title: KO-secondary longRNA rep1

city: Shanghai

first: Fengjuan

last: Zhang

address: 320 Yueyang Road

department: Institute of Biochemistry and Cell Biology

institute: Shanghai Institutes for Biological Sciences, CAS

description: total cellular RNA mixed with exogenous spikein

data_processing:
Raw read1 fastq of smRNA-seq was used to identify small RNAs, which were pre-processed using the fastx_toolkit. After quality filtering, sequencing reads were clipped from the 3' adaptor allowing a minimum match of 10 nt from the 5' end.
Reads unable to match the adaptor sequence or with lengths shorter than 17 bp were discarded, and the remaining reads were mapped to the golden hamster genome (MesAur1.0) by bowtie with parameters –k=100 –v=0. If the sequences mapped to the genome more than 100 loci, we randomly output 100 of all mapped loci. The mapped genome sequences were further aligned to miRNAs, tRNAs, rRNAs, snoRNAs, and snRNAs by bowtie with parameters –a –v=0 --norc.
The remaining 17–32 nt sequences were used to identify piRNAs following a previously described method with slight modifications. The clustering parameters were determined as MinReads = 4 and Eps = 2500 bp by running a series of k-dist analyses of our data with different Eps and MinReads. All of the clusters that satisfied these parameters were considered as piRNA cluster candidates and any overlapping clusters were merged into one cluster. The 17-32 nt unknown reads located in these clusters were defined as piRNA candidates.
The small RNAs were mapped in the following order: miRNA, tRNA, rRNA, snoRNA, snRNA, and piRNA. The reads in each library were normalized with sequencing depth or the count of exogenous spike-ins.
The raw fastq reads of RNA-seq were clipped off the adaptors and quality filtered by trim_galore with parameters --quality 20 --stringency=1 –length=35 --paired (http://tophat.cbcb.umd.edu/). The remaining fastq reads were mapped to the genome or identified transposable element (TE) representative sequences by STAR (version 2.5.3a) with parameters --winAnchorMultimapNmax 10000 --outFilterMultimapNmax 10000. The reads uniquely and multiply mapped with genomic copies less than 10,000 were used for subsequent analysis. Gene abundance was retrieved by RSEM (version 1.3.1) with default parameters.
Genome_build: MesAur1.0
Supplementary_files_format_and_content: tab-delimited text files include useful reads count of smRNAs and each gene count.

organism: Mesocricetus auratus

source_name: secondary follicle stage oocyte

extract_protocol:
Ten MII oocytes of WT and PIWIL1 mutant golden hamster were lysed with lysis buffer composed of 50 mM Tris-HCl (pH 7.4), 150 mM NaCl, 1 mM EDTA, 0.5% NP-40, 0.5 mM DTT, 0.1 U/μl RNase Inhibitor (Thermo Fisher Scientific, Massachusetts, USA) and 0.4 U/μl Proteinase inhibitor cocktail (Sigma, USA) on ice for 10 min. Dynabeads Protein G (Thermo Fisher Scientific, Massachusetts, USA) were washed once with lysis buffer and coupled with 1.5 μg of homemade anti-PIWIL1 or rabbit IgG (Millipore) at RT for 40 min. Oocyte lysates were mixed with antibody-coupled beads and rotated gently at 4°C for 5 h. The beads were then washed three times with lysis buffer and once with PBS. Total RNA from the beads was eluted by adding 4 μl of water and incubating at 72°C for 5 min. The supernatant containing RNA was recovered on a magnetic holder and then used for cDNA library construction. For testis, fresh tissues were homogenized in lysis buffer using Precellys 24 tissue homogenizer (Bertin, USA) and immunoprecipitation was performed as described above. Small RNA libraries were constructed using the single-cell small RNA library construction method as described above.
The single oocytes or embryos were incubated at 72°C for 3 min to release and unfold the small RNAs. After 3’ adapter ligation, 5U of lambda exonuclease and 25U of 5’ deadenylases, which performed better than the combination of RecJf and 5’ deadenylases, were used to remove the excess 3’ adaptor. Then, a 5’ adapter was ligated and small RNAs were reverse transcribed. Pre-amplification was performed and then 1 μl of amplified product was used as a template for final amplification. The amplified libraries were separated on a 6% polyacrylamide gel and 130-160 bp DNA fragments were sliced to recover the library of small RNAs. Long RNA transcriptome libraries was performed following the previously described Smarter-seq2 method with some modifications. In brief, single oocytes or embryos were incubated at 72°C for 3 min to release the RNAs. For every single oocyte or embryo, 0.125 μL 1/100,000 dilution of the ERCC RNA Spike-In Mix (Invitrogen, Cat# 4456740) was used. Following reverse transcription and PCR pre-amplification, cDNA libraries were purified by Agencourt Ampure XP beads (0.8:1 ratio) (Beckman Coulter, Cat#A63881) and 2 ng of purified cDNA was used for a tagmentation reaction with Tn5 transposase as described previously (53). Amplified libraries were purified by Agencourt Ampure XP beads (1:1 ratio).
The small and long RNA libraries were sequenced on a HiSeq X Ten instrument (Illumina, USA) with 2 × 150 run cycles.

tag: breed

value: Syrian

tag: genotype

value: Piwil1 KO

value: secondary follicle stage oocyte


title: WT-MII PIWIL3-IP smRNA

status: Public on Aug 02 2021

type: SRA

state: Shanghai

country: China

library_source: transcriptomic

molecule: total RNA

source_name: MII stage oocyte

extract_protocol:
Ten MII oocytes of WT and PIWIL1 mutant golden hamster were lysed with lysis buffer composed of 50 mM Tris-HCl (pH 7.4), 150 mM NaCl, 1 mM EDTA, 0.5% NP-40, 0.5 mM DTT, 0.1 U/μl RNase Inhibitor (Thermo Fisher Scientific, Massachusetts, USA) and 0.4 U/μl Proteinase inhibitor cocktail (Sigma, USA) on ice for 10 min. Dynabeads Protein G (Thermo Fisher Scientific, Massachusetts, USA) were washed once with lysis buffer and coupled with 1.5 μg of homemade anti-PIWIL1, anti-PIWIL3 or rabbit IgG (Millipore) at RT for 40 min. Oocyte lysates were mixed with antibody-coupled beads and rotated gently at 4°C for 5 h. The beads were then washed three times with lysis buffer and once with PBS. Total RNA from the beads was eluted by adding 4 μl of water and incubating at 72°C for 5 min. The supernatant containing RNA was recovered on a magnetic holder and then used for cDNA library construction. For testis, fresh tissues were homogenized in lysis buffer using Precellys 24 tissue homogenizer (Bertin, USA) and immunoprecipitation was performed as described above. Small RNA libraries were constructed using the single-cell small RNA library construction method as described above.
The single oocytes or embryos were incubated at 72°C for 3 min to release and unfold the small RNAs. After 3’ adapter ligation, 5U of lambda exonuclease and 25U of 5’ deadenylases, which performed better than the combination of RecJf and 5’ deadenylases, were used to remove the excess 3’ adaptor. Then, a 5’ adapter was ligated and small RNAs were reverse transcribed. Pre-amplification was performed and then 1 μl of amplified product was used as a template for final amplification. The amplified libraries were separated on a 6% polyacrylamide gel and 130-160 bp DNA fragments were sliced to recover the library of small RNAs. Long RNA transcriptome libraries was performed following the previously described Smarter-seq2 method with some modifications. In brief, single oocytes or embryos were incubated at 72°C for 3 min to release the RNAs. For every single oocyte or embryo, 0.125 μL 1/100,000 dilution of the ERCC RNA Spike-In Mix (Invitrogen, Cat# 4456740) was used. Following reverse transcription and PCR pre-amplification, cDNA libraries were purified by Agencourt Ampure XP beads (0.8:1 ratio) (Beckman Coulter, Cat#A63881) and 2 ng of purified cDNA was used for a tagmentation reaction with Tn5 transposase as described previously (53). Amplified libraries were purified by Agencourt Ampure XP beads (1:1 ratio).
The small and long RNA libraries were sequenced on a HiSeq X Ten instrument (Illumina, USA) with 2 × 150 run cycles.

tag: strain

value: wild type

tag: treatment

tag: ip antibody

tag: tissue

value: MII stage oocyte

tag: molecule subtype

value: PIWIL3-IP smRNA mixed with exogenous spikein


title: RPMI-8266_DMSO4Aza 1

city: San Francisco

first: Arun

middle: P

last: Wiita

state: CALIFORNIA

address: 185 Berry St, Ste 290/Rm 2410

country: USA

institute: University of California San Francisco

description: RPMI8266_DMSO4Aza-VS-RPMI8266_Aza.DEseq2_Method.GeneDiffExp.xls

data_processing:
For genome mapping, clean reads were mapped to reference genome using HISAT59 with an average of 94.2% mapping across samples.
For gene expression analysis, clean reads were mapped to reference transcripts using Bowtie2 (ref.60) and expression levels calculated using RSEM61.

organism: Homo sapiens

source_name: MM.1S myeloma cell line

growth_protocol: Cell lines were grown in RPMI-1640 medium and passaged twice a week at 5x10^5 cells/ml

extract_protocol:
After treatment, cell lines were washed with PBS twice, pelleted and flash frozen and frozen cell pellets were sent to BGI Genomics for further processing for RNA Seq
RNA extraction, library preparation, and sequencing were performed at BGI (Shenzhen, China).   RNA QC done with Agilent 2100 Bio analyzer and Agilent RNA 6000 Nano kit

treatment_protocol: CRISPR interference cell lines were generated as described in Ramkumar et al 2020. RPMI-8226 cell lines. They were untreated.  RPMI-8226 cell lines were treated with 25 nM  all-trans retinoic acid (ATRA), 2 uM azacytidine, or 10 nM panobinostat.

tag: cell type

value: multiple myeloma cell line

value: 2 uM azacytidine

tag: cell line


title: Rep2_LPLAT1_input

city: Edinburgh

first: Robin

last: Allshire

address: Max Born Crescent

country: United Kingdom

institute: Wellcome Centre for Cell Biology

library_source: genomic

data_processing:
Collapsing. Command: pyFastqDuplicateRemover.py -f paired-end_file_1.fastq -r paired-end_file_2.fastq -o collapsed_file
Alignment. Command: bowtie2 -f -x Tbruceibrucei427  -1  collapsed_paired-end_file_1.fasta - 2 collapsed_paired-end_file_2.fasta > aligned_file.sam
Converting from SAM to BAM format. Command: samtools view -bt Tbruceibrucei427.fasta.fai aligned_file.sam -o aligned_file.bam
Sorting. Command: samtools sort aligned_file.bam -o aligned_sorted_file.bam
Indexing.Command: samtools index aligned_sorted_file.bam
Normalization of IP to input and to library size. Command: bamCompare --operation ratio -b1 aligned_sorted_IP_file.bam -b2 aligned_sorted_input_file.bam -o IP_to_input_ratio.bw --outFileFormat bigwig --binSize 50 --normalizeUsing CPM --scaleFactorsMethod None
Genome_build: HGAP3_Tb427v9.2
Supplementary_files_format_and_content: bigWig files contain information about the peak distribution of each protein across the T. brucei genome

molecule: genomic DNA

organism: Trypanosoma brucei brucei

source_name: cultured cells

growth_protocol: Cell lines were grown at 37 oC and 5% CO2 in HMI-9 medium supplemented with 10% Fetal Calf Serum (Gibco) and 1% Penicillin-Streptomycin (Gibco). Cell lines with tagged proteins were grown in the presence of 5 µg/ml blasticidin.

extract_protocol:
Briefly, 4 x 10^8 parasites were harvested and fixed with 0.8% formaldehyde for 20 min at room temperature. Cells were lysed and sonicated in the presence of 0.2% SDS for 30 cycles (30 s on, 30 s off) using the high setting on a Bioruptor sonicator (Diagenode). Input samples were taken before incubating the rest of the cell lysates overnight with 10 µg rabbit anti-GFP antibody (Thermo Fisher Scientific) and Protein G Dynabeads. The beads were washed and the DNA eluted from them was treated with RNAse and Proteinase K. DNA was purified using a QIAquick PCR Purification Kit (Qiagen).
ChIP-seq libraries were constructed using 0.5-20 ng of immunoprecipitated or input DNA. Following blunt-ending and poly(A)-tailing, NEXTflex (Bioo Scientific) adapters containing barcodes were ligated to each DNA fragment. Fragments were size selected using AMPure beads (Beckman Coulter). The amount of DNA in the resulting libraries was quantified by Qubit fluorometer using Qubit dsDNA HS Assay Kit (Invitrogen). Fragment size distribution was assessed by 2100 Bioanalyzer Instrument (Agilent Technologies) using a Bioanalyzer High Sensitivity DNA Analysis kit (Agilent). Ideally, the libraries had a peak at 300 bp (~ 150 bp fragment DNA + ~ 150 bp adapter sequence). Libraries were sequenced on Illumina MiniSeq, HiSeq or NextSeq. In all cases, 75 bp paired-end sequencing was performed.

value: Lister 427

tag: developmental stage

value: bloodstream slender form

tag: chromatin factor


title: Rep2_LPLAT1_IP

tag: antibody

value: anti-GFP


title: KO-primary longRNA rep1

source_name: primary follicle stage oocyte

value: primary follicle stage oocyte


title: KO-primary longRNA rep2


title: Sample 39

city: St. Louis

first: Blake

middle: C.

last: Meyers

state: MO

address: 975 N Warson Road

institute: Donald Danforth Plant Science Center

data_processing:
FastQC Preprocessing: nohup ./ fastqc <Fastq.gz location> <Fastq.gz location> <As many fasrq.gz files as you want> --outdir=/<output directory location> &
adaptor trimming using rimmomatic version 0.36: ohup java -jar <location of trimmomatic.jar> SE -phred33 <location of fastq.gz file> <output name/location>
aligned to tomato and pepper genome using bowtie2:   nohup bowtie2 -x <Index Name> -U <Fastq file> -S <Alignment Name.sam> --no-unal &
convert from *.sam to *.bam files using samtools: samtools view -Sb <alignment.sam> > <alignment.bam>
sort using samtools: nohup samtools sort <file.bam> -o <sorted file.bam> &
index using samtools: nohup samtools index <sorted file.bam> <sorted file.bai> &
analyze alignments using Bedtools Multicov:   bedtools multicov -D -bams <sorted bam file.bam> -bed <GFF filed.gff> > <Text file.txt> &
Supplementary_files_format_and_content: Sorted, indexed alignments (*.bai). Alignments to tomato genome are named without prefix to the file name. Alignments against pepper genome have "Pepper_" prior to the file name.

organism: Capsicum annuum

source_name: Capsicum annuum variety Big Dipper

extract_protocol:
Trizol total RNA extraction
mRNA was extracted following the NEBNext Poly(A) mRNA Magnetic Isolation Module protocol and libraries were prepared using the NEBNext mRNA Library Prep set for Illumina (New England Biolabs)

value: Stem graft junction

tag: timepoint

value: 5 days after grafting

tag: library

value: Pepper:Pepper graft junction


title: Sample 40


title: RPMI-8266_DMSO4ATRA_1

description: RPMI8266_DMSO4ATRA-VS-RPMI8266_ATRA.DEseq2_Method.GeneDiffExp.xls

value: 25 nM  all-trans retinoic acid (ATRA)


title: KO-secondary longRNA rep2


title: Sample 51

value: 2 weeks after grafting


title: Rep2_HAT3_IP


title: KO-MI longRNA rep3

value: Syrian


title: Rep2_HAT3_input


title: RPMI-8266_Aza 1


title: KO-MII longRNA rep2

value: Piwil1 KO


title: KO-MII longRNA rep1


title: K12_scri_2

description: K12_scri-VS-K12_CD38i.DEseq2_Method.GeneDiffExp.xls


title: Sample 37


title: RPMI-8266_Aza 2


title: RPMI-8266_ATRA2


title: Sample 24

value: 3 days after grafting


title: Sample 38


title: Sample 23


title: K12_scri_1


title: RPMI-8266_ATRA1


title: KO-2C-52PEA longRNA rep4

source_name: 2C embryo at 52PEA

value: 2C embryo at 52PEA


title: KO-GV longRNA rep1

source_name: GV stage oocyte

value: GV stage oocyte


title: K12_CD38i_2


title: KO-GV longRNA rep2


title: Sample 21


title: Rep2_DOT1B_input


title: Rep2_HAT2_input


title: Rep2_CLD1_IP


title: Rep2_DOT1B_IP


title: Rep2_HAT2_IP


title: Sample 7

value: 24 hours after grafting


title: Sample 22


title: KO-2C-52PEA longRNA rep2


title: KO-2C-52PEA longRNA rep1


title: K12_CD38i_1

value: multiple myeloma cell line


title: KO-2C-44PEA longRNA rep4

source_name: 2C embryo at 44PEA

value: 2C embryo at 44PEA


title: Sample 5


title: Rep2_CRD1_IP

value: Lister 427


title: KO-2C-44PEA longRNA rep2


title: Rep2_HAT1_input

value: bloodstream slender form


title: Lung, GC_D3_3B

city: La Jolla

first: Max

last: Chang

state: CA

address: 9500 Gilman Drive

institute: University of California, San Diego

data_processing:
Sequencing reads were aligned to the mouse genome using STAR 2.7.3a.
Gene-level read counts were generated using STAR 2.7.3a.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited file containing raw gene counts

organism: Mus musculus

source_name: Lung

extract_protocol:
Mouse lungs were homogenized in liquid nitrogen. 1 ml Trizol was added per 50-100 mg of tissue and the homogenate was incubated at room temperature for 5 minutes. 200 μl chloroform were added per ml of Trizol, shaken vigorously for 15-30 seconds and incubated at room temperature for 15 minutes. Samples were centrifuged for 15 minutes at 4˚C and 12,000 rcf. The aqueous phase was carefully collected in a separate tube. 500 μl isopropanol was added per 1 ml Trizol, inverted to mix and incubated at room temperature for 5-10 minutes. Samples were transferred to Qiagen RNeasy Spin Columns and RNA was isolated according to the manufacturer’s instructions.
RNA-seq libraries were constructed using the Illumina TruSeq Stranded Total RNA Library Prep Kit.

value: Lung

value: GATM PPMO

tag: infection


title: Rep2_HAT1_IP

value: anti-GFP


title: LUHMES_A30PaSyn_9.1_BS [A30P7_BS]

type: genomic

city: Vancouver

first: Michael

last: Kobor

state: BC

address: 950 W 28th Ave

department: Medical Genetics

country: Canada

institute: University of British Columbia

hyb_protocol: 1.5 μg of DNA per sample was split into two 750 ng aliquots for sodium bisulfite (BS) conversion or oxidative bisulfite (oxBS) conversion using the NuGEN TrueMethyl oxBS Module (NuGEN Technologies Inc.). One aliquot per sample was treated with the oxidation protocol while the second aliquot underwent mock oxidation; all samples were then sodium bisulfite converted according to the manufacturer’s instructions. Samples were hybridized to the Infinium MethylationEPIC Array.

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

data_processing:
GenomeStudio software
Average Beta (after background-subtraction and colour-correction in GenomeStudio software according to standard Illumina protocol).
Unmethylated and methylated signal intensities

label: Cy5 and Cy3

source_name: LUHMES overexpressing A30P human aSyn

label_protocol: Standard Illumina protocol

growth_protocol: Proliferating cells were cultured in Advanced Dulbecco’s modified Eagle’s medium/F12 (DMEM/F12, Gibco, Thermo Fisher Scientific Inc., Waltham, Massachusetts, USA) supplemented with N2 (Gibco), 2 mM L-glutamine (Gibco) and 40 ng/mL recombinant basic fibroblast growth factor (bFGF, R&D Systems Inc., Minneapolis, Minnesota, USA), in pre-coated flasks (Corning Inc., Corning, New York, USA) with 50 g/mL PLO (Sigma-Aldrich, St. Louis, Missouri, USA), at 37ºC in a humidified 5% CO2 atmosphere. Differentiation was achieved by replacing the proliferating medium with DMEM/F12 supplemented with N2 (Gibco), 2 mM L-glutamine (Gibco), 1 g/mL tetracyclin (Sigma-Aldrich), 1 mM dibutyryl cAMP (cAMP, Sigma Aldrich) and 2 ng/mL recombinant human GDNF (R&D Systems). After two days in culture (pre-differentiation), cells were trypsinized and seeded into plates pre-coated with 50 g/mL PLO and 1g/mL fibronectin (Sigma-Aldrich). On the fifth day of differentiation one third of culture medium was refreshed. Cells were harvested after 8 days of differentiation.

extract_protocol: Cell pellets were thawed on dry ice and homogenized with a 20G needle in Qiagen Buffer RLT Plus (QIAGEN Inc.) with β-mercaptoethanol. DNA extractions were performed with the Qiagen AllPrep DNA/RNA Mini Kit as per manufacturer’s instructions.

treatment_protocol: Full-length human aSyn c-DNA (SNCA, NM_000345) or A30P aSyn were subcloned into a second generation bicistronic lenti- viral vector, pWPI (Tronolab, Switzerland), under the chicken/ b-actin (CBA) promoter. All cloned sequences were verified by direct-sequencing (StarSeq). pWPI vector containing only IRES-GFP cassette was used as infection control in all the experiments. Second-generation lentiviral particles were generated as previously described91. Briefly, 293T cells were transiently co-transfected with the modified transfer vector plasmids and second-generation packing system (Tronolab). Supernatant was collected 48-h post-transfection, concentrated by PEG-it Virus Precipitation Solution (System Bioscience) and resuspended in Panserin 402 (PAN). Lentiviral vector titers were quantitatively measured by qPCR using primer sequences specific for the woodchuck hepatitis virus post-transcriptional regulatory element (WPRE), as previously described92. To generate cells expressing aSyn, proliferating LUHMES cells were infected with equimolar amounts of IRES-GFP, WT aSyn-IRES-GFP or A30P aSyn-IRES-GFP lentivirus. Positive green fluorescent cells were selected by fluorescence activated cell sorting (Calibur flow cytometer, BD Biosciences).

value: Lund Human Mesencephalic (LUHMES) cells

tag: passage

tag: conversion

value: Bisulfite

value: A30P aSyn


title: Rep2_CLD1_input


title: KO-2C-44PEA longRNA rep1

tag: breed


title: Rep2_BDF7_input


title: Rep2_BDF6_IP


title: Sample 8

value: Stem graft junction

value: Pepper:Pepper graft junction


title: AMO scri_2

description: AMO_scri-VS-AMO_CD38i.DEseq2_Method.GeneDiffExp.xls


title: KO-2C-33PEA longRNA rep3

source_name: 2C embryo at 33PEA

value: Syrian

tag: genotype

value: Piwil1 KO

value: 2C embryo at 33PEA


title: AMO CD38i_2


title: AMO CD38i_1


title: Rep2_BDF7_IP

tag: strain


title: KO-2C-52PEA longRNA rep3

tag: treatment

value: 2C embryo at 52PEA


title: Sample 6

value: 24 hours after grafting


title: Rep2_BDF5_IP


title: KO-2C-33PEA longRNA rep2


title: KO-2C-33PEA longRNA rep1


title: KO-2C-44PEA longRNA rep3


title: Rep2_BDF6_input


title: LUHMES_A30PaSyn_3.2_BS [A30P8_BS]


title: AMO scri_1

value: multiple myeloma cell line


title: Rep2_BDF5_input


title: KO-1C-9PEA longRNA rep4

source_name: 1C embryo at 9PEA

value: 1C embryo at 9PEA


title: LUHMES_A30PaSyn_7.2_BS [A30P2_BS]


title: KO-1C-9PEA longRNA rep3


title: LUHMES_A30PaSyn_6_BS [A30P5_BS]


title: Rep2_BDF4_IP

value: Lister 427


title: Lung, GP_D3_B

value: mock


title: Rep2_CRD1_input

value: bloodstream slender form


title: LUHMES_WTaSyn_9.1_BS [WT8_BS]

source_name: LUHMES overexpressing WT human aSyn

value: WT aSyn


title: LUHMES_A30PaSyn_5.1_BS [A30P4_BS]


title: Rep2_BDF3_IP

value: anti-GFP


title: KO-1C-9PEA longRNA rep1


title: Rep2_BDF3_input


title: WT-secondary longRNA rep3

value: wild type

value: secondary follicle stage oocyte


title: Lung, SC_D3_2B

value: Lung

value: control (scramble) PPMO


title: Lung, GC_D3_2B

value: GATM PPMO


title: LUHMES_A30PaSyn_3.1_BS [A30P3_BS]

value: Lund Human Mesencephalic (LUHMES) cells

value: Bisulfite

value: A30P aSyn


title: Lung, GP_D3_3B


title: Lung, GC_D3_N


title: Lung, SC_D3_N


title: WT-secondary longRNA rep2

value: Syrian


title: Lung, GP_D3_N


title: Lung, GP_D3_2B


title: LUHMES_A30PaSyn_1.1_BS [A30P1_BS]


title: Lung, SP_D3_3B

description:
SP_D3_3B
QC failure: ignored in final analysis


title: LUHMES_A30PaSyn_2.1_BS [A30P6_BS]


title: Lung, GC_D3_B


title: LUHMES_WTaSyn_8_BS [WT7_BS]


title: Rep2_BDF1_input


title: Lung, SC_D3_3B


title: LUHMES_WTaSyn_7.2_BS [WT6_BS]


title: KO-1C-9PEA longRNA rep2

value: Piwil1 KO


title: WT-primary longRNA rep2

value: primary follicle stage oocyte


title: WT-primary longRNA rep1


title: LUHMES_WTaSyn_1.2_BS [WT2_BS]


title: Rep2_BDF2_IP


title: LUHMES_WTaSyn_6_BS [WT1_BS]


title: WT-MII longRNA rep3

value: MII stage oocyte


title: LUHMES_WTaSyn_1.1_BS [WT5_BS]


title: Lung, SP_D3_N


title: WT-primary longRNA rep3


title: WT-MII longRNA rep1


title: WT-secondary longRNA rep1


title: LUHMES_WTaSyn_3.1_BS [WT4_BS]


title: Rep2_BDF2_input

value: Lister 427


title: Lung, SC_D3_B


title: Rep2_BDF4_input


title: LUHMES_GFP_8.1_BS [GFP7_BS]

source_name: Control LUHMES

value: GFP (control)


title: Rep2_BDF1_IP

value: bloodstream slender form


title: LUHMES_WTaSyn_2.1_BS [WT3_BS]

value: WT aSyn


title: Lung, SP_D3_B

value: mock


title: Rep1_DMT_input

value: TbDMT


title: HPN-7

city: Los Angeles

first: Zarko

last: Manojlovic

state: California

address: 1450 Biggy St

institute: University of Southern California

data_processing:
FASTQ files were converted using BCL2FASTQ v1.8.4.
RNAseq data was aligned using STAR v2.5.3a.
Genome_build: mm9 (MGSCv37)
Supplementary_files_format_and_content: *htSeqCounts.txt: Tab-delimited text files include STAR raw counts; standard STAR htSeqCounts file output.

source_name: PrimaryMelanoma

extract_protocol:
AllPrep Mini Kit (QIAGEN).
NEBNext® Ultra™ II Directional RNA Library Prep Kit (E7765).
Dual index

value: Primary melanoma


title: Lung, SP_D3_2B

value: Lung


title: Rep2_AGO1_IP

value: anti-GFP


title: WT-GV longRNA rep3

value: wild type

value: GV stage oocyte


title: LUHMES_GFP_10.1_BS [GFP5_BS]

value: Lund Human Mesencephalic (LUHMES) cells

value: Bisulfite


title: WT-MII longRNA rep2

value: Syrian


title: HPN-7_Lya

source_name: Cervical

value: Metastatic melanoma (cervical)


title: LUHMES_GFP_2.1_BS [GFP6_BS]


title: LUHMES_GFP_3.1_BS [GFP3_BS]


title: WT-GV longRNA rep1


title: HPN-6


title: Rep1_DMT_IP


title: Rep2_AGO1_input


title: WT-GV longRNA rep2


title: HPN-6_Ly


title: HPN-7_Lyb

source_name: Inguinal

value: Metastatic melanoma (Inguinal)


title: Rep1_Sir2rp2_IP


title: LUHMES_GFP_6_BS [GFP4_BS]


title: HPN-8_Ly

source_name: Brachial

value: Metastatic melanoma (brachial)


title: Rep1_Sir2rp3_IP

value: Lister 427


title: LUHMES_A30PaSyn_3.2_ox [A30P8_ox]

value: Oxidative bisulfite

value: A30P aSyn


title: Rep1_Sir2rp1_input

value: bloodstream slender form


title: WT-4C-52PEA longRNA rep1

value: 2C embryo at 52PEA


title: Rep1_Sir2rp1_IP


title: Rep1_Sir2rp2_input


title: Rep1_Sir2rp3_input


title: WT-4C-52PEA longRNA rep3


title: HPN-4_Ly


title: LUHMES_A30PaSyn_6_ox [A30P5_ox]


title: Rep1_SET29_IP


title: Rep1_SET28_IP


title: WT-4C-52PEA longRNA rep2


title: Rep1_SET29_input


title: LUHMES_A30PaSyn_5.1_ox [A30P4_ox]


title: LUHMES_A30PaSyn_9.1_ox [A30P7_ox]


title: HPN-5_Ly

source_name: Lymph

value: Metastatic melanoma (lymph)


title: LUHMES_GFP_7_BS [GFP2_BS]

value: GFP (control)


title: HPN-5

value: Primary melanoma


title: LUHMES_GFP_1.2_BS [GFP1_BS]


title: HPN-4_Lu

value: Metastatic melanoma (lung)


title: WT-4C-44PEA longRNA rep4

source_name: 4C embryo at 44PEA

value: wild type

value: 4C embryo at 44PEA


title: WT-4C-44PEA longRNA rep2


title: WT-4C-44PEA longRNA rep3


title: LUHMES_A30PaSyn_2.1_ox [A30P6_ox]

value: Lund Human Mesencephalic (LUHMES) cells


title: Rep1_SET27_IP

source_name: cultured cells

value: anti-GFP


title: LUHMES_A30PaSyn_3.1_ox [A30P3_ox]


title: WT-2C-44PEA longRNA rep3

value: Syrian

value: 2C embryo at 44PEA


title: Rep1_SET27_input


title: WT-2C-44PEA longRNA rep2


title: HPN-4


title: LUHMES_A30PaSyn_1.1_ox [A30P1_ox]


title: Rep1_SET28_input


title: HPN-3


title: LUHMES_WTaSyn_9.1_ox [WT8_ox]

value: WT aSyn


title: HPN-2


title: WT-2C-33PEA longRNA rep6

value: 2C embryo at 33PEA


title: HPN-3_Ly

value: Metastatic melanoma (brachial)


title: LUHMES_WTaSyn_8_ox [WT7_ox]

value: Oxidative bisulfite


title: Rep1_SET26_input

value: Lister 427


title: Rep1_SET26_IP

value: bloodstream slender form


title: HPN-3_Lu


title: Rep1_SET25_IP


title: LUHMES_WTaSyn_7.2_ox [WT6_ox]


title: WT-2C-44PEA longRNA rep1


title: LUHMES_A30PaSyn_7.2_ox [A30P2_ox]

value: A30P aSyn


title: HP-7

value: Nme1wt / Nme2wt


title: WT-2C-33PEA longRNA rep4


title: HP-6


title: Rep1_SET25_input


title: WT-2C-33PEA longRNA rep3


title: WT-2C-33PEA longRNA rep5


title: LUHMES_WTaSyn_1.1_ox [WT5_ox]


title: Rep1_SET24_IP


title: WT-4C-44PEA longRNA rep1


title: LUHMES_WTaSyn_3.1_ox [WT4_ox]


title: HP-5


title: WT-2C-33PEA longRNA rep2


title: WT-2C-33PEA longRNA rep1


title: LUHMES_WTaSyn_2.1_ox [WT3_ox]


title: LUHMES_WTaSyn_1.2_ox [WT2_ox]


title: HP-4


title: HP-3


title: HP-9


title: HP-1


title: Rep1_SET24_input


title: LUHMES_WTaSyn_6_ox [WT1_ox]


title: WT-1C-9PEA longRNA rep3

value: 1C embryo at 9PEA


title: Rep1_SET23_IP


title: HPN-1

value: Primary melanoma


title: Rep1_SET22_IP


title: WT-1C-9PEA longRNA rep1


title: LUHMES_GFP_2.1_ox [GFP6_ox]

value: GFP (control)


title: 19744_APP_M

city: Minneapolis

first: Ling

last: Li

state: MN

address: 2001 6th Street SE

department: Experimental and Clinical Pharmacology

institute: University of Minnesota

data_processing:
Base calling was done with RTA3 software in the NovaSeq 6000 system.
3' trimming for Illumina adapters was performed using trimmomatic v0.33, and quality control of reads were performed using FastQC v0.11.7
Sequence reads were aligned to Mus musculus genome (mm10) using HISAT2 v2.1.0.
Cleaned and name-sorted alignments were processed with the featureCounts tool.
Genome_build: mm9
Supplementary_files_format_and_content: A matrix table with raw gene counts of every gene (in ensembl ID and gene symbols) for all 18 samples in CSV format

source_name: Frontal cortex

extract_protocol:
Total RNA was extracted from the frontal cortex using AurumTM Total RNA Fatty and Fibrous Tissue Kit (732-6830; Bio-Rad) following the manufacturer’s instructions. RNA quantity was measured using Quant-iT RiboGreen Assay Kit (Thermofisher), and the quality was determined by the Agilent Bioanalyzer system.
mRNA libraries were prepared following Illumina TruSeq Stranded mRNA library prep workflow

tag: disease model

value: Alzheimer's disease

value: Frontal cortex

tag: Sex

value: Male

tag: rin


title: 19723_APP_F

tag: tissue

value: Female


title: KO-testis PIWIL1-IP smRNA

description: PIWIL1-IP smRNA mixed with exogenous spikein

source_name: testis

value: Syrian

value: Piwil1 KO

tag: ip antibody

value: testis


title: LUHMES_GFP_8.1_ox [GFP7_ox]

tag: cell type

value: Lund Human Mesencephalic (LUHMES) cells


title: Rep1_SET22_input

tag: developmental stage

tag: chromatin factor


title: 19722_APPFCre_F


title: Rep1_SET21_IP

tag: antibody

value: anti-GFP


title: KO-testis IgG-IP smRNA

description: lgG-IP smRNA mixed with exogenous spikein

value: lgG


title: KO-testis input smRNA


title: Rep1_SET20_IP

value: Lister 427


title: LUHMES_GFP_6_ox [GFP4_ox]

value: Oxidative bisulfite


title: 19721_WT_M

value: WT


title: Rep1_SET21_input

value: bloodstream slender form


title: LUHMES_GFP_3.1_ox [GFP3_ox]


title: Rep1_SET23_input


title: 19718_WT_M


title: WT-1C-9PEA longRNA rep2

value: wild type

value: 1C embryo at 9PEA


title: WT-testis input smRNA


title: LUHMES_GFP_1.2_ox [GFP1_ox]

value: GFP (control)


title: 19720_APPFCre_M

value: Alzheimer's disease


title: LUHMES_GFP_7_ox [GFP2_ox]


title: LUHMES_GFP_10.1_ox [GFP5_ox]


title: 19622_WT_F

value: Frontal cortex


title: WT-testis PIWIL1-IP smRNA


title: KO-MII PIWIL1-IP smRNA

source_name: MII stage oocyte

value: MII stage oocyte


title: Rep1_SET20_input


title: Rep1_SET19_IP


title: WT-testis IgG-IP smRNA


title: 19619_APP_M

value: Male


title: Rep1_SET18_IP


title: KO-MII input smRNA

value: Syrian


title: Rep1_SET17_IP


title: 19394_APPFCre_F

value: Female


title: Pool 2 GEX

city: Davis

first: Monica

last: Britton

address: 451 Health Sciences Dr., Rm. 1300

department: Genome Center Service Cores

institute: University of California, Davis

data_processing:
10X Genomics Cell Ranger Software Suite v.4.0.0 was used to process raw fastq files to expression tables and assemble V(D)J clonotypes.
The gene-cell matrix files were analyzed and filtered in R v4.0.3 with Seurat v3.9.9. Individual antibody sample hashtags were used to distinguish cells from the four samples within batch (Normal, Convalescent Covid, MMR and Tdap), requiring at least 100 antibody reads present per cell and tag specificity of >80% to a single sample. V(D)J Clonotypes were linked to the scRNA expression by common cell barcode. The following cell filtering criteria were then applied: gene number greater than 1,000, unique UMI count between 1,000 and 50,000 and mitochondrial gene content < 10%.
After filtering, the matrix for all samples was normalized using ‘LogNormalize’ method with default parameters.
Genome_build: GRCh38-2020-A, GENCODE v32/Ensembl 98
Supplementary_files_format_and_content: tab-separated text files (matrix output from CellRanger), h5 format contains GEX and HTO processed data

source_name: T cells

growth_protocol: PBMCs were isolated from peripheral blood and frozen. After 2 days PBMCs were thawed and CD3+ T cells were isolated and co-cultured with APCs along with antigens in RPMI+10%FCS+1% Pen/Strep.

extract_protocol:
The cells were harvested using Accutase and were aliquoted in 1ml cryopreservation tubes at a concentration of 1.2 million cells/ml and frozen at -80C.
Hashtagged cells were brought to ~1000 cells/ul, pooled equally in sets four samples, and loaded onto the 10x Chromium instrument (10x Genomics) to generate single-cell gel beads in emulsion. For 5’ multiomics including gene expression, TCR-sequencing, and cell-hashing seq, we used the 10x Single Cell V(D) Kit with Feature Barcoding (10x Genomics,Cat# 1000006) along with the Human V(D) Enrichment Kit (10xGenomics,Cat# 10000005) following the manufacturer’sprotocol. Libraries were checked forconcentration using Qubit dsDNA HS assay kit (Fisher Scientific,Cat# Q32854) and size distribution using TapeStation (Agilent). Libraries were then sequenced on NovaSeq (Illumina) to a sequencing depth of50,000 reads per cell for gene expression libraries and 10,000 reads per cell for TCR and hashtag libraries.Cell Ranger reads were aligned to reference GRCh38-2020-A, cellular barcodes were demultiplexed, andunique molecular identifiers and antibody capture were  quantified using 10x Genomics’ Cell Rangersoftware (version 4.0.0).

treatment_protocol: Co-cultures were treated with thefollowing SARS-COV-2 antigens-5μg/ml Spike-S1 subunit (S1-fc), 8.85μg/ml Spike S2 subunit (S2-his),7.8μg/ml Spike S1 receptor binding domain (RBD-fc), 2.35μg/ml Nucleocapsid protein (NC his).InactivatedMeasles, Mumps, Rubella viral preparations were used at of 5μg of total protein/ml, 5μg/ml of heat inactivated Pertussis toxin,Diphtheria toxinandTetanus toxoid.

value: Peripheral blood

value: T cells

tag: disease state

value: pooled sample:healthy control and COVID-19 convalescent patient

value: pooled sample:treated with SARS-CoV-2, MMR or Tdap antigens

tag: hashtag antibodies


title: Pool 1 GEX


title: Pool 2 VDJ

data_processing:
Library strategy: VDJ-seq
10X Genomics Cell Ranger Software Suite v.4.0.0 was used to process raw fastq files to expression tables and assemble V(D)J clonotypes.
The gene-cell matrix files were analyzed and filtered in R v4.0.3 with Seurat v3.9.9. Individual antibody sample hashtags were used to distinguish cells from the four samples within batch (Normal, Convalescent Covid, MMR and Tdap), requiring at least 100 antibody reads present per cell and tag specificity of >80% to a single sample. V(D)J Clonotypes were linked to the scRNA expression by common cell barcode. The following cell filtering criteria were then applied: gene number greater than 1,000, unique UMI count between 1,000 and 50,000 and mitochondrial gene content < 10%.
After filtering, the matrix for all samples was normalized using ‘LogNormalize’ method with default parameters.
Genome_build: GRCh38-2020-A, GENCODE v32/Ensembl 98
Supplementary_files_format_and_content: tab-separated text files (matrix output from CellRanger), h5 format contains GEX and HTO processed data


title: Pool 3 GEX


title: Pool 1 VDJ


title: Pool 3 VDJ


title: Rep1_SET19_input

value: Lister 427


title: Rep1_SET16_IP

value: anti-GFP


title: 19554_APP_F


title: KO-MII IgG-IP smRNA

value: Piwil1 KO

value: lgG


title: Rep1_SET18_input

value: bloodstream slender form


title: WT-MII PIWIL1-IP smRNA

value: wild type


title: KO-testis oxidation smRNA

value: treated by NaIO4

value: testis


title: 19053_WT_F

value: Alzheimer's disease

value: Frontal cortex

value: WT


title: Rep1_SET17_input


title: Rep1_SET15_input


title: 19553_APP_F


title: WT-MII input smRNA

value: Syrian

value: MII stage oocyte


title: Calu-3_CND10_c

city: Higashi-Osaka

first: Kei

last: IIDA

state: Osaka

address: Kowakae 3-4-1

country: Japan

institute: Kindai University

data_processing:
Basecalling was performed with RTAVersion v3.4.4
The seuqence data was mapped to the genome sequence with STAR ver. 2.7.1a.
Genome_build: GRCh38
Supplementary_files_format_and_content: Expression values of refseq gene models were calculated with RSEM ver. 1.3.0.

molecule: polyA RNA

growth_protocol: Calu-3 cells, derived from lung adenocarcinoma, were obtained from American Type Culture Collection (ATCC, Manassas, VA, USA), and cultured in Dulbecco’s modified Eagle’s medium (DMEM) (Nacalai Tesque, Kyoto, Japan) supplemented with 10 % fetal bovine serum, 100 U/mL penicillin, and 100 µg/mL streptomycin. All cells were maintained in an incubator at 37°C with 5% CO2.

extract_protocol:
Total RNA was extracted from HeLa cells using the RNeasy Mini kit (QIAGEN, Hilden, Germany).
TruSeq Stranded mRNA Library Prep Kit; Oligo-dT beads capture polyA tails

treatment_protocol: Calu-3 cells were treated with 0.1% DMSO or 10 μM CaNDY for 18 h.

tag: cell line

value: cancer cell line

tag: tissue source

value: Lung

value: 10 µM CaNDY


title: Calu-3_DMSO_b

value: 0.1% DMSO


title: WT-testis before oxidation smRNA

tag: breed


title: 16975 APP_M

tag: genotype

value: Male


title: 19101_WT_M


title: Rep1_SET16_input

tag: strain

value: Lister 427


title: 16974_APPFCre_M


title: KO-MII oxidation smRNA

value: Piwil1 KO

tag: treatment


title: Calu-3_CND10_a


title: WT-testis oxidation smRNA


title: WT-MII IgG-IP smRNA

value: lgG


title: KO-testis before oxidation smRNA


title: Rep1_SET14_input

value: bloodstream slender form


title: Calu-3_DMSO_c


title: Rep1_SET14_IP

value: anti-GFP


title: Rep1_SET11_IP


title: UMI-4C in zebrafish wt embryos at 48hpf, ptch2_V6 promoter as viewpoint

city: Seville

first: José

middle: M.

last: Santos-Pereira

address: Avda. Manuel Siurot s/n

country: Spain

institute: IBiS, Universidad de Sevilla-CSIC

data_processing:
Library strategy: UMI-4C
Raw fastq files were mapped, and viewpoints were demultiplexed using the R package umi4cpackage (https://bitbucket.org/tanaylab/umi4cpackage)
Contact profiles and domainograms were generated using 'p4cNewProfile' and 'plot.p4cProfile' function of the umi4cpackage with the default parameters and a min_win_cov=10
Bedgraph files were generated using 'p4cExportBedGraph' function of the umi4cpackage with default parameters and min_win_cov (Smoothing parameter) of 10
Genome_build: Zebrafish September 2014 (GRCz10/danRer10)
Supplementary_files_format_and_content: bedgraph files with contact data

organism: Danio rerio

source_name: whole embryo

growth_protocol: Embryos were cultivated at 28°C in E3 medium until desired developmental stage

extract_protocol:
Embryos were fixed in 1% paraformaldehyde and quenched with 0.125M Glycine. Cell were lyses and extracted nuclei were processed for in-situ HiC preparation as previously described (Rao et al. 2014). Briefly, chromatin was digested with DpnII, fragment-ends were blunted and marked with dATP-biotin, followed by proximity ligation. DNA was extracted after cross-link reversal and sonicated in a Covaris M220 sonicator for targeted fragmentation with an average peak size at 500 bp. Proximity ligation products were enriched using Streptavidin-coated beads.
End-repair and A-tailing was performed following standard procedure for Illumina library preparations for paired-end sequencing. 5’-DNA ends were then dephosphorylated using Alkaline Phosphatase, Calf Intestinal. Libraries were then indexed by ligation of TruSeq indexing adapters from Illumina. Non-ligated strand from adapter was removed by denaturation of DNA at 96°C. Final library was prepared using NEBNext High-Fidelity 2X PCR Master Mix (NEB) and ligation junctions for specific viewpoints were enriched using a nested PCR approach as described in Schwartzman et al. 2016. Viewpoint-specific downstream (DS) primers contained P5 sequence at their 5’ end and TruSeq Primer 2.0 (P7) was used to complement adapter sequences for pair-end sequencing.

value: 48 hpf


title: 18973_APPFCre_M

tag: disease model


title: Rep1_SET13_IP


title: HSC CD93- rep2 [ATAC-Seq]

city: Freiburg

first: Asifa

last: Akhtar

address: Stuebeweg 51

department: Chromatin Regulation

country: Germany

institute: Max Planck Institute of Immunobiology and Epigenetics

data_processing:
The ATAC-seq datasets analysis were then performed on the DNA-mapping pipeline described in snakePipes (Bhardwaj et al. 2019). Briefly the adaptors were trimmed from the reads using trimGalore2 following the filtering for uniquely mapped reads and the removal of duplicates. Bowtie2 software was used for mapping using default parameters. Furthermore, the ATAC-seq pipeline from the same tool (Bhardwaj et al., 2019) was applied for open chromatin peak calling using MACS2 tools
Genome_build: mm10
Supplementary_files_format_and_content: peak text file
Supplementary_files_format_and_content: Coverage bigwig file

source_name: Bone Marrow

growth_protocol: Primary cells

extract_protocol:
mouse BM cells were isolated from pooled femora and tibia by flushing them with cold phosphate-buffered saline (PBS) containing 2% FCS. Lysis of erythrocytes was performed using ACK Lysing Buffer (Thermo Fisher Scientific). To deplete lineage-positive cells, we used the MojoSort Mouse Hematopoietic Progenitor Cell Isolation Kit (BioLegend, #48003). Total BM was incubated with a biotin antibody cocktail, followed by incubation with magnetic streptavidin nanobeads from the kit. CD93+ and CD93- HSCs (LSK+CD34-Flt3-CD48-Slam1+) were sorted using an Aria FACS Fusion II cytometer (BD).
CD93+ and CD93- HSCs from 8 week-old male mice were sorted following the Fluorescence-activated cell sorting section. After sorting cells were spinned at 1000 rpm for 5 minutes. Crude nuclei isolation was obtained by resuspending the pellet in 50 µL of cold lysis buffer (10 mM Tris-HCl, pH 7.4, 10 mM NaCl, 3 mM MgCl2, 0.1% IGEPAL CA-630) the samples. The samples were then centrifuged at 500g for 10 minutes at 4oC. Further processing for ATAC-seq was adapted from (Buenrostro et al. 2015). Briefly, the nuclei pellet was resuspended in Tn5 Reaction mix containing 2.5ml of Tn5 from the Nextera DNA Library Prep Kit (Illumina cat. No 15027987), 25ml Buffer 2x and 22.5ml H2O. The tagmentation reaction took place at 37oC shaking at 800rpm. After precisely 30min, the samples were placed on ice and 250ml of PB buffer from the MinElute PCR Purification Kit (cat. No 28004) was added to stop the reaction. DNA purification was followed according to manufacturer’s instructions. Pure DNA was amplified using 16 PCR cycles using the Neb- Next Polymerase (M0541S) for the library amplification.
Ilumina Nextera ATACseq

tag: age

value: 8 weeks old

value: wild type


title: UMI-4C in zebrafish wt embryos at 48hpf, ptch2_V5 promoter as viewpoint


title: 18944_WT_F

value: Alzheimer's disease

value: Frontal cortex

tag: Sex

value: Female

tag: rin


title: Rep1_SET15_IP


title: 18943_APPFCre_F

tag: tissue


title: Calu-3_DMSO_a

tag: cell type


title: Rep1_SET10_IP

tag: developmental stage


title: HSC CD93+ rep2 [ATAC-Seq]


title: KO-MII before oxidation smRNA

value: Syrian

value: MII stage oocyte


title: HSC CD93+ rep1 [ATAC-Seq]


title: WT-MII before oxidation smRNA


title: WT-MII oxidation smRNA

value: treated by NaIO4


title: HSC CD93- rep1 [ATAC-Seq]


title: UMI-4C in zebrafish wt embryos at 48hpf, ptch2_V3 promoter as viewpoint

value: WT


title: Rep1_SET11_input

tag: chromatin factor


title: KO-primary smRNA rep2

source_name: primary follicle stage oocyte

value: primary follicle stage oocyte


title: KO-secondary smRNA rep1

source_name: secondary follicle stage oocyte

value: secondary follicle stage oocyte


title: Rep1_SET10_input

value: Lister 427


title: HSC CD93+ rep2

data_processing:
Reads for mouse bulk RNA-seq datasets were mapped following the default SnakePipes parameters of bulk RNA-seq pipeline (Bhardwaj et al. 2019). In brief, STAR software alignment against mouse genome version GRCm38. The total number of sequenced reads averaged 15 million pairs of which mean alignment of 65 % of the reads were uniquely mapped. Reads were counted with featureCounts (subread-1.5.0-p1). Differential expression analysis was performed with DESEQ2 (v1.26). Multi-FASTA QC statistics indicated data were of high quality and sequencing depth was sufficient to test for differential expression between conditions. Differential genes were called with an FDR threshold of 0.05. Correlations between datasets and graphical output were conducted in an R environment.
Genome_build: mm10
Supplementary_files_format_and_content: DESEQ2_Results
Supplementary_files_format_and_content: DESeq2_hsc_counts_normalized

extract_protocol:
For flow cytometry, mouse BM cells were isolated from pooled femora and tibia by flushing them with cold phosphate-buffered saline (PBS) containing 2% FCS. Lysis of erythrocytes was performed using ACK Lysing Buffer (Thermo Fisher Scientific). To deplete lineage-positive cells, we used the MojoSort Mouse Hematopoietic Progenitor Cell Isolation Kit (BioLegend, #48003). Total BM was incubated with a biotin antibody cocktail, followed by incubation with magnetic streptavidin nanobeads from the kit. CD93+ and CD93- HSCs (LSK+CD34-Flt3-CD48-Slam1+) were sorted using an Aria FACS Fusion II cytometer (BD)
After sorting, primary cells were pelleted at 5000g and lysed in TRIzol (Invitrogen, #15596026). To isolate RNA, chloroform was added followed by extraction and precipitation of the aqueous phase using 5 μg of ribonuclease (RNase)–free glycogen and 0.25 ml of isopropanol. The supernatant was discarded and the pellet was washed twice in 80% ethanol (EtOH) and lastly dissolved in 10 μl of H2O. CD93+ and CD93- HSCs from 8 week-old male mice were sorted following the Fluorescence-activated cell sorting section. RNA was extracted using the PicoKit (Qiagen). The quality between was evaluated using the Fragment analyzer. RNA that passed the QC were then used  to generate libraries using the NEBNext Library Low input library preparation. The manufacturer’s recommendations were followed and the libraries were sequenced on an Illumina NovaSeq6000 sequencer. All sequence data were performed in 3 biological replicates. Having a total depth of 15 millions reads per reads. The reads were conducted at 2 x 50 bp length
NEBNext Library Low input library preparation

treatment_protocol: Not aplicable

value: HSC CD93+


title: UMI-4C in zebrafish wt embryos at 48hpf, ptch2_V4 promoter as viewpoint


title: HSC CD93+ rep3


title: UMI-4C in zebrafish wt embryos at 48hpf, ptch2_V2 promoter as viewpoint


title: Rep1_SET8_IP

tag: antibody


title: UMI-4C in zebrafish wt embryos at 48hpf, ptch2_V1 promoter as viewpoint


title: Rep1_SET9_input


title: HSC CD93+ rep1


title: KO-secondary smRNA rep2

value: Piwil1 KO


title: KO-primary smRNA rep1


title: Calu-3_CND10_b

value: cancer cell line

value: Lung

value: 10 µM CaNDY


title: UMI-4C in zebrafish wt embryos at 48hpf, ptch2 promoter as viewpoint

value: 48 hpf


title: Rep1_SET9_IP

value: anti-GFP

value: bloodstream slender form


title: KO-MII smRNA rep2


title: Rep1_SET8_input


title: HSC CD93- rep3

value: HSC CD93-

value: 8 weeks old

value: wild type


title: HSC CD93- rep1


title: KO-GV smRNA rep2

source_name: GV stage oocyte

value: Syrian

value: GV stage oocyte


title: UMI-4C in zebrafish wt embryos at 48hpf, hoxd_V5 promoter as viewpoint

value: WT


title: Rep1_SET7_IP


title: Rep1_SET13_input


title: KO-GV smRNA rep1


title: UMI-4C in zebrafish wt embryos at 48hpf, hoxd_V6 promoter as viewpoint


title: UMI-4C in zebrafish wt embryos at 48hpf, hoxd_V4 promoter as viewpoint


title: Carma3xpA/+ ES cells, d10, Replicate 3

city: Lausanne

first: Mohamed

last: Nemir

state: Vaud

address: Bugnon 27

department: Cœur et Vaisseau

country: Switzerland

institute: Lausanne University Hospital

data_processing:
base calling were performed using Solexa pipeline v1.8 (Off-Line Base Caller software, v1.8). Sequence quality was examined using the FastQC software.
The trimmed reads (trimmed 5', 3'-adaptor bases using cutadapt [2] ) were aligned to reference genome (mm10) using Hisat2 software
The transcript abundances for each sample was estimated with StringTie [4] , and the FPKM [8] value for gene and transcript level were calculated with R package Ballgown [5–7]
The novel genes and transcripts were predicted from assembled results by comparing to the reference annotation using StringTie and Ballgown, then use CPAT [10] to assess the coding potential of those sequences. Then use rMATS [11] to detecting alternative splicing events and plots.
The expression level (FPKM value) of known genes and transcripts were calculated using ballgown through the
Genome_build: transcript abundances estimated with StringTie. The number of identified genes and transcripts per group was
Supplementary_files_format_and_content: calculated based on the mean of FPKM in group 0.5.

source_name: Carma3xpA/+ ES cells, d10,

growth_protocol: Cells were maintained on MEF in standard ESC medium, consisting of DMEM high-glucose supplemented with 20% FBS , 1% Non-Essential Amino Acids , 0.1mM β-mercaptoethanol and 3000U/ml LIF.

extract_protocol:
Total RNA was isolated using Rneasy kit (Qiagen). RNA quantification and quality control were performed using a NanoDrop ND-1000 and Agilent 2100 Bioanalyzer, respectively.  mRNA was isolated from total RNA with NEBNext® Poly(A) mRNA Magnetic Isolation Module. The mRNA-enriched RNA was used for RNA-seq library preparation using KAPA Stranded RNA-Seq Library Prep Kit (Illumina).
The library preparation procedure included: 1) Fragmentation of the RNA molecules; 2) Reverse transcription to synthesis first strand cDNA; 3) Second strand cDNA synthesis incorporating dUTP; 4) End-repair and A-tailing of the double stranded cDNA; 5) Illumina compatible adapter ligation; 6) PCR amplification and purification for the final RNA-seq library. The completed libraries were qualified on Agilent 2100 Bioanalyzer for concentration, fragment size distribution between 400 _ 600 bp, and adapter dimer contamination. The amount was determined by absolute quantification qPCR method. The barcoded libraries were mixed in equal amounts and used for sequencing on the instrument.
The DNA fragments in well mixed libraries were denatured with 0.1M NaOH to generate single-stranded DNA molecules, loaded onto channels of the flow cell at 8 pM concentration, and amplified in situ using TruSeq SR Cluster Kit v3-cBot-HS (#GD-401-3001, Illumina). Sequencing was carried out using the Illumina Xten/ NovaSeq according to the manufacturer’s instructions. Sequencing was carried out by running 150 cycles.

treatment_protocol: Cardiac differentiation of ESCs was induced by aggregating approx. 1000 cells in hanging drops of 25 µl differentiation medium, consisting of IMDM  supplemented with 200mM L-glutamine, 20% FBS, 6.5 µl of 1-thioglycerol, 1M L-ascorbic acid  and Gentamicin to form embryoid bodies, which wre collected at d3, d6, and d10)

tag: differentiated state

value: embryonic stem cells


title: HSC CD93- rep2


title: UMI-4C in zebrafish wt embryos at 48hpf, hoxd_V3 promoter as viewpoint


title: Rep1_SET7_input


title: Carma3xpA/+ ES cells, d10, Replicate 2


title: Rep1_SET6_IP


title: Carma3xpA/+ ES cells, d10, Replicate 1


title: Carma3xpA/+ ES cells, d6, Replicate 3

source_name: Carma3xpA/+ ES cells, d6,


title: UMI-4C in zebrafish wt embryos at 48hpf, hoxd_V2 promoter as viewpoint


title: Rep1_SET6_input


title: UMI-4C in zebrafish wt embryos at 48hpf, hoxd_V1 promoter as viewpoint


title: KO-2C-52PEA smRNA rep3

source_name: 2C embryo at 52PEA

value: 2C embryo at 52PEA


title: Rep1_SET5_IP

value: Lister 427


title: Carma3xpA/+ ES cells, d6, Replicate 2


title: Rep1_SET5_input


title: UMI-4C in zebrafish wt embryos at 48hpf, hoxd13a promoter as viewpoint


title: Rep1_SET4_IP


title: KO-2C-52PEA smRNA rep1


title: KO-2C-44PEA smRNA rep4

source_name: 2C embryo at 44PEA

value: 2C embryo at 44PEA


title: Carma3xpA/+ ES cells, d6, Replicate 1


title: Rep1_SET4_input


title: UMI-4C in zebrafish wt embryos at 48hpf, hoxa9a promoter as viewpoint


title: KO-2C-52PEA smRNA rep4

value: Piwil1 KO


title: KO-2C-44PEA smRNA rep2


title: UMI-4C in zebrafish wt embryos at 48hpf, hoxd9a promoter as viewpoint


title: UMI-4C in zebrafish wt embryos at 48hpf, hoxa5a promoter as viewpoint


title: Rep1_SET3_IP


title: UMI-4C in zebrafish wt embryos at 48hpf, hoxd4a promoter as viewpoint


title: KO-2C-44PEA smRNA rep1


title: UMI-4C in zebrafish ctcf mutant embryos at 48hpf, ptch2_V6 promoter as viewpoint

value: ctcf -/-


title: Rep1_SET3_input


title: KO-2C-33PEA smRNA rep2

source_name: 2C embryo at 33PEA

value: 2C embryo at 33PEA


title: KO-2C-33PEA smRNA rep1


title: Carma3xpA/+ ES cells, d0, Replicate 2

description:
TODO
mESC-Hetero-D0-Rep2

source_name: Carma3xpA/+ ES cells, d0,


title: KO-1C-9PEA smRNA rep2

source_name: 1C embryo at 9PEA

value: 1C embryo at 9PEA


title: Rep1_LCM1_IP

source_name: cultured cells


title: UMI-4C in zebrafish ctcf mutant embryos at 48hpf, ptch2_V4 promoter as viewpoint

value: 48 hpf


title: Carma3xpA/+ ES cells, d3, Replicate 1

description:
TODO
mESC-Hetero-D3-Rep1

source_name: Carma3xpA/+ ES cells, d3,


title: Carma3xpA/+ ES cells, d0, Replicate 3

description:
TODO
mESC-Hetero-D0-Rep3


title: Rep1_SET1_IP

value: anti-GFP


title: WT ES cells, d10, Replicate 3

source_name: WT ES cells, d10,

value: wildtype


title: Carma3xpA/+ ES cells, d0, Replicate 1

description:
TODO
mESC-Hetero-D0-Rep1


title: UMI-4C in zebrafish ctcf mutant embryos at 48hpf, ptch2_V3 promoter as viewpoint


title: Carma3xpA/+ ES cells, d3, Replicate 2

description:
TODO
mESC-Hetero-D3-Rep2


title: UMI-4C in zebrafish ctcf mutant embryos at 48hpf, ptch2_V2 promoter as viewpoint


title: Rep1_LCM1_input

value: bloodstream slender form


title: KO-2C-52PEA smRNA rep2


title: KO-2C-44PEA smRNA rep3


title: KO-1C-9PEA smRNA rep1


title: WT ES cells, d10, Replicate 2


title: Rep1_JMJ1_IP


title: UMI-4C in zebrafish ctcf mutant embryos at 48hpf, ptch2_V5 promoter as viewpoint


title: UMI-4C in zebrafish ctcf mutant embryos at 48hpf, ptch2_V1 promoter as viewpoint


title: KO-1C-9PEA smRNA rep3


title: WT-secondary smRNA rep3

value: secondary follicle stage oocyte


title: WT ES cells, d10, Replicate 1


title: Rep1_SET1_input


title: WT ES cells, d6, Replicate 3

source_name: WT ES cells, d6,


title: UMI-4C in zebrafish ctcf mutant embryos at 48hpf, ptch2 promoter as viewpoint


title: Rep1_JMJ1_input


title: WT-secondary smRNA rep2

value: wild type


title: UMI-4C in zebrafish ctcf mutant embryos at 48hpf, hoxd_V6 promoter as viewpoint


title: Rep1_HDAC4_IP


title: WT ES cells, d6, Replicate 2


title: Rep1_HDAC4_input


title: Carma3xpA/+ ES cells, d3, Replicate 3

description:
TODO
mESC-Hetero-D3-Rep3


title: WT-secondary smRNA rep1

value: Syrian


title: Rep1_HDAC2_IP


title: WT-primary smRNA  rep3

value: primary follicle stage oocyte


title: UMI-4C in zebrafish ctcf mutant embryos at 48hpf, hoxd_V4 promoter as viewpoint


title: Rep1_HDAC2_input


title: WT ES cells, d6, Replicate 1


title: WT ES cells, d3, Replicate 3

source_name: WT ES cells, d3,


title: UMI-4C in zebrafish ctcf mutant embryos at 48hpf, hoxd_V3 promoter as viewpoint

source_name: whole embryo


title: WT-primary smRNA rep2


title: Rep1_HDAC1_input


title: WT-primary smRNA rep1


title: WT ES cells, d3, Replicate 1


title: Rep1_HDAC1_IP


title: UMI-4C in zebrafish ctcf mutant embryos at 48hpf, hoxd_V2 promoter as viewpoint


title: WT-MII smRNA rep2

source_name: MII stage oocyte

value: MII stage oocyte


title: WT-MII smRNA rep3


title: UMI-4C in zebrafish ctcf mutant embryos at 48hpf, hoxd_V1 promoter as viewpoint


title: Rep1_NAT2_IP


title: WT ES cells, d0, Replicate 2

source_name: WT ES cells, d0,

value: embryonic stem cells


title: WT ES cells, d0, Replicate 1


title: Rep1_NAT3_IP


title: KO-MII smRNA rep1


title: UMI-4C in zebrafish ctcf mutant embryos at 48hpf, hoxd13a promoter as viewpoint


title: WT ES cells, d3, Replicate 2


title: UMI-4C in zebrafish ctcf mutant embryos at 48hpf, hoxd4a promoter as viewpoint


title: WT-GV smRNA rep2

value: GV stage oocyte


title: WT-GV smRNA rep3


title: WT-GV smRNA rep1


title: WT-MII smRNA rep1


title: Rep1_NAT2_input

value: Lister 427


title: UMI-4C in zebrafish ctcf mutant embryos at 48hpf, hoxa9a promoter as viewpoint


title: Rep1_LPLAT1_IP


title: UMI-4C in zebrafish ctcf mutant embryos at 48hpf, hoxa5a promoter as viewpoint


title: Rep1_LPLAT1_input


title: HiChIP in zebrafish wild-type embryos at 48hpf, replicate 2

data_processing:
Library strategy: Hi-ChIP
Reads from biological replicates were pooled and aligned using GEM
Ligation events were detected using TADbit and filtered for non-ligated and self-ligated events
Binary multiresolution hic files were generated using Juicer Tools Pre
Genome_build: Zebrafish September 2014 (GRCz10/danRer10)
Supplementary_files_format_and_content: multiresolution hic files

extract_protocol:
Embryos were fixed in 1% paraformaldehyde and quenched with 0.125M Glycine. Cell were lyses and extracted nuclei were processed for HiChIP preparation as previously described (Mumbach et al. 2016). Briefly, chromatin was digested with DpnII, fragment-ends were blunted and marked with dATP-biotin, followed by proximity ligation. Chromatin was sonicated in a Covaris M220 sonicator for fragments around 300 bp and immunoprecipitated with anti-H3K4me3 (abcam). DNA was extracted after cross-link reversal and biotinylated products were recovered with streptavidin-coated beads, TAGmented with Tn5 transposase and purified for library preparation.
Preparation of HiChIP libraries was performed as described for ATAC-seq assays in Buenrostro et al., 2015

value: WT


title: UMI-4C in zebrafish ctcf mutant embryos at 48hpf, hoxd_V5 promoter as viewpoint


title: WT-4C-52PEA smRNA rep2

source_name: 4C embryo at 52PEA

value: 4C embryo at 52PEA


title: BECs_poly(I:C)+imiquimod_rep3

type: RNA

city: Lund

first: Juan

middle: José

last: Nieto-Fontarigo

address: Sölvegatan 17

department: Experimental Medical Science

country: Sweden

institute: Lund University

data_processing: Data was normalised to seven house-keeping genes (PPIA, RPL19, OAZ1, EEF1G, HPRT1, TUBB, TBP), selected using the geNorm algorithm, and differential gene expression and pathway analysis were performed. All analysis was performed with nSolver software (NanoString technologies, Santa Clara, USA) and PANTHER classification system.

source_name: Human bronchial epithelial cells, poly (I:C)-imiquimod-stimulated

growth_protocol: Human bronchial epithelial cells from asthmatics were obtained by bronchoscopy using a standard outpatient procedure with a flexible bronchoscope (Olympus BF-1TQ180/BF-1TH190, Olympus, Hamburg, Germany). After brushing bronchial epithelial cells (BECs) were isolated and expanded in vitro  in collagen-coated T25 flasks containing 5 mL of bronchial epithelium growth medium (BEGM, Lonza, Walkersville, MD, USA) and after being confluent, BECs were passaged with trypsin to T75 flasks and further expanded. At passage 2, BECS were seeded into 12-well plates (Nunc, Life Technologies, Carlsbad, CA, USA) stimulations were initiated at 70-80% confluency.

extract_protocol: Cell lysates were collected for gene expression analysis. Total RNA was isolated from cell lysates using RNeasy Plus mini kit (Qiagen, Hilden, Germany) according to manufacturer’s protocol and 1 µg RNA was reversely transcribed into cDNA with Precision Nanoscript Reverse Transcription kit (PrimerDesign, Southampton, UK). RNA quality was measured using a bioanalyser (Agilent technologies, Santa Clara, USA). Then a panel of 579 mRNAs involved in the human immune response (NanoString Immunology Human V2 panel) was analysed.

treatment_protocol: 10 μg/mL Poly (I:C) (InvivoGen, San Diego, US) was used as viral mimic to stimulate the cells for 24h in combination (treatment group) or not with  10 µg/mL imiquimod (Tocris Bioscience, Bristol, UK)

value: Bronchial epithelial cells


title: BECs_poly(I:C)_rep3

scan_protocol: All analysis was performed with nSolver software (NanoString technologies, Santa Clara, USA)

source_name: Human bronchial epithelial cells, poly (I:C)-stimulated


title: WT-4C-52PEA smRNA rep3

data_processing:
Raw read1 fastq of smRNA-seq was used to identify small RNAs, which were pre-processed using the fastx_toolkit. After quality filtering, sequencing reads were clipped from the 3' adaptor allowing a minimum match of 10 nt from the 5' end.
Reads unable to match the adaptor sequence or with lengths shorter than 17 bp were discarded, and the remaining reads were mapped to the golden hamster genome (MesAur1.0) by bowtie with parameters –k=100 –v=0. If the sequences mapped to the genome more than 100 loci, we randomly output 100 of all mapped loci. The mapped genome sequences were further aligned to miRNAs, tRNAs, rRNAs, snoRNAs, and snRNAs by bowtie with parameters –a –v=0 --norc.
The remaining 17–32 nt sequences were used to identify piRNAs following a previously described method with slight modifications. The clustering parameters were determined as MinReads = 4 and Eps = 2500 bp by running a series of k-dist analyses of our data with different Eps and MinReads. All of the clusters that satisfied these parameters were considered as piRNA cluster candidates and any overlapping clusters were merged into one cluster. The 17-32 nt unknown reads located in these clusters were defined as piRNA candidates.
The small RNAs were mapped in the following order: miRNA, tRNA, rRNA, snoRNA, snRNA, and piRNA. The reads in each library were normalized with sequencing depth or the count of exogenous spike-ins.
The raw fastq reads of RNA-seq were clipped off the adaptors and quality filtered by trim_galore with parameters --quality 20 --stringency=1 –length=35 --paired (http://tophat.cbcb.umd.edu/). The remaining fastq reads were mapped to the genome or identified transposable element (TE) representative sequences by STAR (version 2.5.3a) with parameters --winAnchorMultimapNmax 10000 --outFilterMultimapNmax 10000. The reads uniquely and multiply mapped with genomic copies less than 10,000 were used for subsequent analysis. Gene abundance was retrieved by RSEM (version 1.3.1) with default parameters.
Genome_build: MesAur1.0
Supplementary_files_format_and_content: tab-delimited text files include useful reads count of smRNAs and each gene count.

extract_protocol:
Ten MII oocytes of WT and PIWIL1 mutant golden hamster were lysed with lysis buffer composed of 50 mM Tris-HCl (pH 7.4), 150 mM NaCl, 1 mM EDTA, 0.5% NP-40, 0.5 mM DTT, 0.1 U/μl RNase Inhibitor (Thermo Fisher Scientific, Massachusetts, USA) and 0.4 U/μl Proteinase inhibitor cocktail (Sigma, USA) on ice for 10 min. Dynabeads Protein G (Thermo Fisher Scientific, Massachusetts, USA) were washed once with lysis buffer and coupled with 1.5 μg of homemade anti-PIWIL1 or rabbit IgG (Millipore) at RT for 40 min. Oocyte lysates were mixed with antibody-coupled beads and rotated gently at 4°C for 5 h. The beads were then washed three times with lysis buffer and once with PBS. Total RNA from the beads was eluted by adding 4 μl of water and incubating at 72°C for 5 min. The supernatant containing RNA was recovered on a magnetic holder and then used for cDNA library construction. For testis, fresh tissues were homogenized in lysis buffer using Precellys 24 tissue homogenizer (Bertin, USA) and immunoprecipitation was performed as described above. Small RNA libraries were constructed using the single-cell small RNA library construction method as described above.
The single oocytes or embryos were incubated at 72°C for 3 min to release and unfold the small RNAs. After 3’ adapter ligation, 5U of lambda exonuclease and 25U of 5’ deadenylases, which performed better than the combination of RecJf and 5’ deadenylases, were used to remove the excess 3’ adaptor. Then, a 5’ adapter was ligated and small RNAs were reverse transcribed. Pre-amplification was performed and then 1 μl of amplified product was used as a template for final amplification. The amplified libraries were separated on a 6% polyacrylamide gel and 130-160 bp DNA fragments were sliced to recover the library of small RNAs. Long RNA transcriptome libraries was performed following the previously described Smarter-seq2 method with some modifications. In brief, single oocytes or embryos were incubated at 72°C for 3 min to release the RNAs. For every single oocyte or embryo, 0.125 μL 1/100,000 dilution of the ERCC RNA Spike-In Mix (Invitrogen, Cat# 4456740) was used. Following reverse transcription and PCR pre-amplification, cDNA libraries were purified by Agencourt Ampure XP beads (0.8:1 ratio) (Beckman Coulter, Cat#A63881) and 2 ng of purified cDNA was used for a tagmentation reaction with Tn5 transposase as described previously (53). Amplified libraries were purified by Agencourt Ampure XP beads (1:1 ratio).
The small and long RNA libraries were sequenced on a HiSeq X Ten instrument (Illumina, USA) with 2 × 150 run cycles.


title: HiChIP in zebrafish wild-type embryos at 48hpf, replicate 1


title: Rep1_HAT3_input


title: Rep1_HAT3_IP


title: WT-4C-52PEA smRNA rep1


title: HiChIP in zebrafish ctcf mutant embryos at 48hpf, replicate 2

description: HiChIP_K4me3_48h_ctcf_comb_downsampled.hic

value: ctcf -/-


title: Rep1_HAT1_input


title: BECs_poly(I:C)+imiquimod_rep1


title: HiChIP in zebrafish ctcf mutant embryos at 48hpf, replicate 1


title: BECs_poly(I:C)_rep2


title: BECs_control_rep2

source_name: Human bronchial epithelial cells, unstimulated


title: WT-4C-44PEA smRNA rep2

source_name: 4C embryo at 44PEA

value: 4C embryo at 44PEA


title: WT-4C-44PEA smRNA rep3


title: Rep1_HAT1_IP


title: BECs_control_rep3


title: Rep1_DOT1B_IP


title: WT-4C-44PEA smRNA rep1


title: WT-4C-44PEA smRNA rep4


title: RNA-seq in zebrafish wild-type embryos at 48hpf, replicate 2

data_processing:
Reads were aligned against reference genome using STAR software
Read counts per gene were calculated using htseq-count script from HTSeq tools software package
Genome_build: Zebrafish September 2014 (GRCz10/danRer10)
Supplementary_files_format_and_content: Individual counts files (reads per gene)

growth_protocol: Embryos were grown at 28°C in E3 medium until desired developmental stage

extract_protocol: RNA was extracted using TRIsure (Bioline) and treated with TURBO DNA free kit (Invitrogen)

treatment_protocol: Injection of tp53 morpholino was performed at 1-cell stage

value: 48 hpf


title: WT-2C-44PEA smRNA rep3

source_name: 2C embryo at 44PEA

value: 2C embryo at 44PEA


title: WT-2C-44PEA smRNA rep2


title: HiC in zebrafish ctcf mutant embryos at 24hpf, replicate 2

description:
Hi-C
HiC_24h_ctcf_comb.hic

data_processing:
Reads from biological replicates were pooled and aligned using BWA
Ligation events were detected using Pairtools and filtered for non-ligated and self-ligated events
Binary multiresolution hic files were generated using Juicer Tools Pre
Genome_build: Zebrafish September 2014 (GRCz10/danRer10)
Supplementary_files_format_and_content: multiresolution hic files

extract_protocol:
Embryos were fixed in 1% paraformaldehyde and quenched with 0.125M Glycine. Cell were lyses and extracted nuclei were processed for in-situ HiC preparation as previously described (Rao et al. 2014). Briefly, chromatin was digested with DpnII, fragment-ends were blunted and marked with dATP-biotin, followed by proximity ligation. DNA was extracted after cross-link reversal and sonicated in a Covaris M220 sonicator for fragments between 150-600 bp. Proximity ligation products were enriched using Streptavidin-coated beads.
End-repair, A-tailing and ligation of TruSeq indexing adapters followed standard procedure for Illumina library preparations for paired-end sequencing. Final library was prepared using NEBNext High-Fidelity 2X PCR Master Mix (NEB) and standard TruSeq Primer 1.0 (P5) and TruSeq Primer 2.0 (P7).

value: 24 hpf


title: RNA-seq in zebrafish wild-type embryos at 48hpf, replicate 1


title: BECs_poly(I:C)_rep1


title: BECs_poly(I:C)+imiquimod_rep2


title: RNA-seq in zebrafish wild-type embryos at 48hpf, injected with morpholino against tp53, replicate 2

value: tp53 morpholino


title: ChIP-seq in zebrafish wild-type embryos at 48hpf, replicate 2

description: ChIP-seq

data_processing:
Reads were aligned using Bowtie
Peaks were called using MACS2 software with  q<0.001
Genome_build: Zebrafish September 2014 (GRCz10/danRer10)
Supplementary_files_format_and_content: Called peaks in narrowPeak format

extract_protocol:
Embryos were fixed in 1% paraformaldehide and quenched with 0.125M Glycine. Nuclei were extracted and lysed, and chromatin sonicated in a Covaris M220 sonicator to an average of 300bp fragments. Sonicated chromatin was divided in 6 aliquots and incubated overnight at 4ºC with 2µg of antibody per aliquiot. Immunoprecipitated chromatin was then incubated with magnetic beads, washed, TAGmented with Tn5 transposase (Schmidl et al., 2015) and eluted from beads. Then, chromatin was decrosslinked and DNA was purified using Minelute kit (Qiagen)
Preparation of ChIPmentation libraries was performed as described for ATAC-seq assays in Buenrostro et al., 2015


title: BECs_control_rep1


title: HiC in zebrafish ctcf mutant embryos at 24hpf, replicate 1

description:
Hi-C
HiC_24h_ctcf_comb.hic


title: WT-2C-44PEA smRNA rep1


title: RNA-seq in zebrafish wild-type embryos at 48hpf, injected with morpholino against tp53, replicate 1


title: MiSeq_Method2 schizont parasites unenriched

city: Khlong Nung

first: Pavita

last: Kaewprommal

state: Pathum Thani

department: NBT

country: Thailand

institute: NSTDA

data_processing:
Filtered reads were mapped to the combined reference genome (Pf3D7_SIRvome_combined_correct.fasta) with HISAT2, guided by annotations in the Pf3D7_SIRvome_combined.gtf file.M2752841) were pre-processed by adapter sequence in the 3'  end of reads was trimmed and low quality reads removed using fastp with default settings.
Normalized depth values for each library at all positions and the associated enrichment scores were calculated from mapped sense-strand reads (read 1 only) of method1 and method2.  P-values of enrichment at each nucleotide were calculated using the ToNER program with the combine p-value option.
Genome_build: Pf3D7_SIRvome_combined_correct.fasta
Supplementary_files_format_and_content: Tab-delimited text files of position, normalized depth and enrichment score for each library.

organism: Plasmodium falciparum

source_name: In vitro cultured malaria parasite

growth_protocol:
Plasmodium falciparum strain K1 was cultured in vitro in human O+ erythrocytes and medium containing pooled human serum and buffered RPMI as described in (Trager and Jensen, 1976). Cultured parasites were synchronized to early ring stages by two sorbitol enrichments (Lambros and Vanderberg, 1979). Parasites were harvested immediately (ring stage), 20 h (trophozoite stage) and 40 h (schizont stage) after the second sorbitol enrichment.   The parasites were liberated from the host cell by treatment with 0.1% (w/v) saponin.
[enrichment protocol ] Enrichment of full-length cDNA: The GST-PfeIF4E protein, which has been demonstrated to possess 5′ mRNA cap binding activity (Shaw et al., 2007), was used for enrichment of full-length cDNA. GST-PfeIF4E protein was expressed as recombinant protein in E. coli and purified by SP-sepharose cation exchange chromatography as described in (Shaw et al., 2007). For each full-length cDNA enrichment, approximately 400 μg of SP-sepharose purified GST-PfeIF4E protein was immobilized on 100 μL of glutathione magnetic beads (Thermo Scientific) in RNase-free phosphate-buffered saline (PBS, Ambion). The glutathione magnetic beads were washed four times with 1 mL of PBS to remove unbound protein, and then resuspended in 100 μL of PBS. The remainder of the desalted mRNA/cDNA was incubated with bead-bound GST-PfeIF4E protein for 20 min at 25°C with agitation (750 rpm Thermomixer). The beads were then washed thrice with 1 mL PBS and the mRNA/cDNA eluted using 100 μL of a solution comprising 1% sodium dodecyl sulfate/0.2 M sodium chloride. The eluted mRNA/cDNA was purified by Tris-buffered phenol:chloroform extraction and desalted on a Amicon-30 micro column (Ambion). RNA was removed from enriched and unenriched cDNA by alkaline hydrolysis (15 min treatment at 65°C with 0.2 N NaOH). Alkaline-treated cDNA was neutralized with 1 M Tris pH 7 solution and the first-strand cDNA purified using an Amicon-30 micro column (Ambion). Desalted single-stranded cDNA was concentrated in a Speedvac.

extract_protocol:
Parasite total RNA was obtained using Trizol reagent according to the manufacturer’s instructions (Invitrogen). Purified total RNA was stored in 75% ethanol at -80°C prior to use. On the day of library preparation, total RNA was dried and then resuspended in nuclease-free water. Total RNA concentration was estimated by Nanodrop ND1000 measurement assuming A260 = 1.0 is equivalent to 40 μg/mL RNA. Up to 100 μg of total RNA was used for mRNA enrichment using a Dynabeads oligo dT25 mRNA kit (Thermo), which enriches for mRNA with oligo dT magnetic beads. The oligo dT-enriched mRNA was then further enriched for 5′ capped mRNA by treatment with 1 unit of XRN-1 nuclease (New England Biolabs) for 30 min at 37°C. XRN-1 enriched mRNA was purified by acidic phenol:chloroform extraction and ethanol precipitation. The mRNA was redissolved in 20 μL of nuclease-free water and genomic DNA was removed using a Turbo DNA-free kit (Ambion).
[5' adapter ligation method: method1] A ribo-G tail of was added to the purified single-stranded cDNA primed with RTNGS1 using terminal transferase (TdT, New England Biolabs). The tail length is limited to three or four Gs (Schmidt and Mueller, 1996). The TdT tailing reactions contained 2 mM GTP, 0.25 mM CoCl2, 1 unit of TdT enzyme in 1x TdT enzyme buffer and first-strand cDNA. TdT reactions were performed in 20 μL reaction volumes for 20 min at 37°C. Ribo-tailed cDNA was purified by ethanol precipitation. Double-stranded DNA adapter was made by combining 80 pmol each of NGS1 and NGS1comp oligonucleotides in a volume of 200 μL with 10 mM NaCl and 10 mM Tris pH 8.0. The NGS1 oligonucleotide is 5′-phosphorylated to act as a donor in ligation and blocked with a three-carbon spacer at the 3′ end to prevent concatamerization of adapters. Annealing was accomplished by heating the mixture for 3 min at 80°C followed by slow cooling to 25°C (0.1°C/min). Double-stranded DNA adapter was ligated to first-strand cDNA using T4 RNA ligase 2 (RNL2, New England Biolabs). This enzyme preferentially ligates a 5′-phosphate donor from a double-stranded RNA or DNA to an RNA acceptor (Bullard and Bowater, 2006). Therefore, it should ligate double-stranded DNA adapter preferentially to ribo-G tailed cDNA. The ligation reactions contained 20 pmol of DNA adapter, 7.5% (w/v) PEG6000, 1x RNL2 enzyme buffer, 0.25 μL (units) of RNL2 enzyme and first strand cDNA. The ligation reactions were performed for 99 cycles of 37°C for 30 s, 22°C for 30 s. After the completion of the RNL2 adapter ligation reactions, cDNA was purified using 25 μL Streptavidin M280 magnetic beads following the manufacturer’s recommendations (Invitrogen). Synthesis of second-strand cDNA was performed on the beads using T7 DNA polymerase following the manufacturer’s recommendations (New England Biolabs). The beads were resuspended in 50 μL of T7 reaction mix (0.3 mM dNTPs, 2.5 units T7 DNA polymerase, 1x T7 DNA polymerase buffer). The reaction was performed for 15 min at 37°C.  The reaction was terminated by washing the beads in 0.4 ml of washing solution (40 mM Tris pH 8.0, 10 mM MgCl2).The second-strand cDNA was eluted from the beads by heating for 3 min at 99°C in a suspension of 50 μL 1x Sodium Saline Citrate (150 mM sodium chloride, 15 mM trisodium citrate pH 7.0).
[5' adapter ligation method: method2] Purified first strand cDNA primed with RTCIRC in which RNA had been removed by alkaline treatment was circularized with 100 U of CircLigaseII enzyme, 2.5 mM MnCl2, 1 M betaine, and 1x CircLigaseII buffer in a reaction volume of 20 μL as recommended by the manufacturer (Epicentre Biotechnologies). The reaction was incubated at 60°C for 1 h and ligated cDNA purified using 0.5x volume of AMPure beads (Beckman Coulter).
cDNA synthesis: A sample of approximately 1 µg of mRNA (estimated by Nanodrop measurement) was fragmented by heating at 94°C for 5 min in 1x first-strand cDNA synthesis buffer supplied with SuperscriptIII reverse transcriptase enzyme (Invitrogen). Fragmented mRNA was chilled on ice prior to reverse-transcription with 50 pmol of 5′ tagged random primer (RTNGS1 oligo for 5′ adapter ligation method 1, RTCIRC oligo for 5′ adapter ligation method2) with SuperscriptIII as described by the manufacturer in a final volume of 20 μL. Method 1 reverse transcription reactions also contained 40 μM biotin-11-dUTP (Thermo Scientific) to label first-strand cDNA with biotin. After addition of SuperscriptIII enzyme, reactions were heated to 25°C for 5 min, followed by heating to 37°C for 30 min, followed by 50°C for 30 min. First-strand cDNA was diluted to 100 μL with 10 mM Tris 1 mM EDTA and digested with 1 μL of RNaseA/T1 mix (Thermo scientific) for 10 min at 25°C to remove incompletely reverse-transcribed RNA. The mRNA/cDNA hybrid was purified by proteinase K treatment, phenol:chloroform extraction and desalting on a Amicon-30 column (Ambion). The volume of desalted mRNA/cDNA hybrid was adjusted to 100 μL with nuclease-free water. A 20 μL sample of desalted mRNA/cDNA was kept for processing as the unenriched control sample. Library purification and Illumina sequencing: Adapter-ligated cDNA was used as a template for PCR amplification make sequencing library DNA. PCRs contained 12.5 pmol each of PE1 and Scriptseq primers, 200 µM dNTPs, 2 mM MgCl2, 0.5 units of Platinum taq enzyme (Invitrogen) and 1x Platinum taq buffer in a reaction volume of 50 μL. The PCR program used was 94°C for 90 s, followed by 18-25 cycles of 94°C for 10 s, 60°C for 60 s. PCR products were separated in 1.5% agarose gel, and DNA molecules 400-600 bp in size were excised from the gel and purified using a MinElute kit (Qiagen). DNA was quantified using a QuantIT HS kit (Invitrogen).  Libraries were pooled in equimolar ratios according to the ScriptSeq index primer recommendations (Illumina). Pooled libraries were processed with 1% Illumina phiX174 control and loaded onto MiSeq flow cells at 10 pM. 150 bp paired-end sequencing was performed using standard sequencing primers as recommended by the manufacturer (Illumina). For sequencing of libraries prepared from cDNA ligated to 5′ adapter using method1, the sequencing “recipe” for the MiSeq instrument was modified to perform the first four sequencing cycles as “dark”, meaning no data are recorded for the purpose of identifying sequencing clusters. This modification was necessary since the G-tail added by TdT during library construction provides insufficient diversity for generation of high density clusters. Without this modification, there will be loss of data in the cluster identification step (clusters passing filter quality control) of Illumina sequencing.

value: schizont

tag: full-length cdna enrichment

value: unenriched

tag: 5' adapter ligation method


title: MiSeq_Method2 trophozoite parasites unenriched

value: trophozoite


title: RNA-seq in zebrafish ctcf mutant embryos at 48hpf, replicate 2


title: RNA-seq in zebrafish ctcf mutant embryos at 48hpf, replicate 1


title: WT-2C-33PEA smRNA rep5

source_name: 2C embryo at 33PEA

value: Syrian

value: wild type

value: 2C embryo at 33PEA


title: WT-2C-33PEA smRNA rep6


title: MiSeq_Method2 schizont parasites enriched

value: enriched


title: WT-2C-33PEA smRNA rep3


title: MiSeq_Method2 ring parasites unenriched

value: ring


title: RNA-seq in zebrafish ctcf mutant embryos at 48hpf, injected with morpholino against tp53, replicate 2


title: MiSeq_Method2 ring parasites enriched


title: MiSeq_Method1 schizont parasites enriched


title: WT-2C-33PEA smRNA rep4


title: WT-2C-33PEA smRNA rep2


title: ChIP-seq in zebrafish wild-type embryos at 48hpf, replicate 1

description: ChIP-seq

value: WT


title: RNA-seq in zebrafish wild-type embryos at 24hpf, replicate 2


title: MiSeq_Method1 schizont parasites unenriched


title: MiSeq_Method1 trophozoite parasites enriched


title: WT-2C-33PEA smRNA rep1


title: MiSeq_Method2 trophozoite parasites enriched


title: WT-1C-9PEA smRNA rep2

source_name: 1C embryo at 9PEA

value: 1C embryo at 9PEA


title: MiSeq_Method1 trophozoite parasites unenriched


title: WT-1C-9PEA smRNA rep3


title: RNA-seq in zebrafish ctcf mutant embryos at 24hpf, replicate 2


title: HiC in zebrafish ctcf mutant embryos at 48hpf, replicate 1


title: RNA-seq in zebrafish wild-type embryos at 24hpf, replicate 1


title: MiSeq_Method1 ring parasites unenriched


title: RNA-seq in zebrafish ctcf mutant embryos at 48hpf, injected with morpholino against tp53, replicate 1


title: HiC in zebrafish ctcf mutant embryos at 48hpf, replicate 2


title: RNA-seq in zebrafish ctcf mutant embryos at 24hpf, replicate 1


title: HighTemp_4h_C

status: Public on Aug 01 2021

first: Ru

state: Missouri

address: 95 N Warson Rd

description: RZ_196_CKDL200150383-1a-AK8596-AK10751_H7NJHBBXX_L2

data_processing:
Single-end reads were trimmed and quality checked using Trim Galore (version 0.6.2)
Trimmed reads from each library were mapped and processed for transcript quantification using Salmon (version 1.1.0) in quasi-m,apping mode with a transcriptome index build from the Setaria viridis transcript and genome files (Sviridis_311_v2, Phytozome v12.1)
Salmon outputs were imported into R using the Bioconductor package tximport (1.16.0) to extract gene-level expression values represented by transcript per million (TPM) for each gene across every time point, tissue, and treatment group sampled
Genes that met minimum read count cutoffs of at least 10 raw reads in at least 10% of samples (14,302 genes) were included in differential expression analysis using DeSeq2, FDR < 0.05. High light or high temperature treatments were compared to the control condition from the same time point.
Genome_build: Sviridis_500_v2.1.transcript.fa
Supplementary_files_format_and_content: tab-delimited text files include TPM values for each Sample
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

organism: Setaria viridis

source_name: HighTemp_4h_mid leaf samples

growth_protocol: Samples were grown in controlled environmental chamber at constant 31°C, 50% humidity, ambient CO2, 12 hour photoperiod, leaf level light intensity of 250 umol photons m-2s-1 for 13 days prior to treatments as described above.  Seeds were germinated on Jolly Gardener C/V Growing Mix and fertilized with Jack's 15-5-15 with an Electrical Conductivity of 1.4.  At 7 days after sowing, seeds were transplated to 3.14' x 3.18' x 3.27' pots.

extract_protocol:
For each biolgoical replicate, 2cm mid-leaf segments from two plants for each time point and treatment were collected from 4th fully expanded true leaves into screw cap tubes with grinding bead and immediately frozen into liquid nitrogen and stored at -80oC.  Frozen samples were homogonized using paint shaker.  RNA was extracted using Trizol method with all centrifugation at 4oC and 11,000 RCT.  1ml of Trizol reagent was added to homogenized leaf tissue and resuspended, then 200uL of Chloroform:Isoamyl alcohol (25:1) was added and vortexed.  Tubes were centrifuged for 15 min. 6-- uL from the aqueous layer was transferred to a clean tube with equal volume Chloroform:Osoamyl alcohol, vortexed, and centrifuged for 5 min. 450uL of aqueous layer was transferred to 0.7x volume 100% Isoporopanol, mixed well, and chilled for 30 min at -20oC. Samles were centrifuged for 15 min to pellet RNA.  Supernatent was decanted and RNA pelled was rinsed twice with ice-cold 75% ethanol with a 2-min centrifiugation following each rinse. RNA was dried in a laminar flow hood until residual ethanol evaporated and was resuspended in 50uL nuclease free H2O. RNA was quantified using NanoDrop and Qubit RNA Broad Range Assay Kit. RNA integrity was verified using a Bioanalyzer Nano Assay.
RNA samples were diluted to 200 ng/uL in nuclease free H2O for a total of 1 uG RNA.  Libraries were generated with the Quantseq 3' mRNA-seq library prep kit FWD for Illumina. Libraries were generated according to manufacturer's instruction. Cycle count for library amplification for 1 ug mRNA was tested using the PCR add-on kit for Illumina. qPCR was performed and a cycle count of 13 was determined for the amplification of all libraries. For library amplification, the Lexogen i5 6nt Dual Indexing Add-on Kit was used in addition to the standard kit to allow libraries to have a unique combination of i5 and i7 indices.  All libararies were quantified using Qubit dsDNA High Sensitivity Assay Kit with the Qubit 3.0 machine.  Prepared libararies were pooled to equimolar concentrations based on Qubit assay reads.  Poolec libaries were submitted to Novogene to be sequenced on the Illumina HiSeq 4000 platform.

value: High tempearture of 40°C

tag: time point

value: 4 hours

value: Mid leaf samples


title: MiSeq_Method1 ring parasites enriched


title: HighLight_4h_D

description: RZ_193_CKDL200150383-1a-AK1061-AK10751_H7NJHBBXX_L2

source_name: HighLight_4h_mid leaf samples

value: High light of 900 μmol photons m-2 s-1


title: WT-1C-9PEA smRNA rep1

tag: breed


title: HighLight_4h_B

description: RZ_191_CKDL200150383-1a-AK2325-AK10751_H7NJHBBXX_L2


title: HighTemp_4h_B

description: RZ_195_CKDL200150383-1a-AK1524-AK10751_H7NJHBBXX_L2


title: HighLight_4h_C

description: RZ_192_CKDL200150383-1a-AK5219-AK2941_H7NJHBBXX_L2


title: Control_4h_B

description: RZ_187_CKDL200150383-1a-AK1177-AK2941_H7NJHBBXX_L2

source_name: Control_4h_mid leaf samples

value: control, 31°C 250μmol photons m-2 s-1


title: Control_4h_D

description: RZ_189_CKDL200150383-1a-AK969-AK2941_H7NJHBBXX_L2


title: HighLight_4h_A

description: RZ_190_CKDL200150383-1a-AK2184-AK10751_H7NJHBBXX_L2


title: HighTemp_2h_C

description: RZ_184_CKDL200150383-1a-AK8599-AK10751_H7NJHBBXX_L2

source_name: HighTemp_2h_mid leaf samples

value: 2 hours


title: HighTemp_2h_D

description: RZ_185_CKDL200150383-1a-AK1208-AK10751_H7NJHBBXX_L2


title: Control_4h_C

description: RZ_188_CKDL200150383-1a-AK2328-AK2941_H7NJHBBXX_L2


title: Control_4h_A

description: RZ_186_CKDL200150383-1a-AK870-AK2941_H7NJHBBXX_L2


title: HighTemp_4h_D

description: RZ_197_CKDL200150383-1a-AK393-AK10751_H7NJHBBXX_L2


title: HighTemp_2h_A

description: RZ_182_CKDL200150383-1a-AK3590-AK2941_H7NJHBBXX_L2


title: HighTemp_2h_B

description: RZ_183_CKDL200150383-1a-AK5276-AK2941_H7NJHBBXX_L2


title: HighTemp_4h_A

description: RZ_194_CKDL200150383-1a-AK5330-AK2941_H7NJHBBXX_L2


title: HighLight_2h_D

description: RZ_181_CKDL200150383-1a-AK1899-AK10751_H7NJHBBXX_L2

source_name: HighLight_2h_mid leaf samples


title: HighLight_2h_C

description: RZ_180_CKDL200150383-1a-AK5328-AK2941_H7NJHBBXX_L2


title: Control_2h_A

description: RZ_174_CKDL200150383-1a-AK2178-AK2941_H7NJHBBXX_L2

source_name: Control_2h_mid leaf samples


title: Control_2h_B

description: RZ_175_CKDL200150383-1a-AK2183-AK2941_H7NJHBBXX_L2


title: HighTemp_1h_C

description: RZ_172_CKDL200150383-1a-AK5325-AK10751_H7NJHBBXX_L2

source_name: HighTemp_1h_mid leaf samples

value: 1 hour


title: HighTemp_1h_B

description: RZ_171_CKDL200150383-1a-AK3637-AK2941_H7NJHBBXX_L2


title: Control_2h_C

description: RZ_176_CKDL200150383-1a-AK1171-AK2941_H7NJHBBXX_L2


title: HighTemp_1h_A

description: RZ_170_CKDL200150383-1a-AK2133-AK2941_H7NJHBBXX_L2


title: HIghTemp_1h_D

description: RZ_173_CKDL200150383-1a-AK2791-AK10751_H7NJHBBXX_L2

source_name: HIghTemp_1h_mid leaf samples


title: HighLight_1h_D

description: RZ_169_CKDL200150383-1a-AK2326-AK10751_H7NJHBBXX_L2

source_name: HighLight_1h_mid leaf samples


title: Rep1_NAT3_input

data_processing:
Collapsing. Command: pyFastqDuplicateRemover.py -f paired-end_file_1.fastq -r paired-end_file_2.fastq -o collapsed_file
Alignment. Command: bowtie2 -f -x Tbruceibrucei427  -1  collapsed_paired-end_file_1.fasta - 2 collapsed_paired-end_file_2.fasta > aligned_file.sam
Converting from SAM to BAM format. Command: samtools view -bt Tbruceibrucei427.fasta.fai aligned_file.sam -o aligned_file.bam
Sorting. Command: samtools sort aligned_file.bam -o aligned_sorted_file.bam
Indexing.Command: samtools index aligned_sorted_file.bam
Normalization of IP to input and to library size. Command: bamCompare --operation ratio -b1 aligned_sorted_IP_file.bam -b2 aligned_sorted_input_file.bam -o IP_to_input_ratio.bw --outFileFormat bigwig --binSize 50 --normalizeUsing CPM --scaleFactorsMethod None
Genome_build: HGAP3_Tb427v9.2
Supplementary_files_format_and_content: bigWig files contain information about the peak distribution of each protein across the T. brucei genome

source_name: cultured cells

extract_protocol:
Briefly, 4 x 10^8 parasites were harvested and fixed with 0.8% formaldehyde for 20 min at room temperature. Cells were lysed and sonicated in the presence of 0.2% SDS for 30 cycles (30 s on, 30 s off) using the high setting on a Bioruptor sonicator (Diagenode). Input samples were taken before incubating the rest of the cell lysates overnight with 10 µg rabbit anti-GFP antibody (Thermo Fisher Scientific) and Protein G Dynabeads. The beads were washed and the DNA eluted from them was treated with RNAse and Proteinase K. DNA was purified using a QIAquick PCR Purification Kit (Qiagen).
ChIP-seq libraries were constructed using 0.5-20 ng of immunoprecipitated or input DNA. Following blunt-ending and poly(A)-tailing, NEXTflex (Bioo Scientific) adapters containing barcodes were ligated to each DNA fragment. Fragments were size selected using AMPure beads (Beckman Coulter). The amount of DNA in the resulting libraries was quantified by Qubit fluorometer using Qubit dsDNA HS Assay Kit (Invitrogen). Fragment size distribution was assessed by 2100 Bioanalyzer Instrument (Agilent Technologies) using a Bioanalyzer High Sensitivity DNA Analysis kit (Agilent). Ideally, the libraries had a peak at 300 bp (~ 150 bp fragment DNA + ~ 150 bp adapter sequence). Libraries were sequenced on Illumina MiniSeq, HiSeq or NextSeq. In all cases, 75 bp paired-end sequencing was performed.

value: Lister 427

value: bloodstream slender form


title: HighLight_2h_B

description: RZ_179_CKDL200150383-1a-AK5193-AK2941_H7NJHBBXX_L2


title: HighLight_1h_C

description: RZ_168_CKDL200150383-1a-AK8598-AK2941_H7NJHBBXX_L2


title: Control_2h_D

description: RZ_177_CKDL200150383-1a-AK2748-AK2941_H7NJHBBXX_L2


title: Control_1h_C

description: RZ_164_CKDL200150383-1a-AK1299-AK2941_H7NJHBBXX_L2

source_name: Control_1h_mid leaf samples


title: HighLight_1h_B

description: RZ_167_CKDL200150383-1a-AK5335-AK2941_H7NJHBBXX_L2


title: UMI-4C in zebrafish ctcf mutant embryos at 48hpf, hoxd9a promoter as viewpoint

source_name: whole embryo

value: 48 hpf

tag: genotype

value: ctcf -/-


title: Control_1h_A

description: RZ_162_CKDL200150383-1a-AK2182-AK2941_H7NJHBBXX_L2

tag: strain


title: Control_1h_D

description: RZ_165_CKDL200150383-1a-AK2024-AK10751_H7NJHBBXX_L2

tag: treatment


title: Control_0h_C

description: RZ_152_CKDL200150383-1a-AK2181-AK2941_H7NJHBBXX_L2

source_name: Control_0h_mid leaf samples

value: 0 hours


title: Control_1h_B

description: RZ_163_CKDL200150383-1a-AK2180-AK10751_H7NJHBBXX_L2


title: Control_0h_D

description: RZ_153_CKDL200150383-1a-AK6548-AK2941_H7NJHBBXX_L2


title: Control_0h_B

description: RZ_151_CKDL200150383-1a-AK1958-AK10751_H7NJHBBXX_L2


title: Control_0h_A

description: RZ_150_CKDL200150383-1a-AK1946-AK2941_H7NJHBBXX_L2


title: HighLight_2h_A

description: RZ_178_CKDL200150383-1a-AK2682-AK2941_H7NJHBBXX_L2


title: HighLight_1h_A

description: RZ_166_CKDL200150383-1a-AK1523-AK2941_H7NJHBBXX_L2


title: WT ES cells, d0, Replicate 3

source_name: WT ES cells, d0,

value: wildtype

value: embryonic stem cells


title: Arrest6

city: Cleveland

first: Cody

last: Rutledge

state: OH

address: 2103 Cornell Road

department: Medicine

institute: CWRU

hyb_protocol: Samples were hybridized with Clariom S Assay (Affymetrix)

scan_protocol: Array scanning was performed according to the manufacturer's instruction (Affymetrix)

data_processing: Raw data were processed with the Exon Array Computational Tool (ExACT) (Affymetrix) for background correction and normalization.

label: biotin

source_name: Arrest

label_protocol: Single-stranded cDNA was generated from the amplified cRNA with the WT cDNA Synthesis Kit (Affymetrix) and then fragmented and labeled with the WT Terminal Labeling Kit (Affymetrix).

growth_protocol: 8 week old male and female C57/BL6 mice

extract_protocol: RNA was isolated from 10 mg homogenized tissue with the RNeasy Mini Kit (Qiagen), according to the manufacturer’s instructions. Inclusion of 10 mL/L of the RNase inhibitor NucleoGuard (AmpTec) in the lysis buffer improved RNA yield and recoveries of long transcripts. All samples were treated with TURBO DNA-free (Ambion) to remove trace amounts of genomic DNA. A 2-round amplification was performed with the ExpressArt TRinucleotide mRNA Amplification Kit (AmpTec) according to the manufacturer’s instructions.

treatment_protocol: Sham surgery vs 8 min cardiac arrest + resuscitation

value: F

tag: batch

value: B

value: Arrest

value: heart


title: Arrest7

value: M


title: Arrest5


title: Arrest8


title: Arrest3

value: A


title: Arrest2


title: Arrest4


title: Arrest1


title: Sham7

source_name: Sham

value: Sham


title: Sham3


title: serum 34 SH89S29_Cell2

city: Kamakura

first: Satoshi

last: Kondo

state: Kanagawa

address: Tebiro 6-10-1

department: New Projects Development Division

institute: Toray Industries,Inc.

hyb_protocol: Hybridized for 16 h at 32 C with rotary shake (250 rpm). Hybridization buffer and washing protocol was followed by the protocol supplied by TORAY Industries, Inc..

scan_protocol: 3D-Gene Scanner ((Toray Industries Inc., Tokyo, Japan) was used for scanning. Images were quantified using Extraction(Toray Industries Inc., Tokyo, Japan).

data_processing: The raw data of each spot was normalized by substitution with a mean intensity of the background signal determined by all blank spots’ signal intensities of 95% confidence intervals.

source_name: healthy individual

label_protocol: Extracted total RNA was labeled with Cy5 using the 3D-Gene miRNA labeling kit (Toray Industries Inc., Tokyo, Japan).

growth_protocol: All samples have not been used steroid for over three months.

extract_protocol: RNA samples were extracted from serum using 3D-Gene extraction reagent from liquid sample(Toray Industries Inc., Tokyo, Japan).

treatment_protocol: A sample of venous blood (~5.0 mL) was collected from each patient enrolled in this study. The samples were placed in tubes and centrifuged (8000 rpm, 4 °C, 15 min) to collect the serum, which was stored at −80 °C until further analysis. Surgically biopsied specimens of IgG4-ROD and orbital MALT lymphoma were delivered immediately to the laboratory and stored at −80 °C until the assay.

tag: diagnosis

value: healthy individual

value: serum

tag: age

tag: swollen eyelid

value: N

tag: diplopia

tag: decrease of vision

tag: other organ lesion


title: serum 32 SH89S28_Cell1

tag: tissue

tag: Sex


title: Sham4


title: serum 33 SH89S29_Cell1


title: Ly6C-Hi+CF_Rep3

city: Baltimore

first: Daniela

last: Cihakova M.D. Ph.D. D(ABMLI)

state: MD

address: 720 Rutland Avenue

department: Pathology-Immunopathology

institute: The Johns Hopkins University School of Medicine

hyb_protocol: Hybridization was 16hrs at 45° C with rotation (60rpm) as described by Affymetrix in their GeneChip Expression Analysis Technical Manual

scan_protocol: Using the Affymetrix GeneChip Scanner 3000 7G and default parameters described by the manufacturer in their GeneChip Expression Analysis Technical Manual

data_processing: Affymetrix CEL files were extracted with the Partek GS 6.6 platform and their data RMA and quantile-normalized to create log2 transcript signal values that were used in subsequent two-tailed one-way ANOVA analysis.

source_name: Ly6Chi + CF

label_protocol: The Affymetrix3' IVT Pico Kit kit was used with the Affymetrix protocol.

growth_protocol: Cells were plated in DMEM (Gibco)  with 20% FBS (GE Healthcare Life Sciences), nonessential amino acids (Sigma), Penicillin/Streptomycin, 2mM L-Glutamine, and 25mM HEPES (all Quality Biological). Non-adherent cells were washed away after 1h. Fibroblasts from second passage were used in experiments.

extract_protocol: Total RNA was extracted using QIAGEN miRNeasy kit mini columns and QIAGEN protocol.

treatment_protocol: Recombinant mouse IL-17A cytokines at 50 ng/mL (Peprotech) were used after second passage of the fibroblasts.

value: spleen

tag: cell type

value: Ly6Chi monocytes

tag: culture protocol

value: splenic monocytes co-cultured with cardiac fibroblasts

value: control


title: serum 35 SH89S29_Cell3


title: Sham2


title: Sham6


title: Ly6C-Lo+CF_Rep2

source_name: Ly6lo + CF

value: Ly6lo monocytes


title: Sham5


title: Sham8


title: Ly6C-Hi+CF+Il17A_Rep3

source_name: Ly6Chi + CF + IL-17

value: IL-17A stimulation


title: serum 26 SH88131_Cell1


title: serum 25 SH87Z38_Cell3


title: serum 24 SH8XB59_Cell4

source_name: orbital MALT lymphoma

value: orbital MALT lympoma

value: P


title: Ly6C-Lo+CF_Rep3


title: Ly6C-Hi+CF_Rep2


title: Ly6C-Lo+CF_Rep1


title: serum 21 SH87Z36_Cell2

value: F


title: serum 28 SH88131_Cell3


title: serum 29 SH88131_Cell4


title: serum 27 SH88131_Cell2


title: serum 30 SH88138_Cell4


title: serum 19 SH87Z28_Cell3

value: abdomen lymph node


title: serum 12 SH87Z04_Cell4


title: serum 14 SH87Z10_Cell2


title: serum 22 SH8XB57_Cell4


title: Sham1

value: heart


title: serum 18 SH87Z27_Cell1


title: serum 16 SH87Z18_Cell4


title: serum 17 SH87Z23_Cell3

value: mediastinal lymph nodes


title: serum 15 SH87Z17_Cell2

value: M


title: serum 23 SH8XB58_Cell1


title: serum 13 SH87Z06_Cell1


title: Ly6C-Hi+CF_Rep1


title: serum 20 SH87Z34_Cell2