title: Fbxl19_fl_KO_RA_rep1

city: Oxford

first: Emilia

last: Dimitrova

address: South Parks Road

department: Biochemistry

institute: University of Oxford

data_processing:
rRNA reads were initially removed by aligning the data to mouse rRNA genomic sequences (GenBank: BK000964.3) using bowtie2. The rRNA-depleted reads were next aligned against mm10 genome using the STAR RNA-seq aligner (Dobin et al., 2012). To improve mapping of nascent, intronic sequences, a second alignment step with bowtie2 was included using the reads which failed to map using STAR. PCR duplicates were removed using samtools (Li et al., 2009).
Genome_build: mm10
Supplementary_files_format_and_content: Stranded bigWig files representing genome coverage for merged biological triplicate.

growth_protocol: Fbxl19fl/fl mouse ES cells were cultured on gelatine-coated dishes in DMEM (Thermo scientific) supplemented with 15% fetal bovine serum (BioSera), L-Glutamine, beta-mercaptoethanol, non-essential amino acids, penicillin/streptomycin (Thermo scientific) and 10ng/mL leukemia-inhibitory factor.

extract_protocol:
For labelling of nascent RNA transcripts, cells were grown in 15cm culture dishes. Labelling was performed for 20 minutes at 37°C by the addition of 50mM 4-thiouridine (T4509, Sigma) to the culture medium. After the incubation, the medium was removed and RNA was isolated using TRIzol reagent (Thermo scientific) following manufacturer’s instructions. The total RNA was treated with TURBO DNA-free kit (Ambion, Thermo scientific) in order to remove contaminating genomic DNA. 300µg RNA was biotinylated using 600 µg Biotin-HPDP (21341, Pierce, Thermo scientific) in Biotinylation buffer (100mM Tris-HCl pH 7.4, 10mM EDTA). The reaction was carried out for one and half hour on a rotor at room temperature. Unincorporated Biotin-HPDP was removed by chloroform/isoamylalcohol (24:1, Sigma) wash followed by isopropanol precipitation of the biotinylated RNA. Labelled biotinylated RNA was isolated using µMacs Streptavidin Kit (130-074-101, Miltenyi) following manufacturer’s instructions and purified using RNeasy MinElute Cleanup kit (Qiagen). The quality of the RNA was confirmed using the RNA pico Bioanalyser kit (Agilent).
Up to 1µg purified 4sU-labelled RNA was used to prepare libraries for 4sU-seq. Ribosomal RNA was removed using NEBNext® rRNA Depletion Kit and libraries were prepared using NEBNext® Ultra™ Directional RNA Library Prep Kit for Illumina (NEB) following manufacturer’s instructions. Library quality was assessed using the High-sensitivity DS DNA Bioanalyser kit (Agilent) and the concentration was measured by quantitative PCR using KAPA Library quantification standards for Illumina (KAPA Bioasystems). All RNA-seq experiments were carried out in biological triplicates. RNA-seq libraries were sequenced as 76 paired-end reads on Illumina NextSeq500 platform using NextSeq® 500/550 High Output Kit v2 (150 cycles).

treatment_protocol: Fbxl19fl/fl ES cells were treated with 800nM 4-hydroxytamoxifen (Sigma) for 72 hours in order to delete the CxxC domain. For differentiation of ES cells, 4x10^4 cells/cm2 were allowed to attached to gelatinised dishes (~12 hours) and treated with 1µM retinoic acid (Sigma-Aldrich) in EC-10 medium (DMEM supplemented with 10% fetal bovine serum, L-Glutamine, beta-mercaptoethanol, non-essential amino acids and penicillin/streptomycin) for 72 hours.

value: mouse embryonic stem cells

tag: passage

tag: treated with

value: 800nM 4-hydroxytamoxifen for 72 h

tag: differentiation

value: 1µM retinoic acid for 72 hrs

tag: molecule subtype

value: nascent RNA


title: Fbxl19_fl_KO_RA_rep2

status: Public on Jun 08 2018

type: SRA

country: United Kingdom

library_source: transcriptomic

molecule: total RNA

organism: Mus musculus

tag: cell line

tag: cell type

tag: replicate


title: Fbxl19_fl_KO_RA_rep3


title: Fbxl19_fl_WT_RA_rep3

value: none (untreated)


title: Fbxl19_fl_WT_RA_rep2


title: Fbxl19_fl_WT_RA_rep1


title: Fbxl19fl_72hrTAM_rep3

value: no


title: 496_02

city: La Jolla

first: Gene

last: Yeo

state: CA

address: 2880 Torrey Pines Scenic Dr. Room 3805/Yeo Lab

country: USA

institute: UCSD

data_processing:
Library strategy: eCLIP-seq
Takes output from raw files.  Run to trim off both 5’ and 3’ adapters on both reads. Command: quality-cutoff 6  -m 18  -a NNNNNAGATCGGAAGAGCACACGTCTGAACTCCAGTCAC  -g CTTCCGATCTACAAGTT -g CTTCCGATCTTGGTCCT  -A AACTTGTAGATCGGA -A AGGACCAAGATCGGA -A ACTTGTAGATCGGAA -A GGACCAAGATCGGAA -A CTTGT  AGATCGGAAG -A GACCAAGATCGGAAG -A TTGTAGATCGGAAGA -A ACCAAGATCGGAAGA -A TGTAGATCGGAAGAG -A CCAAGATCGGAAGAG -A GTAGATCGGAAGAGC -A CAAGATCGGAAGAGC -A TAGATCGGAAGAGCG -A AAGATCGGAAGAGCG -A AGATCGGAAGAGCGT -A GATCGGAAGAGCGTC -A ATCGGAAGAGCGTCG -A TCGGAAGAGCGTCGT -A CGGAAGAGCGTCGTG -A GGAAGAGCGTCGTGT  -o /full/path/to/files/file_R1.C01.fastq.gz.adapterTrim.fastq.gz  -p /full/path/to/files/file_R2.C01.fastq.gz.adapterTrim.fastq.gz  /full/path/to/files/file_R1.C01.fastq.gz /full/path/to/files/file_R2.C01.fastq.gz > /full/path/to/files/file_R1.C01.fastq.gz.adapterTrim.metrics
Takes output from cutadapt round 1. Run to trim off the 3’ adapters on read 2, to control for double ligation events. Command: cutadapt -f fastq --match-read-wildcards  --times 1  -e 0.1  -O 5  --quality-cutoff 6  -m 18  -A AACTTGTAGATCGGA -A AGGACCAAGATCGGA -A ACTTGTAGATCGGAA -A GGACCAAGATCGGAA -A CTTGTAGATCGGAAG -A GACCAAGATCGGAAG -A TTGTAGATCGGAAGA -A ACCAAGATCGGAAGA -A TGTAGATCGGAAGAG -A CCAAGATCGGAAGAG -A GTAGATCGGAAGAGC -A CAAGATCGGAAGAGC -A TAGATCGGAAGAGCG -A AAGATCGGAAGAGCG -A AGATCGGAAGAGCGT -A GATCGGAAGAGCGTC -A ATCGGAAGAGCGTCG -A TCGGAAGAGCGTCGT -A CGGAAGAGCGTCGTG -A GGAAGAGCGTCGTGT  -o /full/path/to/files/file_R1.C01.fastq.gz.adapterTrim.round2.fastq.gz  -p /full/path/to/files/file_R2.C01.fastq.gz.adapterTrim.round2.fastq.gz  /full/path/to/files/file_R1.C01.fastq.gz.adapterTrim.fastq.gz  /full/path/to/files/file_R2.C01.fastq.gz.adapterTrim.fastq.gz > /full/path/to/files/file_R1.C01.fastq.gz.adapterTrim.round2.metrics
Takes output from cutadapt round 2.  Maps to human specific version of RepBase used to remove repetitive elements, helps control for spurious artifacts from rRNA (& other) repetitive reads.  Command: STAR  --runMode alignReads  --runThreadN 16  --genomeDir /path/to/RepBase_human_database_file --genomeLoad LoadAndRemove  --readFilesIn /full/path/to/files/file_R1.C01.fastq.gz.adapterTrim.round2.fastq.gz /full/path/to/files/file_R2.C01.fastq.gz.adapterTrim.round2.fastq.gz --outSAMunmapped Within  --outFilterMultimapNmax 30  --outFilterMultimapScoreRange 1  --outFileNamePrefix /full/path/to/files/file_R1.C01.fastq.gz.adapterTrim.round2.rep.bam --outSAMattributes All  --readFilesCommand zcat  --outStd BAM_Unsorted  --outSAMtype BAM Unsorted  --outFilterType BySJout  --outReadsUnmapped Fastx  --outFilterScoreMin 10  --outSAMattrRGline ID:foo  --alignEndsType EndToEnd > /full/path/to/files/file_R1.C01.fastq.gz.adapterTrim.round2.rep.bam
Takes output from STAR rmRep.  Maps unique reads to the human genome.  Command: STAR  --runMode alignReads  --runThreadN 16  --genomeDir  /path/to/STAR_database_file --genomeLoad LoadAndRemove  --readFilesIn  /full/path/to/files/file_R1.C01.fastq.gz.adapterTrim.round2.rep.bamUnmapped.out.mate1  /full/path/to/files/file_R1.C01.fastq.gz.adapterTrim.round2.rep.bamUnmapped.out.mate2  --outSAMunmapped Within  --outFilterMultimapNmax 1  --outFilterMultimapScoreRange 1  --outFileNamePrefix /full/path/to/files/file_R1.C01.fastq.gz.adapterTrim.round2.rmRep.bam  --outSAMattributes All  --outStd BAM_Unsorted  --outSAMtype BAM Unsorted  --outFilterType BySJout  --outReadsUnmapped Fastx  --outFilterScoreMin 10  --outSAMattrRGline ID:foo  --alignEndsType EndToEnd > /full/path/to/files/file_R1.C01.fastq.gz.adapterTrim.round2.rmRep.bam
takes output from STAR genome mapping.  Custom random-mer-aware script for PCR duplicate removal. Command: barcode_collapse_pe.py  --bam /full/path/to/files/file_R1.C01.fastq.gz.adapterTrim.round2.rmRep.bam  --out_file /full/path/to/files/file_R1.C01.fastq.gz.adapterTrim.round2.rmRep.rmDup.bam  --metrics_file /full/path/to/files/file_R1.C01.fastq.gz.adapterTrim.round2.rmRep.rmDup.metrics
Takes output from barcode collapse PE.  Sorts resulting bam file for use downstream.  Command: java  -Xmx2048m  -XX:+UseParallelOldGC  -XX:ParallelGCThreads=4  -XX:GCTimeLimit=50  -XX:GCHeapFreeLimit=10  -Djava.io.tmpdir=/full/path/to/files/.queue/tmp  -cp /path/to/gatk/dist/Queue.jar  net.sf.picard.sam.SortSam  INPUT=/full/path/to/files/file_R1.C01.fastq.gz.adapterTrim.round2.rmRep.rmDup.bam  TMP_DIR=/full/path/to/files/.queue/tmp  OUTPUT=/full/path/to/files/file_R1.C01.fastq.gz.adapterTrim.round2.rmRep.rmDup.sorted.bam  VALIDATION_STRINGENCY=SILENT  SO=coordinate  CREATE_INDEX=true
Takes output from sortSam, makes bam index for use downstream.  Command: samtools index  /full/path/to/files/file_R1.C01.fastq.gz.adapterTrim.round2.rmRep.rmDup.sorted.bam  /full/path/to/files/file_R1.C01.fastq.gz.adapterTrim.round2.rmRep.rmDup.sorted.bam.bai
Takes inputs from multiple final bam files.  Merges the two technical replicates for further downstream analysis.  Command: samtools  merge  /full/path/to/files/CombinedID.merged.bam  /full/path/to/files/file_R1.C01.fastq.gz.adapterTrim.round2.rmRep.rmDup.sorted.bam /full/path/to/files/file_R1.D08.fastq.gz.adapterTrim.round2.rmRep.rmDup.sorted.bam
Takes output from sortSam, makes bam index for use downstream.  Command: samtools  index  /full/path/to/files/CombinedID.merged.bam  /full/path/to/files/CombinedID.merged.bam.bai
Takes output from sortSam.  Only outputs the second read in each pair for use with single stranded peak caller.  This is the final bam file to perform analysis on.  Command: samtools view -hb -f 128  /full/path/to/files/CombinedID.merged.bam  >  /full/path/to/files/CombinedID.merged.r2.bam
Takes results from samtools view.  Calls peaks on those files.  Command: clipper  -b /full/path/to/files/CombinedID.merged.r2.bam  -s hg19  -o /full/path/to/files/CombinedID.merged.r2.peaks.bed  --bonferroni  --superlocal  --threshold-method binomial  --save-pickle
Genome_build: hg19
Supplementary_files_format_and_content: bed format, contains clusters of predicted RBP binding

organism: Homo sapiens

growth_protocol: HepG2 cells were grown under standard conditions (DMEM + 10% FBS + Pen/Strep (100U / mL)). K562 cells were grown in suspension in standard media (RPMI + 10% FBS + Pen/Strep (100U / mL)).

extract_protocol:
Cells were lysed in iCLIP lysis buffer, followed by limited digestion with RNase I (Ambion), immunoprecipitation of RBP-RNA complexes with a specific antibody of interest (Protein G sheep anti-rabbit Dynabeads), and stringent washes.
After dephosphorylation with FastAP (Thermo Fisher) and T4 PNK (NEB), a barcoded RNA adapter is ligated to the 3’ end (T4 RNA Ligase, NEB) (at this step, multiple replicates of the same RBP, or potentially RBPs of similar size and bound RNA amount, can be uniquely barcoded and pooled after ligation to simplify downstream steps - see Supplementary Fig. 2A). Ligations are performed on-bead (to allow washing away unincorporated adapter) in high concentration of PEG8000, which improves ligation efficiency to > 90%. Samples are then run on standard protein gels and transferred to nitrocellulose membranes, and a region 75 kDa (~150 nt of RNA) above the protein size is isolated and proteinase K (NEB) treated to isolate RNA. RNA is reverse transcribed with AffinityScript (Agilent), and treated with ExoSAP-IT (Affymetrix) to remove excess oligonucleotides. A second DNA adapter (containing a random-mer of 5 (N5) or 10 (N10) random bases at the 5’ end) is then ligated to the cDNA fragment 3’ end (T4 RNA Ligase, NEB), performed with high concentration of PEG8000 (to improve ligation efficiency) and DMSO (to decrease inhibition of ligation due to secondary structure). After cleanup (Dynabeads MyOne Silane, ThermoFisher), an aliquot of each sample is first subjected to qPCR (to identify the proper number of PCR cycles), and then the remainder is PCR amplified (Q5, NEB) and size selected via agarose gel electrophoresis.

treatment_protocol: While plated, HepG2 cells were crosslinked with UV (254 nm, 400 mJ/cm2). HepG2 cells were then isolated with cell scrapers, pelleted at 200g, and snap frozen. K562 suspension cells were pelleted at 200g and resuspended in 1X PBS to 20 million cells per mL. 60 million cells in 3 mL were UV crosslinked (254 nm, 400 mJ/cm2) per 10 cm dish, pelleted, and snap frozen.

tag: barcodes

tag: antibody

value: AATF

tag: antibody catalog#

tag: antibody lot#


title: Fbxl19fl_UNT_rep3


title: Fbxl19fl_UNT_rep2


title: Fbxl19fl_72hrTAM_rep2


title: Fbxl19flfl_OHT_Input_rep1

library_source: genomic

data_processing:
Sequencing reads were aligned to the mouse genome (mm10) using bowtie2 (Langmead and Salzberg, 2012) the '-no-mixed' and '-no-discordant' options, and non-uniquely mapping reads were discarded . PCR duplicates were removed using samtools (Li et al., 2009).
Peak calling was performed using the MACS2 function with the “--broad” option using the biological replicates with matched input. Peak overlapping with a custom “blacklist” of artificially high genomic regions were discarded. Only peaks called in both replicates were considered.
Genome_build: mm10
Supplementary_files_format_and_content: Biological replicates were randomly downsampled to the same number of reads for each individual replicate and merged for visualisation. Bigwig files were generated using MACS2

molecule: genomic DNA

extract_protocol:
Chromatin immunoprecipitation was performed as described previously (Farcas et al., 2012) with slight modifications. Cells were fixed for 45 min with 2mM DSG (Thermo scientific) in PBS and 12.5 min with 1% formaldehyde (methanol-free, Thermo scientific). Reactions were quenched by the addition of glycine to a final concentration of 125µM. After cell lysis and chromatin extraction, chromatin was sonicated using a BioRuptor Pico sonicator (Diagenode), followed by centrifugation at 16,000×g for 20min at 4°C. 200µg chromatin diluted in ChIP dilution buffer (1% Triton-X100, 1mM EDTA, 20mM Tris-HCl (pH 8.0), 150mM NaCl) was used per IP. Chromatin was precleared with protein A Dynabeads blocked with 0.2 mg/ml BSA and 50 µg/ml yeast tRNA and incubated with the respective antibodies overnight at 4°C. Antibody-bound chromatin was purified using blocked protein A Dynabeads for 3 hours at 4°C. ChIP washes were performed as described previously (Farcas et al., 2012). ChIP DNA was eluted in ChIP elution buffer (1% SDS, 100mM NaHCO3) and reversed cross-linked overnight at 65°C with 200mM NaCl and RNase A (Sigma). The reverse cross-linked samples were treated with 20ug/ml Proteinase K and purified using ChIP DNA Clean&Concentrator™ kit (Zymo research).
ChIP DNA material was sheared with BioRuptor Pico sonicator to obtain DNA fragments of average size 200-800 bp. ChIPseq libraries were prepared with  30-40ng of ChIP DNA material using NEBNext Ultra DNA Library Prep Kit.

treatment_protocol: To generate Fbxl19ΔCXXC ES cells, cells were treated with 800nM 4-hydroxytamoxifen for 96 hours

value: Fbxl19 fl/fl

value: 800nM 4-hydroxytamoxifen for 96 h

value: input control


title: Fbxl19fl_UNT_rep1


title: Fbxl19flfl_OHT_CDK8_rep2

value: CDK8 (Bethyl Laboratories, A302-500A, lot A302-500A-1)


title: Fbxl19flfl_UNT_Input_rep2


title: Fbxl19flfl_OHT_CDK8_rep1


title: Fbxl19flfl_UNT_Input_rep1


title: Fbxl19flfl_UNT_CDK8_rep2


title: Fbxl19flfl_UNT_CDK8_rep1


title: stage16 rep1

city: Taipei

first: Jia-Ming

last: Chang

address: NO.64, Sec. 2, ZhiNan Rd., Wenshan District

department: Department of Computer Science

country: Taiwan

institute: National Chengchi University

description: HiC stage16 rep1

data_processing:
library strategy: HiC-seq
Paired-end reads were mapped to the Drosophila melanogaster genome (assembly dm3) using the bowtie program with parameters (-t -a -m 1 --best).  Unmapped or non-unique mapped reads were discarded.
We then divided read pairs into four groups: SS (reads mapping to the same restriction fragment, or to two adjacent restriction fragments); S2 (reads in which both ends mapped precisely on the DpnII site); S1 (reads in which one of the ends mapped precisely on the DpnII site); S0 (reads in which both ends did not map precisely to a DpnII site). SS, S2 and S1 pairs were discarded from subsequent analysis.
Mapped reads were then associated with the first restriction fragment end encountered when moving from the mapped position in the appropriate strand.
All subsequent analysis was done in the space of fragment end pairs. The Drosophila genome contains 464,246 restriction fragments. After discarding low mappability fragments 301,687 fragments are left (and each defines two fragment ends).
A model accounting for systematic biases in contact probability was constructed as previously (Yaffe and Tanay; Nature Genetics, 43, p.1059-65). Briefly, we used the local G+C content of up to 200 bp from the restriction site (agc, bgc), and the DpnII restriction fragment lengths (alen, blen), to correct for systematic biases in Hi-C coverage by modeling: P(Xa,b) = Pprior x Flen(alen,blen) x Fgc(agc,bgc).
We estimated maximum likelihood model parameters (the matrices Flen and Fgc) through application of an iterative algorithm as described, using 20 bins for G+C content and 20 bins for fragment length.
Genome_build: dm3

Supplementary_files_format_and_content: *.bins: the real genomic co-ordinates of the involved *bins (e.g. C1-8_160000.bins.txt.gz - chromosome coordinates for 160 kb paired bins);
cbin - the identity of the bin
chr - chromosome
from.coord - start co-ordinate of bin
to.coord - end co-ordinate of the bin
count - the number of fends contained within the bin

Supplementary_files_format_and_content: *.n_contact: give the contact score maps for *kb paired bins (e.g. C1-8_160000.n_contact.txt.gz - observed and expected interaction scores for 160 kb paired bins);
cbin1 - the identity of the first bin
cbin2 - the identity of the second bin
expected_count - the number of counts expected for this pairwise bin combination, based on the technical normalisation
observed_count - the number of tags counted from the Hi-C dataset for this pairwise bin combination

organism: Drosophila melanogaster

source_name: stage16 embryo

growth_protocol: Oregon-R w1118 flies were grown in standard cornmeal yeast extract media at 25°C. Embryos are collected from cage with apple juice plate supplemented with yeast.

extract_protocol:
embryos were collected in a saline buffer (0.03% Triton X-100, 0.4% NaCl) 16-18 hr after egg laying, then de-chorionated for 5 min in fresh bleach. Embryos were sorted with a Union Biometra COPAS Large Particle Sorter (Union Biometra Inc, Holliston, MA). sorted embryos were washed with n-heptane and fixed with 2% formaldehyde.
For the steps after the fixation of sorted embryos, we basically followed the in situ Hi-C protocol previously reported (Rao et al., 2014). Briefly, fixed nuclei were digested overnight at 37°C using 500 U of DpnII. After biotin filling, proximity ligation was carried out for 4 hr at 18°C with 2000 U T4 DNA Ligase, and after reverse-crosslinking, DNA was purified with ethanol precipitation and sheared to 300-400 bp fragments using a Covaris S220 sonicator.
Ligation fragments with biotin were pulled-down using MyOne Streptavidin T1 beads (ThermoFisher Cat.N: 65602), end-repaired and adenylated as described. Fragments were then ligated with NEXTflex adaptors (Bioo Scientific, Cat.N: 514101) and amplified by PCR using KAPA HiFi Library Ampification Kit (Kapa Biosystems, Cat.N: KK2620) for 8 cycles. DNA size-selection (300-800 bp) was done using AMPure XP beads (Agencourt, Cat.N: A63881).

tag: strain

value: Oregon-R w1118

tag: genotype/variation

value: wild type

tag: developmental stage

value: embryonic stage 16


title: cycles1-8 rep2

description:
HiC cycles1-8 rep2
Please note that the processed data was generated from both replicates (*rep1 and *rep2) and linked to 'rep 1' sample records (i.e. cycles1-8 rep1).

source_name: cycles1-8 embryo

extract_protocol:
embryos were collected in a saline buffer (0.03% Triton X-100, 0.4% NaCl) 30 minutes after egg laying, then embryos were hand sorted based on their morphology. sorted embryos were washed with n-heptane and fixed with 2% formaldehyde.
For the steps after the fixation of sorted embryos, we basically followed the in situ Hi-C protocol previously reported (Rao et al., 2014). Briefly, fixed nuclei were digested overnight at 37°C using 500 U of DpnII. After biotin filling, proximity ligation was carried out for 4 hr at 18°C with 2000 U T4 DNA Ligase, and after reverse-crosslinking, DNA was purified with ethanol precipitation and sheared to 300-400 bp fragments using a Covaris S220 sonicator.
Ligation fragments with biotin were pulled-down using MyOne Streptavidin T1 beads (ThermoFisher Cat.N: 65602), end-repaired and adenylated as described. Fragments were then ligated with NEXTflex adaptors (Bioo Scientific, Cat.N: 514101) and amplified by PCR using KAPA HiFi Library Ampification Kit (Kapa Biosystems, Cat.N: KK2620) for 8 cycles. DNA size-selection (300-800 bp) was done using AMPure XP beads (Agencourt, Cat.N: A63881).

value: embryo cleavage cycles 1-8


title: stages5-8 rep2

description:
HiC stages5-8 rep2
Please note that the processed data was generated from both replicates (*rep1 and *rep2) and linked to 'rep 1' sample records (i.e. stages5-8 rep1).

source_name: stages5-8 embryo

extract_protocol:
embryos were collected in a saline buffer (0.03% Triton X-100, 0.4% NaCl) after 60 minutes of egg laying and 105 minutes of incubation, then embryos were hand sorted based on their morphology. sorted embryos were washed with n-heptane and fixed with 2% formaldehyde.
For the steps after the fixation of sorted embryos, we basically followed the in situ Hi-C protocol previously reported (Rao et al., 2014). Briefly, fixed nuclei were digested overnight at 37°C using 500 U of DpnII. After biotin filling, proximity ligation was carried out for 4 hr at 18°C with 2000 U T4 DNA Ligase, and after reverse-crosslinking, DNA was purified with ethanol precipitation and sheared to 300-400 bp fragments using a Covaris S220 sonicator.
Ligation fragments with biotin were pulled-down using MyOne Streptavidin T1 beads (ThermoFisher Cat.N: 65602), end-repaired and adenylated as described. Fragments were then ligated with NEXTflex adaptors (Bioo Scientific, Cat.N: 514101) and amplified by PCR using KAPA HiFi Library Ampification Kit (Kapa Biosystems, Cat.N: KK2620) for 8 cycles. DNA size-selection (300-800 bp) was done using AMPure XP beads (Agencourt, Cat.N: A63881).

value: embryonic stages 5-8


title: cycle14 late rep2

description:
HiC cycle14 late rep2
Please note that the processed data was generated from both replicates (*rep1 and *rep2) and linked to 'rep 1' sample records (i.e. cycle14 late rep1).

source_name: cycle14 late embryo

value: embryo cleavage cycle 14 late


title: Fbxl19fl_72hrTAM_rep1

value: mouse embryonic stem cells


title: cycles9-13 rep2

description:
HiC cycles9-13 rep2
Please note that the processed data was generated from both replicates (*rep1 and *rep2) and linked to 'rep 1' sample records (i.e. cycles9-13 rep1).

source_name: cycles9-13 embryo

extract_protocol:
embryos were collected in a saline buffer (0.03% Triton X-100, 0.4% NaCl) after 30 minutes of egg laying and 50 minutes of incubation, then embryos were hand sorted based on their morphology. sorted embryos were washed with n-heptane and fixed with 2% formaldehyde.
For the steps after the fixation of sorted embryos, we basically followed the in situ Hi-C protocol previously reported (Rao et al., 2014). Briefly, fixed nuclei were digested overnight at 37°C using 500 U of DpnII. After biotin filling, proximity ligation was carried out for 4 hr at 18°C with 2000 U T4 DNA Ligase, and after reverse-crosslinking, DNA was purified with ethanol precipitation and sheared to 300-400 bp fragments using a Covaris S220 sonicator.
Ligation fragments with biotin were pulled-down using MyOne Streptavidin T1 beads (ThermoFisher Cat.N: 65602), end-repaired and adenylated as described. Fragments were then ligated with NEXTflex adaptors (Bioo Scientific, Cat.N: 514101) and amplified by PCR using KAPA HiFi Library Ampification Kit (Kapa Biosystems, Cat.N: KK2620) for 8 cycles. DNA size-selection (300-800 bp) was done using AMPure XP beads (Agencourt, Cat.N: A63881).

value: embryo cleavage cycles 9-13


title: cycle14 early rep2

description:
HiC cycle14 early rep2
Please note that the processed data was generated from both replicates (*rep1 and *rep2) and linked to 'rep 1' sample records (i.e. cycle14 early rep1).

source_name: cycle14 early embryo

value: embryo cleavage cycle 14 early


title: E14_Input_rep2

description: E14 embryonic stem cell line stabily expressing FS2-tagged transgene

data_processing:
Sequencing reads were aligned to the mouse genome (mm10) using bowtie2 (Langmead and Salzberg, 2012) the '-no-mixed' and '-no-discordant' options, and non-uniquely mapping reads were discarded. PCR duplicates were removed using samtools (Li et al., 2009).
Peak calling was performed using the MACS2 function with the “--broad” option using the biological replicates with matched input. Peak overlapping with a custom “blacklist” of artificially high genomic regions were discarded.
Genome_build: mm10
Supplementary_files_format_and_content: Biological replicates were randomly downsampled to the same number of reads for each individual replicate and merged for visualisation. Bigwig files were generated using MACS2

growth_protocol: E14 mouse ES cells, stably expressing the respective epitope-tagged FBXL19 transgene, were cultured on gelatine-coated dishes in DMEM (Thermo scientific) supplemented with 15% fetal bovine serum (BioSera), L-Glutamine, beta-mercaptoethanol, non-essential amino acids, penicillin/streptomycin (Thermo scientific) and 10ng/mL leukemia-inhibitory factor in the presence of 1 µg/ml puromycin

extract_protocol:
Chromatin immunoprecipitation was performed as described previously (Farcas et al., 2012) with slight modifications. Cells were fixed for 45 min with 2mM DSG (Thermo scientific) in PBS and 12.5 min with 1% formaldehyde (methanol-free, Thermo scientific). Reactions were quenched by the addition of glycine to a final concentration of 125µM. After cell lysis and chromatin extraction, chromatin was sonicated using a BioRuptor Pico sonicator (Diagenode), followed by centrifugation at 16,000×g for 20min at 4°C. 200µg chromatin diluted in ChIP dilution buffer (1% Triton-X100, 1mM EDTA, 20mM Tris-HCl (pH 8.0), 150mM NaCl) was used per IP. Chromatin was precleared with protein A Dynabeads blocked with 0.2 mg/ml BSA and 50 µg/ml yeast tRNA and incubated with the respective antibodies overnight at 4°C. Antibody-bound chromatin was purified using blocked protein A Dynabeads for 3 hours at 4°C. ChIP washes were performed as described previously (Farcas et al., 2012). ChIP DNA was eluted in ChIP elution buffer (1% SDS, 100mM NaHCO3) and reversed cross-linked overnight at 65°C with 200mM NaCl and RNase A (Sigma). The reverse cross-linked samples were treated with 20ug/ml Proteinase K and purified using ChIP DNA Clean&Concentrator™ kit (Zymo research).
ChIP DNA was sheared with Bioruptor sonicator to generate DNA fragments between 100-350bp. Libraries were prepared using the NEBNext Fast DNA fragmentation and library preparation kit for Ion Torrent (NEB, E6285S) following manufacturer’s instructions. Briefly, 30-40ng ChIP or input DNA material was used. Libraries were size-selected for 250bp fragments using 2% E-gel SizeSelect gel (Thermo scientific) . Templates were generated with Ion PI™ Template OT2 200 kit v3 and Ion PI™ Sequencing 200 kit v3, or with Ion PI IC 200 kit (Thermo scientrific). Libraries were sequenced on the Ion Proton Sequencer using Ion PI™ chips v2 (Thermo scientific)

value: embryonic stem cell line

tag: transgene

value: Input

tag: fs2-tagged fbxl19 genotype

value: Input DNA


title: EV_FS2_rep3

value: empty vector control

value: rabbit FS2 antibody (Farcas et al. 2012)


title: cycles1-8 rep1

description: HiC cycles1-8 rep1


title: cycle14 late rep1

description: HiC cycle14 late rep1


title: stages5-8 rep1

description: HiC stages5-8 rep1


title: cycle14 early rep1

description: HiC cycle14 early rep1


title: Fbxl19flfl_OHT_Input_rep2

value: Fbxl19 fl/fl

value: 800nM 4-hydroxytamoxifen for 96 h


title: E14_Input_rep1


title: EV_FS2_rep1


title: EV_FS2_rep2


title: cycles9-13 rep1

description: HiC cycles9-13 rep1


title: ΔCxxC_FBXL19_FS2_rep2

value: CxxC deletion mutant


title: ΔCxxC_FBXL19_FS2_rep1


title: S3

city: Paris

first: Rachel

last: Legendre

address: 28, rue du docteur Roux

department: Research and Resource Center for Scientific Informatics

country: France

institute: Institut Pasteur

data_processing:
RNA-Seq reads were cleaned of adapter sequences and low-quality sequences using an in-house program (https://github.com/baj12/clean_ngs). Only sequences at least 25 nt in length were considered for further analysis.
Tophat version 1.4.1.1, with default parameters, was used for alignment on the reference genome (Entamoeba histolytica retrieved from amoebaDB1.2).
Genes were counted using HTSeq-count version 0.6.1 (parameters: -t exon -i gene_id -m intersection-nonempty -s no).
Count data were then analyzed using R version 3.2.2 and the Bioconductor package DESeq2 version 1.10.0. The normalization and dispersion estimation were performed with DESeq2 using the default parameters but statistical tests for differential expression were performed without applying the independent filtering algorithm.
Genome_build: Entamoeba histolytica retrieved from amoebaDB1.2
Supplementary_files_format_and_content: matrix of count from HTSeq-count

organism: Entamoeba histolytica

source_name: trophozoites

growth_protocol: E. histolytica trophozoites strain HM-1:IMSS were grown under axenic conditions in Diamond’s TYI S-33 medium at 37◦C. Trophozoites in the exponential phase of growth were used in all experiments.

extract_protocol:
Total RNAs were isolated by Trizol reagent (Sigma) according to the recommendations of the manufacturer.
Libraries were constructed using Truseq mRNA-Seq Library Preparation Kit (Illumina) following manufacturer’s recommendations and were quality controlled using Agilent Bioanalyzer.
Sequencing was performed on a HiSeq 2500 (Illumina) to obtain 65 base single-end reads.

treatment_protocol: Trophozoites preincubated with bacteria (1×106 trophozoites/1×109 bacteria) were incubated for 30 min in Diamond’s TYI S-33 medium without serum at 37◦C. Trophozoites exposed to OS (1×106 trophozoites/ml) were incubated for 60 min in Diamond’s TYI S-33 medium without serum at 37◦C amended with 2.5 mM hydrogen peroxide (H2O2) (Merck, Germany). For the determination of E.histolytica LD50 for H2O2, different concentrations of H2O2 (0 to 5 mM) were used. Trophozoites exposed to an acute NS (1×106 trophozoites/ml) were incubated for 60 min in Diamond’s TYI S-33 medium without serum at 37◦C amended with 350 μM S-Nitrosoglutathione (GSNO) (Sigma-Aldrich, Israel).

tag: state

tag: oxydative stress

value: with OS (+OS)

tag: sample id

value: Sample 3


title: S2

value: Sample 2


title: K49A_FBXL19_FS2_rep2

value: K49A FS2-FBXL19

value: CxxC point mutant

tag: passage


title: K49A_FBXL19_FS2_rep1


title: Khcy-ChIPSeq

city: Beijing

first: Qin

last: Zhang

address: 2 YaBao Road，Chao Yang Distinct

country: China

institute: Capital Institute of Pediatrics

data_processing:
After sequencing data was delivered, we did data filtering first, which could remove low quality reads, N reads and adaptor sequences,  and get clean data. Then, we mapped clean data to reference genome when we made sure the data quantity of clean data was qualified. Also, we needed to make a quality test about  the alignment. Then we used the alignment result to calling peak. Later, we used the peak information for standard bioinformatics analysis and personalized bioinformatics analysis
Data filtering includes removing adaptor sequences, contamination and low-quality reads from raw reads. These reads were detected by BGI programs. Low-quality  reads include three types, and the read which could be accord with anyone of the three types will be removed。Clean Parameter: SOAPnuke1.5.0  filter -l 20 -q 0.5 -n 0.1 -i -c 22
After filtering, the Clean data was then mapped to the reference genome by SOAPaligner/SOAP2 (Version: 2.21t). SOAP2 is a member of the SOAP (Short  Oligonucleotide Analysis Package). It is an updated version of SOAP software for short oligonucleotide alignment. The program features in super fast and accurate  alignment for huge amounts of short reads generated by Illumina/Solexa Genome Analyzer. In the pipeline, clean reads are aligned to the reference sequence by  using SOAP2 aligner. No more than 2 mismatches are allowed in the alignment
MACS (Model-based Analysis for ChIP -Seq, version: MACS-1.4.2) : The candidate Peak region was extended to be long enough for modeling.
Genome_build: mm9

source_name: Mouse neural stem cells

growth_protocol: NE4C cells are an established cell line

extract_protocol:
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody.
Libraries were prepared according to Illumina's instructions accompanying the DNA Sample Kit (Part# 0801-0303). Briefly, DNA was end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment (32 to 52 exo minus) and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3’ end. After adapter ligation DNA was PCR amplified with Illumina primers for 15 cycles and library fragments of ~250 bp (insert plus adaptor and PCR primer sequences) were band isolated from an agarose gel. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Genome Analyzer following the manufacturer's protocols.

treatment_protocol: NE4C are cultured in Eagle MEM  and seeded in a plate that had been precoated with poly-L-lysine

tag: tissue

value: Mouse neural stem cells

tag: chip antibody

value: Hcy


title: stage16 rep2

description:
HiC stage16 rep2
Please note that the processed data was generated from both replicates (*rep1 and *rep2) and linked to 'rep 1' sample records (i.e. stage16 rep1).

extract_protocol:
embryos were collected in a saline buffer (0.03% Triton X-100, 0.4% NaCl) 16-18 hr after egg laying, then late embryos were hand sorted. sorted embryos were washed with n-heptane and fixed with 2% formaldehyde.
For the steps after the fixation of sorted embryos, we basically followed the in situ Hi-C protocol previously reported (Rao et al., 2014). Briefly, fixed nuclei were digested overnight at 37°C using 500 U of DpnII. After biotin filling, proximity ligation was carried out for 4 hr at 18°C with 2000 U T4 DNA Ligase, and after reverse-crosslinking, DNA was purified with ethanol precipitation and sheared to 300-400 bp fragments using a Covaris S220 sonicator.
Ligation fragments with biotin were pulled-down using MyOne Streptavidin T1 beads (ThermoFisher Cat.N: 65602), end-repaired and adenylated as described. Fragments were then ligated with NEXTflex adaptors (Bioo Scientific, Cat.N: 514101) and amplified by PCR using KAPA HiFi Library Ampification Kit (Kapa Biosystems, Cat.N: KK2620) for 8 cycles. DNA size-selection (300-800 bp) was done using AMPure XP beads (Agencourt, Cat.N: A63881).

value: Oregon-R w1118

value: wild type

value: embryonic stage 16


title: h3k4me3-ChIPSeq


title: S1

value: Sample 1


title: L3


title: WT_FBXL19_FS2_rep3

tag: cell line

tag: cell type

value: embryonic stem cell line

value: WT FS2-FBXL19

value: wild-type


title: L2


title: L1


title: K79-Hcy-ChIPSeq


title: WT_FBXL19_FS2_rep1

value: rabbit FS2 antibody (Farcas et al. 2012)

tag: replicate


title: EF3


title: WT_FBXL19_FS2_rep2

tag: antibody


title: HDF161_SIPS_day21

city: Vienna

first: Markus

last: Schosserer

address: Waehringer Strasse 10

department: Center for Pathobiochemistry and Genetics

country: Austria

institute: Medical University of Vienna

description: miRNA-Seq

data_processing:
base calling and adapter trimming: bcl2fastq
mapping: bowtie2
abundance quantification: exq_ngs_mircount (internal Exiqon tool)
miRNA prediction: exq_ngs_mirpred (internal Exiqon tool)
Genome_build: human (Hsa) miRbase 20, assembly version: GRCm38
Supplementary_files_format_and_content: miRNA abundance meassurement (.tsv)

source_name: abdominal skin

growth_protocol: Fibroblasts were isolated from abdominoplasties and cultivated in DMEM/Ham's F12 supplemented with 4 mM L-glutamine and 10% fetal calf serum at 37°C, 7% CO2 and ambient oxygen. Cells were usually passaged twice a week at a 1:2 ratio.

extract_protocol:
Total RNA was isolated with QIAzol Reagent (Qiagen) and RNA was automatically extracted by QIAcube technology based on miRNeasy Mini kit (Qiagen, 217004). RNA concentration and quality was analysed with a Bioanalyzer 2100 using the RNA 6000 Nano Kit (Agilent Technologies).
Intracellular small RNA cDNA library for Illumina Sequencing was synthesized according to the manual provided by NEBNext® Small RNA Library Prep Set for Illumina® (Multiplex Compatible) (NEB, E7330S). From initially 1 µg of total RNA, small RNA fragments of approximately 18 – 36 nucleotides were purified on a 10% TBE gel, quantified by 2100 Bioanalyzer  (Agilent) and equimolar amounts were pooled and sent to Exiqon (Denmark) for Illumina RNA-Seq.

treatment_protocol: Fibroblasts with 15-26 poplation doublings were seeded at 3,500 cells /cm2. SIPS was induced with chronic subtoxic concentrations of 100 uM H2O2 for 9 days (4 days treatment, 2 days break, 5 days treatment). Nontreated control cells reached quiescent (Q) by contact inhibtion by the end of the treatment. Media change of Q cells was done at day 4, 7 and 11.

value: abdominal skin

tag: cell stage

value: H2O2 induced senescence

tag: recovery [days]


title: EF1

tag: strain

value: with OS (+OS)


title: HDF161_quiescent_day21

description: miRNA-Seq

value: quiescent


title: HDF161_SIPS_day7

description: miRNA-Seq


title: HDF161_quiescent_day7

description: miRNA-Seq


title: EC1

value: Trophozoites+E.coli O55


title: HDF85_SIPS_day21

description: miRNA-Seq


title: EC3

value: Trophozoites+E.coli O57

value: Sample 3


title: NI+OS_C

value: NI=non-infected

value: Sample C


title: HDF85_SIPS_day7

description: miRNA-Seq


title: T3

value: Trophozoites alone


title: EF2

value: Sample 2


title: EC2

value: Trophozoites+E.coli O56


title: T1

value: Sample 1


title: HDF85_quiescent_day21

description: miRNA-Seq


title: NI-OS_C

value: without OS (-OS)


title: NI+OS_B

value: Sample B


title: HDF76_SIPS_day21

description: miRNA-Seq


title: NI-OS_B


title: NI+OS_A

value: Sample A


title: HDF76_SIPS_day7

description: miRNA-Seq


title: NI-OS_A


title: LB+OS_C

value: LB=Live E.coli O60


title: T2


title: HDF76_quiescent_day7

description: miRNA-Seq

value: abdominal skin


title: LB+OS_A

value: LB=Live E.coli O56


title: LB+OS_B

value: LB=Live E.coli O58

value: with OS (+OS)


title: LB-OS_C

value: LB=Live E.coli O59


title: LB-OS_B

value: LB=Live E.coli O57


title: LB-OS_A

value: LB=Live E.coli O55


title: KB+OS_A

value: KB=killed E.coli O55


title: KB-OS_B


title: KB+OS_B


title: KB+OS_C

value: Sample C


title: KB-OS_C


title: Normal control-NE4C-RNAseq

data_processing:
Clean-tags were mapped to the reference genome and genes available at the Mice Genome
For gene expression analysis, the matched reads were calculated and then normalized to RPKM using RESM software
The significance of the differential expression of genes was defined by the bioinformatics service of BGI according to the combination of the absolute value of log2-Ratio ≥1 and FDR ≤ 0.001.
Genome_build: mm9

extract_protocol:
normal cultured NE4C and HTL treated NE4C were collected and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard BGISEQ protocols

value: Mouse neural stem cells


title: treatment_513.2hr

city: Cambridge

first: Charles

middle: Arthur

last: Whittaker

state: MA

institute: Koch Institute

data_processing:
Sequencing run with HiSeq Control Software (HCS) version 2.2.38 and Real Time Analysis (RTA) version 1.18.61
Fastq sequences prepared with bcl2fastq version 2.15.0
Sequence alignment and preparation of expected_count and FPKM abundance measurements done using bowtie version 1.0.1, RSEM version 1.2.15 and samtools/0.1.19 with the UCSC known genes annotation file from the mm9 assembly
Genome_build: mm9
Supplementary_files_format_and_content: Processed data files are tab delimited files with RSEM expected counts and FPKM data for each UCSC transcript or transcripts.

source_name: CD11c+ Siglec-F+ alveolar macrophages

growth_protocol: The bronchoalveolar lavage (BAL) fluids of C57BL/6J were flushed and the BAL fluids from 3 mice were pooled together as one sample for sorting the CD11c+ Siglec-F+ alveolar macrophages. Then the cells were cultured in complete RPMI and incubated at 37 celsius degree with or without hematin treatment for 2 hours with 5% CO2.

extract_protocol:
The RNA were extracted by the RNeasy Micro kit (Qiagen).
1 ug RNA processed with Illumina TruSeq followed by cDNA processing on SPRIworks
RNA-Seq 50 nucleotide single-ended reads with 6 nucleotide indicies

treatment_protocol: Hematin was dissolved in 0.1 M NaOH following the Mannual (Sigma). The cells treated with the solvent or 40 μM hematin were defined as mock and treated.

tag: treatment

value: 40 μM Hematin for 2 hours


title: treatment_514.2hr


title: control_515.2hr

value: mock


title: treatment_516.2hr


title: control_517.2hr


title: HDF85_quiescent_day7

description: miRNA-Seq

value: quiescent


title: control_518.2hr


title: KB-OS_A

value: without OS (-OS)


title: HTLtreatment-NE4C-RNAseq


title: HDF76_quiescent_day21

description: miRNA-Seq


title: Mouse fed ND for 16 weeks rep1

status: Public on Jun 07 2018

city: Seoul

first: Je Kyung

last: Seong

department: Veterinary Medicine

country: South Korea

institute: Seoul National University

data_processing:
low quality bases were trimmed at 3' end of read by 'trimmomatic v0.33'
Processed reads were mapped onto mouse genome (mm10/GRCm38) by using 'TopHat v2.0.13'
Read counts were calculated by 'HTSeq v0.6.0'
FPKM was calculated according to the instruction of Mortazavi et al. 2008 Nat Methods
Genome_build: mm10
Supplementary_files_format_and_content: Processed_Data_raw_read_counts.txt

source_name: epididymal white adipose tissue

extract_protocol:
Total RNA extracted from lysate of epididymal white adipose tissue (each sample 60~70 mg)
Library was prepared Following manufacturer's instruction (TruSeq RNA Sample Preparation Kit (Illumina, Sandiago, CA))

tag: age

value: 21 weeks

tag: treatment period

value: 16 weeks

tag: diet

value: normal diet


title: Mouse fed ND for 16 weeks rep3


title: Mouse fed HFD for 4 weeks rep2

value: high fat diet(60% kcal fat)


title: Mouse fed HFD for 4 weeks rep3


title: Mouse fed HFD for 4 weeks rep1


title: Mouse fed ND for 8 weeks after feeding HFD rep3


title: Mouse fed ND for 16 weeks rep2


title: Mouse fed ND for 8 weeks after feeding HFD rep2


title: Mouse re-fed HFD for 4 weeks after weight loss rep3


title: Mouse fed ND for 8 weeks after feeding HFD rep1


title: Mouse re-fed HFD for 4 weeks after weight loss rep2


title: Mouse re-fed HFD for 4 weeks after weight loss rep1


title: Mouse fed ND for 12 weeks rep1

value: 17 weeks

value: 12 weeks


title: Mouse fed ND for 12 weeks rep2


title: Mouse fed ND for 4 weeks after feeding HFD rep3


title: Mouse fed ND for 8 weeks rep2

value: 13 weeks

value: 8 weeks


title: day1_2

city: Charlottesville

first: Christopher

last: Overall

state: Virginia

address: 409 Lane Road

department: Neuroscience

institute: University of Virginia

data_processing:
Base calling an quality scoring performed by real-Time Analysis (RTA) v2.
Raw FASTQ sequencing reads were chastity filtered to remove clusters having outlying intensity corresponding to bases other than the called base.
Filtered reads were assessed for quality using FastQC
Reads were splice-aware aligned to the UCSC mm9 genome using STAR
Reads overlapping Gencode mm9 gene regions were counted using HTSeq.
Genome_build: mm9
Supplementary_files_format_and_content: Tab-delimited text file with the raw counts.

source_name: day1_MACS sorted microglia

growth_protocol: Adult C57BL/6J mice were purchased from Jackson Labs and house in our vivarium prior to use.

extract_protocol:
RNA was extracted using the RNAqueous Micro Kit (Ambion)
All RNA sample processing (including linear RNA amplification and cDNA library generation) and RNA-seq was performed by HudsonAlpha Genomic Services Laboratory

treatment_protocol: no treatment

tag: strain background

value: 2-3 months

tag: genotype

value: wild type

tag: Sex

value: male

value: one day post bilateral optic nerve crush injury

value: lateral geniculate nucleus (LGN)

tag: cell subtype

value: MACS sorted microglia


title: control_2

source_name: Control_MACS sorted microglia

value: Uninjured


title: day3_3

source_name: day3_MACS sorted microglia

value: three days post bilateral optic nerve crush injury


title: Mouse fed ND for 8 weeks rep3


title: Mouse fed ND for 4 weeks after feeding HFD rep1


title: day1_1


title: Mouse fed ND for 4 weeks after feeding HFD rep2


title: day3_2


title: Mouse fed HFD for 8 weeks rep3


title: Mouse fed ND for 8 weeks rep1


title: Mouse fed HFD for 8 weeks rep1


title: day3_1


title: control_1


title: Initial time point on weight cycling progress rep2

value: 5 weeks

value: 0 weeks


title: Mouse fed HFD for 8 weeks rep2


title: Initial time point on weight cycling progress rep3


title: Initial time point on weight cycling progress rep1


title: 32_340_GGGT_8N_L4

city: Haifa

first: Ayelet

last: Lamm

address: Technion st

department: Biology

country: Israel

institute: Technion

description:
small RNA
8N identifier
The barcode can be found in each sequence according to the number indicated in the sample name: sequences in samples which include "8N" in their title start with 8 random bases, followed by their barcode, and sequences in samples which include "0N" in their title begin with their barcode.

data_processing:
Library strategy: QsRNA-seq
Filter sequences with irrelevant barcodes
Split relevant sequences by barcode
Remove the linker from each sequence
DEseq package in R (http://www.r-project.org) was used from the data obtained from bowtie to identify differentially expressed miRNAs.
Genome_build: miRBase WBcel235
Supplementary_files_format_and_content: Suppl_Table_3.xlsx (Deseq table)

organism: Caenorhabditis elegans

source_name: whole worm

growth_protocol: worms were grown at 20°C on enriched NGM with OP50 as food

extract_protocol:
Synchronized Embryos or L4 larval worms were washed several times to avoid contamination with bacteria, snap-freezed at liquid nitrogen, and grinded to powder in a liquid nitrogen -prechilled mortar and pestle. High-molecular weight and Low-molecular weight RNA fractions were isolated using miRVana miRNA isolation kit Applied Biosystems (Ambion).
The protocol includes ligation of a total pool of small RNAs first to 3’ adapter pre-adenylated 3’ adapter without ATP, followed by ligation to a 5’-adapter containing 4-nt RNA barcode to allow multiplexing and 8 random nucleotide UMI, reverse transcription and amplification using primers complementary to the 5’ and 3’ adapters, baring Illumina barcodes. 3 size-selection steps are performed, separation of small RNA (20-30b) from longer RNA species and separation, after each one of the two ligations, of small RNA ligated to adapter(s) from free adapter/adapter dimer. All the separations performed on SPRI beads using a proprietary combination of two crowding agents, PEG and Isopropanol. The resulting Libraries were sequenced using 50 bp SR sequencing mode on the HiSeq 2500 platform (Illumina).

treatment_protocol: Embryos were isolated from gravid N2 adults by treatment with sodium hypochlorite solution. To obtain synchronized L4 worms, embryos were incubated in M9 media without food at 20 °C for 24h. Hutched synchronized L1 were grown until they reached L4 larval stage.

tag: Stage

tag: bio replicate no


title: 30_419_ATAC_8N_HuBr

description:
small RNA
8N identifier
The barcode can be found in each sequence according to the number indicated in the sample name: sequences in samples which include "8N" in their title start with 8 random bases, followed by their barcode, and sequences in samples which include "0N" in their title begin with their barcode.
The paper describes a new method for siRNA sequencing.  C. elegans was used as the main test case.  This specific human brain sample was used  to show that the new method works on a published RNA sample.

source_name: brain

tag: tissue

value: brain


title: Mouse fed ND for 12 weeks rep3

value: normal diet


title: 28_333_AGCG_8N_E

value: Embryo


title: 28_334_CGTC_8N_L4


title: 32_335_CTGG_8N_E


title: 26_342_TATG_0N_L4

description:
small RNA
no identifier (0N)
The barcode can be found in each sequence according to the number indicated in the sample name: sequences in samples which include "8N" in their title start with 8 random bases, followed by their barcode, and sequences in samples which include "0N" in their title begin with their barcode.

tag: tech replicate no


title: day1_3

tag: cell type


title: 26_339_ACTT_0N_L4


title: 26_340_GGGT_0N_L4


title: 26_334_CGTC_0N_E


title: Long-term light exposed rep2

city: Chengdu

first: xungang

last: wang

address: No.9 Section 4, Renmin Nan Road

institute: Chengdu Institute of Biology, Chinese Academy of Sciences

description:
Sample 12
30 hours light exposure

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence;The total clean reads from all libraries were assembled using Trinity as a reference transcriptome.
The expression level of each unigene was expressed as fragments per kilobase of exon model per million mapped reads (FPKM).
Genome_build: de novo
Supplementary_files_format_and_content: XLSX file includes FPKM values for all Samples
Supplementary_files_format_and_content: fasta file includes the sequences of all unigenes

organism: Oreolalax rhodostigmatus

source_name: Skin, eyeball and liver

growth_protocol: Tadpoles were collected in the caves.

extract_protocol:
Total RNA of each sample was extracted and purified using Trizol (Invitrogen, Carlsbad, CA, USA) following the manufacturer’s instructions. After purified with poly-T oligo-attached magnetic beads, the mRNAs were fragmented.
First-strand cDNA was synthesized using random hexamer primers and M-MuLV Reverse Transcriptase (RNase H−). Second-strand cDNA synthesis was subsequently performed using DNA Polymerase I and RNase H. The remaining overhangs were converted into blunt ends via exonuclease/polymerase activities. After adenylation of the 3′ ends of the DNA fragments, NEBNext Adaptors with a hairpin loop structure were ligated to prepare for hybridization. To preferentially select cDNA fragments of 150–200 bp in length, the library fragments were purified with AMPure XP system (Beckman Coulter, Beverly, USA). Then, 3 μl USER Enzyme (NEB, USA) was used with size-selected, adaptor-ligated cDNA at 37 °C for 15 min followed by 5 min at 95 °C before PCR. Then, PCR was performed with a Phusion High-Fidelity DNA polymerase, universal PCR primers and Index (X) primer. Finally, PCR products were purified (AMPure XP system), and library quality was assessed on the Agilent Bioanalyzer 2100 system. The clustering of the index-coded samples was performed on a cBot Cluster Generation System using the TruSeq PE Cluster Kit v3-cBot-HS (Illumina) according to the manufacturer’s instructions. After cluster generation, the library preparations were sequenced on an Illumina HiSeq 2500 platform by NovoGene (Beijing), and paired-end reads were generated.

tag: developmental stage

value: Gosner stage 25

tag: collection sites

value: Shizhu County, Chongqing City, China (30.25 N, 108.35 E)


title: 25_422_CAAT_8N_L4


title: 25_335_CTGG_8N_L4


title: 24_334_CGTC_8N_E


title: 24_421_TTCT_8N_L4


title: 26_333_AGCG_0N_E


title: Long-term light exposed rep1

description:
Sample 11
30 hours light exposure

value: Shizhu County, Chongqing City, China (30.25 N, 108.34 E)


title: Long-term light exposed rep3

description:
Sample 13
30 hours light exposure

value: Shizhu County, Chongqing City, China (30.25 N, 108.36 E)


title: 23_333_AGCG_8N_L4


title: 24_333_AGCG_8N_E


title: 23_448_AAGA_8N_E


title: Short-term light exposed rep6

description:
Sample 10
4 hours light exposure

value: Shizhu County, Chongqing City, China (30.25 N, 108.33 E)


title: Short-term light exposed rep5

description:
Sample 9
4 hours light exposure

value: Shizhu County, Chongqing City, China (30.25 N, 108.32 E)


title: Short-term light exposed rep1

description:
Sample 5
4 hours light exposure

value: Shizhu County, Chongqing City, China (30.25 N, 108.28 E)


title: Short-term light exposed rep2

description:
Sample 6
4 hours light exposure

value: Shizhu County, Chongqing City, China (30.25 N, 108.29 E)


title: Short-term light exposed rep3

description:
Sample 7
4 hours light exposure

value: Shizhu County, Chongqing City, China (30.25 N, 108.30 E)


title: Dark/Control rep4

description:
Sample 4
Dark

value: Shizhu County, Chongqing City, China (30.25 N, 108.27 E)


title: Dark/Control rep1

description:
Sample 1
Dark

value: Shizhu County, Chongqing City, China (30.25 N, 108.24 E)


title: Dark/Control rep2

description:
Sample 2
Dark

value: Shizhu County, Chongqing City, China (30.25 N, 108.25 E)


title: Dark/Control rep3

description:
Sample 3
Dark

value: Shizhu County, Chongqing City, China (30.25 N, 108.26 E)


title: 26_335_CTGG_0N_E


title: AF22 iPS-derived neuro-epithelial stem cells

status: Public on Jun 06 2018

city: Uppsala

first: Fredrik

middle: Johansson

last: Swartling

address: Dag Hammarskjölds väg 20

department: Immunology, Genetics and Pathology

country: Sweden

institute: Uppsala University

description:
AF22
Processed_expression_HAc_HAsp_AF22.tsv

data_processing:
All human RNA sequence reads were mapped against the human genome assembly GRCh37/hg19 using STAR v2.4.0 in a two step aproach previously described by Veeneman, B.A., et al. in Bioinformatics, 2016. Mice RNA sequence reads were mapped against mm9 in identical way.
Unmapped reads were realigned using Bowtie2 v2.2 and default parameters
Duplicate reads were removed with Piccard v1.127 and default parameters
The transcriptome were assembled and the expression profile quantified with Cufflinks v2.2.1 and default parameters
Comparison of transcriptomes and their expression levels where performed using Cuffcompare and Cuffdiff
Genome_build: hg19, mm9
Supplementary_files_format_and_content: Tab delimeted files with FPKM values

source_name: iPS-derived neuro-epithelial stem cells

growth_protocol: MB002 were maintained in culture media made up of 1:1 (v/v) DMEM/F-12 (Gibco) and Neurobasal -A media (Gibco, #10888-022) supplemented with HEPES, sodium pyruvate, non-essential amino acid, L-glutamine, B27, 20 ng/mL EGF, 20 ng/mL basic-fibroblast growth factor, Heparin, and 10 ng/mL leukemia inhibitory factor, PeSt. GTML2 were maintained in culture media made up of Neurobasal -A media (Gibco, #10888-022) supplemented with L-glutamine, B27, 20 ng/mL EGF, 20 ng/mL basic-fibroblast growth factor, PeSt.

extract_protocol:
Cells were lysed in Trizol (Life Technologies) and RNA was prepared using Qiagen RNeasy Mini Kit (Qiagen) according to manufacturer´s recommendations.
RNA-Seq were prepared for sequencing using standard Ion-Torrent protocols.

treatment_protocol: MB002 and GTML2 were treated 6h with DMSO, 500nM JQ1, 500nM Milciclib alone or in combination; GTML2 was also treated 6h with 1 ug/mL doxycycline. All compounds were added in the regular propagation culture medium (described above) for 2 & 6 hours pior to being collected for extraction.

tag: cell line


title: HA-sp

description:
HA-sp
Processed_expression_HAc_HAsp_AF22.tsv

source_name: Human astrocyte from spine


title: MB002 DMSO 2h 2

description:
MB002 DMSO 2h 2
Processed_expression_MB_treat_and_cell_lines.tsv

source_name: Medulloblastoma cell line

value: DMSO


title: MB002 DMSO 2h 3

description:
MB002 DMSO 2h 3
Processed_expression_MB_treat_and_cell_lines.tsv


title: MB002 DMSO 2h 1

description:
MB002 DMSO 2h 1
Processed_expression_MB_treat_and_cell_lines.tsv


title: D283 DMSO 2h 3

description:
D283 DMSO 2h 3
Processed_expression_MB_treat_and_cell_lines.tsv


title: D283 DMSO 2h 1

description:
D283 DMSO 2h 1
Processed_expression_MB_treat_and_cell_lines.tsv


title: D283 DMSO 2h 2

description:
D283 DMSO 2h 2
Processed_expression_MB_treat_and_cell_lines.tsv


title: CHLA259 DMSO 2h3

description:
CHLA259 DMSO 2h3
Processed_expression_MB_treat_and_cell_lines.tsv


title: CHLA259 DMSO 2h 2

description:
CHLA259 DMSO 2h 2
Processed_expression_MB_treat_and_cell_lines.tsv


title: CHLA259 DMSO 2h 1

description:
CHLA259 DMSO 2h 1
Processed_expression_MB_treat_and_cell_lines.tsv


title: Kelly DMSO 2h 3

description:
Kelly DMSO 2h 3
Processed_expression_MB_treat_and_cell_lines.tsv

source_name: Neuroblastoma cell line

value: Kelly


title: sd425 DMSO 2h 2

description:
sd425 DMSO 2h 2
Processed_expression_MB_treat_and_cell_lines.tsv


title: DAOY DMSO 2h 3

description:
DAOY DMSO 2h 3
Processed_expression_MB_treat_and_cell_lines.tsv

value: DAOY


title: DAOY DMSO 2h 2

description:
DAOY DMSO 2h 2
Processed_expression_MB_treat_and_cell_lines.tsv


title: sd425 DMSO 2h 1

description:
sd425 DMSO 2h 1
Processed_expression_MB_treat_and_cell_lines.tsv


title: Short-term light exposed rep4

description:
Sample 8
4 hours light exposure

value: Shizhu County, Chongqing City, China (30.25 N, 108.31 E)


title: Kelly DMSO 2h 2

description:
Kelly DMSO 2h 2
Processed_expression_MB_treat_and_cell_lines.tsv


title: Sai2 DMSO 2h 3

description:
Sai2 DMSO 2h 3
Processed_expression_MB_treat_and_cell_lines.tsv

source_name: Sai cell line


title: DAOY DMSO 2h 1

description:
DAOY DMSO 2h 1
Processed_expression_MB_treat_and_cell_lines.tsv


title: HA-c

description:
HA-c
Processed_expression_HAc_HAsp_AF22.tsv

source_name: Human astrocyte from cerebellum


title: MB002 JQMilciclib 6h 3

description:
MB002 JQPHA 6h 3
Processed_expression_MB_treat_and_cell_lines.tsv

value: JQ1 and Milciclib


title: sd425 DMSO 2h 3

description:
sd425 DMSO 2h 3
Processed_expression_MB_treat_and_cell_lines.tsv


title: MB002 Milciclib 6h 1

description:
MB002 PHA 6h 1
Processed_expression_MB_treat_and_cell_lines.tsv

value: Milciclib


title: Kelly DMSO 2h 1

description:
Kelly DMSO 2h 1
Processed_expression_MB_treat_and_cell_lines.tsv


title: MB002 JQ1 6h 1

description:
MB002 JQ1 6h 1
Processed_expression_MB_treat_and_cell_lines.tsv


title: Sai2 DMSO 2h 2

description:
Sai2 DMSO 2h 2
Processed_expression_MB_treat_and_cell_lines.tsv


title: MB002 DMSO 6h 3

description:
MB002 DMSO 6h 3
Processed_expression_MB_treat_and_cell_lines.tsv


title: MB002 JQMilciclib 6h 1

description:
MB002 JQPHA 6h 1
Processed_expression_MB_treat_and_cell_lines.tsv


title: MB002 DMSO 6h 1

description:
MB002 DMSO 6h 1
Processed_expression_MB_treat_and_cell_lines.tsv


title: MB002 JQMilciclib 6h 2

description:
MB002 JQPHA 6h 2
Processed_expression_MB_treat_and_cell_lines.tsv


title: MB002 Milciclib 6h 2

description:
MB002 PHA 6h 2
Processed_expression_MB_treat_and_cell_lines.tsv


title: MB002 JQ1 6h 3

description:
MB002 JQ1 6h 3
Processed_expression_MB_treat_and_cell_lines.tsv


title: GTML2 JQMilciclib 6h 2

description:
GTML2 JQPHA 6h 2
Processed_expression_GTML2.tsv

source_name: GTML medulloblastoma tumor


title: MB002 Milciclib 6h 3

description:
MB002 PHA 6h 3
Processed_expression_MB_treat_and_cell_lines.tsv


title: GTML2 JQMilciclib 6h 3

description:
GTML2 JQPHA 6h 3
Processed_expression_GTML2.tsv


title: MB002 JQ1 6h 2

description:
MB002 JQ1 6h 2
Processed_expression_MB_treat_and_cell_lines.tsv


title: GTML2 Dox 6h 3

description:
GTML2 Dox 6h 3
Processed_expression_GTML2.tsv

value: Doxycykline


title: GTML2 JQMilciclib 6h 1

description:
GTML2 JQPHA 6h 1
Processed_expression_GTML2.tsv


title: Sai2 DMSO 2h 1

description:
Sai2 DMSO 2h 1
Processed_expression_MB_treat_and_cell_lines.tsv


title: GTML2 Milciclib 6h 2

description:
GTML2 PHA 6h 2
Processed_expression_GTML2.tsv


title: GTML2 Milciclib 6h 1

description:
GTML2 PHA 6h 1
Processed_expression_GTML2.tsv


title: GTML2 Milciclib 6h 3

description:
GTML2 PHA 6h 3
Processed_expression_GTML2.tsv


title: GTML2 JQ1 6h 3

description:
GTML2 JQ1 6h 3
Processed_expression_GTML2.tsv


title: CD45- 48h Irf7KO

city: Tel-Aviv

first: Irit

last: Gat-Viks

address: Tel-Aviv

department: Department of Cell Research and Immunology

institute: Tel-Aviv University

description:
Single cell 3' RNA seq
experimental_design.txt

data_processing:
Single-cells were mapped to a joint reference of both the mouse and the influenza genome
Reads mapped at multiple positions were omitted.
We recorded reads that were mapped to either influenza segments or to exonic regions of mouse genes based on the UCSC transcripts annotation.
The expression level was calculated for each single cell based on the number of UMIs (unique molecular identifiers).
Filtered reads with cell-barcoding errors and UMIs that contained more than 1 error that may be due to sequencing or amplification errors.
Genome_build: Mouse: genome build mm9; influenza: NCBI records- NC_002016, NC_002017, NC_002018, NC_002019, NC_002020, NC_002021, NC_002022, NC_002023.
Supplementary_files_format_and_content: tab-delimited text files. Each file includes the number of UMIs obtained for each cell for all genes

source_name: CD45- Influenza-treated 48h p.i Irf7KO

extract_protocol:
Single-cell were sorted into 384-well cell capture plates containing 2μL of lysis solution and barcoded poly(T) reverse transcription (RT) primers for single-cell RNA-seq (Jaitin et al., 2014; Paul et al., 2015)
Single-cell libraries were prepared as previously described (Jaitin et al., 2014; Paul et al., 2015)

treatment_protocol: Mice were treated with PBS or PR8 H1N1 influenza virus (A/Puerto Rico/8/34) and sacrificed at 48h or 72h post infection

tag: infection

tag: time

value: CD45- cells


title: CD45+ 48h Irf7KO

source_name: CD45+ Influenza-treated 48h p.i Irf7KO

value: PR8 H1N1 influenza virus (A/Puerto Rico/8/34)

value: CD45+ cells


title: GTML2 Dox 6h 2

description:
GTML2 Dox 6h 2
Processed_expression_GTML2.tsv

tag: treatment


title: GTML2 JQ1 6h 1

description:
GTML2 JQ1 6h 1
Processed_expression_GTML2.tsv


title: sALS_33_Input

data_processing:
Takes output from raw files.  Run to trim off both 5’ and 3’ adapters on both reads. Command: quality-cutoff 6  -m 18  -a NNNNNAGATCGGAAGAGCACACGTCTGAACTCCAGTCAC  -g CTTCCGATCTACAAGTT -g CTTCCGATCTTGGTCCT  -A AACTTGTAGATCGGA -A AGGACCAAGATCGGA -A ACTTGTAGATCGGAA -A GGACCAAGATCGGAA -A CTTGT  AGATCGGAAG -A GACCAAGATCGGAAG -A TTGTAGATCGGAAGA -A ACCAAGATCGGAAGA -A TGTAGATCGGAAGAG -A CCAAGATCGGAAGAG -A GTAGATCGGAAGAGC -A CAAGATCGGAAGAGC -A TAGATCGGAAGAGCG -A AAGATCGGAAGAGCG -A AGATCGGAAGAGCGT -A GATCGGAAGAGCGTC -A ATCGGAAGAGCGTCG -A TCGGAAGAGCGTCGT -A CGGAAGAGCGTCGTG -A GGAAGAGCGTCGTGT  -o /full/path/to/files/file_R1.C01.fastq.gz.adapterTrim.fastq.gz  -p /full/path/to/files/file_R2.C01.fastq.gz.adapterTrim.fastq.gz  /full/path/to/files/file_R1.C01.fastq.gz /full/path/to/files/file_R2.C01.fastq.gz > /full/path/to/files/file_R1.C01.fastq.gz.adapterTrim.metrics
Takes output from cutadapt round 1. Run to trim off the 3’ adapters on read 2, to control for double ligation events. Command: cutadapt -f fastq --match-read-wildcards  --times 1  -e 0.1  -O 5  --quality-cutoff 6  -m 18  -A AACTTGTAGATCGGA -A AGGACCAAGATCGGA -A ACTTGTAGATCGGAA -A GGACCAAGATCGGAA -A CTTGTAGATCGGAAG -A GACCAAGATCGGAAG -A TTGTAGATCGGAAGA -A ACCAAGATCGGAAGA -A TGTAGATCGGAAGAG -A CCAAGATCGGAAGAG -A GTAGATCGGAAGAGC -A CAAGATCGGAAGAGC -A TAGATCGGAAGAGCG -A AAGATCGGAAGAGCG -A AGATCGGAAGAGCGT -A GATCGGAAGAGCGTC -A ATCGGAAGAGCGTCG -A TCGGAAGAGCGTCGT -A CGGAAGAGCGTCGTG -A GGAAGAGCGTCGTGT  -o /full/path/to/files/file_R1.C01.fastq.gz.adapterTrim.round2.fastq.gz  -p /full/path/to/files/file_R2.C01.fastq.gz.adapterTrim.round2.fastq.gz  /full/path/to/files/file_R1.C01.fastq.gz.adapterTrim.fastq.gz  /full/path/to/files/file_R2.C01.fastq.gz.adapterTrim.fastq.gz > /full/path/to/files/file_R1.C01.fastq.gz.adapterTrim.round2.metrics
Takes output from cutadapt round 2.  Maps to human specific version of RepBase used to remove repetitive elements, helps control for spurious artifacts from rRNA (& other) repetitive reads.  Command: STAR  --runMode alignReads  --runThreadN 16  --genomeDir /path/to/RepBase_human_database_file --genomeLoad LoadAndRemove  --readFilesIn /full/path/to/files/file_R1.C01.fastq.gz.adapterTrim.round2.fastq.gz /full/path/to/files/file_R2.C01.fastq.gz.adapterTrim.round2.fastq.gz --outSAMunmapped Within  --outFilterMultimapNmax 30  --outFilterMultimapScoreRange 1  --outFileNamePrefix /full/path/to/files/file_R1.C01.fastq.gz.adapterTrim.round2.rep.bam --outSAMattributes All  --readFilesCommand zcat  --outStd BAM_Unsorted  --outSAMtype BAM Unsorted  --outFilterType BySJout  --outReadsUnmapped Fastx  --outFilterScoreMin 10  --outSAMattrRGline ID:foo  --alignEndsType EndToEnd > /full/path/to/files/file_R1.C01.fastq.gz.adapterTrim.round2.rep.bam
Takes output from STAR rmRep.  Maps unique reads to the human genome.  Command: STAR  --runMode alignReads  --runThreadN 16  --genomeDir  /path/to/STAR_database_file --genomeLoad LoadAndRemove  --readFilesIn  /full/path/to/files/file_R1.C01.fastq.gz.adapterTrim.round2.rep.bamUnmapped.out.mate1  /full/path/to/files/file_R1.C01.fastq.gz.adapterTrim.round2.rep.bamUnmapped.out.mate2  --outSAMunmapped Within  --outFilterMultimapNmax 1  --outFilterMultimapScoreRange 1  --outFileNamePrefix /full/path/to/files/file_R1.C01.fastq.gz.adapterTrim.round2.rmRep.bam  --outSAMattributes All  --outStd BAM_Unsorted  --outSAMtype BAM Unsorted  --outFilterType BySJout  --outReadsUnmapped Fastx  --outFilterScoreMin 10  --outSAMattrRGline ID:foo  --alignEndsType EndToEnd > /full/path/to/files/file_R1.C01.fastq.gz.adapterTrim.round2.rmRep.bam
takes output from STAR genome mapping.  Custom random-mer-aware script for PCR duplicate removal. Command: barcode_collapse_pe.py  --bam /full/path/to/files/file_R1.C01.fastq.gz.adapterTrim.round2.rmRep.bam  --out_file /full/path/to/files/file_R1.C01.fastq.gz.adapterTrim.round2.rmRep.rmDup.bam  --metrics_file /full/path/to/files/file_R1.C01.fastq.gz.adapterTrim.round2.rmRep.rmDup.metrics
Takes output from barcode collapse PE.  Sorts resulting bam file for use downstream.  Command: java  -Xmx2048m  -XX:+UseParallelOldGC  -XX:ParallelGCThreads=4  -XX:GCTimeLimit=50  -XX:GCHeapFreeLimit=10  -Djava.io.tmpdir=/full/path/to/files/.queue/tmp  -cp /path/to/gatk/dist/Queue.jar  net.sf.picard.sam.SortSam  INPUT=/full/path/to/files/file_R1.C01.fastq.gz.adapterTrim.round2.rmRep.rmDup.bam  TMP_DIR=/full/path/to/files/.queue/tmp  OUTPUT=/full/path/to/files/file_R1.C01.fastq.gz.adapterTrim.round2.rmRep.rmDup.sorted.bam  VALIDATION_STRINGENCY=SILENT  SO=coordinate  CREATE_INDEX=true
Takes output from sortSam, makes bam index for use downstream.  Command: samtools index  /full/path/to/files/file_R1.C01.fastq.gz.adapterTrim.round2.rmRep.rmDup.sorted.bam  /full/path/to/files/file_R1.C01.fastq.gz.adapterTrim.round2.rmRep.rmDup.sorted.bam.bai
Takes inputs from multiple final bam files.  Merges the two technical replicates for further downstream analysis.  Command: samtools  merge  /full/path/to/files/CombinedID.merged.bam  /full/path/to/files/file_R1.C01.fastq.gz.adapterTrim.round2.rmRep.rmDup.sorted.bam /full/path/to/files/file_R1.D08.fastq.gz.adapterTrim.round2.rmRep.rmDup.sorted.bam
Takes output from sortSam, makes bam index for use downstream.  Command: samtools  index  /full/path/to/files/CombinedID.merged.bam  /full/path/to/files/CombinedID.merged.bam.bai
Takes output from sortSam.  Only outputs the second read in each pair for use with single stranded peak caller.  This is the final bam file to perform analysis on.  Command: samtools view -hb -f 128  /full/path/to/files/CombinedID.merged.bam  >  /full/path/to/files/CombinedID.merged.r2.bam
Takes results from samtools view.  Calls peaks on those files.  Command: clipper  -b /full/path/to/files/CombinedID.merged.r2.bam  -s hg19  -o /full/path/to/files/CombinedID.merged.r2.peaks.bed  --bonferroni  --superlocal  --threshold-method binomial  --save-pickle
Genome_build: hg19
Supplementary_files_format_and_content: bed format, contains clusters of predicted RBP binding

source_name: human frontal cortex

extract_protocol:
Ftcx were lysed in iCLIP lysis buffer, followed by limited digestion with RNase I (Ambion), immunoprecipitation of RBP-RNA complexes with a specific antibody of interest (Protein G sheep anti-rabbit Dynabeads), and stringent washes.
After dephosphorylation with FastAP (Thermo Fisher) and T4 PNK (NEB), a barcoded RNA adapter is ligated to the 3’ end (T4 RNA Ligase, NEB) (at this step, multiple replicates of the same RBP, or potentially RBPs of similar size and bound RNA amount, can be uniquely barcoded and pooled after ligation to simplify downstream steps - see Supplementary Fig. 2A). Ligations are performed on-bead (to allow washing away unincorporated adapter) in high concentration of PEG8000, which improves ligation efficiency to > 90%. Samples are then run on standard protein gels and transferred to nitrocellulose membranes, and a region 75 kDa (~150 nt of RNA) above the protein size is isolated and proteinase K (NEB) treated to isolate RNA. RNA is reverse transcribed with AffinityScript (Agilent), and treated with ExoSAP-IT (Affymetrix) to remove excess oligonucleotides. A second DNA adapter (containing a random-mer of 5 (N5) or 10 (N10) random bases at the 5’ end) is then ligated to the cDNA fragment 3’ end (T4 RNA Ligase, NEB), performed with high concentration of PEG8000 (to improve ligation efficiency) and DMSO (to decrease inhibition of ligation due to secondary structure). After cleanup (Dynabeads MyOne Silane, ThermoFisher), an aliquot of each sample is first subjected to qPCR (to identify the proper number of PCR cycles), and then the remainder is PCR amplified (Q5, NEB) and size selected via agarose gel electrophoresis.

treatment_protocol: Human frontal cortex (ftcx) was dissected < 6h after death and frozen at -70°C. For preparation ftcx was homogenized in liquid nitrogen and crosslinked in PBS with  UV (254 nm, 400 mJ/cm2). Homogenzied and crosslinked ftcx was stored at -80°C.

value: frontal cortex


title: control_4_Input


title: control_39_Input


title: sALS_30_Input


title: GTML2 DMSO 6h 2

description:
GTML2 DMSO 6h 2
Processed_expression_GTML2.tsv


title: GTML2 JQ1 6h 2

description:
GTML2 JQ1 6h 2
Processed_expression_GTML2.tsv


title: CD45+ 48h replicate II

source_name: CD45+ Influenza-treated 48h p.i replicate II

value: wild-type


title: MB002 DMSO 6h 2

description:
MB002 DMSO 6h 2
Processed_expression_MB_treat_and_cell_lines.tsv


title: CD45- 72h

source_name: CD45- Influenza-treated 72h p.i


title: control_4_IP

tag: antibody

tag: antibody manufacturer

value: Bethyl

tag: in-line barcodes

value: A01=AAGCAAT; B06=GGCTTGT


title: CD45+ PBS-treated

source_name: CD45+ PBS-treated

tag: genotype

value: control


title: CD45+ 72h

source_name: CD45+ Influenza-treated 72h p.i


title: CD45- PBS-treated

source_name: CD45- PBS-treated


title: GTML2 DMSO 6h 1

description:
GTML2 DMSO 6h 1
Processed_expression_GTML2.tsv


title: CD45- 48h replicate II

source_name: CD45- Influenza-treated 48h p.i replicate II


title: sALS_33_IP

value: C01=ACAAGTT; D08=TGGTCCT


title: sALS_32_IP


title: sALS_32_Input


title: CD45- 48h replicate I

source_name: CD45- Influenza-treated 48h p.i replicate I


title: unfertilized eggs_PolyA plus

city: Singapore

first: Jun Wei

last: Pek

address: 1 Research Link National University of Singapore

country: Singapore

institute: Temasek Life Sciences Laboratory

data_processing:
Sequenced and aligned reads were passed through a Perl filtering algorithm to determine if they were internal to an intron or overlapped with the 5' or 3' junction of each intron in the Drosophila melanogaster (dm3) genome. Each intron was indexed and reads that aligned to the index were parsed and counted to determine molecule size. Sequence information was then extracted for each putative molecule, and pairwise aligned using Blast (43). Positive Blast hits were then aligned with Clustalw2 to determine actual sequence alignment for further downstream analysis (44).
Genome_build: dm3
Supplementary_files_format_and_content: readcounts.xlsx contains the read counts of the individual sisRNA candidates

source_name: unfertilized eggs

extract_protocol:
RNA was extraction in accordance to Trizol protocol.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: unfertilized egg

value: y w

tag: rna fraction

value: rRNA-depleted total RNA, polyA-plus fraction


title: unfertilized eggs_Total RNA

value: rRNA-depleted total RNA


title: sALS_30_IP


title: control_39_IP


title: koc5

city: New York

first: Robert

middle: F

last: Schwabe

state: NY

address: 1150 st Nicholas Av

department: Medicine

institute: Columbia University

data_processing:
Bases were called with RTA (Illumina).
Adaptors were trimmed and reads were converted from BCL to Fasta format with bcl2fastq (version 1.8.4).
Reads were mapped to the genome with Bowtie version 2.2.4 and Tophat2 2.1.0 .
Reads in each gene were counted with HTSeq-0.6.1 .
Genome_build: mm9
Supplementary_files_format_and_content: .txt file with raw counts for each gene

source_name: Liver tumor tissue from HMGB1 deleted mouse  (Hgmb1Dhep)

extract_protocol:
RNA was isolated from liver tissues by column purification and on-column DNAse treatment (High Pure RNA tissue kit from Roche Diagnostics, ref 12033674001) isolation kit (Life Technologies).
A poly-A pull-down was used to enrich mRNAs from total RNA samples (200ng-1ug per sample, RIN>8 required)
Libraries were constructed using the Illumina TruSeq RNA prep kit according to manufacturer’s instructions.

tag: genotype/variation

value: HMGB1 deleted  (Hgmb1Dhep)

value: Liver tumor


title: S137235

city: boston

first: qiong

last: xu

address: CLS Building 3 Blackfan Circle

institute: dana farber cancer institute

data_processing:
Alignment was performed using TopHat2 against human genome assembly hg19 with default settings.
Kallisto was used for quantification of transcript-level expression, which was reported as TPM.
Genome_build: hg19 (GRCh37)
Supplementary_files_format_and_content: *tsv: Tab-separated text files contain transcript-level expression, represented as TPM.

source_name: Lung adenocarcinoma

extract_protocol:
Reference: Life Technologies Corporation | Carlsbad, CA 92008 USA cat# 15596018.
1 ug of total RNA (RNA integrity number varying from 1 to 8.9) underwent ribosomal depletion and TruSeq library preparation according to instruction provided by Illumina (TruSeq® Stranded Total RNA LT, cat#RS-122-2202), with 6 cycles of PCR. Samples were barcoded and run on a Hiseq 2500 in a 50bp/50bp Paired end run, using the TruSeq SBS Kit v3 (Illumina). On average, 74 million paired reads was generated per sample, 24% of the data mapped to the transcriptome (range from 5 to 34%).

value: Lung adenocarcinoma

tag: suv


title: S138002


title: wtnc3

source_name: Normal liver from control C57Bl/6 mice

value: Normal liver


title: CD45+ 48h replicate I

source_name: CD45+ Influenza-treated 48h p.i replicate I


title: unfertilized eggs_PolyA minus

value: rRNA-depleted total RNA, polyA-minus fraction


title: GTML2 DMSO 6h 3

description:
GTML2 DMSO 6h 3
Processed_expression_GTML2.tsv

value: DMSO


title: koc2


title: wtnc2


title: koc6


title: wtnc1


title: S137591


title: koc4


title: S137038


title: wtc3

source_name: Liver tumor tissue from floxed control mouse  (Hgmb1fl/fl)

value: floxed control  (Hgmb1fl/fl)


title: S136782


title: wtc5


title: wtc2


title: koc3


title: S137399


title: koc1


title: S137758


title: wtc4


title: wtc6


title: S137757


title: S137246


title: S136605


title: wtc1


title: S137687


title: S137343


title: S136877


title: S137788


title: S137147


title: WT_HZ2186

status: Public on Jun 05 2018

first: Ayush

middle: T

last: Raman

address: 75 Ames St

department: Epigenomics Program

institute: Broad Institute of MIT and Harvard

description: RNA-Seq

data_processing:
RNA sequencing was performed using Illumina HiSeq 2000. All sequencing was done by the Genomic and RNA Profiling Core at the Baylor College of Medicine. For each sample, about 90 to 110 million pairs of 100 bp reads were generated. Raw reads were first groomed by trimming the adapters before mapping to reference genome. Trimmed reads were aligned to the Mus musculus genome (Gencode mm10; version M10) using STAR aligner v2.4.2a (Dobin et al., 2013) with default parameters. The overall mappability for all 6 samples was above 90%. The read counts per gene were obtained using the quantMode function in STAR. These read counts are analogous to the expression level of the gene. Using the obtained raw counts, normalization and differential gene analysis were carried out using the DESeq2 (Love et al., 2014) package in the R environment. DESeq2 allows us to test for gene expression changes between samples in different conditions using more robust shrinkage estimation for dispersion and fold changes (Love et al., 2014). The default negative binomial generalized linear model with Wald test implemented in the package was used to identify significant differentially expression genes.
Genome_build: Gencode mm10; version M10
Supplementary_files_format_and_content: For RNA-Seq, raw counts and differential expression gene list across 750 genes is provided.

source_name: Cellebellum

growth_protocol: All mice used in this study were FVB.129 F1-hybrids. They were group-housed with up to five mice per cage. They were maintained on a 14h light:10h dark cycle (light on at 06:00) with standard mouse chow and water ad libitum in our AAALAS-accredited facility. All research and animal care procedures were approved by the Baylor College of Medicine Institutional Animal Care and Use Committee.

extract_protocol:
We performed RNA extraction and purification from the cerebellum of male mice 8 to 9 weeks of age (three biological replicates of wild type and Mecp2-null) using the Aurum™ Total RNA Fatty and Fibrous Tissue Kit (Bio-Rad 7326830) per the manufacturer’s instructions. Genomic DNA was eliminated using an on-column DNase digestion step. RNA quality was assessed using the Agilent 2100 Bioanalyzer system prior to library preparation for deep sequencing or use of the total RNA for Nanostring nCounter quantification.
RNA library preparation was performed using the cerebellar RNA from 3 wildtype and 3 Mecp2-null mice. We used the Illumina TruSeq Stranded mRNA library preparation protocol (publication number 15031047, rev. E) and 250ng of total RNA was used to make each library, and ERCC RNA Spike-In Mix 1 or 2 (Thermo Fisher 4456740) was added to the samples prior to library preparation according to the manufacturers instructions. Samples were paired end sequenced (PE100) on a HiSeq2500 in high-output mode using the v4 sequencing kit (Illumina; SBS: FC-401-4003, paired-end flow cell: PE-401-4001).

tag: strain

value: FVB.129 F1-hybrids

tag: age

value: 8-9 weeks

tag: genotypes

value: WT

tag: platform

value: Illumina HiSeq 2000


title: S136609

tag: tissue


title: S136903


title: WT_HZ2188

description: RNA-Seq


title: S137513


title: WT_HZ2185

description: RNA-Seq


title: KO_HZ2183

description: RNA-Seq

value: Mecp2 KO


title: Mili-ip

city: Shanghai

first: Fengjuan

state: Shanghai

address: 320 Yueyang Road

department: Institute of Biochemistry and Cell Biology

institute: Shanghai Institutes for Biological Sciences, CAS

description: total cellular RNA

data_processing:
Illumina Casava1.7 software used for basecalling.
The raw fastq data was pre-processed using a common procedure. After quality filtering, sequencing reads were clipped from the 3’ adaptor allowing a minimum match of 10nt. Reads unable to match the 3' adaptor sequence or with lengths shorter than 17 bp were discarded.
The useful reads were mapped to the mouse genome by bowtie (bowite options –v 0 –k 100) (Langmead et al. 2009). The mapped genome sequences were further aligned to known miRNAs, tRNAs, rRNAs, snoRNAs and snRNAs by bowtie. The remaining 25~32 nt sequences were used to identify piRNAs following the method described previously (Inuk Jung et al 2014) with slight modifications. The clustering parameters were determined as MinReads = 4 and Eps = 2500 bp by running a series of k-dist analysis with different Eps and MinReads in our own data. After clustering all remaining 25~32nt sequences with the determined parameters, all candidate clusters were considered as piRNA clusters without any further scoring and filtering.
Only the reads that exactly matched the 5’ start site of annotated miRNAs and has ≤2 nt deletions or additional sequences derived from pri-miRNAs at the 3’ ends were counted as miRNAs. The count of each miRNAs, piRNAs and tRNA, rRNA, snRNA-derived sequences was normalized to the count of methylated spike-in. The small RNAs were mapped in the following order: miRNA, tRNA, rRNA, snoRNA, snRNA and piRNA
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include useful reads count for each sample.

source_name: cultured SSC (spermatogonia stem cell)

growth_protocol: SSCs were dissociated from a 15-day-old C57BL/6× DBA2 F1 male mouse carrying transgenic actin-EGFP genes. The colonies of SSC were trypsinized and plated on MEF feeder cells in 24-well plate with SF medium.

extract_protocol:
Total cellular RNA was extracted using TRIzol reagent (Takara). 4 μg total RNAs with 2 X 10-6 pmol spike-ins mixture from wild type SSC and mhen1 knock-out SSC were treated by 2 μl freshly dissolved NaIO4 (200 mM), kept on ice for 1 hr in the dark. Then the RNAs were precipitated and dissolved in DEPC-treated water for small RNA library construction.
0.5 μg of RNA with or without NaIO4 treatment was used to construct a small RNA library according to the Illumina protocol.
High-throughput RNA sequencing was performed using Hi-Seq2500 with 50 running circles.

treatment_protocol: Plasmid encoding spCas9 and sgRNAs (20 µg) targeting mHen1 and Mili were transiently transfected into SSCs with Amaxa Cell Line Nucleofector Kit L as described previously. Single SSC colonies were picked and verified by Sanger sequencing.

value: wild type

value: ip by mili anti-body (MABE363, Millipore)


title: hen1 knock-out

description: total cellular RNA mixed with exogenous spikein


title: wild type


title: wild type treated by NaIO4

value: treated by NaIO4


title: S137783


title: S136698


title: Tumor from ApcMin/+/Macrod2+/+ mouse_6

city: Parkville

first: Oliver

last: Sieber

state: VIC

address: 1G Royal Parade

country: Australia

institute: Walter and Eliza Hall Insitute of Medical Reseach

data_processing:
trimmed adaptors using Trimmomatic, reads <50 bp removed (v0.22)
tophat -g 1 -library-type fr-firststrand mm10 <fastq.gz> (v2.0.8)
featureCounts -a mm10_ucsc.gtf -t exon -g gene_name -s 2 (subread-1.4.5-p1-Linux-x86_64)
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include read counts and rpkms for each Sample

molecule: polyA RNA

source_name: epithelial tumor from large intestine

growth_protocol: ApcMin/+/Macrod2+/+, ApcMin/+/Macrod2-/+, ApcMin/+/Macrod2-/- mice were maintained in colonies at the WEHI animal facility.

extract_protocol:
On autopsy of knock-out mice, the intestinal tract was removed and tumors resected. Total RNA was extracted using the AllPrep DNA/RNA Mini kit (Qiagen).
TruSeq Stranded Total RNA Library Preparation Kit

tag: Sex

value: Male

value: intestinal tumor


title: Tumor from ApcMin/+/Macrod2+/+ mouse_5


title: Tumor from ApcMin/+/Macrod2-/+ mouse_6


title: Tumor from ApcMin/+/Macrod2-/+ mouse_5


title: Tumor from ApcMin/+/Macrod2-/- mouse_6


title: Tumor from ApcMin/+/Macrod2+/+ mouse_4


title: Tumor from ApcMin/+/Macrod2+/+ mouse_3


title: Tumor from ApcMin/+/Macrod2-/- mouse_4


title: KO_HZ2187

description: RNA-Seq


title: mili knock-out

value: mili-/-


title: KO_HZ2184

description: RNA-Seq


title: Tumor from ApcMin/+/Macrod2-/+ mouse_3


title: Tumor from ApcMin/+/Macrod2+/+ mouse_2


title: Tumor from ApcMin/+/Macrod2-/+ mouse_2


title: Tumor from ApcMin/+/Macrod2-/- mouse_1


title: hen1 knock-out treated by NaIO4


title: Tumor from ApcMin/+/Macrod2-/+ mouse_1


title: Tumor from ApcMin/+/Macrod2-/- mouse_2


title: Tumor from ApcMin/+/Macrod2+/+ mouse_1


title: Tumor from ApcMin/+/Macrod2-/- mouse_5


title: FTOC_RA_2

city: Worcester

first: Rene

last: Maehr

address: 55 Lake Ave N

department: Program in Molecular Medicine

institute: UMass Medical School

description: Read 1 contains the barcode and Read 2 contains biological sequence

data_processing:
Base calling was performed using Illumina RTA version 2.4.11.
FASTQ's from resequenced runs were concatenated prior to processing.
Alignment and quantification were performed using the STAR aligner v2.4.2, Picard tools v1.96, Samtools v1.3, and Drop-seq tools v1.0.
Analysis step: Convert to SAM  Software package:  Picard tools   Command name:  FastqToSam.jar Parameters used:  --
Analysis step: Tag cell barcode  Software package:  DropSeq tools  Command name: TagBamWithReadSequenceExtended  Parameters used:  BASE_QUALITY=10, BARCODED_READ=1, NUM_BASES_BELOW_QUALITY=1,  DISCARD_READ=False
Analysis step: Tag molecular barcode  Software package:  DropSeq tools  Command name: TagBamWithReadSequenceExtended Parameters used:  BASE_QUALITY=10, BARCODED_READ=1, NUM_BASES_BELOW_QUALITY=1,  DISCARD_READ=True
Analysis step: Remove low-quality barcodes  Software package:  DropSeq tools  Command name:   FilterBAM  Parameters used:     --
Analysis step: Remove polyA tail  Software package:  DropSeq tools  Command name:   PolyATrimmer               Parameters used:  MISMATCHES=0, NUM_BASES=6
Analysis step: Convert to FASTQ  Software package:  Picard tools   Command name:   SamToFastq.jar             Parameters used:     --
Analysis step: Align reads to exome  Software package:  STAR  Command name:   --  Parameters used: --
Analysis step: Sort BAM to speed merging  Software package:  Picard tools  Command name:   SortSam.jar                 Parameters used:     --
Analysis step: Merge barcode and alignment info  Software package:  Picard tools  Command name:   MergeBamAlignment.jar       Parameters used:  INCLUDE_SECONDARY_ALIGNMENTS=False
Analysis step: Label read with exon  Software package:  DropSeq tools  Command name:   TagReadWithGeneExon        Parameters used:     --
Analysis step: Screen for bead errors  Software package:  DropSeq tools  Command name:  DetectBeadSynthesisErrors  Parameters used: NUM_BARCODES=2000
Analysis step: Form DGE matrix  Software package:  DropSeq tools  Command name:   DigitalExpression          Parameters used: MIN_NUM_GENES_PER_CELL=1000
The procedure was repeated with a  T-Cell receptor (TCR) contig added to the reference genome and the following two steps were used to generate improved TCR counts.
Analysis step: Subset reads aligning to TCR contig Software package: Samtools Command name: view Parameters used:  -bh
Analysis step: Form TCR-specific DGE matrix  Software package:  DropSeq tools  Command name:   DigitalExpression          Parameters used: MIN_NUM_GENES_PER_CELL=1 READ_MQ=1
Genome_build: For initial DGE calculations, mm10 was used. For TCR-specific DGE's, an artificial TCR contig was added.  The FASTA with the TCR sequence is available on the series record.
Supplementary_files_format_and_content: Processed files are digital gene expression matrices containing UMI counts. They are represented as dense matrices in (gzipped) tab-delimited text files. Each column is labeled with a cell barcode and each row is labeled with a gene.

growth_protocol: Thymic lobes were isolated from timed mouse embryos.

extract_protocol:
Thymic lobes were mechanically isolated, dissociated in trypsin, depleted of RBC's (only some samples), washed and stained with 7AAD cell viability dye, and 7AAD negative single cells were sorted on a BD FACSARIA.
Libraries were prepared according to the Drop-seq lab protocol version 3.1 (Macosko and Goldman, December 2015, McCarroll Lab).  Final libraries were sequenced on an Illumina NextSeq 500 using high-output 75-cycle kits.

tag: background strain

value: wildtype

value: Fetal thymic organ culture

tag: developmental day

value: E13.5 + 3 days in culture

tag: rbc lysis buffer

value: Biolegend Cat# 420301

value: Retinoic acid (1 µM; Sigma, R2625)


title: FTOC_PBSDMSO_2

tag: treatment

value: Control


title: FTOC_RA_1


title: FTOC_PBSDMSO_1


title: Rag1KO_wholeThy_2

value: B6.129S7-Rag1 tm1Mom/J

value: thymus

value: eBioscience Cat# 00-4333-57


title: FTOC_RA_3


title: Rag1KO_wholeThy_1


title: Tumor from ApcMin/+/Macrod2-/- mouse_3


title: Tumor from ApcMin/+/Macrod2-/+ mouse_4

source_name: epithelial tumor from small intestine


title: Endocrine progenitors at e14.5_ATAC-seq_2

city: Houston

first: Malgorzata

last: Borowiak

address: 1 Baylor Plaza

institute: Baylor College of Medicine

data_processing:
Reads mapped to mm9 genome using Bowtie2 with default paired-end settings
Non-nuclear and unmapped reads discarded
picard MarkDuplicates to remove duplicate reads
Peak calling using Homer (findPeaks -style factor) on the merged BAM file of all e14.5 and e16.5 replicates
Blacklisted regions from mm9 were removed from comprehensive peak file
Reads were counted for each condition from the comprehensive peak file using bedtools (mulicov module)
DEseq2 was used for differential accessibility analysis with the multicov file as input
Genome_build: mm9
Supplementary_files_format_and_content: bedGraph.gz of processed bam file, generated using homer makeUCSC

source_name: Ngn3-eGFP+ e14.5 cells

extract_protocol:
Cells resuspended in transposase-containing reaction mixture with 0.05% digitonin before tagmentation at 37 degrees C for 30 minutes with 300rpm agitation. DNA was then purified with a Qiagen MinElute reaction cleanup kit.
As described in Buenrostro JD et al., 2013 Nature Methods

tag: developmental stage

value: pancreas

tag: cell type

value: Ngn3-eGFP+ cells


title: Endocrine progenitors at e14.5_ATAC-seq_1


title: FTOC_PBSDMSO_3


title: Endocrine progenitors at e16.5_ATAC-seq_1

source_name: Ngn3-eGFP+ e16.5 cells


title: Endocrine progenitors at e16.5_ATAC-seq_2


title: Endocrine progenitors at e14.5_ATAC-seq_3


title: e16.5 EP 10

description:
single e16.5 mouse EPs
e16_10

data_processing:
First MATQ-seq amplification primers are trimmed off the reads using Skewer.
Extra 14 based are further trimmed to remove the UMI sequence and extra bases from the reads.
The trimmed reads are then mapped using STAR algorithm.
The uniquely mapped reads are assigned to the genes using HTseq-count.
Based the assigned reads, the UMI for unique amplicons are retrieved and counted for each gene.
The amplicons per million amplicons (APM), similar to reads per million reads (RPM) are calculated and used to quantify the gene expression in single cells. For detailed procedures, please refer to Sheng et al. (2016).
Genome_build: mm9
Supplementary_files_format_and_content: text file with APM

source_name: e16.5 endocrine progenitor (Ngn3-eGFP+ cell) from Ngn3-eGFP mouse

extract_protocol:
After flow sorting, Ngn3-eGFP+ cells were collected in RPMI medium. We used mouth pipette to pick single cells into PCR tubes with MATQ-seq lysis buffer (Sheng et al., 2017).
MATQ-seq was then performed to amplify the whole transcriptome of single cells. After second strand synthesis, the input and yield of each sample was quantified by qPCR. Highly degraded samples or samples with multiple cells were discarded. After PCR amplification, we performed library preparation and data analysis according to the previous publication (Sheng et al., 2017). Duplex specific Nuclease was used to remove the majority of ribosomal cDNA.

value: Endocrine progenitors


title: e16.5 EP 9

description:
single e16.5 mouse EPs
e16_9


title: e16.5 EP 6

description:
single e16.5 mouse EPs
e16_6


title: e16.5 EP 5

description:
single e16.5 mouse EPs
e16_5


title: e16.5 EP 7

description:
single e16.5 mouse EPs
e16_7


title: e16.5 EP 11

description:
single e16.5 mouse EPs
e16_11


title: e16.5 EP 4

description:
single e16.5 mouse EPs
e16_4


title: e16.5 EP 2

description:
single e16.5 mouse EPs
e16_2


title: e14.5 EP 15

description:
single e14.5 mouse EPs
e14_15

source_name: e14.5 endocrine progenitor (Ngn3-eGFP+ cell) from Ngn3-eGFP mouse


title: e16.5 EP 1

description:
single e14.5 mouse EPs
e16_1


title: Endocrine progenitors at e16.5_ATAC-seq_3


title: e14.5 EP 14

description:
single e14.5 mouse EPs
e14_14


title: e14.5 EP 13

description:
single e14.5 mouse EPs
e14_13


title: e14.5 EP 9

description:
single e14.5 mouse EPs
e14_9


title: e16.5 EP 12

description:
single e16.5 mouse EPs
e16_12


title: e14.5 EP 10

description:
single e14.5 mouse EPs
e14_10


title: e14.5 EP 12

description:
single e14.5 mouse EPs
e14_12


title: e14.5 EP 11

description:
single e14.5 mouse EPs
e14_11


title: e14.5 EP 6

description:
single e14.5 mouse EPs
e14_6


title: e14.5 EP 8

description:
single e14.5 mouse EPs
e14_8


title: e14.5 EP 7

description:
single e14.5 mouse EPs
e14_7


title: e14.5 EP 2

description:
single e14.5 mouse EPs
e14_2


title: e16.5 EP 8

description:
single e16.5 mouse EPs
e16_8


title: e14.5 EP 4

description:
single e14.5 mouse EPs
e14_4


title: e16.5 EP 3

description:
single e16.5 mouse EPs
e16_3


title: e16.5 mouse pancreas_Drop-seq

data_processing:
Sequencing data was handled as described in Shekhar et. al. (2016).
FastQ files were converted to BAMs with Picard tools (MergeSamFiles) and then used is input for STAR alignment, cell barcode correction, and digital gene expression (DGE) matrix generation via the Drop-seq tools software package (available at http://mccarrolllab.com/dropseq/).
DGEs from each experiment were merged and then we imported the comprehensive DGE into Seurat (version 1.4.0.5) where normalization was performed according to package default settings.
Batch effects were corrected for by regressing out the number of molecules per cell and the percentage of mapped mitochondrial reads with the RegressOut function (Seurat package).
Principle components analysis (PCA) was performed and significant PCs were used as input for graph-based clustering.
And 2-dimensional visualization of the multi-dimensional data set was done with tSNE.
Differential expression of the individual clusters was performed using the likelihood-ratio test for single cell gene expression.
Genome_build: mm10
Supplementary_files_format_and_content: Matrix is digital gene expression matrix of raw UMI counts aligned to mm10.

extract_protocol:
Lysis in droplets
Illumina Nextera XT

value: whole mouse pancreas

value: ICR


title: e14.5 EP 3

description:
single e14.5 mouse EPs
e14_3


title: e14.5 EP 5

description:
single e14.5 mouse EPs
e14_5


title: mutant replicate 5

city: Storrs

first: Rahul

middle: N

last: Kanadia

state: CT

address: 75 N. Eagleville Road

department: Physiology and Neurobiology

institute: University of Connecticut

data_processing:
Reads were aligned to mm10 genome using Hisat2 (with parameters --no discordant and --no-mixed).
Single nucleotide variations were called using SNVQ and a new reference genome was generated.
Reads were aligned to new reference genome using Hisat2 (with parameters --no-discordant and --no-mixed).
Fragments per kilobase per million mapped reads (FPKM) values were calculated using IsoEM2.
Differential gene expression was determined using IsoDE2 (P<0.01).
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: *txt: Tab-delimited text files with FPKM values for each sample.

source_name: dorsal telencephalon, U11 mutant

extract_protocol:
Dorsal telencephalon was dissected, and RNA was extracted using Trizol.
Total RNA library was prepared by Illumina TruSeq Stranded Total RNA Library Sample Prep Kit (RS-122-2201) with Ribo-Zero to remove ribosomal RNA.

tag: strain/background

value: dorsal telencephalon

value: Embryonic day 12


title: mutant replicate 3


title: mutant replicate 2


title: mutant replicate 1


title: mutant replicate 4


title: e14.5 mouse pancreas_Drop-seq


title: control replicate 5

source_name: dorsal telencephalon, control


title: control replicate 3


title: control replicate 4


title: control replicate 2


title: control replicate 1


title: e14.5 EP 1

description:
single e14.5 mouse EPs
e14_1