title: Untagged_CRAC

status: Public on Aug 01 2018

city: Basel

first: Alex

middle: Charles

last: Tuck

address: Maulbeerstrasse 66

country: Switzerland

institute: Friedrich Miescher Institute for Biomedical Research

description: Illumina i7 index: in-line barcode NNNNGTGAGC (L5Bb)

data_processing:
Library strategy: CRAC-seq
Single-cell RNA-seq data processing: Paired-end reads were preprocessed using Trimmomatic, with the following settings: ILLUMINACLIP:Nextera_PE_adapters.fa:2:30:10:1:true LEADING:28 TRAILING:28 SLIDINGWINDOW:1:28 MINLEN:50. The reads were then aligned to mm10 using gsnap version 2015-09-29 with the following settings: --suboptimal-levels=5 -n 1 -Q –nofails, and providing splice sites from a reference file including Ensembl annotations (GRCm38 release 75) and lncRNA annotations from "Ab initio reconstruction of cell type-specific transcriptomes in mouse reveals the conserved multi-exonic structure of lincRNAs. Guttman M, Garber M, Levin JZ, Donaghey J, Robinson J, Adiconis X, Fan L, Koziol MJ, Gnirke A, Nusbaum C, Rinn JL, Lander ES, Regev A. Nat Biotechnol. 2010 May;28(5):503-10" and "The evolution of lncRNA repertoires and expression patterns in tetrapods. Necsulea A, Soumillon M, Warnefors M, Liechti A, Daish T, Zeller U, Baker JC, Grützner F, Kaessmann H. Nature. 2014 Jan 30;505(7485):635-40".
Bulk RNA-seq data processing for ES to NPC timecourse: reads were mapped to mm10 using tophat version 2.0.14 with the settings --mate-inner-dist -30 --mate-std-dev 80 --library-type fr-firststrand , and providing a --transcriptome-index from a reference file including Ensembl annotations (GRCm38 release 75) and lncRNA annotations from "Ab initio reconstruction of cell type-specific transcriptomes in mouse reveals the conserved multi-exonic structure of lincRNAs. Guttman M, Garber M, Levin JZ, Donaghey J, Robinson J, Adiconis X, Fan L, Koziol MJ, Gnirke A, Nusbaum C, Rinn JL, Lander ES, Regev A. Nat Biotechnol. 2010 May;28(5):503-10" and "The evolution of lncRNA repertoires and expression patterns in tetrapods. Necsulea A, Soumillon M, Warnefors M, Liechti A, Daish T, Zeller U, Baker JC, Grützner F, Kaessmann H. Nature. 2014 Jan 30;505(7485):635-40". Uniquely mapping reads from concordant read pairs were retained by filtering for a quality of 50 and the 0x2 flag (samtools view -b -q 50 -f 0x2).
Bulk RNA-seq data for cell lines with HHRz integrations or deletions: reads were mapped to mm10 using gsnap-2015-09-29 and the settings --suboptimal-levels=5 -B 5 -t 8 -n 1 -Q --nofails, and providing splice sites from a reference file including Ensembl annotations (GRCm38 release 75) and lncRNA annotations from "Ab initio reconstruction of cell type-specific transcriptomes in mouse reveals the conserved multi-exonic structure of lincRNAs. Guttman M, Garber M, Levin JZ, Donaghey J, Robinson J, Adiconis X, Fan L, Koziol MJ, Gnirke A, Nusbaum C, Rinn JL, Lander ES, Regev A. Nat Biotechnol. 2010 May;28(5):503-10" and "The evolution of lncRNA repertoires and expression patterns in tetrapods. Necsulea A, Soumillon M, Warnefors M, Liechti A, Daish T, Zeller U, Baker JC, Grützner F, Kaessmann H. Nature. 2014 Jan 30;505(7485):635-40".
Bulk RNA-seq data for actinomycin D timecourse (half life calculations): reads were mapped to mm10 using gsnap-2015-09-29 and the settings --suboptimal-levels=5 -B 5 -t 8 -n 1 -Q --nofails, and providing splice sites from a reference file including Ensembl annotations (GRCm38 release 75) and lncRNA annotations from "Ab initio reconstruction of cell type-specific transcriptomes in mouse reveals the conserved multi-exonic structure of lincRNAs. Guttman M, Garber M, Levin JZ, Donaghey J, Robinson J, Adiconis X, Fan L, Koziol MJ, Gnirke A, Nusbaum C, Rinn JL, Lander ES, Regev A. Nat Biotechnol. 2010 May;28(5):503-10" and "The evolution of lncRNA repertoires and expression patterns in tetrapods. Necsulea A, Soumillon M, Warnefors M, Liechti A, Daish T, Zeller U, Baker JC, Grützner F, Kaessmann H. Nature. 2014 Jan 30;505(7485):635-40".
CRAC and NET-seq data:  Sequencing reads were preprocessed for standard analyses as follows:
(i) The 3’ adapter was removed (if present) using fastx_clipper.
(ii) Low quality sequence was removed using the fastx toolkit, specifically fastq_quality_trimmer -t 25, fastq_quality_filter -q 20 -p 90 and fastx_artifacts_filter.
(iii) Reads with identical sequence and 5’ inline unique molecule identifier, UMI, were collapsed, as they are likely to arise from duplication during PCR.
(iv) For CRAC, low complexity regions were trimmed from the 3’ end of reads (regions of 2 nt or more where 80 % or more of the sequence comprises one nucleotide). This is because many Mtr4-bound RNA fragments contain non-genome-encoded oligo(A) tails that can lead to apparently unique mapping of repeat RNAs.
(v) Homopolymers and dinucleotide-rich sequences were removed using prinseq-lite, with settings -min_len 18 -lc_threshold 20 -lc_method dust.
To obtain a set of reads that do not map to repetitive regions of the genome or small non-coding RNAs (e.g. retrotransposons, tRNAs, snoRNAs, rRNA), we then filtered reads as follows. Reads were mapped separately, using novoalign, to three indexes: (i) the mm10 genome, (ii) mm10 protein-coding transcripts (cDNAs), and (iii) pseudochromosomes assembled from RepeatMasker repeats, the ribosomal DNA repeat (Grozdanov et al, 2003) and gencode.vM9 small non-coding RNAs (e.g. miRNA, snoRNA, snRNA, rRNA). “Nonrepeat” reads were then defined as those that mapped better to the mm10 genome or cDNAs, than to any of the repeat RNAs or small non-coding RNAs.
We then mapped reads (either after standard preprocessing, or “nonrepeat” reads filtered as described) using bowtie2 (mode: --sensitive) with mm10.
Genome_build: mm10
Supplementary_files_format_and_content: bigWig files for single-cell RNA-seq: alignments were converted to bigWig files using picard-tools and bedtools, accounting for library size by dividing the depth at each position by the number of mapped reads then multiplying by 1000000.
bigWig files for bulk RNA-seq of the ES to NPC differentiation: IGVtools was used to convert BAM files into bigWig format. The bigWigs are not normalised for library size, and one bigWig file is provided for plus and minus strand mapping reads.
bigWig files for bulk RNA-seq of cell lines with HHRz integrations or deletions were generated from BAM files using bedtools, accounting for library size by dividing the depth at each position by the number of mapped reads then multiplying by 1000000.
bigWig files for bulk RNA-seq of cells treated with actinomycin D for RNA half life calculations were generated from BAM files using bedtools, accounting for library size by dividing the depth at each position by the number of mapped reads then multiplying by 1000000.
bigWig files for CRAC and NET-seq data: generally, bigWig files were obtained by taking uniquely mapping reads and converting to bigWig with samtools and bedtools. The "mixed" bigWig files contain data from replicate experiments that has been combined prior to generating the bigWig

source_name: mouse embryonic stem cell

growth_protocol: Cells were cultured on gelatin-coated dishes in serum+LIF medium (DMEM, 0.1 mM non-essential amino acids, 1 mM sodium pyruvate, 2 mM L-glutamine, 15 % (v/v) fetal bovine serum, 0.1 mM beta-mercaptoethanol, 50 μg/ml penicillin, 80 μg/ml streptomycin and home-made LIF conditioned medium)

extract_protocol: 2x15cm dishes of mESCs were crosslinked, cells lysed in mild RIPA buffer, a tandem purification with FLAG and then Streptavidin beads performed, including RNase digestion, TSAP treatment, PNK treatment, and linker ligations while on the Streptavidin beads. The RNPs were eluted by heating in loading buffer, and resolved by SDS-PAGE and transfer to a nitrocellulose membrane. The region corresponding to the (radiolabelled) RNP was then cut out, RNA extracted using Proteinase K and then phenol:choloroform, and then cDNA synthesis and PCR performed. The final library was purified on a Metaphor agarose 3 % gel. The 5' linker includes an in-line barcode, followed by AGC at the 3' end.

tag: genetic background

value: mES159 Rosa26Cre-ERT2/BirA-V5

tag: visual annotation for single cell data


title: NETSeq

type: SRA

description:
NETSeq_rep1
NETSeq_rep2

library_source: transcriptomic

data_processing:
Library strategy: NET-seq
Single-cell RNA-seq data processing: Paired-end reads were preprocessed using Trimmomatic, with the following settings: ILLUMINACLIP:Nextera_PE_adapters.fa:2:30:10:1:true LEADING:28 TRAILING:28 SLIDINGWINDOW:1:28 MINLEN:50. The reads were then aligned to mm10 using gsnap version 2015-09-29 with the following settings: --suboptimal-levels=5 -n 1 -Q –nofails, and providing splice sites from a reference file including Ensembl annotations (GRCm38 release 75) and lncRNA annotations from "Ab initio reconstruction of cell type-specific transcriptomes in mouse reveals the conserved multi-exonic structure of lincRNAs. Guttman M, Garber M, Levin JZ, Donaghey J, Robinson J, Adiconis X, Fan L, Koziol MJ, Gnirke A, Nusbaum C, Rinn JL, Lander ES, Regev A. Nat Biotechnol. 2010 May;28(5):503-10" and "The evolution of lncRNA repertoires and expression patterns in tetrapods. Necsulea A, Soumillon M, Warnefors M, Liechti A, Daish T, Zeller U, Baker JC, Grützner F, Kaessmann H. Nature. 2014 Jan 30;505(7485):635-40".
Bulk RNA-seq data processing for ES to NPC timecourse: reads were mapped to mm10 using tophat version 2.0.14 with the settings --mate-inner-dist -30 --mate-std-dev 80 --library-type fr-firststrand , and providing a --transcriptome-index from a reference file including Ensembl annotations (GRCm38 release 75) and lncRNA annotations from "Ab initio reconstruction of cell type-specific transcriptomes in mouse reveals the conserved multi-exonic structure of lincRNAs. Guttman M, Garber M, Levin JZ, Donaghey J, Robinson J, Adiconis X, Fan L, Koziol MJ, Gnirke A, Nusbaum C, Rinn JL, Lander ES, Regev A. Nat Biotechnol. 2010 May;28(5):503-10" and "The evolution of lncRNA repertoires and expression patterns in tetrapods. Necsulea A, Soumillon M, Warnefors M, Liechti A, Daish T, Zeller U, Baker JC, Grützner F, Kaessmann H. Nature. 2014 Jan 30;505(7485):635-40". Uniquely mapping reads from concordant read pairs were retained by filtering for a quality of 50 and the 0x2 flag (samtools view -b -q 50 -f 0x2).
Bulk RNA-seq data for cell lines with HHRz integrations or deletions: reads were mapped to mm10 using gsnap-2015-09-29 and the settings --suboptimal-levels=5 -B 5 -t 8 -n 1 -Q --nofails, and providing splice sites from a reference file including Ensembl annotations (GRCm38 release 75) and lncRNA annotations from "Ab initio reconstruction of cell type-specific transcriptomes in mouse reveals the conserved multi-exonic structure of lincRNAs. Guttman M, Garber M, Levin JZ, Donaghey J, Robinson J, Adiconis X, Fan L, Koziol MJ, Gnirke A, Nusbaum C, Rinn JL, Lander ES, Regev A. Nat Biotechnol. 2010 May;28(5):503-10" and "The evolution of lncRNA repertoires and expression patterns in tetrapods. Necsulea A, Soumillon M, Warnefors M, Liechti A, Daish T, Zeller U, Baker JC, Grützner F, Kaessmann H. Nature. 2014 Jan 30;505(7485):635-40".
Bulk RNA-seq data for actinomycin D timecourse (half life calculations): reads were mapped to mm10 using gsnap-2015-09-29 and the settings --suboptimal-levels=5 -B 5 -t 8 -n 1 -Q --nofails, and providing splice sites from a reference file including Ensembl annotations (GRCm38 release 75) and lncRNA annotations from "Ab initio reconstruction of cell type-specific transcriptomes in mouse reveals the conserved multi-exonic structure of lincRNAs. Guttman M, Garber M, Levin JZ, Donaghey J, Robinson J, Adiconis X, Fan L, Koziol MJ, Gnirke A, Nusbaum C, Rinn JL, Lander ES, Regev A. Nat Biotechnol. 2010 May;28(5):503-10" and "The evolution of lncRNA repertoires and expression patterns in tetrapods. Necsulea A, Soumillon M, Warnefors M, Liechti A, Daish T, Zeller U, Baker JC, Grützner F, Kaessmann H. Nature. 2014 Jan 30;505(7485):635-40".
CRAC and NET-seq data:  Sequencing reads were preprocessed for standard analyses as follows:
(i) The 3’ adapter was removed (if present) using fastx_clipper.
(ii) Low quality sequence was removed using the fastx toolkit, specifically fastq_quality_trimmer -t 25, fastq_quality_filter -q 20 -p 90 and fastx_artifacts_filter.
(iii) Reads with identical sequence and 5’ inline unique molecule identifier, UMI, were collapsed, as they are likely to arise from duplication during PCR.
(iv) For CRAC, low complexity regions were trimmed from the 3’ end of reads (regions of 2 nt or more where 80 % or more of the sequence comprises one nucleotide). This is because many Mtr4-bound RNA fragments contain non-genome-encoded oligo(A) tails that can lead to apparently unique mapping of repeat RNAs.
(v) Homopolymers and dinucleotide-rich sequences were removed using prinseq-lite, with settings -min_len 18 -lc_threshold 20 -lc_method dust.
To obtain a set of reads that do not map to repetitive regions of the genome or small non-coding RNAs (e.g. retrotransposons, tRNAs, snoRNAs, rRNA), we then filtered reads as follows. Reads were mapped separately, using novoalign, to three indexes: (i) the mm10 genome, (ii) mm10 protein-coding transcripts (cDNAs), and (iii) pseudochromosomes assembled from RepeatMasker repeats, the ribosomal DNA repeat (Grozdanov et al, 2003) and gencode.vM9 small non-coding RNAs (e.g. miRNA, snoRNA, snRNA, rRNA). “Nonrepeat” reads were then defined as those that mapped better to the mm10 genome or cDNAs, than to any of the repeat RNAs or small non-coding RNAs.
We then mapped reads (either after standard preprocessing, or “nonrepeat” reads filtered as described) using bowtie2 (mode: --sensitive) with mm10.
Genome_build: mm10
Supplementary_files_format_and_content: bigWig files for single-cell RNA-seq: alignments were converted to bigWig files using picard-tools and bedtools, accounting for library size by dividing the depth at each position by the number of mapped reads then multiplying by 1000000.
bigWig files for bulk RNA-seq of the ES to NPC differentiation: IGVtools was used to convert BAM files into bigWig format. The bigWigs are not normalised for library size, and one bigWig file is provided for plus and minus strand mapping reads.
bigWig files for bulk RNA-seq of cell lines with HHRz integrations or deletions were generated from BAM files using bedtools, accounting for library size by dividing the depth at each position by the number of mapped reads then multiplying by 1000000.
bigWig files for bulk RNA-seq of cells treated with actinomycin D for RNA half life calculations were generated from BAM files using bedtools, accounting for library size by dividing the depth at each position by the number of mapped reads then multiplying by 1000000.
bigWig files for CRAC and NET-seq data: generally, bigWig files were obtained by taking uniquely mapping reads and converting to bigWig with samtools and bedtools. The "mixed" bigWig files contain data from replicate experiments that has been combined prior to generating the bigWig

molecule: total RNA

organism: Mus musculus

extract_protocol: The protocol of Nojima et al, Cell. 2015 Apr 23;161(3):526-540, was followed


title: All_miRNA

status: Public on Aug 02 2018

city: Dalian

first: Hongjun

last: Li

address: 42 Linghe Street

country: China

institute: National Marine Environmental Monitoring Center

description: MicroRNA

data_processing:
Hiseq 2500 SE used for basecalling
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then alignment with the database of genebank, Rfam and genome of Mactra chinensis.
miRDeeps used for analysis and identification the cleans and its expression.
Genome_build: fast and effective prediction of microRNA/target duplexes. Rehmsmeier M, Steffen P, Hochsmann M, Giegerich R RNA.2004 Oct: 10(10):1507-1517.
Supplementary_files_format_and_content: fasta file with sequences and .mrd text files with with read counts and scores.

organism: Mactra chinensis

source_name: Gill

extract_protocol:
The gill was collected and immersed into RNA-EZ Reagents D RNA-Be-Locker A, then stored at −80℃ and RNA was harvested using Trizol reagent. NEB Multiple Small RNA Library Pre Set Kit for Illumina was used for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: tissue

value: Gills

tag: treatment

tag: hours


title: Mtr4_CRAC_rep3

value: mES159 Rosa26Cre-ERT2/BirA-V5 Mtr4 3xFlagAvi clone 35


title: non-acclimated (ck)

city: Hangzhou

first: Lu

last: Wang

state: Zhejiang

address: 9th, South Meiling Road

description: miRNA

data_processing:
After the sequence tags from Solexa sequencing went through the data cleaning by removing the low quality tags (i.e., tags less than 18 nt and tags whose adaptors were null) and contaminants (adaptors and polyA)
After removing adaptor sequences of the left high-quality small RNA reads with exact matches to the adaptor sequences, reads were mapped to the C. sinenesis unigene dataset using SOAP2.
The sequences were used through BLASTn search of the NCBI Genebank database and Rfam database to remove the rRNAs, tRNAs, snRNAs and snoRNAs.
The unique small RNA sequences left were searched against the miRNase database v19.0 and were considered to be known miRNAs with up to two mismatches.The sequences that didn’t map to any known miRNAs were analyzed for predictions to identify novel miRNAs
The sequences that didn’t map to any known miRNAs were analyzed for predictions to identify novel miRNAs
Supplementary_files_format_and_content: fasta files and text files

organism: Camellia sinensis

source_name: leaf

growth_protocol: Tea plants (‘Camellia sinensis (L.) O. Kuntze cv. ‘Longjing 43’) were grown in the Tea Research Institute, Chinese Academy of Agricultural Sciences (TRI, CAAS, N 30°10', E 120°5'), Hangzhou, China, were used in this study.

extract_protocol:
To construct small RNA libraries, total RNA was extracted using the Trizol (Invitrogen) according to the manufacturer's protocols and RNase –Free DNase I was used to remove genomic DNA contimination.
For each sample, the 18-30 nt small RNAs were ligated with 5' and 3' RNA adapter by T4 RNA ligase (TaKaRa) after they were purified by electrophoretic separation on a 15% TBE-urea denaturing PAGE gel, and at each step purified by urea PAGE gel electrophoretic separation. The RNA was subsequently transcribed to single-stranded cDNA using Superscript II reverse transcriptase (Invitrogen). Thereafter the cDNA was used as templates for double-stranded cDNA synthesis by PCR amplification using primers that anneal to adapters. The purified DNA was sequenced on a Solexa sequencer (Illumina).

treatment_protocol: The natural cold acclimation treatment and samples collection was performed.Two samples, including ones that were non-acclimated (CK, the date for sample collection was 1st December, 2010) and fully acclimated (CA1, the date was 29th December, 2010), were used for libraries preparation and further analyses.

value: mature leaves

value: non-acclimated

tag: sampling date

value: 1st December, 2010

tag: cultivar

value: Longjing 43


title: I2 TRhi

city: Houston

first: Maria

last: Bettini

state: TX

address: 1102 Bates St

country: USA

institute: Baylor College of Medicine

data_processing:
NextSeq Control Software v2.0 used for base calling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm10 using TopHat Alignment v1.0.0
Fragment per kilobase million of library size (FPKM) were calculated using Cufflinks Assembly & DE v1.1.0
Genome_build: RefSeq mm10

source_name: regulatory T cells

extract_protocol:
TritonX-100 cell lysis, reverse transcription, cDNA amplification
Nextera XT

tag: strain

value: NOD

value: pancreatic islets

tag: age

tag: genotype

value: NOD (WT)

tag: cell type

value: regulatory T cells


title: Mtr4_CRAC_rep2

description: Illumina i7 index: in-line barcode NNNNCTAGC (L5Ca)


title: I1 TRlo


title: ActD_timecourse_rep3_time30

data_processing:
Single-cell RNA-seq data processing: Paired-end reads were preprocessed using Trimmomatic, with the following settings: ILLUMINACLIP:Nextera_PE_adapters.fa:2:30:10:1:true LEADING:28 TRAILING:28 SLIDINGWINDOW:1:28 MINLEN:50. The reads were then aligned to mm10 using gsnap version 2015-09-29 with the following settings: --suboptimal-levels=5 -n 1 -Q –nofails, and providing splice sites from a reference file including Ensembl annotations (GRCm38 release 75) and lncRNA annotations from "Ab initio reconstruction of cell type-specific transcriptomes in mouse reveals the conserved multi-exonic structure of lincRNAs. Guttman M, Garber M, Levin JZ, Donaghey J, Robinson J, Adiconis X, Fan L, Koziol MJ, Gnirke A, Nusbaum C, Rinn JL, Lander ES, Regev A. Nat Biotechnol. 2010 May;28(5):503-10" and "The evolution of lncRNA repertoires and expression patterns in tetrapods. Necsulea A, Soumillon M, Warnefors M, Liechti A, Daish T, Zeller U, Baker JC, Grützner F, Kaessmann H. Nature. 2014 Jan 30;505(7485):635-40".
Bulk RNA-seq data processing for ES to NPC timecourse: reads were mapped to mm10 using tophat version 2.0.14 with the settings --mate-inner-dist -30 --mate-std-dev 80 --library-type fr-firststrand , and providing a --transcriptome-index from a reference file including Ensembl annotations (GRCm38 release 75) and lncRNA annotations from "Ab initio reconstruction of cell type-specific transcriptomes in mouse reveals the conserved multi-exonic structure of lincRNAs. Guttman M, Garber M, Levin JZ, Donaghey J, Robinson J, Adiconis X, Fan L, Koziol MJ, Gnirke A, Nusbaum C, Rinn JL, Lander ES, Regev A. Nat Biotechnol. 2010 May;28(5):503-10" and "The evolution of lncRNA repertoires and expression patterns in tetrapods. Necsulea A, Soumillon M, Warnefors M, Liechti A, Daish T, Zeller U, Baker JC, Grützner F, Kaessmann H. Nature. 2014 Jan 30;505(7485):635-40". Uniquely mapping reads from concordant read pairs were retained by filtering for a quality of 50 and the 0x2 flag (samtools view -b -q 50 -f 0x2).
Bulk RNA-seq data for cell lines with HHRz integrations or deletions: reads were mapped to mm10 using gsnap-2015-09-29 and the settings --suboptimal-levels=5 -B 5 -t 8 -n 1 -Q --nofails, and providing splice sites from a reference file including Ensembl annotations (GRCm38 release 75) and lncRNA annotations from "Ab initio reconstruction of cell type-specific transcriptomes in mouse reveals the conserved multi-exonic structure of lincRNAs. Guttman M, Garber M, Levin JZ, Donaghey J, Robinson J, Adiconis X, Fan L, Koziol MJ, Gnirke A, Nusbaum C, Rinn JL, Lander ES, Regev A. Nat Biotechnol. 2010 May;28(5):503-10" and "The evolution of lncRNA repertoires and expression patterns in tetrapods. Necsulea A, Soumillon M, Warnefors M, Liechti A, Daish T, Zeller U, Baker JC, Grützner F, Kaessmann H. Nature. 2014 Jan 30;505(7485):635-40".
Bulk RNA-seq data for actinomycin D timecourse (half life calculations): reads were mapped to mm10 using gsnap-2015-09-29 and the settings --suboptimal-levels=5 -B 5 -t 8 -n 1 -Q --nofails, and providing splice sites from a reference file including Ensembl annotations (GRCm38 release 75) and lncRNA annotations from "Ab initio reconstruction of cell type-specific transcriptomes in mouse reveals the conserved multi-exonic structure of lincRNAs. Guttman M, Garber M, Levin JZ, Donaghey J, Robinson J, Adiconis X, Fan L, Koziol MJ, Gnirke A, Nusbaum C, Rinn JL, Lander ES, Regev A. Nat Biotechnol. 2010 May;28(5):503-10" and "The evolution of lncRNA repertoires and expression patterns in tetrapods. Necsulea A, Soumillon M, Warnefors M, Liechti A, Daish T, Zeller U, Baker JC, Grützner F, Kaessmann H. Nature. 2014 Jan 30;505(7485):635-40".
CRAC and NET-seq data:  Sequencing reads were preprocessed for standard analyses as follows:
(i) The 3’ adapter was removed (if present) using fastx_clipper.
(ii) Low quality sequence was removed using the fastx toolkit, specifically fastq_quality_trimmer -t 25, fastq_quality_filter -q 20 -p 90 and fastx_artifacts_filter.
(iii) Reads with identical sequence and 5’ inline unique molecule identifier, UMI, were collapsed, as they are likely to arise from duplication during PCR.
(iv) For CRAC, low complexity regions were trimmed from the 3’ end of reads (regions of 2 nt or more where 80 % or more of the sequence comprises one nucleotide). This is because many Mtr4-bound RNA fragments contain non-genome-encoded oligo(A) tails that can lead to apparently unique mapping of repeat RNAs.
(v) Homopolymers and dinucleotide-rich sequences were removed using prinseq-lite, with settings -min_len 18 -lc_threshold 20 -lc_method dust.
To obtain a set of reads that do not map to repetitive regions of the genome or small non-coding RNAs (e.g. retrotransposons, tRNAs, snoRNAs, rRNA), we then filtered reads as follows. Reads were mapped separately, using novoalign, to three indexes: (i) the mm10 genome, (ii) mm10 protein-coding transcripts (cDNAs), and (iii) pseudochromosomes assembled from RepeatMasker repeats, the ribosomal DNA repeat (Grozdanov et al, 2003) and gencode.vM9 small non-coding RNAs (e.g. miRNA, snoRNA, snRNA, rRNA). “Nonrepeat” reads were then defined as those that mapped better to the mm10 genome or cDNAs, than to any of the repeat RNAs or small non-coding RNAs.
We then mapped reads (either after standard preprocessing, or “nonrepeat” reads filtered as described) using bowtie2 (mode: --sensitive) with mm10.
Genome_build: mm10
Supplementary_files_format_and_content: bigWig files for single-cell RNA-seq: alignments were converted to bigWig files using picard-tools and bedtools, accounting for library size by dividing the depth at each position by the number of mapped reads then multiplying by 1000000.
bigWig files for bulk RNA-seq of the ES to NPC differentiation: IGVtools was used to convert BAM files into bigWig format. The bigWigs are not normalised for library size, and one bigWig file is provided for plus and minus strand mapping reads.
bigWig files for bulk RNA-seq of cell lines with HHRz integrations or deletions were generated from BAM files using bedtools, accounting for library size by dividing the depth at each position by the number of mapped reads then multiplying by 1000000.
bigWig files for bulk RNA-seq of cells treated with actinomycin D for RNA half life calculations were generated from BAM files using bedtools, accounting for library size by dividing the depth at each position by the number of mapped reads then multiplying by 1000000.
bigWig files for CRAC and NET-seq data: generally, bigWig files were obtained by taking uniquely mapping reads and converting to bigWig with samtools and bedtools. The "mixed" bigWig files contain data from replicate experiments that has been combined prior to generating the bigWig

extract_protocol: 300,000 mESCs were seeded per well of 2 6-well dishes and grown for 48 hr in serum + LIF medium. The medium was replaced by fresh medium containing 5 μM Actinomycin D (from a 5 mg/ml stock in DMSO) and the cells incubated for 30, 90 or 240 min. A mock treatment (240 min = "time 0" samples) was included, using medium with the same amount of DMSO but no Actinomycin D. After the indicated times, the wells were washed twice with 37 °C PBS, and RNA extracted using the Agilent Absolutely RNA miniprep kit. ERCC RNA spike-ins were added to the lysis buffer (1.7 μl of a 1:10 dilution per sample) before it was added to the cells. Ribosomal RNA was then depleted with the ribo-zero rRNA removal kit and high throughput sequencing libraries prepared using the ScriptSeq V2 RNA-Seq Library Preparation Kit.


title: ActD_timecourse_rep3_time0


title: ActD_timecourse_rep3_time240


title: S1 TRlo

value: spleen


title: ActD_timecourse_rep3_time90


title: ActD_timecourse_rep2_time30


title: ActD_timecourse_rep2_time240


title: cold-acclimated (ca_1)

institute: Tea Research Institute, Chinese Academy of Agricultural Sciences

description: miRNA

value: cold-acclimated

value: 29th December, 2010


title: ActD_timecourse_rep2_time90


title: Pdgfra-GFP positive cells E13.5 Brain 1

city: Stockholm

first: David

last: van Bruggen

state: Stockholm

address: Scheeles väg 2

department: MBB

country: Sweden

institute: Karolinska Institutet

description: STRT fluidigm sequence prep

data_processing:
Read processing was performed as described (Islam et al., Nat Methods. 2014 Feb;11(2):163-6), RNA molecules (UMIs) supported only by a single read ("singleton molecules") were removed.
The first 6 bases of each read represent the random Unique Molecular Identifier used for molecule counting. After follows three or more Gs, stemming from the template switching at the mRNA 5' end during first strand cDNA sythesis.
Genome_build: Genome_build: UCSC mm10
Supplementary_files_format_and_content: Total transcript counts per gene for each individual cell

molecule: polyA RNA

source_name: Pdgfra-GFP positive cells from Mouse Brain

extract_protocol:
Forebrain and spinal cord were excised and tissue was mechanical dissociated in HBSS with ions using 3 different Pasteur pipettes of decreasing diameter
Variable, see sample
Illumina’s TruSeq Stranded Total RNA Library Prep Kit was used according to manufacturer’s instructions. Three pooled biological replicates were sequenced for each developmental stage and brain region, and a total of 38 - 66 million 150 bp strand-specific paired-end reads were generated for each replicate, comprising a total of 620.5 million reads across all datasets


title: ActD_timecourse_rep2_time0


title: ActD_timecourse_rep1_time90


title: ActD_timecourse_rep1_time240


title: Mtr4_CRAC_2i_rep1

growth_protocol: Cells were cultured on gelatin-coated dishes in serum+LIF+2i medium (DMEM, 0.1 mM non-essential amino acids, 1 mM sodium pyruvate, 2 mM L-glutamine, 15 % (v/v) fetal bovine serum, 0.1 mM beta-mercaptoethanol, 50 μg/ml penicillin, 80 μg/ml streptomycin and home-made LIF conditioned medium, plus 1 μM MEK inhibitor PD 0325901 (Tocris) and 3 μM GSK3 inhibitor CHIR99021 (Calbiochem))


title: ActD_timecourse_rep1_time0


title: XLOC_023934-8-1E

extract_protocol: For bulk RNA sequencing of mESC ribozyme cell lines, RNA was extracted using the Agilent Absolutely RNA Miniprep kit, ribosomal RNA depleted using the ribo-zero rRNA removal kit and libraries prepared using the ScriptSeq V2 RNA-Seq Library Preparation Kit.

value: mES159 XLOC_023934 HHRz/HHRz


title: XLOC_023934-8-9F


title: S2 TRlo


title: XLOC_021390-7-5C

value: mES159 XLOC_021390 HHRz/HHRz


title: Mtr4_CRAC_rep1

value: mES159 Rosa26Cre-ERT2/BirA-V5 Mtr4 1xFlagAvi


title: XLOC_021390-7-1D


title: XLOC_021390-7-1C


title: WT-2H


title: WT-2B


title: TunaSite1-18-2G

value: mES159 Tuna HHRz/HHRz (site 1)


title: ActD_timecourse_rep1_time30


title: Tuna-18del-2E

value: mES159 Tuna -/-


title: TunaSite2-18-3D

value: mES159 Tuna HHRz/HHRz (site 2)


title: Pvt1-2alt-6G

value: mES159 Pvt1 HHRz/HHRz (site 2)


title: Pvt1-2del-2A


title: TunaSite1-18-6B


title: Pvt1-2alt-6F


title: TunaSite1-18-3C


title: Pvt1-2-5A

value: mES159 Pvt1 HHRz/HHRz (site 1)


title: Pvt1-2-4H


title: Pcgf6-12-1B


title: Miat-25del-2C

value: mES159 Miat -/-


title: lincEnc1-16del-1D

value: mES159 lncEnc1 -/-


title: Miat-25del-4A


title: Pcgf6-12-5B


title: XLOC_023934-8-4E


title: Pcgf6-12-2B


title: lincEnc1-16-2D

value: mES159 lncEnc1 HHRz/HHRz


title: Pvt1-2-2E


title: lincEnc1-16del-3C


title: WT


title: lincEnc1-16del-2D


title: lincEnc1-16-4B


title: lincEnc1-16-2B


title: Tuna-18del-3B


title: Miat-25del-3G


title: linc1611delta-10del-4G


title: linc1611delta-10del-6E


title: linc1611-10-4H

value: mES159 linc1611 HHRz/HHRz


title: linc1611-10-3H


title: linc1611-10-5G


title: linc1611delta-10del-4D


title: linc1611-10-12C


title: linc1611-10-5E


title: linc1611-10-12D


title: linc1543-24del-4H


title: linc1543-24del-1H


title: linc1543-24del-1E


title: linc1611-10-12B


title: linc1611-10-11A


title: linc1543-24-3E

value: mES159 linc1543 HHRz/HHRz


title: linc1509Site1-19-6B

value: mES159 linc1509 HHRz/HHRz (site 1)


title: linc1543-24-2C


title: linc1509Site2-19-5A

value: mES159 linc1509 HHRz/HHRz (site 2)


title: linc1509Site2-19-4E


title: linc1509Site1-19-4E


title: linc1509Site1-19-1C


title: linc1509Site1-19-5G


title: linc1503-3del-6G


title: linc1503-3del-1C


title: linc1503-3del-6D


title: linc1503-3del-6C


title: linc1503-3-2C

value: mES159 linc1503 HHRz/HHRz


title: linc1503-3-5C


title: linc1611delta-10del-5H


title: linc1503-3-1B


title: linc1405delta-9del-4C


title: linc1405delta-9del-3F


title: linc1405delta-9del-3D


title: linc1405delta-9del-5B


title: linc1405delta-9del-2E


title: linc1405-9-5D

value: mES159 linc1405 HHRz/HHRz


title: linc1405-9-5A


title: linc1405-9-5E


title: linc1405-9-3D


title: linc1405-9-2D


title: linc1509Site2-19-6E


title: linc1405delta-9del-2A


title: linc1400-4mut-6D

value: mES159 linc1400 HHRz*/HHRz*


title: linc1400-4mut-3A


title: linc1400-4del-2A


title: linc1400-4mut-3E


title: linc1400-4del-1G


title: linc1503-3-1E


title: linc1400-4del-1B


title: linc1400-4-7D

value: mES159 linc1400 HHRz/HHRz


title: linc1405delta-9del-6G


title: linc1400-4-7C


title: linc1400-4-6B


title: linc1400-4-4C


title: linc1400-4-1B


title: linc1400-4-11B


title: linc1333-17-6E

value: mES159 linc1333 HHRz/HHRz


title: linc1333-17-4E


title: linc1333-17-3E


title: linc1296-6mut-6E

value: mES159 linc1296 HHRz*/HHRz*


title: linc1296-6mut-6D


title: linc1296-6mut-5F


title: linc1296-6mut-6A


title: linc1296-6mut-1D


title: linc1296-6del-2H


title: linc1296-6del-2E


title: linc1296-6-5F

value: mES159 linc1296 HHRz/HHRz


title: linc1296-6-4C


title: linc1296-6-4D


title: linc1296-6-3C


title: linc1296-6-3B


title: linc1400-4-3D


title: linc1296-6-2C


title: linc1251-1mut-3D

value: mES159 linc1251 HHRz*/HHRz*


title: linc1333-17-6H


title: linc1251-1mut-1A


title: linc1296-6-2G


title: linc1251-1-5D

value: mES159 linc1251 HHRz/HHRz


title: linc1296-6-11E


title: linc1400-4-1H


title: linc1251-1mut-2F


title: linc1251-1-2B


title: G9a-22-3C

value: mES159 G9a HHRz/HHRz


title: linc1333-17-1F


title: G9a-22-2C


title: linc1296-6mut-5A


title: linc1251-1-1B


title: linc1296-6del-2B


title: G9a-22-2H


title: Firre-5del-2C

value: mES159 Firre -/-


title: G9a-22-2B


title: Firre-5-5G

value: mES159 Firre HHRz/HHRz


title: Firre-5del-3C


title: Firre-5del-3A


title: Firre-5-5B


title: Firre-5-2E


title: Firre-5-1B


title: DGCR8-23-6F

value: mES159 DGCR8 HHRz/HHRz


title: DGCR8-23-5E


title: Clpp-13-4B


title: DGCR8-23-2F


title: 7SK-26mut-4H

value: mES159 7SK HHRz*/HHRz*


title: 7SK-26mut-2A


title: 7SK-26-6G

value: mES159 7SK HHRz/HHRz


title: 7SK-26-1B


title: scRNAseq_072_cell_96

description:
Illumina i7 index: N710-CGAGGCTG
Illumina i5 index: S508-CTAAGCCT

source_name: neural precursor cell (day 8)

growth_protocol: NPCs were derived from mESCs according to Bibel M. Richter J. Schrenk K. Tucker K.L. Staiger V. Korte M. Goetz M. Barde Y.A. Differentiation of mouse embryonic stem cells into a defined neuronal lineage. Nat. Neurosci. 2004;7:1003–1009.

extract_protocol: For single cell RNA sequencing, 4000 cells were loaded onto a 10-17 μm Fluidigm C1 Single Cell mRNA Seq IFC, and cells captured according to manufacturer’s instructions. The captured cells were manually annotated under a microscope, to identify capture chambers containing cell debris, dead cells, no cells or multiple cells. Reverse transcription and cDNA preamplification was then performed in the 10-17 μm Fluidigm C1 Single Cell mRNA Seq IFC using the SMARTer Ultra Low RNA Kit for the Fluidigm C1 System and Advantage 2 PCR kit. cDNA was harvested and diluted to 0.1-0.3 ng/μl. Sequencing libraries were then prepared using the Nextera XT DNA Sample Preparation Kit and Nextera XT DNA Sample Preparation Index Kit according to the Fluidigm instructions, “Using the C1™ Single-Cell Auto Prep System to Generate mRNA from Single Cells and Libraries for Sequencing.” The 96 libraries from one IFC were pooled and 150 bp paired-end sequencing performed on the Illumina HiSeq2000.

value: CB9 (Cast/EiJ x C57BL/6J)


title: Firre-5del-2A


title: scRNAseq_072_cell_94

description:
Illumina i7 index: N711-AAGAGGCA
Illumina i5 index: S508-CTAAGCCT


title: scRNAseq_072_cell_90

description:
Illumina i7 index: N710-CGAGGCTG
Illumina i5 index: S507-AAGGAGTA


title: scRNAseq_072_cell_88

description:
Illumina i7 index: N711-AAGAGGCA
Illumina i5 index: S507-AAGGAGTA


title: scRNAseq_072_cell_86

description:
Illumina i7 index: N705-GGACTCCT
Illumina i5 index: S507-AAGGAGTA


title: scRNAseq_072_cell_87

description:
Illumina i7 index: N704-TCCTGAGC
Illumina i5 index: S507-AAGGAGTA


title: scRNAseq_072_cell_82

description:
Illumina i7 index: N711-AAGAGGCA
Illumina i5 index: S506-ACTGCATA


title: scRNAseq_072_cell_80

description:
Illumina i7 index: N705-GGACTCCT
Illumina i5 index: S506-ACTGCATA


title: scRNAseq_072_cell_93

description:
Illumina i7 index: N704-TCCTGAGC
Illumina i5 index: S508-CTAAGCCT


title: scRNAseq_072_cell_95

description:
Illumina i7 index: N712-GTAGAGGA
Illumina i5 index: S508-CTAAGCCT


title: scRNAseq_072_cell_92

description:
Illumina i7 index: N705-GGACTCCT
Illumina i5 index: S508-CTAAGCCT


title: scRNAseq_072_cell_79

description:
Illumina i7 index: N706-TAGGCATG
Illumina i5 index: S506-ACTGCATA


title: scRNAseq_072_cell_85

description:
Illumina i7 index: N706-TAGGCATG
Illumina i5 index: S507-AAGGAGTA


title: scRNAseq_072_cell_81

description:
Illumina i7 index: N704-TCCTGAGC
Illumina i5 index: S506-ACTGCATA


title: scRNAseq_072_cell_84

description:
Illumina i7 index: N710-CGAGGCTG
Illumina i5 index: S506-ACTGCATA


title: scRNAseq_072_cell_89

description:
Illumina i7 index: N712-GTAGAGGA
Illumina i5 index: S507-AAGGAGTA


title: scRNAseq_072_cell_76

description:
Illumina i7 index: N711-AAGAGGCA
Illumina i5 index: S505-GTAAGGAG


title: scRNAseq_072_cell_77

description:
Illumina i7 index: N712-GTAGAGGA
Illumina i5 index: S505-GTAAGGAG


title: scRNAseq_072_cell_78

description:
Illumina i7 index: N710-CGAGGCTG
Illumina i5 index: S505-GTAAGGAG


title: scRNAseq_072_cell_73

description:
Illumina i7 index: N706-TAGGCATG
Illumina i5 index: S505-GTAAGGAG


title: scRNAseq_072_cell_75

description:
Illumina i7 index: N704-TCCTGAGC
Illumina i5 index: S505-GTAAGGAG


title: scRNAseq_072_cell_72

description:
Illumina i7 index: N711-AAGAGGCA
Illumina i5 index: S504-AGAGTAGA


title: scRNAseq_072_cell_74

description:
Illumina i7 index: N705-GGACTCCT
Illumina i5 index: S505-GTAAGGAG


title: scRNAseq_072_cell_91

description:
Illumina i7 index: N706-TAGGCATG
Illumina i5 index: S508-CTAAGCCT


title: scRNAseq_072_cell_71

description:
Illumina i7 index: N712-GTAGAGGA
Illumina i5 index: S504-AGAGTAGA


title: scRNAseq_072_cell_70

description:
Illumina i7 index: N710-CGAGGCTG
Illumina i5 index: S504-AGAGTAGA


title: scRNAseq_072_cell_68

description:
Illumina i7 index: N705-GGACTCCT
Illumina i5 index: S504-AGAGTAGA


title: scRNAseq_072_cell_69

description:
Illumina i7 index: N706-TAGGCATG
Illumina i5 index: S504-AGAGTAGA


title: scRNAseq_072_cell_83

description:
Illumina i7 index: N712-GTAGAGGA
Illumina i5 index: S506-ACTGCATA


title: scRNAseq_072_cell_65

description:
Illumina i7 index: N712-GTAGAGGA
Illumina i5 index: S503-TATCCTCT


title: scRNAseq_072_cell_67

description:
Illumina i7 index: N704-TCCTGAGC
Illumina i5 index: S504-AGAGTAGA


title: scRNAseq_072_cell_66

description:
Illumina i7 index: N711-AAGAGGCA
Illumina i5 index: S503-TATCCTCT


title: scRNAseq_072_cell_62

description:
Illumina i7 index: N705-GGACTCCT
Illumina i5 index: S503-TATCCTCT


title: scRNAseq_072_cell_63

description:
Illumina i7 index: N706-TAGGCATG
Illumina i5 index: S503-TATCCTCT


title: scRNAseq_072_cell_58

description:
Illumina i7 index: N710-CGAGGCTG
Illumina i5 index: S502-CTCTCTAT


title: scRNAseq_072_cell_59

description:
Illumina i7 index: N712-GTAGAGGA
Illumina i5 index: S502-CTCTCTAT


title: scRNAseq_072_cell_60

description:
Illumina i7 index: N711-AAGAGGCA
Illumina i5 index: S502-CTCTCTAT


title: scRNAseq_072_cell_61

description:
Illumina i7 index: N704-TCCTGAGC
Illumina i5 index: S503-TATCCTCT


title: scRNAseq_072_cell_64

description:
Illumina i7 index: N710-CGAGGCTG
Illumina i5 index: S503-TATCCTCT


title: scRNAseq_072_cell_55

description:
Illumina i7 index: N704-TCCTGAGC
Illumina i5 index: S502-CTCTCTAT


title: scRNAseq_072_cell_54

description:
Illumina i7 index: N711-AAGAGGCA
Illumina i5 index: S501-TAGATCGC


title: scRNAseq_072_cell_52

description:
Illumina i7 index: N710-CGAGGCTG
Illumina i5 index: S501-TAGATCGC


title: Tuna-18del-1E

value: mES159 Tuna -/-


title: scRNAseq_072_cell_51

description:
Illumina i7 index: N706-TAGGCATG
Illumina i5 index: S501-TAGATCGC


title: scRNAseq_072_cell_45

description:
Illumina i7 index: N703-AGGCAGAA
Illumina i5 index: S508-CTAAGCCT


title: scRNAseq_072_cell_48

description:
Illumina i7 index: N709-GCTACGCT
Illumina i5 index: S508-CTAAGCCT

value: debris


title: scRNAseq_072_cell_43

description:
Illumina i7 index: N701-TAAGGCGA
Illumina i5 index: S508-CTAAGCCT


title: scRNAseq_072_cell_44

description:
Illumina i7 index: N702-CGTACTAG
Illumina i5 index: S508-CTAAGCCT


title: scRNAseq_072_cell_47

description:
Illumina i7 index: N708-CAGAGAGG
Illumina i5 index: S508-CTAAGCCT

value: multi


title: scRNAseq_072_cell_46

description:
Illumina i7 index: N707-CTCTCTAC
Illumina i5 index: S508-CTAAGCCT


title: scRNAseq_072_cell_42

description:
Illumina i7 index: N709-GCTACGCT
Illumina i5 index: S507-AAGGAGTA


title: scRNAseq_072_cell_40

description:
Illumina i7 index: N707-CTCTCTAC
Illumina i5 index: S507-AAGGAGTA


title: scRNAseq_072_cell_41

description:
Illumina i7 index: N708-CAGAGAGG
Illumina i5 index: S507-AAGGAGTA


title: scRNAseq_072_cell_38

description:
Illumina i7 index: N702-CGTACTAG
Illumina i5 index: S507-AAGGAGTA


title: scRNAseq_072_cell_37

description:
Illumina i7 index: N701-TAAGGCGA
Illumina i5 index: S507-AAGGAGTA


title: scRNAseq_072_cell_39

description:
Illumina i7 index: N703-AGGCAGAA
Illumina i5 index: S507-AAGGAGTA

value: small


title: scRNAseq_072_cell_57

description:
Illumina i7 index: N706-TAGGCATG
Illumina i5 index: S502-CTCTCTAT


title: scRNAseq_072_cell_35

description:
Illumina i7 index: N708-CAGAGAGG
Illumina i5 index: S506-ACTGCATA


title: scRNAseq_072_cell_34

description:
Illumina i7 index: N707-CTCTCTAC
Illumina i5 index: S506-ACTGCATA


title: scRNAseq_072_cell_56

description:
Illumina i7 index: N705-GGACTCCT
Illumina i5 index: S502-CTCTCTAT


title: scRNAseq_072_cell_49

description:
Illumina i7 index: N704-TCCTGAGC
Illumina i5 index: S501-TAGATCGC


title: scRNAseq_072_cell_32

description:
Illumina i7 index: N702-CGTACTAG
Illumina i5 index: S506-ACTGCATA


title: scRNAseq_072_cell_31

description:
Illumina i7 index: N701-TAAGGCGA
Illumina i5 index: S506-ACTGCATA


title: scRNAseq_072_cell_28

description:
Illumina i7 index: N707-CTCTCTAC
Illumina i5 index: S505-GTAAGGAG


title: scRNAseq_072_cell_33

description:
Illumina i7 index: N703-AGGCAGAA
Illumina i5 index: S506-ACTGCATA

value: empty


title: scRNAseq_072_cell_30

description:
Illumina i7 index: N709-GCTACGCT
Illumina i5 index: S505-GTAAGGAG


title: scRNAseq_072_cell_27

description:
Illumina i7 index: N703-AGGCAGAA
Illumina i5 index: S505-GTAAGGAG


title: scRNAseq_072_cell_26

description:
Illumina i7 index: N702-CGTACTAG
Illumina i5 index: S505-GTAAGGAG


title: scRNAseq_072_cell_25

description:
Illumina i7 index: N701-TAAGGCGA
Illumina i5 index: S505-GTAAGGAG


title: scRNAseq_072_cell_24

description:
Illumina i7 index: N707-CTCTCTAC
Illumina i5 index: S504-AGAGTAGA


title: scRNAseq_072_cell_50

description:
Illumina i7 index: N705-GGACTCCT
Illumina i5 index: S501-TAGATCGC


title: scRNAseq_072_cell_22

description:
Illumina i7 index: N709-GCTACGCT
Illumina i5 index: S504-AGAGTAGA


title: scRNAseq_072_cell_21

description:
Illumina i7 index: N701-TAAGGCGA
Illumina i5 index: S504-AGAGTAGA


title: scRNAseq_072_cell_23

description:
Illumina i7 index: N708-CAGAGAGG
Illumina i5 index: S504-AGAGTAGA


title: scRNAseq_072_cell_36

description:
Illumina i7 index: N709-GCTACGCT
Illumina i5 index: S506-ACTGCATA


title: scRNAseq_072_cell_18

description:
Illumina i7 index: N707-CTCTCTAC
Illumina i5 index: S503-TATCCTCT


title: scRNAseq_072_cell_20

description:
Illumina i7 index: N702-CGTACTAG
Illumina i5 index: S504-AGAGTAGA


title: scRNAseq_072_cell_19

description:
Illumina i7 index: N703-AGGCAGAA
Illumina i5 index: S504-AGAGTAGA


title: scRNAseq_072_cell_17

description:
Illumina i7 index: N708-CAGAGAGG
Illumina i5 index: S503-TATCCTCT


title: scRNAseq_072_cell_16

description:
Illumina i7 index: N709-GCTACGCT
Illumina i5 index: S503-TATCCTCT


title: scRNAseq_072_cell_13

description:
Illumina i7 index: N703-AGGCAGAA
Illumina i5 index: S503-TATCCTCT


title: scRNAseq_072_cell_11

description:
Illumina i7 index: N708-CAGAGAGG
Illumina i5 index: S502-CTCTCTAT


title: scRNAseq_072_cell_12

description:
Illumina i7 index: N707-CTCTCTAC
Illumina i5 index: S502-CTCTCTAT


title: scRNAseq_072_cell_14

description:
Illumina i7 index: N702-CGTACTAG
Illumina i5 index: S503-TATCCTCT


title: scRNAseq_072_cell_10

description:
Illumina i7 index: N709-GCTACGCT
Illumina i5 index: S502-CTCTCTAT


title: scRNAseq_072_cell_53

description:
Illumina i7 index: N712-GTAGAGGA
Illumina i5 index: S501-TAGATCGC


title: scRNAseq_072_cell_7

description:
Illumina i7 index: N703-AGGCAGAA
Illumina i5 index: S502-CTCTCTAT


title: scRNAseq_072_cell_9

description:
Illumina i7 index: N701-TAAGGCGA
Illumina i5 index: S502-CTCTCTAT

value: double


title: scRNAseq_072_cell_6

description:
Illumina i7 index: N707-CTCTCTAC
Illumina i5 index: S501-TAGATCGC


title: scRNAseq_072_cell_8

description:
Illumina i7 index: N702-CGTACTAG
Illumina i5 index: S502-CTCTCTAT


title: scRNAseq_072_cell_3

description:
Illumina i7 index: N701-TAAGGCGA
Illumina i5 index: S501-TAGATCGC


title: scRNAseq_072_cell_4

description:
Illumina i7 index: N709-GCTACGCT
Illumina i5 index: S501-TAGATCGC


title: scRNAseq_072_cell_5

description:
Illumina i7 index: N708-CAGAGAGG
Illumina i5 index: S501-TAGATCGC


title: scRNAseq_072_cell_1

description:
Illumina i7 index: N703-AGGCAGAA
Illumina i5 index: S501-TAGATCGC


title: scRNAseq_072_cell_2

description:
Illumina i7 index: N702-CGTACTAG
Illumina i5 index: S501-TAGATCGC


title: scRNAseq_071_cell_96

description:
Illumina i7 index: N710-CGAGGCTG
Illumina i5 index: S508-CTAAGCCT

value: BC8 (C57BL/6J x Cast/EiJ)


title: scRNAseq_071_cell_94

description:
Illumina i7 index: N711-AAGAGGCA
Illumina i5 index: S508-CTAAGCCT


title: scRNAseq_072_cell_15

description:
Illumina i7 index: N701-TAAGGCGA
Illumina i5 index: S503-TATCCTCT


title: scRNAseq_071_cell_88

description:
Illumina i7 index: N711-AAGAGGCA
Illumina i5 index: S507-AAGGAGTA


title: scRNAseq_071_cell_91

description:
Illumina i7 index: N706-TAGGCATG
Illumina i5 index: S508-CTAAGCCT


title: scRNAseq_071_cell_89

description:
Illumina i7 index: N712-GTAGAGGA
Illumina i5 index: S507-AAGGAGTA


title: scRNAseq_071_cell_92

description:
Illumina i7 index: N705-GGACTCCT
Illumina i5 index: S508-CTAAGCCT


title: scRNAseq_071_cell_87

description:
Illumina i7 index: N704-TCCTGAGC
Illumina i5 index: S507-AAGGAGTA


title: scRNAseq_071_cell_85

description:
Illumina i7 index: N706-TAGGCATG
Illumina i5 index: S507-AAGGAGTA


title: scRNAseq_071_cell_84

description:
Illumina i7 index: N710-CGAGGCTG
Illumina i5 index: S506-ACTGCATA


title: scRNAseq_071_cell_86

description:
Illumina i7 index: N705-GGACTCCT
Illumina i5 index: S507-AAGGAGTA


title: scRNAseq_071_cell_80

description:
Illumina i7 index: N705-GGACTCCT
Illumina i5 index: S506-ACTGCATA


title: scRNAseq_071_cell_82

description:
Illumina i7 index: N711-AAGAGGCA
Illumina i5 index: S506-ACTGCATA


title: scRNAseq_071_cell_81

description:
Illumina i7 index: N704-TCCTGAGC
Illumina i5 index: S506-ACTGCATA


title: scRNAseq_071_cell_79

description:
Illumina i7 index: N706-TAGGCATG
Illumina i5 index: S506-ACTGCATA


title: scRNAseq_071_cell_78

description:
Illumina i7 index: N710-CGAGGCTG
Illumina i5 index: S505-GTAAGGAG


title: scRNAseq_071_cell_76

description:
Illumina i7 index: N711-AAGAGGCA
Illumina i5 index: S505-GTAAGGAG


title: scRNAseq_071_cell_74

description:
Illumina i7 index: N705-GGACTCCT
Illumina i5 index: S505-GTAAGGAG


title: scRNAseq_071_cell_77

description:
Illumina i7 index: N712-GTAGAGGA
Illumina i5 index: S505-GTAAGGAG


title: scRNAseq_071_cell_95

description:
Illumina i7 index: N712-GTAGAGGA
Illumina i5 index: S508-CTAAGCCT


title: scRNAseq_071_cell_93

description:
Illumina i7 index: N704-TCCTGAGC
Illumina i5 index: S508-CTAAGCCT


title: scRNAseq_071_cell_73

description:
Illumina i7 index: N706-TAGGCATG
Illumina i5 index: S505-GTAAGGAG


title: scRNAseq_071_cell_75

description:
Illumina i7 index: N704-TCCTGAGC
Illumina i5 index: S505-GTAAGGAG


title: scRNAseq_071_cell_72

description:
Illumina i7 index: N711-AAGAGGCA
Illumina i5 index: S504-AGAGTAGA


title: scRNAseq_071_cell_71

description:
Illumina i7 index: N712-GTAGAGGA
Illumina i5 index: S504-AGAGTAGA


title: scRNAseq_071_cell_68

description:
Illumina i7 index: N705-GGACTCCT
Illumina i5 index: S504-AGAGTAGA


title: scRNAseq_071_cell_67

description:
Illumina i7 index: N704-TCCTGAGC
Illumina i5 index: S504-AGAGTAGA


title: scRNAseq_071_cell_90

description:
Illumina i7 index: N710-CGAGGCTG
Illumina i5 index: S507-AAGGAGTA


title: scRNAseq_071_cell_65

description:
Illumina i7 index: N712-GTAGAGGA
Illumina i5 index: S503-TATCCTCT


title: scRNAseq_071_cell_64

description:
Illumina i7 index: N710-CGAGGCTG
Illumina i5 index: S503-TATCCTCT


title: scRNAseq_071_cell_66

description:
Illumina i7 index: N711-AAGAGGCA
Illumina i5 index: S503-TATCCTCT


title: scRNAseq_071_cell_62

description:
Illumina i7 index: N705-GGACTCCT
Illumina i5 index: S503-TATCCTCT


title: scRNAseq_071_cell_63

description:
Illumina i7 index: N706-TAGGCATG
Illumina i5 index: S503-TATCCTCT


title: scRNAseq_071_cell_59

description:
Illumina i7 index: N712-GTAGAGGA
Illumina i5 index: S502-CTCTCTAT


title: scRNAseq_071_cell_58

description:
Illumina i7 index: N710-CGAGGCTG
Illumina i5 index: S502-CTCTCTAT


title: scRNAseq_071_cell_60

description:
Illumina i7 index: N711-AAGAGGCA
Illumina i5 index: S502-CTCTCTAT


title: scRNAseq_071_cell_61

description:
Illumina i7 index: N704-TCCTGAGC
Illumina i5 index: S503-TATCCTCT


title: scRNAseq_071_cell_56

description:
Illumina i7 index: N705-GGACTCCT
Illumina i5 index: S502-CTCTCTAT


title: scRNAseq_071_cell_55

description:
Illumina i7 index: N704-TCCTGAGC
Illumina i5 index: S502-CTCTCTAT


title: scRNAseq_071_cell_57

description:
Illumina i7 index: N706-TAGGCATG
Illumina i5 index: S502-CTCTCTAT


title: scRNAseq_071_cell_53

description:
Illumina i7 index: N712-GTAGAGGA
Illumina i5 index: S501-TAGATCGC


title: scRNAseq_071_cell_83

description:
Illumina i7 index: N712-GTAGAGGA
Illumina i5 index: S506-ACTGCATA


title: scRNAseq_071_cell_69

description:
Illumina i7 index: N706-TAGGCATG
Illumina i5 index: S504-AGAGTAGA


title: scRNAseq_071_cell_54

description:
Illumina i7 index: N711-AAGAGGCA
Illumina i5 index: S501-TAGATCGC


title: scRNAseq_071_cell_70

description:
Illumina i7 index: N710-CGAGGCTG
Illumina i5 index: S504-AGAGTAGA


title: scRNAseq_071_cell_52

description:
Illumina i7 index: N710-CGAGGCTG
Illumina i5 index: S501-TAGATCGC


title: scRNAseq_071_cell_50

description:
Illumina i7 index: N705-GGACTCCT
Illumina i5 index: S501-TAGATCGC


title: scRNAseq_071_cell_45

description:
Illumina i7 index: N703-AGGCAGAA
Illumina i5 index: S508-CTAAGCCT


title: scRNAseq_071_cell_47

description:
Illumina i7 index: N708-CAGAGAGG
Illumina i5 index: S508-CTAAGCCT

value: dead


title: scRNAseq_071_cell_49

description:
Illumina i7 index: N704-TCCTGAGC
Illumina i5 index: S501-TAGATCGC


title: scRNAseq_071_cell_48

description:
Illumina i7 index: N709-GCTACGCT
Illumina i5 index: S508-CTAAGCCT


title: scRNAseq_071_cell_51

description:
Illumina i7 index: N706-TAGGCATG
Illumina i5 index: S501-TAGATCGC


title: scRNAseq_071_cell_43

description:
Illumina i7 index: N701-TAAGGCGA
Illumina i5 index: S508-CTAAGCCT


title: scRNAseq_071_cell_42

description:
Illumina i7 index: N709-GCTACGCT
Illumina i5 index: S507-AAGGAGTA


title: scRNAseq_071_cell_40

description:
Illumina i7 index: N707-CTCTCTAC
Illumina i5 index: S507-AAGGAGTA


title: scRNAseq_071_cell_38

description:
Illumina i7 index: N702-CGTACTAG
Illumina i5 index: S507-AAGGAGTA


title: scRNAseq_071_cell_41

description:
Illumina i7 index: N708-CAGAGAGG
Illumina i5 index: S507-AAGGAGTA


title: scRNAseq_071_cell_37

description:
Illumina i7 index: N701-TAAGGCGA
Illumina i5 index: S507-AAGGAGTA


title: scRNAseq_071_cell_36

description:
Illumina i7 index: N709-GCTACGCT
Illumina i5 index: S506-ACTGCATA


title: scRNAseq_071_cell_34

description:
Illumina i7 index: N707-CTCTCTAC
Illumina i5 index: S506-ACTGCATA


title: scRNAseq_071_cell_32

description:
Illumina i7 index: N702-CGTACTAG
Illumina i5 index: S506-ACTGCATA


title: scRNAseq_071_cell_33

description:
Illumina i7 index: N703-AGGCAGAA
Illumina i5 index: S506-ACTGCATA


title: scRNAseq_071_cell_46

description:
Illumina i7 index: N707-CTCTCTAC
Illumina i5 index: S508-CTAAGCCT


title: scRNAseq_071_cell_29

description:
Illumina i7 index: N708-CAGAGAGG
Illumina i5 index: S505-GTAAGGAG


title: scRNAseq_071_cell_30

description:
Illumina i7 index: N709-GCTACGCT
Illumina i5 index: S505-GTAAGGAG


title: scRNAseq_071_cell_31

description:
Illumina i7 index: N701-TAAGGCGA
Illumina i5 index: S506-ACTGCATA


title: scRNAseq_071_cell_27

description:
Illumina i7 index: N703-AGGCAGAA
Illumina i5 index: S505-GTAAGGAG


title: scRNAseq_071_cell_44

description:
Illumina i7 index: N702-CGTACTAG
Illumina i5 index: S508-CTAAGCCT


title: scRNAseq_071_cell_26

description:
Illumina i7 index: N702-CGTACTAG
Illumina i5 index: S505-GTAAGGAG


title: scRNAseq_071_cell_22

description:
Illumina i7 index: N709-GCTACGCT
Illumina i5 index: S504-AGAGTAGA


title: scRNAseq_071_cell_24

description:
Illumina i7 index: N707-CTCTCTAC
Illumina i5 index: S504-AGAGTAGA


title: scRNAseq_071_cell_23

description:
Illumina i7 index: N708-CAGAGAGG
Illumina i5 index: S504-AGAGTAGA


title: scRNAseq_071_cell_20

description:
Illumina i7 index: N702-CGTACTAG
Illumina i5 index: S504-AGAGTAGA


title: scRNAseq_071_cell_16

description:
Illumina i7 index: N709-GCTACGCT
Illumina i5 index: S503-TATCCTCT


title: scRNAseq_071_cell_21

description:
Illumina i7 index: N701-TAAGGCGA
Illumina i5 index: S504-AGAGTAGA


title: scRNAseq_071_cell_19

description:
Illumina i7 index: N703-AGGCAGAA
Illumina i5 index: S504-AGAGTAGA


title: scRNAseq_071_cell_18

description:
Illumina i7 index: N707-CTCTCTAC
Illumina i5 index: S503-TATCCTCT


title: scRNAseq_071_cell_15

description:
Illumina i7 index: N701-TAAGGCGA
Illumina i5 index: S503-TATCCTCT


title: scRNAseq_071_cell_39

description:
Illumina i7 index: N703-AGGCAGAA
Illumina i5 index: S507-AAGGAGTA


title: scRNAseq_071_cell_17

description:
Illumina i7 index: N708-CAGAGAGG
Illumina i5 index: S503-TATCCTCT


title: scRNAseq_071_cell_14

description:
Illumina i7 index: N702-CGTACTAG
Illumina i5 index: S503-TATCCTCT


title: scRNAseq_071_cell_13

description:
Illumina i7 index: N703-AGGCAGAA
Illumina i5 index: S503-TATCCTCT


title: scRNAseq_071_cell_12

description:
Illumina i7 index: N707-CTCTCTAC
Illumina i5 index: S502-CTCTCTAT


title: scRNAseq_071_cell_10

description:
Illumina i7 index: N709-GCTACGCT
Illumina i5 index: S502-CTCTCTAT


title: scRNAseq_071_cell_35

description:
Illumina i7 index: N708-CAGAGAGG
Illumina i5 index: S506-ACTGCATA


title: scRNAseq_071_cell_11

description:
Illumina i7 index: N708-CAGAGAGG
Illumina i5 index: S502-CTCTCTAT


title: scRNAseq_071_cell_28

description:
Illumina i7 index: N707-CTCTCTAC
Illumina i5 index: S505-GTAAGGAG


title: scRNAseq_071_cell_9

description:
Illumina i7 index: N701-TAAGGCGA
Illumina i5 index: S502-CTCTCTAT


title: scRNAseq_071_cell_8

description:
Illumina i7 index: N702-CGTACTAG
Illumina i5 index: S502-CTCTCTAT


title: scRNAseq_071_cell_5

description:
Illumina i7 index: N708-CAGAGAGG
Illumina i5 index: S501-TAGATCGC


title: scRNAseq_071_cell_25

description:
Illumina i7 index: N701-TAAGGCGA
Illumina i5 index: S505-GTAAGGAG


title: scRNAseq_071_cell_4

description:
Illumina i7 index: N709-GCTACGCT
Illumina i5 index: S501-TAGATCGC


title: scRNAseq_071_cell_6

description:
Illumina i7 index: N707-CTCTCTAC
Illumina i5 index: S501-TAGATCGC


title: scRNAseq_071_cell_3

description:
Illumina i7 index: N701-TAAGGCGA
Illumina i5 index: S501-TAGATCGC


title: scRNAseq_071_cell_2

description:
Illumina i7 index: N702-CGTACTAG
Illumina i5 index: S501-TAGATCGC


title: scRNAseq_071_cell_1

description:
Illumina i7 index: N703-AGGCAGAA
Illumina i5 index: S501-TAGATCGC


title: scRNAseq_069_cell_94

description:
Illumina i7 index: N712-GTAGAGGA
Illumina i5 index: S508-CTAAGCCT

source_name: neural precursor cell (day 6)


title: scRNAseq_069_cell_96

description:
Illumina i7 index: N710-CGAGGCTG
Illumina i5 index: S508-CTAAGCCT


title: scRNAseq_069_cell_95

description:
Illumina i7 index: N711-AAGAGGCA
Illumina i5 index: S508-CTAAGCCT


title: scRNAseq_069_cell_89

description:
Illumina i7 index: N711-AAGAGGCA
Illumina i5 index: S507-AAGGAGTA


title: scRNAseq_069_cell_91

description:
Illumina i7 index: N706-TAGGCATG
Illumina i5 index: S508-CTAAGCCT


title: scRNAseq_069_cell_92

description:
Illumina i7 index: N705-GGACTCCT
Illumina i5 index: S508-CTAAGCCT


title: scRNAseq_069_cell_93

description:
Illumina i7 index: N704-TCCTGAGC
Illumina i5 index: S508-CTAAGCCT


title: scRNAseq_069_cell_87

description:
Illumina i7 index: N704-TCCTGAGC
Illumina i5 index: S507-AAGGAGTA


title: scRNAseq_069_cell_84

description:
Illumina i7 index: N710-CGAGGCTG
Illumina i5 index: S506-ACTGCATA


title: scRNAseq_069_cell_81

description:
Illumina i7 index: N704-TCCTGAGC
Illumina i5 index: S506-ACTGCATA


title: scRNAseq_069_cell_80

description:
Illumina i7 index: N705-GGACTCCT
Illumina i5 index: S506-ACTGCATA


title: scRNAseq_071_cell_7

description:
Illumina i7 index: N703-AGGCAGAA
Illumina i5 index: S502-CTCTCTAT


title: scRNAseq_069_cell_74

description:
Illumina i7 index: N705-GGACTCCT
Illumina i5 index: S505-GTAAGGAG


title: scRNAseq_069_cell_75

description:
Illumina i7 index: N704-TCCTGAGC
Illumina i5 index: S505-GTAAGGAG


title: scRNAseq_069_cell_76

description:
Illumina i7 index: N712-GTAGAGGA
Illumina i5 index: S505-GTAAGGAG


title: scRNAseq_069_cell_77

description:
Illumina i7 index: N711-AAGAGGCA
Illumina i5 index: S505-GTAAGGAG


title: scRNAseq_069_cell_79

description:
Illumina i7 index: N706-TAGGCATG
Illumina i5 index: S506-ACTGCATA


title: scRNAseq_069_cell_73

description:
Illumina i7 index: N706-TAGGCATG
Illumina i5 index: S505-GTAAGGAG


title: scRNAseq_069_cell_70

description:
Illumina i7 index: N710-CGAGGCTG
Illumina i5 index: S504-AGAGTAGA


title: scRNAseq_069_cell_72

description:
Illumina i7 index: N712-GTAGAGGA
Illumina i5 index: S504-AGAGTAGA


title: scRNAseq_069_cell_90

description:
Illumina i7 index: N710-CGAGGCTG
Illumina i5 index: S507-AAGGAGTA


title: scRNAseq_069_cell_88

description:
Illumina i7 index: N712-GTAGAGGA
Illumina i5 index: S507-AAGGAGTA


title: scRNAseq_069_cell_65

description:
Illumina i7 index: N711-AAGAGGCA
Illumina i5 index: S503-TATCCTCT


title: scRNAseq_069_cell_63

description:
Illumina i7 index: N706-TAGGCATG
Illumina i5 index: S503-TATCCTCT


title: scRNAseq_069_cell_86

description:
Illumina i7 index: N705-GGACTCCT
Illumina i5 index: S507-AAGGAGTA


title: scRNAseq_069_cell_62

description:
Illumina i7 index: N705-GGACTCCT
Illumina i5 index: S503-TATCCTCT


title: scRNAseq_069_cell_78

description:
Illumina i7 index: N710-CGAGGCTG
Illumina i5 index: S505-GTAAGGAG


title: scRNAseq_069_cell_60

description:
Illumina i7 index: N712-GTAGAGGA
Illumina i5 index: S502-CTCTCTAT


title: scRNAseq_069_cell_82

description:
Illumina i7 index: N712-GTAGAGGA
Illumina i5 index: S506-ACTGCATA


title: scRNAseq_069_cell_59

description:
Illumina i7 index: N711-AAGAGGCA
Illumina i5 index: S502-CTCTCTAT


title: scRNAseq_069_cell_68

description:
Illumina i7 index: N705-GGACTCCT
Illumina i5 index: S504-AGAGTAGA


title: scRNAseq_069_cell_67

description:
Illumina i7 index: N704-TCCTGAGC
Illumina i5 index: S504-AGAGTAGA


title: scRNAseq_069_cell_57

description:
Illumina i7 index: N706-TAGGCATG
Illumina i5 index: S502-CTCTCTAT


title: scRNAseq_069_cell_64

description:
Illumina i7 index: N710-CGAGGCTG
Illumina i5 index: S503-TATCCTCT


title: scRNAseq_069_cell_66

description:
Illumina i7 index: N712-GTAGAGGA
Illumina i5 index: S503-TATCCTCT


title: scRNAseq_069_cell_52

description:
Illumina i7 index: N710-CGAGGCTG
Illumina i5 index: S501-TAGATCGC


title: scRNAseq_069_cell_61

description:
Illumina i7 index: N704-TCCTGAGC
Illumina i5 index: S503-TATCCTCT


title: scRNAseq_072_cell_29

description:
Illumina i7 index: N708-CAGAGAGG
Illumina i5 index: S505-GTAAGGAG


title: scRNAseq_069_cell_56

description:
Illumina i7 index: N705-GGACTCCT
Illumina i5 index: S502-CTCTCTAT


title: scRNAseq_069_cell_58

description:
Illumina i7 index: N710-CGAGGCTG
Illumina i5 index: S502-CTCTCTAT


title: scRNAseq_069_cell_51

description:
Illumina i7 index: N706-TAGGCATG
Illumina i5 index: S501-TAGATCGC


title: scRNAseq_069_cell_54

description:
Illumina i7 index: N712-GTAGAGGA
Illumina i5 index: S501-TAGATCGC


title: scRNAseq_069_cell_43

description:
Illumina i7 index: N701-TAAGGCGA
Illumina i5 index: S508-CTAAGCCT


title: scRNAseq_069_cell_44

description:
Illumina i7 index: N702-CGTACTAG
Illumina i5 index: S508-CTAAGCCT


title: scRNAseq_069_cell_47

description:
Illumina i7 index: N708-CAGAGAGG
Illumina i5 index: S508-CTAAGCCT


title: scRNAseq_069_cell_41

description:
Illumina i7 index: N708-CAGAGAGG
Illumina i5 index: S507-AAGGAGTA


title: scRNAseq_069_cell_50

description:
Illumina i7 index: N705-GGACTCCT
Illumina i5 index: S501-TAGATCGC


title: scRNAseq_069_cell_49

description:
Illumina i7 index: N704-TCCTGAGC
Illumina i5 index: S501-TAGATCGC


title: scRNAseq_069_cell_48

description:
Illumina i7 index: N709-GCTACGCT
Illumina i5 index: S508-CTAAGCCT


title: scRNAseq_069_cell_45

description:
Illumina i7 index: N703-AGGCAGAA
Illumina i5 index: S508-CTAAGCCT


title: scRNAseq_069_cell_46

description:
Illumina i7 index: N707-CTCTCTAC
Illumina i5 index: S508-CTAAGCCT


title: scRNAseq_069_cell_53

description:
Illumina i7 index: N711-AAGAGGCA
Illumina i5 index: S501-TAGATCGC


title: scRNAseq_069_cell_42

description:
Illumina i7 index: N709-GCTACGCT
Illumina i5 index: S507-AAGGAGTA


title: scRNAseq_069_cell_40

description:
Illumina i7 index: N707-CTCTCTAC
Illumina i5 index: S507-AAGGAGTA


title: scRNAseq_069_cell_38

description:
Illumina i7 index: N702-CGTACTAG
Illumina i5 index: S507-AAGGAGTA


title: scRNAseq_069_cell_55

description:
Illumina i7 index: N704-TCCTGAGC
Illumina i5 index: S502-CTCTCTAT


title: scRNAseq_069_cell_35

description:
Illumina i7 index: N708-CAGAGAGG
Illumina i5 index: S506-ACTGCATA


title: scRNAseq_069_cell_37

description:
Illumina i7 index: N701-TAAGGCGA
Illumina i5 index: S507-AAGGAGTA


title: scRNAseq_069_cell_36

description:
Illumina i7 index: N709-GCTACGCT
Illumina i5 index: S506-ACTGCATA


title: scRNAseq_069_cell_28

description:
Illumina i7 index: N707-CTCTCTAC
Illumina i5 index: S505-GTAAGGAG


title: scRNAseq_069_cell_30

description:
Illumina i7 index: N709-GCTACGCT
Illumina i5 index: S505-GTAAGGAG


title: scRNAseq_069_cell_34

description:
Illumina i7 index: N707-CTCTCTAC
Illumina i5 index: S506-ACTGCATA


title: scRNAseq_069_cell_25

description:
Illumina i7 index: N701-TAAGGCGA
Illumina i5 index: S505-GTAAGGAG


title: scRNAseq_069_cell_23

description:
Illumina i7 index: N708-CAGAGAGG
Illumina i5 index: S504-AGAGTAGA


title: scRNAseq_069_cell_27

description:
Illumina i7 index: N703-AGGCAGAA
Illumina i5 index: S505-GTAAGGAG


title: scRNAseq_069_cell_32

description:
Illumina i7 index: N702-CGTACTAG
Illumina i5 index: S506-ACTGCATA


title: scRNAseq_069_cell_29

description:
Illumina i7 index: N708-CAGAGAGG
Illumina i5 index: S505-GTAAGGAG


title: scRNAseq_069_cell_24

description:
Illumina i7 index: N707-CTCTCTAC
Illumina i5 index: S504-AGAGTAGA


title: scRNAseq_069_cell_22

description:
Illumina i7 index: N709-GCTACGCT
Illumina i5 index: S504-AGAGTAGA


title: scRNAseq_069_cell_26

description:
Illumina i7 index: N702-CGTACTAG
Illumina i5 index: S505-GTAAGGAG


title: scRNAseq_069_cell_17

description:
Illumina i7 index: N708-CAGAGAGG
Illumina i5 index: S503-TATCCTCT


title: scRNAseq_069_cell_31

description:
Illumina i7 index: N701-TAAGGCGA
Illumina i5 index: S506-ACTGCATA


title: scRNAseq_069_cell_21

description:
Illumina i7 index: N701-TAAGGCGA
Illumina i5 index: S504-AGAGTAGA


title: scRNAseq_069_cell_39

description:
Illumina i7 index: N703-AGGCAGAA
Illumina i5 index: S507-AAGGAGTA


title: scRNAseq_069_cell_20

description:
Illumina i7 index: N702-CGTACTAG
Illumina i5 index: S504-AGAGTAGA


title: scRNAseq_069_cell_14

description:
Illumina i7 index: N702-CGTACTAG
Illumina i5 index: S503-TATCCTCT


title: scRNAseq_069_cell_16

description:
Illumina i7 index: N709-GCTACGCT
Illumina i5 index: S503-TATCCTCT


title: scRNAseq_069_cell_15

description:
Illumina i7 index: N701-TAAGGCGA
Illumina i5 index: S503-TATCCTCT


title: scRNAseq_069_cell_33

description:
Illumina i7 index: N703-AGGCAGAA
Illumina i5 index: S506-ACTGCATA


title: scRNAseq_069_cell_13

description:
Illumina i7 index: N703-AGGCAGAA
Illumina i5 index: S503-TATCCTCT


title: scRNAseq_069_cell_5

description:
Illumina i7 index: N708-CAGAGAGG
Illumina i5 index: S501-TAGATCGC


title: scRNAseq_069_cell_4

description:
Illumina i7 index: N709-GCTACGCT
Illumina i5 index: S501-TAGATCGC


title: scRNAseq_069_cell_1

description:
Illumina i7 index: N703-AGGCAGAA
Illumina i5 index: S501-TAGATCGC


title: scRNAseq_069_cell_11

description:
Illumina i7 index: N708-CAGAGAGG
Illumina i5 index: S502-CTCTCTAT


title: scRNAseq_069_cell_2

description:
Illumina i7 index: N702-CGTACTAG
Illumina i5 index: S501-TAGATCGC


title: scRNAseq_069_cell_9

description:
Illumina i7 index: N701-TAAGGCGA
Illumina i5 index: S502-CTCTCTAT


title: scRNAseq_069_cell_19

description:
Illumina i7 index: N703-AGGCAGAA
Illumina i5 index: S504-AGAGTAGA


title: scRNAseq_069_cell_8

description:
Illumina i7 index: N702-CGTACTAG
Illumina i5 index: S502-CTCTCTAT


title: scRNAseq_066_cell_94

description:
Illumina i7 index: N712-GTAGAGGA
Illumina i5 index: S508-CTAAGCCT


title: scRNAseq_069_cell_6

description:
Illumina i7 index: N707-CTCTCTAC
Illumina i5 index: S501-TAGATCGC


title: scRNAseq_069_cell_10

description:
Illumina i7 index: N709-GCTACGCT
Illumina i5 index: S502-CTCTCTAT


title: scRNAseq_069_cell_3

description:
Illumina i7 index: N701-TAAGGCGA
Illumina i5 index: S501-TAGATCGC


title: scRNAseq_066_cell_88

description:
Illumina i7 index: N712-GTAGAGGA
Illumina i5 index: S507-AAGGAGTA


title: scRNAseq_066_cell_89

description:
Illumina i7 index: N711-AAGAGGCA
Illumina i5 index: S507-AAGGAGTA


title: scRNAseq_069_cell_7

description:
Illumina i7 index: N703-AGGCAGAA
Illumina i5 index: S502-CTCTCTAT


title: scRNAseq_066_cell_95

description:
Illumina i7 index: N711-AAGAGGCA
Illumina i5 index: S508-CTAAGCCT


title: scRNAseq_066_cell_91

description:
Illumina i7 index: N706-TAGGCATG
Illumina i5 index: S508-CTAAGCCT


title: scRNAseq_066_cell_96

description:
Illumina i7 index: N710-CGAGGCTG
Illumina i5 index: S508-CTAAGCCT


title: scRNAseq_069_cell_12

description:
Illumina i7 index: N707-CTCTCTAC
Illumina i5 index: S502-CTCTCTAT


title: scRNAseq_066_cell_93

description:
Illumina i7 index: N704-TCCTGAGC
Illumina i5 index: S508-CTAAGCCT


title: scRNAseq_066_cell_90

description:
Illumina i7 index: N710-CGAGGCTG
Illumina i5 index: S507-AAGGAGTA


title: scRNAseq_066_cell_86

description:
Illumina i7 index: N705-GGACTCCT
Illumina i5 index: S507-AAGGAGTA


title: scRNAseq_066_cell_87

description:
Illumina i7 index: N704-TCCTGAGC
Illumina i5 index: S507-AAGGAGTA


title: scRNAseq_066_cell_92

description:
Illumina i7 index: N705-GGACTCCT
Illumina i5 index: S508-CTAAGCCT


title: scRNAseq_066_cell_85

description:
Illumina i7 index: N706-TAGGCATG
Illumina i5 index: S507-AAGGAGTA


title: scRNAseq_066_cell_84

description:
Illumina i7 index: N710-CGAGGCTG
Illumina i5 index: S506-ACTGCATA


title: scRNAseq_066_cell_80

description:
Illumina i7 index: N705-GGACTCCT
Illumina i5 index: S506-ACTGCATA


title: scRNAseq_066_cell_81

description:
Illumina i7 index: N704-TCCTGAGC
Illumina i5 index: S506-ACTGCATA


title: scRNAseq_066_cell_70

description:
Illumina i7 index: N710-CGAGGCTG
Illumina i5 index: S504-AGAGTAGA


title: scRNAseq_066_cell_78

description:
Illumina i7 index: N710-CGAGGCTG
Illumina i5 index: S505-GTAAGGAG


title: scRNAseq_066_cell_67

description:
Illumina i7 index: N704-TCCTGAGC
Illumina i5 index: S504-AGAGTAGA


title: scRNAseq_066_cell_82

description:
Illumina i7 index: N712-GTAGAGGA
Illumina i5 index: S506-ACTGCATA


title: scRNAseq_066_cell_69

description:
Illumina i7 index: N706-TAGGCATG
Illumina i5 index: S504-AGAGTAGA


title: scRNAseq_066_cell_76

description:
Illumina i7 index: N712-GTAGAGGA
Illumina i5 index: S505-GTAAGGAG


title: scRNAseq_069_cell_18

description:
Illumina i7 index: N707-CTCTCTAC
Illumina i5 index: S503-TATCCTCT


title: scRNAseq_066_cell_77

description:
Illumina i7 index: N711-AAGAGGCA
Illumina i5 index: S505-GTAAGGAG


title: scRNAseq_066_cell_75

description:
Illumina i7 index: N704-TCCTGAGC
Illumina i5 index: S505-GTAAGGAG


title: scRNAseq_066_cell_74

description:
Illumina i7 index: N705-GGACTCCT
Illumina i5 index: S505-GTAAGGAG


title: scRNAseq_066_cell_65

description:
Illumina i7 index: N711-AAGAGGCA
Illumina i5 index: S503-TATCCTCT


title: scRNAseq_066_cell_83

description:
Illumina i7 index: N711-AAGAGGCA
Illumina i5 index: S506-ACTGCATA


title: scRNAseq_066_cell_71

description:
Illumina i7 index: N711-AAGAGGCA
Illumina i5 index: S504-AGAGTAGA


title: scRNAseq_066_cell_72

description:
Illumina i7 index: N712-GTAGAGGA
Illumina i5 index: S504-AGAGTAGA


title: scRNAseq_066_cell_63

description:
Illumina i7 index: N706-TAGGCATG
Illumina i5 index: S503-TATCCTCT


title: scRNAseq_066_cell_61

description:
Illumina i7 index: N704-TCCTGAGC
Illumina i5 index: S503-TATCCTCT


title: scRNAseq_066_cell_68

description:
Illumina i7 index: N705-GGACTCCT
Illumina i5 index: S504-AGAGTAGA


title: scRNAseq_066_cell_62

description:
Illumina i7 index: N705-GGACTCCT
Illumina i5 index: S503-TATCCTCT


title: scRNAseq_066_cell_64

description:
Illumina i7 index: N710-CGAGGCTG
Illumina i5 index: S503-TATCCTCT


title: scRNAseq_066_cell_79

description:
Illumina i7 index: N706-TAGGCATG
Illumina i5 index: S506-ACTGCATA


title: scRNAseq_066_cell_66

description:
Illumina i7 index: N712-GTAGAGGA
Illumina i5 index: S503-TATCCTCT


title: scRNAseq_066_cell_56

description:
Illumina i7 index: N705-GGACTCCT
Illumina i5 index: S502-CTCTCTAT


title: scRNAseq_066_cell_57

description:
Illumina i7 index: N706-TAGGCATG
Illumina i5 index: S502-CTCTCTAT


title: scRNAseq_066_cell_73

description:
Illumina i7 index: N706-TAGGCATG
Illumina i5 index: S505-GTAAGGAG


title: scRNAseq_066_cell_54

description:
Illumina i7 index: N712-GTAGAGGA
Illumina i5 index: S501-TAGATCGC


title: scRNAseq_069_cell_69

description:
Illumina i7 index: N706-TAGGCATG
Illumina i5 index: S504-AGAGTAGA


title: scRNAseq_069_cell_85

description:
Illumina i7 index: N706-TAGGCATG
Illumina i5 index: S507-AAGGAGTA


title: scRNAseq_066_cell_59

description:
Illumina i7 index: N711-AAGAGGCA
Illumina i5 index: S502-CTCTCTAT


title: scRNAseq_066_cell_60

description:
Illumina i7 index: N712-GTAGAGGA
Illumina i5 index: S502-CTCTCTAT


title: scRNAseq_066_cell_49

description:
Illumina i7 index: N704-TCCTGAGC
Illumina i5 index: S501-TAGATCGC


title: scRNAseq_069_cell_71

description:
Illumina i7 index: N711-AAGAGGCA
Illumina i5 index: S504-AGAGTAGA


title: scRNAseq_066_cell_55

description:
Illumina i7 index: N704-TCCTGAGC
Illumina i5 index: S502-CTCTCTAT


title: scRNAseq_066_cell_58

description:
Illumina i7 index: N710-CGAGGCTG
Illumina i5 index: S502-CTCTCTAT


title: scRNAseq_066_cell_46

description:
Illumina i7 index: N707-CTCTCTAC
Illumina i5 index: S508-CTAAGCCT


title: scRNAseq_066_cell_53

description:
Illumina i7 index: N711-AAGAGGCA
Illumina i5 index: S501-TAGATCGC


title: scRNAseq_066_cell_51

description:
Illumina i7 index: N706-TAGGCATG
Illumina i5 index: S501-TAGATCGC


title: scRNAseq_066_cell_47

description:
Illumina i7 index: N708-CAGAGAGG
Illumina i5 index: S508-CTAAGCCT


title: scRNAseq_066_cell_50

description:
Illumina i7 index: N705-GGACTCCT
Illumina i5 index: S501-TAGATCGC


title: scRNAseq_066_cell_48

description:
Illumina i7 index: N709-GCTACGCT
Illumina i5 index: S508-CTAAGCCT


title: scRNAseq_066_cell_41

description:
Illumina i7 index: N708-CAGAGAGG
Illumina i5 index: S507-AAGGAGTA


title: scRNAseq_069_cell_83

description:
Illumina i7 index: N711-AAGAGGCA
Illumina i5 index: S506-ACTGCATA


title: scRNAseq_066_cell_44

description:
Illumina i7 index: N702-CGTACTAG
Illumina i5 index: S508-CTAAGCCT


title: scRNAseq_066_cell_42

description:
Illumina i7 index: N709-GCTACGCT
Illumina i5 index: S507-AAGGAGTA


title: scRNAseq_066_cell_45

description:
Illumina i7 index: N703-AGGCAGAA
Illumina i5 index: S508-CTAAGCCT


title: scRNAseq_066_cell_52

description:
Illumina i7 index: N710-CGAGGCTG
Illumina i5 index: S501-TAGATCGC


title: scRNAseq_066_cell_40

description:
Illumina i7 index: N707-CTCTCTAC
Illumina i5 index: S507-AAGGAGTA


title: scRNAseq_066_cell_39

description:
Illumina i7 index: N703-AGGCAGAA
Illumina i5 index: S507-AAGGAGTA


title: scRNAseq_066_cell_36

description:
Illumina i7 index: N709-GCTACGCT
Illumina i5 index: S506-ACTGCATA


title: scRNAseq_066_cell_34

description:
Illumina i7 index: N707-CTCTCTAC
Illumina i5 index: S506-ACTGCATA


title: scRNAseq_066_cell_35

description:
Illumina i7 index: N708-CAGAGAGG
Illumina i5 index: S506-ACTGCATA


title: scRNAseq_066_cell_37

description:
Illumina i7 index: N701-TAAGGCGA
Illumina i5 index: S507-AAGGAGTA


title: scRNAseq_066_cell_38

description:
Illumina i7 index: N702-CGTACTAG
Illumina i5 index: S507-AAGGAGTA


title: scRNAseq_066_cell_31

description:
Illumina i7 index: N701-TAAGGCGA
Illumina i5 index: S506-ACTGCATA


title: scRNAseq_066_cell_33

description:
Illumina i7 index: N703-AGGCAGAA
Illumina i5 index: S506-ACTGCATA


title: scRNAseq_066_cell_30

description:
Illumina i7 index: N709-GCTACGCT
Illumina i5 index: S505-GTAAGGAG


title: scRNAseq_066_cell_28

description:
Illumina i7 index: N707-CTCTCTAC
Illumina i5 index: S505-GTAAGGAG


title: scRNAseq_066_cell_24

description:
Illumina i7 index: N707-CTCTCTAC
Illumina i5 index: S504-AGAGTAGA


title: scRNAseq_066_cell_19

description:
Illumina i7 index: N703-AGGCAGAA
Illumina i5 index: S504-AGAGTAGA


title: scRNAseq_066_cell_21

description:
Illumina i7 index: N701-TAAGGCGA
Illumina i5 index: S504-AGAGTAGA


title: scRNAseq_066_cell_25

description:
Illumina i7 index: N701-TAAGGCGA
Illumina i5 index: S505-GTAAGGAG


title: scRNAseq_066_cell_20

description:
Illumina i7 index: N702-CGTACTAG
Illumina i5 index: S504-AGAGTAGA


title: scRNAseq_066_cell_26

description:
Illumina i7 index: N702-CGTACTAG
Illumina i5 index: S505-GTAAGGAG


title: scRNAseq_066_cell_27

description:
Illumina i7 index: N703-AGGCAGAA
Illumina i5 index: S505-GTAAGGAG


title: scRNAseq_066_cell_23

description:
Illumina i7 index: N708-CAGAGAGG
Illumina i5 index: S504-AGAGTAGA


title: scRNAseq_066_cell_22

description:
Illumina i7 index: N709-GCTACGCT
Illumina i5 index: S504-AGAGTAGA


title: scRNAseq_066_cell_17

description:
Illumina i7 index: N708-CAGAGAGG
Illumina i5 index: S503-TATCCTCT


title: scRNAseq_066_cell_18

description:
Illumina i7 index: N707-CTCTCTAC
Illumina i5 index: S503-TATCCTCT


title: scRNAseq_066_cell_16

description:
Illumina i7 index: N709-GCTACGCT
Illumina i5 index: S503-TATCCTCT


title: scRNAseq_066_cell_32

description:
Illumina i7 index: N702-CGTACTAG
Illumina i5 index: S506-ACTGCATA


title: scRNAseq_066_cell_15

description:
Illumina i7 index: N701-TAAGGCGA
Illumina i5 index: S503-TATCCTCT


title: scRNAseq_066_cell_29

description:
Illumina i7 index: N708-CAGAGAGG
Illumina i5 index: S505-GTAAGGAG


title: scRNAseq_066_cell_13

description:
Illumina i7 index: N703-AGGCAGAA
Illumina i5 index: S503-TATCCTCT


title: scRNAseq_066_cell_11

description:
Illumina i7 index: N708-CAGAGAGG
Illumina i5 index: S502-CTCTCTAT


title: scRNAseq_066_cell_9

description:
Illumina i7 index: N701-TAAGGCGA
Illumina i5 index: S502-CTCTCTAT


title: scRNAseq_066_cell_12

description:
Illumina i7 index: N707-CTCTCTAC
Illumina i5 index: S502-CTCTCTAT


title: scRNAseq_066_cell_14

description:
Illumina i7 index: N702-CGTACTAG
Illumina i5 index: S503-TATCCTCT


title: scRNAseq_066_cell_8

description:
Illumina i7 index: N702-CGTACTAG
Illumina i5 index: S502-CTCTCTAT


title: scRNAseq_066_cell_7

description:
Illumina i7 index: N703-AGGCAGAA
Illumina i5 index: S502-CTCTCTAT


title: scRNAseq_066_cell_5

description:
Illumina i7 index: N708-CAGAGAGG
Illumina i5 index: S501-TAGATCGC


title: scRNAseq_066_cell_6

description:
Illumina i7 index: N707-CTCTCTAC
Illumina i5 index: S501-TAGATCGC


title: scRNAseq_066_cell_10

description:
Illumina i7 index: N709-GCTACGCT
Illumina i5 index: S502-CTCTCTAT


title: scRNAseq_066_cell_2

description:
Illumina i7 index: N702-CGTACTAG
Illumina i5 index: S501-TAGATCGC


title: scRNAseq_066_cell_3

description:
Illumina i7 index: N701-TAAGGCGA
Illumina i5 index: S501-TAGATCGC


title: scRNAseq_066_cell_1

description:
Illumina i7 index: N703-AGGCAGAA
Illumina i5 index: S501-TAGATCGC


title: scRNAseq_065_cell_95

description:
Illumina i7 index: N711-AAGAGGCA
Illumina i5 index: S508-CTAAGCCT


title: scRNAseq_065_cell_94

description:
Illumina i7 index: N712-GTAGAGGA
Illumina i5 index: S508-CTAAGCCT

value: burst


title: scRNAseq_065_cell_92

description:
Illumina i7 index: N705-GGACTCCT
Illumina i5 index: S508-CTAAGCCT


title: scRNAseq_065_cell_93

description:
Illumina i7 index: N704-TCCTGAGC
Illumina i5 index: S508-CTAAGCCT


title: scRNAseq_065_cell_91

description:
Illumina i7 index: N706-TAGGCATG
Illumina i5 index: S508-CTAAGCCT


title: scRNAseq_065_cell_89

description:
Illumina i7 index: N711-AAGAGGCA
Illumina i5 index: S507-AAGGAGTA


title: scRNAseq_065_cell_90

description:
Illumina i7 index: N710-CGAGGCTG
Illumina i5 index: S507-AAGGAGTA


title: scRNAseq_066_cell_4

description:
Illumina i7 index: N709-GCTACGCT
Illumina i5 index: S501-TAGATCGC


title: scRNAseq_065_cell_87

description:
Illumina i7 index: N704-TCCTGAGC
Illumina i5 index: S507-AAGGAGTA


title: scRNAseq_065_cell_86

description:
Illumina i7 index: N705-GGACTCCT
Illumina i5 index: S507-AAGGAGTA


title: scRNAseq_065_cell_96

description:
Illumina i7 index: N710-CGAGGCTG
Illumina i5 index: S508-CTAAGCCT


title: scRNAseq_065_cell_83

description:
Illumina i7 index: N711-AAGAGGCA
Illumina i5 index: S506-ACTGCATA


title: scRNAseq_065_cell_85

description:
Illumina i7 index: N706-TAGGCATG
Illumina i5 index: S507-AAGGAGTA


title: scRNAseq_065_cell_84

description:
Illumina i7 index: N710-CGAGGCTG
Illumina i5 index: S506-ACTGCATA


title: scRNAseq_065_cell_80

description:
Illumina i7 index: N705-GGACTCCT
Illumina i5 index: S506-ACTGCATA


title: scRNAseq_065_cell_77

description:
Illumina i7 index: N711-AAGAGGCA
Illumina i5 index: S505-GTAAGGAG


title: scRNAseq_065_cell_78

description:
Illumina i7 index: N710-CGAGGCTG
Illumina i5 index: S505-GTAAGGAG


title: scRNAseq_065_cell_79

description:
Illumina i7 index: N706-TAGGCATG
Illumina i5 index: S506-ACTGCATA


title: scRNAseq_065_cell_76

description:
Illumina i7 index: N712-GTAGAGGA
Illumina i5 index: S505-GTAAGGAG


title: scRNAseq_065_cell_73

description:
Illumina i7 index: N706-TAGGCATG
Illumina i5 index: S505-GTAAGGAG


title: scRNAseq_065_cell_82

description:
Illumina i7 index: N712-GTAGAGGA
Illumina i5 index: S506-ACTGCATA


title: scRNAseq_065_cell_88

description:
Illumina i7 index: N712-GTAGAGGA
Illumina i5 index: S507-AAGGAGTA


title: scRNAseq_065_cell_74

description:
Illumina i7 index: N705-GGACTCCT
Illumina i5 index: S505-GTAAGGAG


title: scRNAseq_065_cell_71

description:
Illumina i7 index: N711-AAGAGGCA
Illumina i5 index: S504-AGAGTAGA


title: scRNAseq_065_cell_70

description:
Illumina i7 index: N710-CGAGGCTG
Illumina i5 index: S504-AGAGTAGA


title: scRNAseq_065_cell_69

description:
Illumina i7 index: N706-TAGGCATG
Illumina i5 index: S504-AGAGTAGA


title: scRNAseq_065_cell_72

description:
Illumina i7 index: N712-GTAGAGGA
Illumina i5 index: S504-AGAGTAGA


title: scRNAseq_065_cell_75

description:
Illumina i7 index: N704-TCCTGAGC
Illumina i5 index: S505-GTAAGGAG


title: scRNAseq_065_cell_68

description:
Illumina i7 index: N705-GGACTCCT
Illumina i5 index: S504-AGAGTAGA


title: scRNAseq_065_cell_66

description:
Illumina i7 index: N712-GTAGAGGA
Illumina i5 index: S503-TATCCTCT


title: scRNAseq_065_cell_65

description:
Illumina i7 index: N711-AAGAGGCA
Illumina i5 index: S503-TATCCTCT


title: scRNAseq_065_cell_81

description:
Illumina i7 index: N704-TCCTGAGC
Illumina i5 index: S506-ACTGCATA


title: scRNAseq_065_cell_62

description:
Illumina i7 index: N705-GGACTCCT
Illumina i5 index: S503-TATCCTCT


title: scRNAseq_065_cell_63

description:
Illumina i7 index: N706-TAGGCATG
Illumina i5 index: S503-TATCCTCT


title: scRNAseq_065_cell_61

description:
Illumina i7 index: N704-TCCTGAGC
Illumina i5 index: S503-TATCCTCT


title: scRNAseq_065_cell_60

description:
Illumina i7 index: N712-GTAGAGGA
Illumina i5 index: S502-CTCTCTAT


title: scRNAseq_065_cell_58

description:
Illumina i7 index: N710-CGAGGCTG
Illumina i5 index: S502-CTCTCTAT


title: scRNAseq_065_cell_55

description:
Illumina i7 index: N704-TCCTGAGC
Illumina i5 index: S502-CTCTCTAT


title: scRNAseq_065_cell_54

description:
Illumina i7 index: N712-GTAGAGGA
Illumina i5 index: S501-TAGATCGC


title: scRNAseq_065_cell_53

description:
Illumina i7 index: N711-AAGAGGCA
Illumina i5 index: S501-TAGATCGC


title: scRNAseq_065_cell_67

description:
Illumina i7 index: N704-TCCTGAGC
Illumina i5 index: S504-AGAGTAGA


title: scRNAseq_065_cell_52

description:
Illumina i7 index: N710-CGAGGCTG
Illumina i5 index: S501-TAGATCGC


title: scRNAseq_066_cell_43

description:
Illumina i7 index: N701-TAAGGCGA
Illumina i5 index: S508-CTAAGCCT


title: scRNAseq_065_cell_59

description:
Illumina i7 index: N711-AAGAGGCA
Illumina i5 index: S502-CTCTCTAT


title: scRNAseq_065_cell_46

description:
Illumina i7 index: N707-CTCTCTAC
Illumina i5 index: S508-CTAAGCCT


title: scRNAseq_065_cell_48

description:
Illumina i7 index: N709-GCTACGCT
Illumina i5 index: S508-CTAAGCCT


title: scRNAseq_065_cell_49

description:
Illumina i7 index: N704-TCCTGAGC
Illumina i5 index: S501-TAGATCGC


title: scRNAseq_065_cell_51

description:
Illumina i7 index: N706-TAGGCATG
Illumina i5 index: S501-TAGATCGC


title: scRNAseq_065_cell_41

description:
Illumina i7 index: N708-CAGAGAGG
Illumina i5 index: S507-AAGGAGTA


title: scRNAseq_065_cell_64

description:
Illumina i7 index: N710-CGAGGCTG
Illumina i5 index: S503-TATCCTCT


title: scRNAseq_065_cell_43


title: scRNAseq_065_cell_45

description:
Illumina i7 index: N703-AGGCAGAA
Illumina i5 index: S508-CTAAGCCT


title: scRNAseq_065_cell_38

description:
Illumina i7 index: N702-CGTACTAG
Illumina i5 index: S507-AAGGAGTA


title: scRNAseq_065_cell_37

description:
Illumina i7 index: N701-TAAGGCGA
Illumina i5 index: S507-AAGGAGTA


title: scRNAseq_065_cell_39

description:
Illumina i7 index: N703-AGGCAGAA
Illumina i5 index: S507-AAGGAGTA


title: scRNAseq_065_cell_56

description:
Illumina i7 index: N705-GGACTCCT
Illumina i5 index: S502-CTCTCTAT


title: scRNAseq_065_cell_35

description:
Illumina i7 index: N708-CAGAGAGG
Illumina i5 index: S506-ACTGCATA


title: scRNAseq_065_cell_36

description:
Illumina i7 index: N709-GCTACGCT
Illumina i5 index: S506-ACTGCATA


title: scRNAseq_065_cell_32

description:
Illumina i7 index: N702-CGTACTAG
Illumina i5 index: S506-ACTGCATA


title: scRNAseq_065_cell_31

description:
Illumina i7 index: N701-TAAGGCGA
Illumina i5 index: S506-ACTGCATA


title: scRNAseq_065_cell_34

description:
Illumina i7 index: N707-CTCTCTAC
Illumina i5 index: S506-ACTGCATA


title: scRNAseq_065_cell_44

description:
Illumina i7 index: N702-CGTACTAG
Illumina i5 index: S508-CTAAGCCT


title: scRNAseq_065_cell_50

description:
Illumina i7 index: N705-GGACTCCT
Illumina i5 index: S501-TAGATCGC


title: scRNAseq_065_cell_29

description:
Illumina i7 index: N708-CAGAGAGG
Illumina i5 index: S505-GTAAGGAG


title: scRNAseq_065_cell_26

description:
Illumina i7 index: N702-CGTACTAG
Illumina i5 index: S505-GTAAGGAG


title: scRNAseq_065_cell_27

description:
Illumina i7 index: N703-AGGCAGAA
Illumina i5 index: S505-GTAAGGAG


title: scRNAseq_065_cell_28

description:
Illumina i7 index: N707-CTCTCTAC
Illumina i5 index: S505-GTAAGGAG


title: scRNAseq_065_cell_57

description:
Illumina i7 index: N706-TAGGCATG
Illumina i5 index: S502-CTCTCTAT


title: scRNAseq_065_cell_47

description:
Illumina i7 index: N708-CAGAGAGG
Illumina i5 index: S508-CTAAGCCT


title: scRNAseq_065_cell_42

description:
Illumina i7 index: N709-GCTACGCT
Illumina i5 index: S507-AAGGAGTA


title: scRNAseq_065_cell_40

description:
Illumina i7 index: N707-CTCTCTAC
Illumina i5 index: S507-AAGGAGTA


title: scRNAseq_065_cell_25

description:
Illumina i7 index: N701-TAAGGCGA
Illumina i5 index: S505-GTAAGGAG


title: scRNAseq_065_cell_30

description:
Illumina i7 index: N709-GCTACGCT
Illumina i5 index: S505-GTAAGGAG


title: scRNAseq_065_cell_23

description:
Illumina i7 index: N708-CAGAGAGG
Illumina i5 index: S504-AGAGTAGA


title: scRNAseq_065_cell_21

description:
Illumina i7 index: N701-TAAGGCGA
Illumina i5 index: S504-AGAGTAGA


title: scRNAseq_065_cell_17

description:
Illumina i7 index: N708-CAGAGAGG
Illumina i5 index: S503-TATCCTCT


title: scRNAseq_065_cell_19

description:
Illumina i7 index: N703-AGGCAGAA
Illumina i5 index: S504-AGAGTAGA


title: scRNAseq_065_cell_20

description:
Illumina i7 index: N702-CGTACTAG
Illumina i5 index: S504-AGAGTAGA


title: scRNAseq_065_cell_13

description:
Illumina i7 index: N703-AGGCAGAA
Illumina i5 index: S503-TATCCTCT


title: scRNAseq_065_cell_18

description:
Illumina i7 index: N707-CTCTCTAC
Illumina i5 index: S503-TATCCTCT


title: scRNAseq_065_cell_33

description:
Illumina i7 index: N703-AGGCAGAA
Illumina i5 index: S506-ACTGCATA


title: scRNAseq_065_cell_16

description:
Illumina i7 index: N709-GCTACGCT
Illumina i5 index: S503-TATCCTCT


title: scRNAseq_065_cell_14

description:
Illumina i7 index: N702-CGTACTAG
Illumina i5 index: S503-TATCCTCT


title: scRNAseq_065_cell_24

description:
Illumina i7 index: N707-CTCTCTAC
Illumina i5 index: S504-AGAGTAGA


title: scRNAseq_065_cell_12

description:
Illumina i7 index: N707-CTCTCTAC
Illumina i5 index: S502-CTCTCTAT


title: scRNAseq_065_cell_9

description:
Illumina i7 index: N701-TAAGGCGA
Illumina i5 index: S502-CTCTCTAT


title: scRNAseq_065_cell_7

description:
Illumina i7 index: N703-AGGCAGAA
Illumina i5 index: S502-CTCTCTAT


title: scRNAseq_065_cell_5

description:
Illumina i7 index: N708-CAGAGAGG
Illumina i5 index: S501-TAGATCGC


title: scRNAseq_065_cell_6

description:
Illumina i7 index: N707-CTCTCTAC
Illumina i5 index: S501-TAGATCGC


title: scRNAseq_065_cell_4

description:
Illumina i7 index: N709-GCTACGCT
Illumina i5 index: S501-TAGATCGC


title: scRNAseq_065_cell_3

description:
Illumina i7 index: N701-TAAGGCGA
Illumina i5 index: S501-TAGATCGC


title: scRNAseq_065_cell_2

description:
Illumina i7 index: N702-CGTACTAG
Illumina i5 index: S501-TAGATCGC


title: scRNAseq_065_cell_15

description:
Illumina i7 index: N701-TAAGGCGA
Illumina i5 index: S503-TATCCTCT


title: scRNAseq_065_cell_8

description:
Illumina i7 index: N702-CGTACTAG
Illumina i5 index: S502-CTCTCTAT


title: scRNAseq_065_cell_1

description:
Illumina i7 index: N703-AGGCAGAA
Illumina i5 index: S501-TAGATCGC


title: scRNAseq_064_cell_96

description:
Illumina i7 index: N710-CGAGGCTG
Illumina i5 index: S508-CTAAGCCT

growth_protocol: Cells were cultured on gelatin-coated dishes in 2i medium (NDiff 227 with 0.33 v/v LIF conditioned medium, 1 μM MEK inhibitor PD 0325901 (Tocris) and 3 μM GSK3 inhibitor CHIR99021 (Calbiochem))


title: scRNAseq_064_cell_92

description:
Illumina i7 index: N705-GGACTCCT
Illumina i5 index: S508-CTAAGCCT


title: scRNAseq_064_cell_94

description:
Illumina i7 index: N712-GTAGAGGA
Illumina i5 index: S508-CTAAGCCT


title: scRNAseq_064_cell_91

description:
Illumina i7 index: N706-TAGGCATG
Illumina i5 index: S508-CTAAGCCT


title: scRNAseq_064_cell_90

description:
Illumina i7 index: N710-CGAGGCTG
Illumina i5 index: S507-AAGGAGTA


title: scRNAseq_065_cell_22

description:
Illumina i7 index: N709-GCTACGCT
Illumina i5 index: S504-AGAGTAGA


title: scRNAseq_064_cell_87

description:
Illumina i7 index: N704-TCCTGAGC
Illumina i5 index: S507-AAGGAGTA


title: scRNAseq_064_cell_88

description:
Illumina i7 index: N712-GTAGAGGA
Illumina i5 index: S507-AAGGAGTA


title: scRNAseq_064_cell_85

description:
Illumina i7 index: N706-TAGGCATG
Illumina i5 index: S507-AAGGAGTA


title: scRNAseq_065_cell_10

description:
Illumina i7 index: N709-GCTACGCT
Illumina i5 index: S502-CTCTCTAT


title: scRNAseq_064_cell_86

description:
Illumina i7 index: N705-GGACTCCT
Illumina i5 index: S507-AAGGAGTA


title: scRNAseq_064_cell_84

description:
Illumina i7 index: N710-CGAGGCTG
Illumina i5 index: S506-ACTGCATA


title: scRNAseq_064_cell_83

description:
Illumina i7 index: N711-AAGAGGCA
Illumina i5 index: S506-ACTGCATA


title: scRNAseq_064_cell_80

description:
Illumina i7 index: N705-GGACTCCT
Illumina i5 index: S506-ACTGCATA


title: scRNAseq_064_cell_81

description:
Illumina i7 index: N704-TCCTGAGC
Illumina i5 index: S506-ACTGCATA


title: scRNAseq_064_cell_78

description:
Illumina i7 index: N710-CGAGGCTG
Illumina i5 index: S505-GTAAGGAG


title: scRNAseq_065_cell_11

description:
Illumina i7 index: N708-CAGAGAGG
Illumina i5 index: S502-CTCTCTAT


title: scRNAseq_064_cell_74

description:
Illumina i7 index: N705-GGACTCCT
Illumina i5 index: S505-GTAAGGAG


title: scRNAseq_064_cell_76

description:
Illumina i7 index: N712-GTAGAGGA
Illumina i5 index: S505-GTAAGGAG


title: scRNAseq_064_cell_77

description:
Illumina i7 index: N711-AAGAGGCA
Illumina i5 index: S505-GTAAGGAG


title: scRNAseq_064_cell_75

description:
Illumina i7 index: N704-TCCTGAGC
Illumina i5 index: S505-GTAAGGAG


title: scRNAseq_064_cell_73

description:
Illumina i7 index: N706-TAGGCATG
Illumina i5 index: S505-GTAAGGAG


title: scRNAseq_064_cell_93

description:
Illumina i7 index: N704-TCCTGAGC
Illumina i5 index: S508-CTAAGCCT


title: scRNAseq_064_cell_95

description:
Illumina i7 index: N711-AAGAGGCA
Illumina i5 index: S508-CTAAGCCT


title: scRNAseq_064_cell_70

description:
Illumina i7 index: N710-CGAGGCTG
Illumina i5 index: S504-AGAGTAGA


title: scRNAseq_064_cell_89

description:
Illumina i7 index: N711-AAGAGGCA
Illumina i5 index: S507-AAGGAGTA


title: scRNAseq_064_cell_79

description:
Illumina i7 index: N706-TAGGCATG
Illumina i5 index: S506-ACTGCATA


title: scRNAseq_064_cell_69

description:
Illumina i7 index: N706-TAGGCATG
Illumina i5 index: S504-AGAGTAGA


title: scRNAseq_064_cell_66

description:
Illumina i7 index: N712-GTAGAGGA
Illumina i5 index: S503-TATCCTCT


title: scRNAseq_064_cell_65

description:
Illumina i7 index: N711-AAGAGGCA
Illumina i5 index: S503-TATCCTCT


title: scRNAseq_064_cell_67

description:
Illumina i7 index: N704-TCCTGAGC
Illumina i5 index: S504-AGAGTAGA


title: scRNAseq_064_cell_82

description:
Illumina i7 index: N712-GTAGAGGA
Illumina i5 index: S506-ACTGCATA


title: scRNAseq_064_cell_71

description:
Illumina i7 index: N711-AAGAGGCA
Illumina i5 index: S504-AGAGTAGA


title: scRNAseq_064_cell_61

description:
Illumina i7 index: N704-TCCTGAGC
Illumina i5 index: S503-TATCCTCT


title: scRNAseq_064_cell_63

description:
Illumina i7 index: N706-TAGGCATG
Illumina i5 index: S503-TATCCTCT


title: scRNAseq_064_cell_62

description:
Illumina i7 index: N705-GGACTCCT
Illumina i5 index: S503-TATCCTCT


title: scRNAseq_064_cell_60

description:
Illumina i7 index: N712-GTAGAGGA
Illumina i5 index: S502-CTCTCTAT


title: scRNAseq_064_cell_72

description:
Illumina i7 index: N712-GTAGAGGA
Illumina i5 index: S504-AGAGTAGA


title: scRNAseq_064_cell_59

description:
Illumina i7 index: N711-AAGAGGCA
Illumina i5 index: S502-CTCTCTAT


title: scRNAseq_064_cell_57

description:
Illumina i7 index: N706-TAGGCATG
Illumina i5 index: S502-CTCTCTAT


title: scRNAseq_064_cell_56

description:
Illumina i7 index: N705-GGACTCCT
Illumina i5 index: S502-CTCTCTAT


title: scRNAseq_064_cell_54

description:
Illumina i7 index: N712-GTAGAGGA
Illumina i5 index: S501-TAGATCGC


title: scRNAseq_064_cell_53

description:
Illumina i7 index: N711-AAGAGGCA
Illumina i5 index: S501-TAGATCGC


title: scRNAseq_064_cell_51

description:
Illumina i7 index: N706-TAGGCATG
Illumina i5 index: S501-TAGATCGC


title: scRNAseq_064_cell_50

description:
Illumina i7 index: N705-GGACTCCT
Illumina i5 index: S501-TAGATCGC


title: scRNAseq_064_cell_44

description:
Illumina i7 index: N702-CGTACTAG
Illumina i5 index: S508-CTAAGCCT


title: scRNAseq_064_cell_43

description:
Illumina i7 index: N701-TAAGGCGA
Illumina i5 index: S508-CTAAGCCT


title: scRNAseq_064_cell_49

description:
Illumina i7 index: N704-TCCTGAGC
Illumina i5 index: S501-TAGATCGC


title: scRNAseq_064_cell_45

description:
Illumina i7 index: N703-AGGCAGAA
Illumina i5 index: S508-CTAAGCCT


title: scRNAseq_064_cell_46

description:
Illumina i7 index: N707-CTCTCTAC
Illumina i5 index: S508-CTAAGCCT


title: scRNAseq_064_cell_47

description:
Illumina i7 index: N708-CAGAGAGG
Illumina i5 index: S508-CTAAGCCT


title: scRNAseq_064_cell_68

description:
Illumina i7 index: N705-GGACTCCT
Illumina i5 index: S504-AGAGTAGA


title: scRNAseq_064_cell_64

description:
Illumina i7 index: N710-CGAGGCTG
Illumina i5 index: S503-TATCCTCT


title: scRNAseq_064_cell_52

description:
Illumina i7 index: N710-CGAGGCTG
Illumina i5 index: S501-TAGATCGC


title: scRNAseq_064_cell_42

description:
Illumina i7 index: N709-GCTACGCT
Illumina i5 index: S507-AAGGAGTA


title: scRNAseq_064_cell_58

description:
Illumina i7 index: N710-CGAGGCTG
Illumina i5 index: S502-CTCTCTAT


title: scRNAseq_064_cell_41

description:
Illumina i7 index: N708-CAGAGAGG
Illumina i5 index: S507-AAGGAGTA


title: scRNAseq_064_cell_39

description:
Illumina i7 index: N703-AGGCAGAA
Illumina i5 index: S507-AAGGAGTA


title: scRNAseq_064_cell_31

description:
Illumina i7 index: N701-TAAGGCGA
Illumina i5 index: S506-ACTGCATA


title: scRNAseq_064_cell_32

description:
Illumina i7 index: N702-CGTACTAG
Illumina i5 index: S506-ACTGCATA

value: triple


title: scRNAseq_064_cell_40

description:
Illumina i7 index: N707-CTCTCTAC
Illumina i5 index: S507-AAGGAGTA


title: scRNAseq_064_cell_37

description:
Illumina i7 index: N701-TAAGGCGA
Illumina i5 index: S507-AAGGAGTA


title: scRNAseq_064_cell_34

description:
Illumina i7 index: N707-CTCTCTAC
Illumina i5 index: S506-ACTGCATA


title: scRNAseq_064_cell_48

description:
Illumina i7 index: N709-GCTACGCT
Illumina i5 index: S508-CTAAGCCT


title: scRNAseq_064_cell_35

description:
Illumina i7 index: N708-CAGAGAGG
Illumina i5 index: S506-ACTGCATA


title: scRNAseq_064_cell_33

description:
Illumina i7 index: N703-AGGCAGAA
Illumina i5 index: S506-ACTGCATA


title: scRNAseq_064_cell_55

description:
Illumina i7 index: N704-TCCTGAGC
Illumina i5 index: S502-CTCTCTAT


title: scRNAseq_064_cell_30

description:
Illumina i7 index: N709-GCTACGCT
Illumina i5 index: S505-GTAAGGAG


title: scRNAseq_064_cell_27

description:
Illumina i7 index: N703-AGGCAGAA
Illumina i5 index: S505-GTAAGGAG


title: scRNAseq_064_cell_28

description:
Illumina i7 index: N707-CTCTCTAC
Illumina i5 index: S505-GTAAGGAG


title: scRNAseq_064_cell_26

description:
Illumina i7 index: N702-CGTACTAG
Illumina i5 index: S505-GTAAGGAG


title: scRNAseq_064_cell_38

description:
Illumina i7 index: N702-CGTACTAG
Illumina i5 index: S507-AAGGAGTA


title: scRNAseq_064_cell_20

description:
Illumina i7 index: N702-CGTACTAG
Illumina i5 index: S504-AGAGTAGA


title: scRNAseq_064_cell_16

description:
Illumina i7 index: N709-GCTACGCT
Illumina i5 index: S503-TATCCTCT


title: scRNAseq_064_cell_24

description:
Illumina i7 index: N707-CTCTCTAC
Illumina i5 index: S504-AGAGTAGA


title: scRNAseq_064_cell_29

description:
Illumina i7 index: N708-CAGAGAGG
Illumina i5 index: S505-GTAAGGAG


title: scRNAseq_064_cell_21

description:
Illumina i7 index: N701-TAAGGCGA
Illumina i5 index: S504-AGAGTAGA


title: scRNAseq_064_cell_15

description:
Illumina i7 index: N701-TAAGGCGA
Illumina i5 index: S503-TATCCTCT


title: scRNAseq_064_cell_36

description:
Illumina i7 index: N709-GCTACGCT
Illumina i5 index: S506-ACTGCATA


title: scRNAseq_064_cell_19

description:
Illumina i7 index: N703-AGGCAGAA
Illumina i5 index: S504-AGAGTAGA


title: scRNAseq_064_cell_13

description:
Illumina i7 index: N703-AGGCAGAA
Illumina i5 index: S503-TATCCTCT


title: scRNAseq_064_cell_12

description:
Illumina i7 index: N707-CTCTCTAC
Illumina i5 index: S502-CTCTCTAT


title: scRNAseq_064_cell_11

description:
Illumina i7 index: N708-CAGAGAGG
Illumina i5 index: S502-CTCTCTAT


title: scRNAseq_064_cell_18

description:
Illumina i7 index: N707-CTCTCTAC
Illumina i5 index: S503-TATCCTCT


title: scRNAseq_064_cell_10

description:
Illumina i7 index: N709-GCTACGCT
Illumina i5 index: S502-CTCTCTAT


title: scRNAseq_064_cell_17

description:
Illumina i7 index: N708-CAGAGAGG
Illumina i5 index: S503-TATCCTCT


title: scRNAseq_064_cell_14

description:
Illumina i7 index: N702-CGTACTAG
Illumina i5 index: S503-TATCCTCT


title: scRNAseq_064_cell_7

description:
Illumina i7 index: N703-AGGCAGAA
Illumina i5 index: S502-CTCTCTAT


title: scRNAseq_064_cell_6

description:
Illumina i7 index: N707-CTCTCTAC
Illumina i5 index: S501-TAGATCGC


title: scRNAseq_064_cell_23

description:
Illumina i7 index: N708-CAGAGAGG
Illumina i5 index: S504-AGAGTAGA


title: scRNAseq_064_cell_4

description:
Illumina i7 index: N709-GCTACGCT
Illumina i5 index: S501-TAGATCGC


title: scRNAseq_064_cell_8

description:
Illumina i7 index: N702-CGTACTAG
Illumina i5 index: S502-CTCTCTAT


title: scRNAseq_064_cell_22

description:
Illumina i7 index: N709-GCTACGCT
Illumina i5 index: S504-AGAGTAGA


title: scRNAseq_064_cell_25

description:
Illumina i7 index: N701-TAAGGCGA
Illumina i5 index: S505-GTAAGGAG


title: scRNAseq_064_cell_9

description:
Illumina i7 index: N701-TAAGGCGA
Illumina i5 index: S502-CTCTCTAT


title: scRNAseq_064_cell_1

description:
Illumina i7 index: N703-AGGCAGAA
Illumina i5 index: S501-TAGATCGC


title: scRNAseq_063_cell_96

description:
Illumina i7 index: N710-CGAGGCTG
Illumina i5 index: S508-CTAAGCCT