title: CTRL_E14_Rep2

city: Philadelphia

first: Ricardo

middle: A

last: Linares Saldana

state: PA

address: 3400 civic center blvd

institute: University of Pennsylvania

data_processing:
ATAC seq
Cluster generation, sequencing, and base calling was performed on Illumina NextSeq 500.
Trimming of known adapters and low-quality regions of reads was performed using Fastq-mcf. Sequence quality control was assessed using FastQC.
Reads were aligned to the mm10 genomic assembly using bowtie2 with options: -X 600 --no-mixed --no-discordant. Peaks were called using macs2 callpeak with options: -p 0.1 --nomodel --shift 100 --extsize 200 -B --SPMR --call-summits. Peaks identified in both replicates were considered concordant and kept for further analysis.
Genome_build: mm10
Supplementary_files_format_and_content: bw
Bulk RNA seq
Cluster generation, sequencing, and base calling was performed on Illumina NextSeq 500.
Trimming of known adapters and low-quality regions of reads was performed using Fastq-mcf. Sequence quality control was assessed using FastQC.
Reads were mapped to the mm10 reference mouse genome using STAR (v 2.7.3a) and assigned to Ensembl genes. We quantified gene expression using raw counts and kept the protein coding genes that showed an average FPKM value across the samples >0.5 FPKM. We then performed differential expression gene testing with DESeq25 (v.1.24.0 R package) using default settings.
Genome_build: mm10
Supplementary_files_format_and_content: bw,  counts

source_name: E14 Heart tissue (Cardiomyocyte cells)

extract_protocol:
The microdissected heart was saved in Qiazol. After genotyping was completed, hearts of the appropriate genotype were then processed through the Qiagen RNAeasy kit
Single-end Poly(A)-enriched RNA libraries were prepared with the NEBNext RNA library Prep Kit. High-throughput sequencing was done using a SE75 run on a NextSeq 500 instrument (Illumina).

treatment_protocol: E14 embryos were microdissected from timed pregnant mice and yolk sacs were genotyped to identify relevant embryonic hearts to include in the analysis.

value: Brd4 flox/+ , Tnnt2-Cre

tag: treatment

value: Tamoxifen

tag: type of experiment

value: Bulk RNA seq


title: CTRL_E14_Rep3

status: Public on Sep 30 2021

type: SRA

country: USA

library_source: transcriptomic

molecule: polyA RNA

organism: Mus musculus

tag: genotype


title: BRD4KO_E14_Rep3

value: Brd4 flox/flox , Tnnt2-Cre


title: Donor6_agc

type: RNA

city: Wellington

first: Ellie-May

last: Jarvis

address: Malaghan Institute of Medical Research, PO Box 7060

country: New Zealand

institute: Malaghan Institute of Medical Reseatch

hyb_protocol: Briefly, RNA was hybridised with the Reporter CodeSet for 18 hours at 65 ºC and then incubated with the Capture ProbeSet at 65 ºC  for a further 12 hours.

scan_protocol: Following this, samples were loaded into cartridges via the NanoString PrepStation and RNA quantified via a Digital Analyser.

data_processing: The raw data was imported into nSolver (v3.0, NanoString Technologies, Inc.) and RNA counts normalised to housekeeping genes. Data was then log2-transformed and trimmed to exclude counts greater than 1.5 mean absolute deviations from the median value  using RStudio (RStudio, Inc.).

molecule: total RNA

organism: Homo sapiens

source_name: PBMC

label_protocol: PanCancer Immune nCounter Assay (NanoString Technologies, Inc.) was utilised to label, hybridise and quantify RNA expression according to the manufacturer’s instructions.

growth_protocol: Healthy donor PBMCs isolated using lymphoprep. They were seeded at 3 x 10^5 cells/well and stimuli or media control added.

extract_protocol: RNA was extracted using the Qiagen RNA mini kit according to manufacurer's instructions

treatment_protocol: Innate-like T-cell stimuli used were 200 nM agc for NKT-cell activation, 1 µM 5-A-RU/MG for MAIT-cell activations or 1 µM BrHPP for V[gama]9V[delta]2 T-cell stimulation

tag: disease state

value: healthy

tag: culture

value: agc


title: Donor1_5aru


title: Donor6_5aru


title: BRD4KO_E14_Rep2


title: BRD4KO_E14_Rep1


title: Donor3_5aru


title: Donor5_agc


title: Donor2_agc


title: Donor4_agc


title: Donor1_agc


title: Donor3_agc


title: BRD4KO_TAM_Day5_Rep1

source_name: Heart tissue (Cardiomyocyte cells)

extract_protocol:
Briefly, after proper mouse anesthesia level was reached, thoracotomy was performed, and mouse heart was isolated. The isolated heart was cannulated and perfused with perfusion buffer (120.4 mM NaCl, 14.7 mM KCl, 0.6 mM KH2PO4, 0.6 mM Na2HPO4, 1.2 mM MgSO4, 10 mM Na-HEPES, 4.6 mM NaHCO3, 30 mM taurine, 10 mM 2,3-butanedione monoxime, and 5.5 mM glucose, pH 7.0) in a Langendorff perfusion system (Radnoti 120108EZ) for 5-10 minutes at 37 °C. The cannulated heart was then digested by digestion buffer (perfusion buffer with 300 units/mL collagenase II (Worthington Biochemical) and 50 μM CaCl2) for about 10 min at 37 °C. At the end of digestion, the atria and great vessels were removed and the ventricular tissue was transferred to and gently teased into small pieces in stop buffer (perfusion buffer with 10% fetal bovine serum) at 37 °C. After gently pipetting, cell suspension was passed through a 250uM strainer in a falcon tube and then at 30xg for 3 minutes at room temperature (RT). Then, the supernatant - containing most of the non-cardiomyocytes (CMs) was discarded. CMs were lysed with Qiazol (Qiagen # 79306) and RNA extracted with miRNeasy Mini Kit (Qiagen # 217004).
Paired-end Poly(A)-enriched RNA libraries were prepared with the ovation RNA-seq Universal kit (NuGEN; strand specific). High-throughput sequencing was done using a PE75 run on a NextSeq 500 instrument (Illumina).

treatment_protocol: Administration of intraperitoneal TAM (75 μg/g/day) or vehicle (VEH; corn oil) was performed for 5 consecutive days.

value: Myh6-MCM , Brd4 flox/flox

tag: time point


title: BRD4KO_TAM_Day5_Rep3


title: BRD4KO_TAM_Day5_Rep2


title: BRD4KO_TAM_Day2_Rep3


title: BRD4KO_TAM_Day2_Rep1


title: CTRL_VEH_Day5_Rep2

value: Vehicle


title: CTRL_E14_Rep1


title: Donor6_Media

value: media


title: CTRL_VEH_Day5_Rep3


title: BRD4KO_TAM_Day2_Rep2


title: Donor5_Media


title: Donor2_Media


title: Donor4_Media


title: Donor3_Media


title: Donor1_Media


title: CTRL_VEH_Day2_Rep2


title: CTRL_VEH_Day2_Rep1


title: CTRL_VEH_Day2_Rep3


title: CTRL_VEH_Day5_Rep1


title: CTRL_TAM_CRE_Day5_Rep2


title: CTRL_TAM_CRE_Day2_Rep2


title: CTRL_TAM_CRE_Day5_Rep1


title: CTRL_TAM_CRE_Day2_Rep1


title: CM_TAM1_Day5_Rep1

library_source: genomic

molecule: genomic DNA

extract_protocol:
Briefly, after proper mouse anesthesia level was reached, thoracotomy was performed, and mouse heart was isolated. The isolated heart was cannulated and perfused with perfusion buffer (120.4 mM NaCl, 14.7 mM KCl, 0.6 mM KH2PO4, 0.6 mM Na2HPO4, 1.2 mM MgSO4, 10 mM Na-HEPES, 4.6 mM NaHCO3, 30 mM taurine, 10 mM 2,3-butanedione monoxime, and 5.5 mM glucose, pH 7.0) in a Langendorff perfusion system (Radnoti 120108EZ) for 5-10 minutes at 37 °C. The cannulated heart was then digested by digestion buffer (perfusion buffer with 300 units/mL collagenase II (Worthington Biochemical) and 50 μM CaCl2) for about 10 min at 37 °C. At the end of digestion, the atria and great vessels were removed and the ventricular tissue was transferred to and gently teased into small pieces in stop buffer (perfusion buffer with 10% fetal bovine serum) at 37 °C. After gently pipetting, cell suspension was passed through a 250uM strainer in a falcon tube and then at 30xg for 3 minutes at room temperature (RT). Then, the supernatant - containing most of the non-cardiomyocytes (CMs) was discarded. For performing Assay for Transposase-Accessible Chromatin (ATAC), aliquots of 50,000 cardiomyocytes were lysed with 3 mL of chilled lysis buffer (3.75mM PIPES, 450mM KCl, 1% NP-40, 1% Tween-20, 1% Triton X-100 in water; pH 7.3) for 10 minutes. Nuclear pellets were transposed with 25 µL of Tagment DNA Buffer, 2.5 µL of Tagment DNA Enzyme (Nextera Sample Prep Kit from Illumina; #FC-121-1030), and 22.5 µL of nuclease-free water. Samples were incubated at 37°C for 60 min and then stored at 20°C.
Transposed samples were purified using the QIAGEN MinElute Reaction Cleanup Kit (28204) and amplified using 25 µL of NEBNext High Fidelity 2x PCR Master Mix, 1.25 mM Nextera custom primers with unique barcodes, and nuclease-free water. Samples were amplified using the following PCR conditions: 72°C for 5 min; 98°C for 30 s; and cycled at 98°C for 10 s, 63°C for 30 s and 72°C for 1 min. Half of each sample was amplified for 12 cycles, purified, and assessed by Bioanalyzer (Agilent) for library quality. Sample concentration was quantified by Qubit (Invitrogen) prior to pooling.

value: ATAC seq


title: E13.5 dKO 1

city: Storrs

first: Rahul

middle: N

last: Kanadia

state: CT

address: 75 N. Eagleville Road

department: Physiology and Neurobiology

institute: University of Connecticut

data_processing:
Reads were mapped using Hisat2
Expression calls were made using IsoEM
Differential expression was determined with IsoDE2
Genome_build: mm10
Supplementary_files_format_and_content: tab delimeted text files with gene TPM for each sample

source_name: Dorsal telencephalon

extract_protocol:
Dorsal telencephalons (pallia) were dissected and placed into Trizol. RNA was extracted using Direct-zol RNA Miniprep Plus Kit.
RNA libraries were generated for sequencing through standard Illumina recommended protocols

tag: strain

tag: tissue

value: Dorsal telencephalon

tag: age


title: CM_VEH2_Day5_Rep2


title: CM_VEH1_Day5_Rep1


title: E13.5 dKO 2


title: E13.5 dKO 4


title: E13.5 Rnu11 cKO 4


title: E13.5 dKO 3


title: E13.5 Rnu11 cKO 3


title: E13.5 Rnu11 cKO 2


title: CM_TAM2_Day5_Rep2


title: GC091479_ATGCGCAG-CGTCTAAT

city: Leuven

first: Vincent

last: Pasque

address: Herestraat 49 bus 804

department: Development and Regeneration

country: Belgium

institute: KU Leuven

data_processing:
For allele resolution analyses, reads processed as previously described in (Janiszewski, talon et al). Briefly, reads were mapped to the same reference genome release in which SNP positions were substituted by N base (referred to as N-masked mm10). N-masking was performed with SNPsplit software (Version 0.3.2 released (29-03-2017)) (Krueger and Andrews 2016) supplied with the list of strain-specific SNPs (129S1_SvImJ and CAST_EiJ) from Sanger Mouse Genomes project database (mgp.v5.merged.snps_all.dbSNP142.vcf.gz). N-masking was done in dual hybrid mode and resulted in the identification throughout the entire genome of 20,563,466 SNP positions unique for either strain, of which 634,730 on the X Chromosome. Next, reads were aligned to the N-masked mm10 genome using STAR 2.5.3a with parameters disabling soft-clipping of incompletely aligned reads (--alignEndsType EndToEnd --outSAMattributes NH HI NM MD). Reads aligned to the N-masked reference genome were then split into two BAM files containing only strain-specific reads (on average 10.95% for Mus and 10.25% for Cast of total mapped reads) using SNPsplit (version 0.3.4). Unclassified reads were not used for subsequent allele-specific analysis. Using the allelic BAM files, variant calling files (VCF) were generated using samtools’ mpilup command (version 1.7) (ref), and merged using bcftools (ref)(version 1.5). An allelic count matrix was created by retaining counts from SNP positions and annotating these positions with their respective genes, where only genes covered by 4 SNPs or more are kept. Allelic data was size factor normalized by dividing allele-specific gene counts by total counts of that cell, this was then multiplied by 10000 and log transformed.
Genome_build: mm10
Supplementary_files_format_and_content: iPSC_allelic_count_matrix.csv (contains gene names and allelic counts of the 48 single cells. Each cell can be identified by its "plate_cell" code in the "Characteristics" section. Two columns per cell, one column for Mus musculus castaneus counts, indicated as Ca and another column for Mus musculus mus counts, indicated as X129. Information about the active X is included in column name with biallelic for when 2 X are present, Cast when only the Cast X allele is present and mus when only the Mus X allele is present.)

source_name: iPSCs

growth_protocol: iPSCs were cultured in mouse ESC medium [KnockOut DMEM (Gibco, 10829-018) supplemented with 15% FBS, 1% P/S 10,000 U/mL, 1% GlutaMAX 100×, 1% NEAA 100×, 0.008% (v/v) beta-mercaptoethanol, and mouse LIF] in the presence of ascorbic acid (50 μg/ml final).

extract_protocol:
Cells were FACS sorted into 2.5 μl GpC methylase reaction mix, comprising 1x M.CviPI reaction buffer, 2 U M.CviPI (Bioké, M0227S), 160 μM S-adenosylmethionine (SAM), 1U/μl RNAsein (Thermofisher, AM2694) and 0.1% IGEPAL (Sigma-Aldrich, CA-630). The samples were incubated at 37°C for 15 min to label open chromatin after which 5 μl RLT plus buffer was added. The mRNA was captured using oligo-dT-coated paramagnetic beads on an automated liquid-handling robotics platform (Hamilton), following the G&T-seq procedure [104] with additional wash step. The beads were resuspended in 5 μl reverse transcription mix; 4 mM dNTPs, 1 μM TSO (IDT), 6 mM MgCl2, 1 M Betaine, 1x superscript II First-strand buffer, 5 mM DTT, 2.5 U RNase inhibitor (Thermofisher, R0192) and 50 U superscript II reverse transcriptase (Thermofisher, 18064022) and incubated at 42°C for 2 min with mixing at 2,000 rpm, 42°C for 60 min and 1,500 rpm, 50°C for 30 min and 1,500 rpm and 60°C for 10 min and 1500 rpm. cDNA amplification was performed by adding 7.5 μl cDNA amplification master mix, comprising 1x KAPA HiFi HotStart ReadyMix (KAPA biosystems, KR0370) and 0.1 μM IS PCR primer (IDT), followed by incubation at: 98 °C for 3 min, 23 cycles of 98°C for 20 sec, 67°C for 15 sec, 72°C for 6 min and finally, 72°C for 5 min. The amplified cDNA was purified in a 1:1 ratio using AMPure beads (BeckmanCoulter, A63880)) and eluted in 25 μl nuclease-free water. Library preparation was performed using the Nextera XT kit (Illumina, FC-131-1096) according to manufacturer’s instructions using 1:4th volumes starting from 250pg cDNA. Final libraries were 96-plex pooled and SPRI purified using 0.66:1 ratio and quantified using qPCR while fragment size was assessed on bioanalyzer. Libraries were 192-plex sequenced on an Illumina HiSeq 4000 platform in 50bp single end mode.
single-cell RNA-seq

tag: cell type

value: iPSCs


title: GC091479_TACGCTGC-CGTCTAAT


title: GC091479_CGGAGCCT-TCTCTCCG


title: GC091479_GGAGCTAC-CGTCTAAT


title: GC091479_GCGTAGTA-CGTCTAAT


title: GC091479_GCGTAGTA-TCTCTCCG


title: GC091479_TACGCTGC-TCTCTCCG


title: GC091479_ACTCGCTA-TCTCTCCG


title: GC091479_CGGAGCCT-CGTCTAAT


title: GC091479_ATGCGCAG-CTAAGCCT


title: GC091479_ACTCGCTA-CGTCTAAT


title: GC091479_GGAGCTAC-TCTCTCCG


title: GC091479_ATGCGCAG-TCTCTCCG


title: E13.5 Rnu11 cKO 1


title: E13.5 control 3


title: GC091479_CGGAGCCT-CTAAGCCT


title: E13.5 control 2


title: GC091479_ACTCGCTA-CTAAGCCT


title: GC091479_GCGTAGTA-CTAAGCCT


title: GC091479_TACGCTGC-AAGGAGTA


title: Plate number LC396

city: Parkville

first: Peter

last: Hickey

address: 1G Royal Parade

country: Australia

institute: WEHI

data_processing:
gene and ERCC count matrix generated using scPipe 1.10.0
reads were aligned using Rsubread 2.24.0
Genome_build: GRCm38.p6
Supplementary_files_format_and_content: ERCC count matrix, rows represent ERCC spike-in sequences and each column is a well
Supplementary_files_format_and_content: gene count matrix, rows represent genes and each column is a well
Supplementary_files_format_and_content: sample sheet, rows represent a well and columns contain metadata on the sample in the well

source_name: Mouse retinal endothelial cells

growth_protocol: Mice were intercrossed with the mTmG reporter allele that leads to cre-driven EGFP expression. Control mice were: Hbo1fl/+;Cdh5-creERT2+;mTmG+ and Hbo1iEC/iEC mice were: Hbo1flox/flox;Cdh5-creERT2+;mTmG.

extract_protocol:
Retinas were removed at P6, dissociated into single cells using Liberase TM and Dnase I and stained for PECAM1. PECAM1+EGFP+ cells were flow sorted into a chilled 384-well PCR plate (Greiner, 785290) containing 1.2 μl of primer/lysis mix [20 nM indexed polydT primer (custom made, IDT), 1:6.000.000 dilution of ERCC RNA spike-in mix (Ambion, 4456740), 1 mM dNTPs (NEB, N0446S), 1.2 units SUPERaseIN Rnase Inhibitor (Thermo Fisher, AM2696), DEPC water (Thermo Fisher, AM9920)] using a BD FACSAria III flow cytometer (BD Biosciences, San Jose, CA, USA). Prepared RNA mixture plates were sealed and immediately frozen upside down at -80C.
Single cell transcriptome libraries were generated using the CelSeq2 protocol (Hashimshony et al., 2016 Genome Biol.) with the following adaptations: Second strand synthesis was performed using NEBNext Second Strand Synthesis module (NEB, #E6111S) in a final reaction volume of 8 µl and NucleoMag NGS Clean-up and Size select magnetic beads (Macherey-Nagel, 7449970.5) were used for all DNA purification and size selection steps.

treatment_protocol: Mice were treated with 50 µg tamoxifen on P1 and P2 by intra-gastric injection to induce Cdh5-creERT2 mediated deletion of Hbo1 and drive expression of EGFP

value: Retinal endothelial cells

value: mixed sample (non-demultiplexed):Control;mTmG+ & Hbo1iEC/iEC;mTmG


title: E13.5 control 4


title: GC091479_TACGCTGC-CTAAGCCT


title: Plate number LC392


title: GC091479_GGAGCTAC-CTAAGCCT


title: GC091479_CGGAGCCT-AAGGAGTA


title: E13.5 control 1


title: GC091479_ACTCGCTA-AAGGAGTA


title: Plate number LC294


title: GC091479_TACGCTGC-ACTGCATA


title: GC091479_ATGCGCAG-ACTGCATA


title: Plate number LC279

value: Control;mTmG+


title: GC091479_GCGTAGTA-ACTGCATA


title: GC071398_TCTTACGC-TAGCGCTC

description: smart-seq2 protocol

data_processing:
For non-allele resulotion analyses, reads were mapped to the mouse reference genome (mm10) using STAR 2.5.3a (Dobin et al. 2013) and GENCODE vM16 annotation file. Alignment was performed with default parameters and --sjdbOverhang set to 74 and output to sorted BAM files. Uniquely aligned reads were quantified using the featureCounts function from the R Bioconductor package “Rsubread” (version 1.5.2) (Liao et al. 2019).
For allele resolution analyses, reads processed as previously described in (Janiszewski, talon et al). Briefly, reads were mapped to the same reference genome release in which SNP positions were substituted by N base (referred to as N-masked mm10). N-masking was performed with SNPsplit software (Version 0.3.2 released (29-03-2017)) (Krueger and Andrews 2016) supplied with the list of strain-specific SNPs (129S1_SvImJ and CAST_EiJ) from Sanger Mouse Genomes project database (mgp.v5.merged.snps_all.dbSNP142.vcf.gz). N-masking was done in dual hybrid mode and resulted in the identification throughout the entire genome of 20,563,466 SNP positions unique for either strain, of which 634,730 on the X Chromosome. Next, reads were aligned to the N-masked mm10 genome using STAR 2.5.3a with parameters disabling soft-clipping of incompletely aligned reads (--alignEndsType EndToEnd --outSAMattributes NH HI NM MD). Reads aligned to the N-masked reference genome were then split into two BAM files containing only strain-specific reads (on average 10.95% for Mus and 10.25% for Cast of total mapped reads) using SNPsplit (version 0.3.4). Unclassified reads were not used for subsequent allele-specific analysis. Using the allelic BAM files, variant calling files (VCF) were generated using samtools’ mpilup command (version 1.7) (ref), and merged using bcftools (ref)(version 1.5). An allelic count matrix was created by retaining counts from SNP positions and annotating these positions with their respective genes, where only genes covered by 4 SNPs or more are kept. Allelic data was size factor normalised by dividing allele-specific gene counts by total counts of that cell, this was then multiplied by 10000 and log transformed.
Genome_build: mm10
Supplementary_files_format_and_content: smartseq_norm_counts.csv: text file containing normalized read counts
Supplementary_files_format_and_content: smartseq_annotation.xlsx: spreadsheet containing additional metadata information
Supplementary_files_format_and_content: loom_XCR_5runs.loom: loom file containing both expression and gene regulatory network data together with tSNE embeddings

source_name: MEF to iPSC reprogramming timecourse

growth_protocol: MEFs were cultured in MEF medium [DMEM (Gibco, 41966-554 052) supplemented with 10% (v/v) fetal bovine serum (FBS, Gibco, 10270-106), 1% (v/v) penicillin/streptomycin (P/S, Gibco, 15140-122), 1% (v/v) GlutaMAX (Gibco, 35050-061), 1% (v/v) non-essential amino acids (NEAA, Gibco, 11140-050), and 0.008% (v/v) beta-mercaptoethanol (Sigma-Aldrich, M7522)].   Cells undergoing reprogramming, and iPSCs were cultured in mouse ESC medium [KnockOut DMEM (Gibco, 10829-018) supplemented with 15% FBS, 1% P/S 10,000 U/mL, 1% GlutaMAX 100×, 1% NEAA 100×, 0.008% (v/v) beta-mercaptoethanol, and mouse LIF] in the presence of ascorbic acid (50 μg/ml final).

extract_protocol:
For the isolation of Day 0 time point of single-cell transcriptome analysis, 96 Xi-GFP cells were sorted into a 96-well multiwell plate with 2 µl lysis buffer, followed by initial steps of smart-seq2 protocol (see below). Remaining cells were plated for reprogramming directly after sorting, 50.000 cells per one well of a 12 well plate. Reprogramming was induced by doxycycline (2 μg/ml final) in mouse ESC medium in the presence of ascorbic acid (50 μg/ml final). The medium together with doxycycline and ascorbic acid was replaced every two days and maintained throughout entire reprogramming experiments. To derive iPSCs from picked colonies, the same conditions were used with dox and AA withdrawal after picking. Next, FUT4+ reprogramming intermediates were sorted into single wells, each with 2 µl of the lysis buffer [0,2% Triton X100, 1:20 RRI (Recombinant RNase Inhibitor Takara)] and snap-frozen in -80°C until cells from all timepoints were collected.
All samples were processed following the smart-seq2 protocol (Picelli et al). cDNA synthesis was done starting from 500 pg of input RNA, followed by library preparation from 80 pg of cDNA using the Nextera XT kit (Illumina, FC-131-1096). Indexing was performed with the Nextera XT index Kit V2 (Illumina, FC-131-2003). The quality of cDNA and individual libraries was assessed using an Agilent 2100 Bioanalyzer system.

treatment_protocol: Reprogramming experiments, unless stated otherwise, were performed by conditional induction of lentivirally delivered reprogramming factors. First, passage 1 MEFs at around 70% confluency were transduced with concentrated lentiviral supernatants. Lentiviruses were generated using HEK cells separately for two constructs: tetO-FUW-OSKM, Addgene cat. 20321 (Carey et al. 2009) and FUW-M2rtTA, Addgene cat. 20342 (Hockemeyer et al. 2008) with the calcium precipitation method. Supernatants with lentiviral particles were concentrated using lenti-X-concentrator (Takara, 631231) in 1:100 ratios. Infection with a pool of equal volumes of both constructs was carried out overnight, followed by 12 hours culture in MEF medium and 1:6 split. Cells were then sorted using FACS (described below) in order to isolate homogeneous population with regard to allelic inactivation of the X-GFP transgene (either Xi-GFP or Xa-GFP).

tag: timepoint

tag: initially inactive x allele

value: Cast


title: GC071398_TCTTACGC-TGCAGCTA

description: smart-seq2 protocol


title: GC071398_TCTTACGC-TCGACGTC

description: smart-seq2 protocol


title: Plate number LC280


title: GC071398_TCTTACGC-TACGCTGC

description: smart-seq2 protocol


title: GC091479_GGAGCTAC-ACTGCATA


title: GC091479_ATGCGCAG-AAGGAGTA


title: GC091479_GCGTAGTA-AAGGAGTA


title: GC091479_GGAGCTAC-AAGGAGTA


title: Plate number LC398


title: GC071398_TCTTACGC-GGAGCTAC

description: smart-seq2 protocol


title: GC071398_TCTTACGC-GCGTAGTA

description: smart-seq2 protocol


title: GC091479_ACTCGCTA-ACTGCATA


title: Plate number LC358


title: GC071398_TCTTACGC-CGGAGCCT

description: smart-seq2 protocol


title: GC091479_CGGAGCCT-ACTGCATA


title: GC091479_ATGCGCAG-GTAAGGAG


title: GC091479_TACGCTGC-GTAAGGAG


title: GC091479_CGGAGCCT-GTAAGGAG


title: GC091479_TACGCTGC-TATCCTCT


title: GC071398_TCTTACGC-CCTAAGAC

description: smart-seq2 protocol


title: GC071398_TCTTACGC-ACTGAGCG

description: smart-seq2 protocol


title: GC071398_TCGCATAA-TCGACGTC

description: smart-seq2 protocol


title: GC091479_ACTCGCTA-GTAAGGAG


title: GC071398_TCTTACGC-CGATCAGT

description: smart-seq2 protocol


title: GC071398_TCGCATAA-TAGCGCTC

description: smart-seq2 protocol


title: GC091479_GGAGCTAC-GTAAGGAG


title: GC091479_CGGAGCCT-TATCCTCT


title: GC091479_TACGCTGC-CTCTCTAT


title: GC091479_ATGCGCAG-TATCCTCT


title: GC071398_TCGCATAA-CGATCAGT

description: smart-seq2 protocol


title: GC071398_TCTTACGC-ACTCGCTA

description: smart-seq2 protocol


title: GC071398_TCGCATAA-GGAGCTAC

description: smart-seq2 protocol


title: GC091479_GCGTAGTA-GTAAGGAG


title: GC071398_TCGCATAA-TGCAGCTA

description: smart-seq2 protocol


title: GC071398_TCGCATAA-GCGTAGTA

description: smart-seq2 protocol


title: GC091479_GGAGCTAC-TATCCTCT


title: GC091479_GCGTAGTA-CTCTCTAT


title: GC071398_TCGCATAA-CGGAGCCT

description: smart-seq2 protocol


title: GC091479_GGAGCTAC-CTCTCTAT


title: GC091479_GCGTAGTA-TATCCTCT


title: GC071398_TCGCATAA-ATGCGCAG

description: smart-seq2 protocol


title: GC071398_TATGCAGT-TCGACGTC

description: smart-seq2 protocol

value: Mus


title: GC091479_ACTCGCTA-TATCCTCT


title: GC091479_ATGCGCAG-CTCTCTAT


title: GC071398_TCGCATAA-TACGCTGC

description: smart-seq2 protocol


title: GC091479_CGGAGCCT-CTCTCTAT


title: GC071398_TCTTACGC-ATGCGCAG

description: smart-seq2 protocol


title: GC071398_TATGCAGT-TGCAGCTA

description: smart-seq2 protocol


title: GC071398_TCGCATAA-CCTAAGAC

description: smart-seq2 protocol


title: GC071398_TATGCAGT-GTAGAGGA

description: smart-seq2 protocol


title: GC071398_TCGCATAA-ACTCGCTA

description: smart-seq2 protocol


title: sample6_Mu_S6

city: Chicago

first: Yan

last: Li

state: IL

address: 900 East 57th St.

department: Center for Research Informatics

institute: The University of Chicago

description: Mutant type sample replicate 3

data_processing:
Adapter trime: trim_galore v0.6.5
Alignment: STAR v2.6.1d
Samples gene transcripts assembly: featureCounts
Differentially expressed genes analysis: edgeR
Functional enrichemnt: clusterProfiler
Genome_build: Gencode GRCm38 v25
Supplementary_files_format_and_content: tab-delimited text files include gene features raw counts values summarized by featureCouts for each Sample.

source_name: M14(f/f);Villin-Cre colonic crypt cell RNA

extract_protocol:
Total RNAs were isolated from purified colonic crypt cells; PolyA RNAs were purified using Dynabeads mRNA Purification kit (ThermoFisher Cat # 61006)
Libraries were made based on Takara's instruction using SMARTer Stranded RNA-Seq Kit (Cat # 634836).

value: four week old

value: isolated colonic crypt cells


title: sample3_Wt_S3

description: Wide type sample replicate 3

source_name: M14(f/f) colonic crypt cell RNA


title: GC071398_TATGCAGT-TAGCGCTC

description: smart-seq2 protocol


title: GC071398_TATGCAGT-TCCTGAGC

description: smart-seq2 protocol


title: sample2_Mu

description: single cell RNA

data_processing:
BCL demultiplexing: CellRanger v.3.0.0 mkfastq
alignment, filtering, barcode and UMI counting: CellRanger v.3.0.0 count
Doublet cells detection: DoubletDecon
Downstream analysis: Seurat v3
Genome_build: cellranger builded mouse reference genome basedon Ensembl 93
Supplementary_files_format_and_content: cellranger aligned results in 3 gzipped files for barcodes, features, and matrix respectively

extract_protocol: 10x Genomics protocol


title: GC071398_TATGCAGT-TAGGCATG

description: smart-seq2 protocol


title: FACS endothelial cells Young Sham 21

city: Rochester

first: Mrunal

middle: Kishor

last: Dehankar

state: MN

address: 200 First St. SW

department: Computational genomics

institute: Mayo Clinic

data_processing:
Base calling was performed with the Illumina bcl2fastq
QC was performed on the FASTQ files using RSeQC software (http://rseqc.sourceforge.net/)
The paired end reads were aligned by STAR-2.5.2b aligner
Gene counts were generated using Subread featureCounts (http://subread.sourceforge.net/)
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include raw counts and FPKM values for each gene per sample

source_name: Lung endothelial cells

extract_protocol:
Lungs were perfused, harvested and processed for FACS. Freshly isolated lung endothelial cells were sorted diretly in tubes containing 350 ul of RLT buffer, for RNA isolation and subsequent RNA-seq analysis
Takara Bio SMART-Seq v4 Ultra Low RNA kit to generate cDNA followed with Illumina Nextera lib prep

value: FVB

value: PBS

value: 2 months


title: FACS endothelial cells Young Sham 23


title: sample1_Wt

description: single cell RNA


title: sample4_Mu_S4

description: Mutant type sample replicate 1


title: FACS endothelial cells Young Sham 24


title: GC071398_TCGCATAA-ACTGAGCG

description: smart-seq2 protocol


title: GC071398_TATGCAGT-GGAGCTAC

description: smart-seq2 protocol


title: GC071398_TATGCAGT-GCGTAGTA

description: smart-seq2 protocol


title: sample1_Wt_S1

description: Wide type sample replicate 1


title: GC071398_TATGCAGT-GGACTCCT

description: smart-seq2 protocol


title: FACS endothelial cells Young Bleo 20

value: Bleomycin


title: GC071398_TATGCAGT-TAAGGCGA

description: smart-seq2 protocol


title: sample2_Wt_S2

description: Wide type sample replicate 2


title: GC071398_TATGCAGT-GCTCATGA

description: smart-seq2 protocol


title: neural tube, Wild-type RNA-seq (run2_TC6_WT_RNA_S9_L002)

city: Stanford

first: Gun Woo

last: Byeon

state: CA

address: 279 Campus Dr., Beckman Center B309

institute: Stanford University

description: Replicate 3

data_processing:
Read alignment: For removal of adapter sequences, low quality bases, and short reads, we use cutadapt (Martin, 2011) to trim Illumina adapter sequences and <Q20 bases (parameters -m 18 -a CTGTAGGCACCATCAAT --quality-cutoff=20). For splice-aware alignment using STAR (Dobin et al., 2013), we used STAR to align the reads to a reference genome/transcriptome. STAR reference is built using a combination of mouse genome (mm10), mouse rDNA sequence (GenBank GU372691), and mouse transcript annotations (GENCODE vM18). Only uniquely mapped reads were retained (Parameters --outFilterMultimapNmax 1 --alignEndsType EndToEnd --alignIntronMax 1000000 --alignIntronMin 20 --outFilterMismatchNmax 999 --alignSJDBoverhangMin 1 --alignSJoverhangMin 8). For read quantification, we used bedtools (Quinlan and Hall, 2010) to count alignments over annotated coding regions excluding the first 45 bases from the start codon and last 15 bases from the stop codon.
Genome_build: STAR reference is built using a combination of mouse genome (mm10), mouse rDNA sequence (GenBank GU372691), and mouse transcript annotations (GENCODE vM18).
Supplementary_files_format_and_content: Text file includes read counts across the different regions of each annotated transcript

source_name: neural tube

extract_protocol:
Ribosome profiling was performed following the procedures described before (Fujii et al., 2017). For Ribo-Seq, neural tubes from 1 litter of E11.5 embryos (20-23 somite number from tail to hind limb) were used. The Papain dissociated cells were split into two tubes. One was dissolved by Trizol (Invitrogen, 15596) for RNA seq. Another cell pellet was re-suspended in 0.5 ml of cold lysis buffer (20 mM Tris pH 7.5, 150 mM NaCl, 15 mM MgCl2, 1 % Triton X-100, 1 mM DTT, 8 % Glycerol, 20 Unit/ml TURBO DNase, 100µg/ml Cycloheximide) and incubated for 30 min at 4 °C with occasional vortexing. The lysate was clarified by sequential centrifugation for 5 min at 1,800 g and 10,000 g at 4 °C to remove nuclei and mitochondria. The lysate was then treated with RNase I (Ambion, AM2294) for 30 min at RT to digest mRNAs not protected by the ribosome. The digestion was stopped by adding 4.5 µl of SUPERaseIn RNase Inhibitor (20 U/µl, Ambion AM2696). Lysate was then loaded onto a 1 M sucrose cushion. Ribosomes and ribosome protected fragments (RPFs) were pelleted by ultracentrifugation at 70,000 rpm for 4 hr at 4 ºC by TLA120.2 rotor. The pellet was re-suspended in Trizol (Invitrogen, 15596) and RNAs were extracted by following manufacturer’s protocol. RNA-seq: RNA was extracted from Trizol (Invitrogen, 15596) following manufactuer’s protocol and polyA mRNA was isolated using Oligotex mRNA Mini Kit (Qiagen, 70022) following manufacturer’s protocol. Purified mRNAs were fragmented in alkaline fragmentation buffer (100 mM NaCO3 pH 9.2, 2 mM EDTA).
Ribo-seq/RNA-seq Library production: RPFs and fragmented RNAs were loaded onto a 15% urea gel. 28–31 nt RPFs and 30–50 nt fragmented RNAs were excised from the gel for Ribo-Seq and RNA-Seq respectively. RNAs were eluted, dephosphorylated by PNK (NEB, M0201S), and ligated to the miRNA Cloning linker (NEB, S1315S) by T4 RNA Ligase2 truncated K227Q (NEB, M0242S). Ligated RNA was gel purified and reverse transcribed by Superscript III (Invitrogen, 18080). Gel purified cDNAs were circularized by Circligase (Epicentra, CL4111K) and rRNA sequence were subtracted using biotinylated oligos. Amplification was done using Phusion High Fidelity DNA Polymerase (NEB, M0530S). PCR amplification was performed for 6–7 cycles and products were loaded onto non-denaturing 8 % PAGE gel. DNA fragment were purified for Illumina sequencing.

value: neural tube


title: sample5_Mu_S5

description: Mutant type sample replicate 2


title: GC071398_TATGCAGT-TACGCTGC

description: smart-seq2 protocol


title: GC071398_TATGCAGT-CTCTCTAC

description: smart-seq2 protocol


title: FACS endothelial cells Young Sham 22


title: FACS endothelial cells Young Sham 25


title: GC071398_TATGCAGT-CGTACTAG

description: smart-seq2 protocol


title: FACS endothelial cells Young Bleo 18


title: FACS endothelial cells Young Bleo 19


title: FACS endothelial cells Aged Sham 15

value: 18 months


title: GC071398_TATGCAGT-CGATCAGT

description: smart-seq2 protocol


title: FACS endothelial cells Aged Sham 14


title: GC071398_TATGCAGT-ATGCGCAG

description: smart-seq2 protocol


title: FACS endothelial cells Aged Sham 13


title: GC071398_TATGCAGT-CCTAAGAC

description: smart-seq2 protocol


title: GC071398_TATGCAGT-CGGAGCCT

description: smart-seq2 protocol


title: GC071398_TATGCAGT-ACTGAGCG

description: smart-seq2 protocol


title: FACS endothelial cells Aged Bleo 3


title: GC071398_TATGCAGT-AAGAGGCA

description: smart-seq2 protocol


title: GC071398_TATGCAGT-CGAGGCTG

description: smart-seq2 protocol


title: FACS endothelial cells Aged Bleo 5


title: GC071398_TATGCAGT-ACTCGCTA

description: smart-seq2 protocol


title: GC071398_TACTCCTT-TCGACGTC

description: smart-seq2 protocol


title: FACS endothelial cells Young Bleo 17


title: FACS endothelial cells Aged Bleo 2


title: GC071398_TATGCAGT-ATCTCAGG

description: smart-seq2 protocol


title: GC071398_TACTCCTT-TACGCTGC

description: smart-seq2 protocol


title: GC071398_TACTCCTT-TAGGCATG

description: smart-seq2 protocol


title: GC071398_TATGCAGT-AGGCAGAA

description: smart-seq2 protocol


title: GC071398_TACTCCTT-TAAGGCGA

description: smart-seq2 protocol


title: B2_IP

city: Los Angeles

first: Riki

last: Kawaguchi

address: 760 Westwood Plaza, Room 37-420

department: Department of Psychiatry and Neurology Department of Psychiatry

institute: University of California, Los Angeles

description:
bARK IP replicate 2
StAstroGi_RNAseq

data_processing:
Basecalls/demultiplexing performed using Illumina Bcl2fastq2 v 2.17
Aligned to mm10 using STAR spliced read aligner
Count read using HT-seq with mm10 RefSeq as reference
Normalization (TMM), quantitation (log CPM) and differential expression analysis using limma voom.  Low expressed genes were removed and genes with logCPM greater than 0.5 in at least 4 samples were used for further analysis.
Genome_build: mm10
Supplementary_files_format_and_content: Counts

source_name: brain

extract_protocol:
HA samples underwent DNA depletion and RNA purification with the RNeasy Micro Plus kit (Qiagen). Integrity of the eluted RNA was analyzed by a 2100 Bioanalyzer (Agilent) using the RNA Pico chip. RNA concentration determined by tapestation.
Paired-end libraries for ultiplexed sequencing were generated from 100ng of IP or input RNA using Nugen Ovation RNA-Seq System V2 kit with mRNA enrichment.

value: 9 weeks

tag: Sex

value: male

value: brain

tag: background strain

value: wildtype

tag: expression

value: BetaARK

tag: rna sample type

value: HA IP


title: B4_input

description:
bARK input replicate 4
StAstroGi_RNAseq

value: input


title: D3_IP

description:
bARKD110A IP replicate 3
StAstroGi_RNAseq


title: D4_IP

description:
bARKD110A IP replicate 4
StAstroGi_RNAseq


title: D4_input

description:
bARKD110A input replicate 4
StAstroGi_RNAseq


title: GC071398_TACTCCTT-TGCAGCTA

description: smart-seq2 protocol

value: iPSCs


title: B3_IP

description:
bARK IP replicate 3
StAstroGi_RNAseq


title: B4_IP

description:
bARK IP replicate 4
StAstroGi_RNAseq


title: GC071398_TACTCCTT-TAGCGCTC

description: smart-seq2 protocol

value: Mus


title: GC071398_TACTCCTT-GCTCATGA

description: smart-seq2 protocol


title: FACS endothelial cells Aged Bleo 1


title: B2_input

description:
bARK input replicate 2
StAstroGi_RNAseq


title: B3_input

description:
bARK input replicate 3
StAstroGi_RNAseq


title: B1_input

description:
bARK input replicate 1
StAstroGi_RNAseq


title: GC071398_TACTCCTT-TCCTGAGC

description: smart-seq2 protocol


title: D2_IP

description:
bARKD110A IP replicate 2
StAstroGi_RNAseq


title: B1_IP

description:
bARK IP replicate 1
StAstroGi_RNAseq


title: D3_input

description:
bARKD110A input replicate 3
StAstroGi_RNAseq


title: GC071398_TACTCCTT-GTAGAGGA

description: smart-seq2 protocol


title: GC071398_TACTCCTT-GGACTCCT

description: smart-seq2 protocol


title: GC071398_TACTCCTT-CTCTCTAC

description: smart-seq2 protocol


title: D1_IP

description:
bARKD110A IP replicate 1
StAstroGi_RNAseq


title: CLTP1

city: Warsaw

first: Bartosz

last: Wojtas

address: Pasteura 3

country: Poland

institute: Nencki Institute of Experimental Biology

data_processing:
Basecalling with HCS 2.2.68
Bcl2Fastq processing of bcl files to fastq
Fastq trimming for adapter contamination and low quality reads and aligned with STAR to rn6.fa reference
DESeq2 normalization and statistical analysis
Genome_build: rn6
Supplementary_files_format_and_content: DESeq2 normalized data table, normalized for library size and gene length

organism: Rattus norvegicus

source_name: rat hippocampal culture 1 with induced cLTP

growth_protocol: Primary hippocampal neurons from Wistar rat pups at P0 were cultured in 6-well plates (VWR) or in 24-well plates (VWR) on 12 mm glass coverslips (VWR) coated with poly-D-lysine (Sigma Aldrich) and laminin (Roche)

extract_protocol:
Total RNA was extracted using RNAeasy Mini Kit (Qiagen), according to the company's recommendations (a detailed protocol can be found on the producers website). Briefly, cells from the 6-well plates were disrupted in Buffer RLT and transferred to the RNAse-free tube. RNA was then purified on the spin column, including DNase I step, and eluted with 30 μL of nuclease-free water. Purity and concentration of RNA were measured using  NanoDrop One (Thermo Scientific).
In total, 6 strand-specific RNA libraries for high-throughput sequencing were prepared (three biological replicates for each treatment) using the KAPA Stranded mRNA Sample Preparation Kit according to the manufacturer’s protocol. Briefly, the poly-A containing mRNA molecules were purified from 500ng of total RNA (extracted FACS sorted cells from the brain samples of sham operated and MCAo animals) using poly-T oligo-attached magnetic beads (Kapa Biosystems, MA, USA ) The mRNA was then fragmented and the first-strand cDNA was synthesized using reverse transcriptase and random hexamers. Second cDNA synthesis was performed by removing the RNA template and synthesizing a replacement strand, incorporating dUTP in place of dTTP, to generate double-stranded (ds) cDNA. dsDNA was then subjected to the addition of “A” bases to the 3′ ends and ligation of adapters from NEB followed by uracil digestion in a loop structure of adapter by USER enzyme from NEB (Ipswich, MA, USA). Amplification of fragments with adapters ligated on both ends was performed by PCR using primers containing Truseq barcodes from NEB (Ipswich MA, USA).

treatment_protocol: Chemically-induced long-term potentiation of synaptic transmission (cLTP) was induced according to previously published protocol (Szepesi et al., 2013) by adding 50 μM forskolin (Sigma Aldrich), 50 nM rolipram (Sigma Aldrich), and 200 μM picrotoxin (Sigma Aldrich) to the medium on DIV13-15. As the chemicals were dissolved in DMSO, the same amount of the solvent was added to the medium of the control.

tag: agent

value: induced cLTP

value: hippocampal


title: GC071398_TACTCCTT-CGATCAGT

description: smart-seq2 protocol


title: GC071398_TACTCCTT-CCTAAGAC

description: smart-seq2 protocol


title: D1_input

description:
bARKD110A input replicate 1
StAstroGi_RNAseq


title: GC071398_TACTCCTT-GGAGCTAC

description: smart-seq2 protocol


title: CLTP2

source_name: rat hippocampal culture 2 with induced cLTP


title: GC071398_TACTCCTT-GCGTAGTA

description: smart-seq2 protocol


title: GC054862_10X_RNAseq

data_processing:
Raw read counts were generated using CellRanger (2.1.1) and reference genome and annotation mm10 (1.2.0). Raw read counts matrix was imported to Seurat R package. Only the cell that contained more than 1500 and less than 6000 expressed genes, less than 9% of mitochondrial RNA were retained. Subsequently, reads were normalized using scale factor and log-transformed.
Genome_build: mm10
Supplementary_files_format_and_content: normalized expression matrix in csv

source_name: iPSC reprogramming intermediate

growth_protocol: MEFs were cultured in mouse ESC medium [KnockOut DMEM (Gibco, 10829-018) supplemented with 15% FBS, 1% P/S 10,000 U/mL, 1% GlutaMAX 100×, 1% NEAA 100×, 0.008% (v/v) beta-mercaptoethanol, and mouse LIF]   Cells undergoing reprogramming, and iPSCs were cultured in mouse ESC medium [KnockOut DMEM (Gibco, 10829-018) supplemented with 15% FBS, 1% P/S 10,000 U/mL, 1% GlutaMAX 100×, 1% NEAA 100×, 0.008% (v/v) beta-mercaptoethanol, and mouse LIF] in the presence of ascorbic acid (50 μg/ml final).

extract_protocol:
Cells at Day 16 of reprogramming were washed twice  with PBS without Ca/Mg, detached using 0.25%Trypsin incubated at 37C for 5 minutes; cells were resupsended in 2ml 0.04%BSA/PBS at the concetration of 1 mln cells/ml
To obtain single-cell suspensions, cells at Day 16 of reprogramming were washed twice  with PBS without Ca/Mg, detached using 0.25%Trypsin incubated at 37C for 5 minutes; cells were resupsended in 2ml 0.04%BSA/PBS at the concetration of 1 mln cells/ml.  Single-cell suspensions were converted to barcoded scRNA-seq libraries by using the Chromium Single Cell 3’ Library, Gel Bead & Multiplex Kit and Chip Kit (10x Genomics). Samples were processed using kits pertaining to Chromium V2 chemistry of 10X genomics.  Libraries were sequenced using HiSeq 4000 in paired-end mode.

treatment_protocol: STEMCCA reprogramming was carried out as previously reported (Pasque et al. 2014)

value: Day 16

value: iPSC reprogramming intermediate

tag: barcode suffix


title: CTRL2

source_name: control rat hippocampal culture2 (DMSO solvant treated)

value: DMSO


title: GC054861_10X_RNAseq


title: CTRL1

source_name: control rat hippocampal culture 1 (DMSO solvant treated)


title: CLTP3

source_name: rat hippocampal culture 3 with induced cLTP


title: GC071398_TACTCCTT-ATGCGCAG

description: smart-seq2 protocol


title: GC071398_TACTCCTT-ACTGAGCG

description: smart-seq2 protocol


title: GC071398_TACTCCTT-CGGAGCCT

description: smart-seq2 protocol


title: GC071398_TACTCCTT-ACTCGCTA

description: smart-seq2 protocol


title: GC071398_TACTCCTT-AGGCAGAA

description: smart-seq2 protocol


title: GC071398_TACTCCTT-CGAGGCTG

description: smart-seq2 protocol


title: D2_input

description:
bARKD110A input replicate 2
StAstroGi_RNAseq


title: GC071398_TACTCCTT-AAGAGGCA

description: smart-seq2 protocol


title: CTRL3

source_name: control rat hippocampal culture 3(DMSO solvant treated)


title: GC071398_TAAGGCTC-TGCAGCTA

description: smart-seq2 protocol

value: Cast


title: GC071398_TACTCCTT-CGTACTAG

description: smart-seq2 protocol


title: GC071398_TAAGGCTC-TAGCGCTC

description: smart-seq2 protocol


title: SB02_16-f3-5 (high lithium)

city: London

first: Timothy

last: Powell

address: 16 De Crespigny Park

department: Social, Genetic & Developmental Psychiatry

country: United Kingdom

institute: King's College London

data_processing:
Raw reads were obtained from the sequencing facility and were processed using Trimmomatic 0.38, to prune low quality bases (leading/trailing sequences with phred score < 3, or those with average score < 15 every four bases), or reads below 36 bases in length. Trimmed reads were pseudoaligned to the human reference genome GRCh38 using kallisto. The package tximport was used to import kallisto output files into DESeq2, summarizing transcript-level information to gene-level expression counts utilizing gene information from Ensembl Release 99, imported using biomaRt.
Genome_build: GRCh38
Supplementary_files_format_and_content: deseq2_normalizedcounts.txt contains a matrix corresponding to DESeq2-normalized gene counts for all genes in all samples
Supplementary_files_format_and_content: kallisto_raw_counts.txt contains a matrix corresponding to kallisto raw estimates of gene counts for all genes in all samples

source_name: HPCOA07/03 neural progenitor cells

extract_protocol:
Total RNA was extracted using the Qiagen AllPrep DNA/RNA/Protein Mini Kit (Qiagen, Hilden, Germany). All RNA samples were of good purity and integrity, as indicated by 260/280 ratios of between 1.95 to 2.1, tested using a Nanodrop D1000 spectrophotometer (Thermo Scientific, Wilmington, DE), and RINs > 9, as tested using an Agilent 2100 Bioanalyzer (Agilent Technologies, Berkshire, UK).
Library preparation and RNA-sequencing was performed at The Genomic Centre, King’s College London. Briefly, total RNA samples were submitted to a DNase treatment using the DNA-free™ DNA Removal Kit (Invitrogen, California, USA). Subsequently, 300 ng of total RNA from each sample was submitted for ribosomal RNA depletion using the NEBNext rRNA Depletion kit (New England Biolabs, Massachusetts, USA), and RNA-Seq libraries were constructed using the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina (New England Biolabs). The samples were sequenced in a HiSeq 4000 sequencing system (Illumina).

tag: cell line

value: neural progenitor cells

tag: treatment

value: lithium

tag: dose

tag: biological replicate


title: SB02_12-f2-5 (low lithium)


title: SB02_14-d3-7 (high lithium)


title: SB02_15-e3-5 (high lithium)


title: SB02_11-e2-5 (low lithium)


title: SB02_13-c3-7 (high lithium)


title: SB02_7-e1-5 (control)

value: control


title: GC071398_TAAGGCTC-CCTAAGAC

description: smart-seq2 protocol


title: GC071398_TAAGGCTC-CGATCAGT

description: smart-seq2 protocol


title: GC071398_TAAGGCTC-TACGCTGC

description: smart-seq2 protocol


title: SB02_8-f1-5 (control)


title: GC071398_TAAGGCTC-CGGAGCCT

description: smart-seq2 protocol


title: GC071398_TAAGGCTC-ATGCGCAG

description: smart-seq2 protocol


title: Ex_vivo_Meg_day_11 scRNA-seq

city: Seattle

first: Grigorios

last: Georgolopoulos

state: WA

address: 2211 Elliott Ave #400

institute: Altius Institute

description: 10X Single Cell 3' Reagent Kit V2

data_processing:
Library strategy: scRNA-seq
FASTQ files were demultiplexed using cellranger demux with default parameters
BAM files were generated using 10X Genomics Cellranger V1.3 using default parameters
Gene-barcode (count) matrices were generated using 10X Genomics Cellranger V1.3 using default parameters
Genome_build: GRCh38
Supplementary_files_format_and_content: Cell barcodes in tab separated file
Supplementary_files_format_and_content: Gene list in tab separated file
Supplementary_files_format_and_content: Cell-gene count matrix .mtx formatted

growth_protocol: We used a 2-step erythroid differentiation protocol as described in Giarratana et al., 2011, Blood. Briefly, frozen CD34+ HSPCs are conditioned overnight in serum-free media in the presence of FLT3, TPO and IL3. Cells were then transferred in Step 1, serum-free media supplemented with BSA, Insulin, human-holotransferrin, heparin, hydrocortisone, human recombinant IL-3, hrEPO, and hrSCF and maintained for 7 days. On day 8, cells were transferred to Step 2 media where we withdraw hydrocortisone and IL-3 and maintain the rest of the components. Cells are maintained in Step 2 media until culture termination on day 12. CD34+ HSPCs were differentiated to the megakaryocyte lineage by culturing for 11 days in IMDM based media containing 30ng/mL rhTPO , 1ng/mL rhSCF , 7.5ng/mL rhIL-6 , 13.5ng/mL rhIL-9 , 20% BIT , 40µg/mL LDL , 0.05mM beta mercaptoethanol

extract_protocol:
Frozen culture cell suspension from ex vivo erythroid or megakaryocytic culture or uncultured CD34+ were thawed and resuspended in PBS-BSA aiming for ~5,000 cell per sample
Single cells were lysed in droplets using the 10X Chromium instrument Reverse transcription was performed in droplet and library construction was performed according to the 10X Chromium Single Cell 3' Reagent Kit User Guide Rev A

tag: differentiation day


title: SB02_5-c1-6 (control)


title: SB02_6-d1-7 (control)


title: GC071398_TAAGGCTC-TCGACGTC

description: smart-seq2 protocol


title: GC071398_TAAGGCTC-ACTCGCTA

description: smart-seq2 protocol


title: Ex_vivo_Meg_day_8 scRNA-seq

description: 10X Single Cell 3' Reagent Kit V2


title: GC071398_TAAGGCTC-ACTGAGCG

description: smart-seq2 protocol


title: GC071398_CTTAATAG-TCGACGTC

description: smart-seq2 protocol


title: GC071398_CTTAATAG-TAGCGCTC

description: smart-seq2 protocol


title: Ex_vivo_Ery_day_11 scRNA-seq

description: 10X Single Cell 3' Reagent Kit V1


title: Ex_vivo_Meg_day_4 scRNA-seq

description: 10X Single Cell 3' Reagent Kit V2


title: SB02_10-d2-7 (low lithium)


title: Ex_vivo_Meg_day_2 scRNA-seq

description: 10X Single Cell 3' Reagent Kit V2


title: Ex_vivo_Meg_day_6 scRNA-seq

description: 10X Single Cell 3' Reagent Kit V2


title: GC071398_TAAGGCTC-GCGTAGTA

description: smart-seq2 protocol


title: Ex_vivo_Ery_day_6 scRNA-seq

description: 10X Single Cell 3' Reagent Kit V1


title: GC071398_CTTAATAG-GCGTAGTA

description: smart-seq2 protocol


title: Ex_vivo_Ery_day_8 scRNA-seq

description: 10X Single Cell 3' Reagent Kit V1


title: GC071398_CTTAATAG-CGGAGCCT

description: smart-seq2 protocol


title: GC071398_TAAGGCTC-GGAGCTAC

description: smart-seq2 protocol


title: GC071398_CTTAATAG-GGAGCTAC

description: smart-seq2 protocol


title: Ex_vivo_Ery_day_4 scRNA-seq

description: 10X Single Cell 3' Reagent Kit V1


title: Ex_vivo_Ery_day_2 scRNA-seq

description: 10X Single Cell 3' Reagent Kit V2


title: GC071398_CTTAATAG-TGCAGCTA

description: smart-seq2 protocol


title: GC071398_CTTAATAG-TACGCTGC

description: smart-seq2 protocol


title: GC071398_CTTAATAG-ACTGAGCG

description: smart-seq2 protocol


title: GC071398_CTTAATAG-ATGCGCAG

description: smart-seq2 protocol


title: GC071398_CTTAATAG-CCTAAGAC

description: smart-seq2 protocol


title: Ex_vivo_megakaryocytic_Donor1_Day10 RNA-seq

data_processing:
Basecalling, RTA v3.4.4
Alignments to GRCh38, star v2.4.2a
Annotation, cufflinks v2.2.1, GENCODE v25
Subread, featureCounts v1.5.1
Genome_build: GRCh38
Supplementary_files_format_and_content: Cufflinks FPKM expression levels per gene as a .txt file

growth_protocol: We used a 2-step differentiation protocol as described in Giarratana et al., 2011, Blood. Briefly, frozen CD34+ HSPCs are conditioned overnight in serum-free media in the presence of FLT3, TPO and IL3. Cells were then transferred in Step 1, serum-free media supplemented with BSA, Insulin, human-holotransferrin, heparin, hydrocortisone, human recombinant IL-3, hrEPO, and hrSCF and maintained for 7 days. On day 8, cells were transferred to Step 2 media where we withdraw hydrocortisone and IL-3 and maintain the rest of the components. Cells are maintained in Step 2 media until culture termination on day 12.

extract_protocol:
Approximately 200,000 cells were collected per culture and total RNA was isolated using QIAGEN RNeasy kit per manufacturer's instructions
RNA library was constructed using the Illumina RNA TruSeq Stranded tRNA with Ribo-Zero Globin


title: Ex_vivo_megakaryocytic_Donor3_Day10 RNA-seq


title: CD34_uncultured scRNA-seq

description: 10X Single Cell 3' Reagent Kit V1


title: GC071398_CTTAATAG-ACTCGCTA

description: smart-seq2 protocol


title: GC071398_CTCCTTAC-TGCAGCTA

description: smart-seq2 protocol


title: GC071398_CTCCTTAC-TCGACGTC

description: smart-seq2 protocol


title: Ex_vivo_megakaryocytic_Donor3_Day8 RNA-seq


title: Ex_vivo_megakaryocytic_Donor2_Day9 RNA-seq


title: GC071398_CTCCTTAC-TCCTGAGC

description: smart-seq2 protocol


title: Ex_vivo_megakaryocytic_Donor1_Day8 RNA-seq


title: GC071398_CTCCTTAC-TAGCGCTC

description: smart-seq2 protocol


title: GC071398_CTCCTTAC-TAGGCATG

description: smart-seq2 protocol


title: Ex_vivo_megakaryocytic_Donor2_Day8 RNA-seq


title: Ex_vivo_megakaryocytic_Donor1_Day7 RNA-seq


title: GC071398_CTCCTTAC-GTAGAGGA

description: smart-seq2 protocol


title: GC071398_CTCCTTAC-TACGCTGC

description: smart-seq2 protocol


title: Ex_vivo_megakaryocytic_Donor1_Day9  RNA-seq


title: GC071398_CTCCTTAC-GGAGCTAC

description: smart-seq2 protocol


title: Ex_vivo_megakaryocytic_Donor2_Day5 RNA-seq


title: GC071398_CTTAATAG-CGATCAGT

description: smart-seq2 protocol


title: Ex_vivo_megakaryocytic_Donor3_Day7  RNA-seq


title: Ex_vivo_megakaryocytic_Donor1_Day5  RNA-seq


title: GC071398_CTCCTTAC-GCTCATGA

description: smart-seq2 protocol


title: Ex_vivo_megakaryocytic_Donor3_Day5 RNA-seq


title: GC071398_TACTCCTT-ATCTCAGG

description: smart-seq2 protocol


title: Ex_vivo_megakaryocytic_Donor2_Day7 RNA-seq


title: Ex_vivo_megakaryocytic_Donor1_Day4 RNA-seq


title: GC071398_CTCCTTAC-CGATCAGT

description: smart-seq2 protocol


title: Ex_vivo_megakaryocytic_Donor3_Day6 RNA-seq


title: Ex_vivo_megakaryocytic_Donor3_Day3  RNA-seq


title: GC071398_CTCCTTAC-ATGCGCAG

description: smart-seq2 protocol


title: Ex_vivo_megakaryocytic_Donor2_Day3 RNA-seq


title: Ex_vivo_megakaryocytic_Donor1_Day3 RNA-seq


title: GC071398_CTCCTTAC-ATCTCAGG

description: smart-seq2 protocol


title: Ex_vivo_megakaryocytic_Donor2_Day2  RNA-seq


title: Ex_vivo_megakaryocytic_Donor1_Day6 RNA-seq


title: Ex_vivo_megakaryocytic_Donor2_Day6  RNA-seq


title: GC071398_CTCCTTAC-CGTACTAG

description: smart-seq2 protocol


title: GC071398_CTCCTTAC-ACTGAGCG

description: smart-seq2 protocol


title: Ex_vivo_megakaryocytic_Donor1_Day1  RNA-seq


title: GC071398_CTAGTCGA-TGCAGCTA

description: smart-seq2 protocol


title: GC071398_CTCCTTAC-CTCTCTAC

description: smart-seq2 protocol


title: GC071398_CTCCTTAC-GCGTAGTA

description: smart-seq2 protocol


title: Ex_vivo_megakaryocytic_Donor2_Day0 RNA-seq


title: GC071398_CTCCTTAC-GGACTCCT

description: smart-seq2 protocol


title: GC071398_CTAGTCGA-TACGCTGC

description: smart-seq2 protocol


title: Ex_vivo_erythroid_Donor2_Day12 RNA-seq


title: GC071398_CTAGTCGA-GGAGCTAC

description: smart-seq2 protocol


title: GC071398_CTAGTCGA-GCGTAGTA

description: smart-seq2 protocol


title: GC071398_CTCCTTAC-TAAGGCGA

description: smart-seq2 protocol


title: Ex_vivo_erythroid_Donor1_Day12 RNA-seq


title: Ex_vivo_megakaryocytic_Donor3_Day1 RNA-seq


title: GC071398_CTCCTTAC-CGAGGCTG

description: smart-seq2 protocol


title: GC071398_CTCCTTAC-AGGCAGAA

description: smart-seq2 protocol


title: Ex_vivo_megakaryocytic_Donor2_Day4 RNA-seq


title: Ex_vivo_erythroid_Donor2_Day11 RNA-seq


title: GC071398_CTCCTTAC-ACTCGCTA

description: smart-seq2 protocol


title: GC071398_CTAGTCGA-CCTAAGAC

description: smart-seq2 protocol


title: Ex_vivo_erythroid_Donor3_Day10 RNA-seq


title: GC071398_CTCCTTAC-CCTAAGAC

description: smart-seq2 protocol


title: Ex_vivo_megakaryocytic_Donor2_Day1 RNA-seq


title: Ex_vivo_megakaryocytic_Donor3_Day4 RNA-seq


title: Ex_vivo_erythroid_Donor1_Day10 RNA-seq


title: GC071398_CTAGTCGA-ACTCGCTA

description: smart-seq2 protocol


title: GC071398_CTCCTTAC-CGGAGCCT

description: smart-seq2 protocol


title: Ex_vivo_megakaryocytic_Donor3_Day2 RNA-seq


title: GC071398_CTCCTTAC-AAGAGGCA

description: smart-seq2 protocol


title: Ex_vivo_megakaryocytic_Donor3_Day0 RNA-seq


title: Ex_vivo_megakaryocytic_Donor1_Day2 RNA-seq


title: GC071398_CTAGTCGA-TCGACGTC

description: smart-seq2 protocol


title: GC071398_CGGAGAGA-TCGACGTC

description: smart-seq2 protocol


title: GC071398_CGGAGAGA-TCCTGAGC

description: smart-seq2 protocol


title: Ex_vivo_erythroid_Donor1_Day9 RNA-seq


title: GC071398_CTAGTCGA-TAGCGCTC

description: smart-seq2 protocol


title: Ex_vivo_erythroid_Donor1_Day11 RNA-seq


title: Ex_vivo_erythroid_Donor2_Day8 RNA-seq


title: GC071398_CTAGTCGA-ACTGAGCG

description: smart-seq2 protocol


title: GC071398_CTAGTCGA-CGGAGCCT

description: smart-seq2 protocol


title: GC071398_CTAGTCGA-CGATCAGT

description: smart-seq2 protocol


title: Ex_vivo_erythroid_Donor3_Day11 RNA-seq


title: GC071398_CTAGTCGA-ATGCGCAG

description: smart-seq2 protocol


title: GC071398_CGGAGAGA-TAGCGCTC

description: smart-seq2 protocol


title: GC071398_CGGAGAGA-TACGCTGC

description: smart-seq2 protocol


title: Ex_vivo_erythroid_Donor3_Day7 RNA-seq


title: GC071398_CGGAGAGA-TAAGGCGA

description: smart-seq2 protocol


title: Ex_vivo_megakaryocytic_Donor1_Day0 RNA-seq


title: Ex_vivo_erythroid_Donor3_Day9 RNA-seq


title: GC071398_CGGAGAGA-TAGGCATG

description: smart-seq2 protocol


title: Ex_vivo_erythroid_Donor2_Day9 RNA-seq


title: Ex_vivo_erythroid_Donor3_Day6 RNA-seq


title: Ex_vivo_erythroid_Donor2_Day6 RNA-seq


title: Ex_vivo_erythroid_Donor2_Day7 RNA-seq


title: GC071398_CGGAGAGA-GGACTCCT

description: smart-seq2 protocol


title: GC071398_CGGAGAGA-TGCAGCTA

description: smart-seq2 protocol


title: Ex_vivo_erythroid_Donor2_Day10 RNA-seq


title: Ex_vivo_erythroid_Donor1_Day6 RNA-seq


title: GC071398_CGGAGAGA-GCGTAGTA

description: smart-seq2 protocol


title: GC071398_CGGAGAGA-GTAGAGGA

description: smart-seq2 protocol


title: Ex_vivo_erythroid_Donor3_Day8 RNA-seq


title: GC071398_CGGAGAGA-CTCTCTAC

description: smart-seq2 protocol


title: GC071398_CGGAGAGA-GCTCATGA

description: smart-seq2 protocol


title: GC071398_CGGAGAGA-CGTACTAG

description: smart-seq2 protocol


title: Ex_vivo_erythroid_Donor1_Day8 RNA-seq


title: GC071398_CGGAGAGA-GGAGCTAC

description: smart-seq2 protocol


title: Ex_vivo_erythroid_Donor1_Day7 RNA-seq


title: Ex_vivo_erythroid_Donor1_Day5 RNA-seq


title: GC071398_CGGAGAGA-CGGAGCCT

description: smart-seq2 protocol


title: Ex_vivo_erythroid_Donor2_Day4 RNA-seq


title: GC071398_CGGAGAGA-ATCTCAGG

description: smart-seq2 protocol


title: GC071398_CGGAGAGA-ATGCGCAG

description: smart-seq2 protocol


title: Ex_vivo_erythroid_Donor1_Day4 RNA-seq


title: Ex_vivo_erythroid_Donor3_Day3 RNA-seq


title: Ex_vivo_erythroid_Donor3_Day2 RNA-seq


title: GC071398_CGGAGAGA-CCTAAGAC

description: smart-seq2 protocol


title: Ex_vivo_erythroid_Donor1_Day3 RNA-seq


title: Ex_vivo_erythroid_Donor2_Day3 RNA-seq


title: Ex_vivo_erythroid_Donor2_Day5 RNA-seq


title: Ex_vivo_erythroid_Donor3_Day4 RNA-seq


title: GC071398_CGGAGAGA-ACTCGCTA

description: smart-seq2 protocol


title: Ex_vivo_erythroid_Donor1_Day2 RNA-seq


title: GC071398_CGGAGAGA-AAGAGGCA

description: smart-seq2 protocol


title: Ex_vivo_erythroid_Donor3_Day5 RNA-seq


title: Ex_vivo_erythroid_Donor3_Day1 RNA-seq


title: GC071398_ATTAGACG-TGCAGCTA

description: smart-seq2 protocol


title: GC071398_CGGAGAGA-ACTGAGCG

description: smart-seq2 protocol


title: GC071398_CGGAGAGA-AGGCAGAA

description: smart-seq2 protocol


title: GC071398_CGGAGAGA-CGAGGCTG

description: smart-seq2 protocol


title: GC071398_CGGAGAGA-CGATCAGT

description: smart-seq2 protocol


title: Ex_vivo_erythroid_Donor2_Day2 RNA-seq


title: GC071398_ATTAGACG-TAGGCATG

description: smart-seq2 protocol


title: GC071398_ATTAGACG-TCGACGTC

description: smart-seq2 protocol


title: Ex_vivo_erythroid_Donor3_Day0 RNA-seq


title: GC071398_ATTAGACG-GGAGCTAC

description: smart-seq2 protocol


title: Ex_vivo_erythroid_Donor2_Day1 RNA-seq


title: Ex_vivo_erythroid_Donor1_Day0 RNA-seq


title: CD19+/CD20+ B cells 4, scVDJ-seq

first: Aaron

middle: M

last: Newman

address: 265 Campus Drive

department: Department of Biomedical Data Science

data_processing:
Library strategy: VDJ-seq
The resulting scVDJ-seq data were mapped to reference “refdata-cellranger-vdj-GRCh38-altsensembl-4.0.0”.
The final clonotypes were downloaded from the Loupe VDJ browser versions 3.0.0 and 4.0.0 (10x Genomics).
Genome_build: hg38
Supplementary_files_format_and_content: Text file containing the following columns: cell barcode, BCR chain, CDR3 amino-acid sequence, CDR3 nucloeotide sequence, clonotype ID, flag indicating whether the clone is dominant or not.

source_name: Diffuse large B cell lymphoma

extract_protocol:
Sample was prepared using the Chromium Single Cell V(D)J Enrichment Kit, Human B Cell, and sequenced using Illumina HiSeq 4000
Chromium Single Cell V(D)J Enrichment Kit, Human B Cell, following manufacturer's protocol
Chromium Single Cell 5' Library Construction Kit, following manufacturer's protocol
Chromium Single Cell 5' Feature Barcode Library Kit, Chromium Single Cell A Chip Kit, Chromium i7 Multiplex Kit, following manufacturer's protocol

tag: patient

value: DLBCL

tag: diagnosis

value: ABC DLBCL

tag: coo

value: ABC

value: F


title: CD19+/CD20+ B cells 8, scRNA-seq

description: Sample was prepared using the Single Cell 5’ kit v1, sequenced using Illumina HiSeq 4000, and aligned using Cell Ranger v3.0

data_processing:
The resulting scRNA-seq data were processed with CellRanger (version 2.1, 3.0, and 5.0, 10x Genomics) and mapped to the hg38 reference genome.
Seurat (versions 3.0 and 4.0) was used to process the cell types.
After pre-processing, cell types were annotated in all four samples together (B cells and non-B cell samples for DLBCL007 and DLBCL111), with a clustering resolution parameter of 1.2 and 20 PCA dimensions. This step was repeated for two additional DLBCL samples that were analyzed in a separate batch (DLBCL002 and DLBCL008). Canonical marker genes were used to annotate B cells (MS4A1 and CD79B) and T cells (CD3D and CD3E), with T cells further divided into CD8 T cells (CD8A, CD8B) and CD4 T cells (CD4). Among the latter, follicular helper T cells were defined as the cluster showing highest expression of CXCL13 and regulatory T cells by the highest expression of FOXP3. Myeloid cells were defined by high expression of CD14, FCER1A, and/or FCGR3A and NKs by high expression of GLNY and NKG7 but not CD3D/E. FL and tonsil specimens were analyzed for each sample individually and annotated using the same set of genes listed above.
Genome_build: hg38
Supplementary_files_format_and_content: Matrix with raw gene counts for every gene and every cell
Supplementary_files_format_and_content: Tab-delimited text file including the cell annotations

source_name: Tonsil

extract_protocol:
Chromium Single Cell 5’ Library & Gel Bead Kit, Chromium Next GEM Single Cell 5’ Library & Gel Bead Kit v1.1, following manufacturer’s protocol
Chromium Single Cell 5’ Library Construction Kit following manufacturer’s protocol
Chromium Single Cell 5' Feature Barcode Library Kit, Chromium Single Cell A Chip Kit, Chromium i7 Multiplex Kit, following manufacturer's protocol

tag: tissue

value: Tonsil

tag: cell type

value: B cells

tag: age


title: GC071398_ATTAGACG-GCTCATGA

description: smart-seq2 protocol

tag: timepoint

tag: initially inactive x allele


title: Ex_vivo_erythroid_Donor2_Day0 RNA-seq


title: GC071398_ATTAGACG-TAGCGCTC

description: smart-seq2 protocol

value: iPSCs


title: GC071398_ATTAGACG-CGTACTAG

description: smart-seq2 protocol

value: Mus


title: Ex_vivo_erythroid_Donor1_Day1 RNA-seq


title: CD19-/CD20- non-B cells 6, scRNA-seq

description: Sample was prepared using the Single Cell 5’ kit v1, sequenced using Illumina HiSeq 4000, and aligned using Cell Ranger v2.1

source_name: Follicular lymphoma

value: FL

value: non-B cells

tag: Sex

value: M


title: GC071398_ATTAGACG-CGGAGCCT

description: smart-seq2 protocol

source_name: MEF to iPSC reprogramming timecourse


title: GC071398_ATTAGACG-TAAGGCGA

description: smart-seq2 protocol


title: CD19+/CD20+ B cells 2, scVDJ-seq

value: GCB DLBCL

value: GCB


title: CD19-/CD20- non-B cells 5, scRNA-seq


title: GC071398_ATTAGACG-CGAGGCTG

description: smart-seq2 protocol


title: GC071398_ATTAGACG-TACGCTGC

description: smart-seq2 protocol


title: GC071398_ATTAGACG-GGACTCCT

description: smart-seq2 protocol


title: GC071398_ATTAGACG-CCTAAGAC

description: smart-seq2 protocol


title: GC071398_ATTAGACG-AGGCAGAA

description: smart-seq2 protocol


title: GC071398_ATTAGACG-TCCTGAGC

description: smart-seq2 protocol


title: GC071398_ATTAGACG-ATCTCAGG

description: smart-seq2 protocol


title: CD19+/CD20+ B cells 2, scRNA-seq


title: GC071398_ATTAGACG-GCGTAGTA

description: smart-seq2 protocol


title: CD19-/CD20- non-B cells 8, scRNA-seq


title: K109019_RNASeq

city: Indianapolis

first: Natascia

last: Marino

state: IN

address: 980 W. Walnut St, R3-C238

department: Hematology/Oncology Division

institute: Indiana University School of Medicine

description:
transcriptome profile
K109019_RNASeq

data_processing:
The raw RNA-seq reads were cleaned using Trimmomatic version 0.36 (Bolger et al. 2014) setting the cutoff threshold for average base quality score at 20 over a window of 3 bases. Reads shorter than 20 bases post-trimming were excluded. (parameters: LEADING:20 TRAILING:20 SLIDINGWINDOW:3:20 MINLEN:20)
The cleaned reads were aligned to the human genome reference, GRCh38.p12 using STAR (version STAR_2.5.2b) (Dobin et al. 2013).
Individual gene expression was quantified by counting the number reads mapping to the exon regions of each of the annotated genes from gencode v.28 using featureCounts tool of subread package (version 2.0.0) (Liao et al. 2014). Those reads that mapped to antisense strand, or mapped to multiple regions on the genome or those reads that overlapped with multiple genes were excluded. (parameters: -s 2 -p -B -C)
Genome_build: GRCh38.p12
Supplementary_files_format_and_content: Wiggle files containing deduplicated insert coverage

source_name: Breast

growth_protocol: The breast tissue cores are collected by using a needle biopsy needle (Hologic, Marlborough, MA). The skin is cleaned, then numbed with lidocaine. The physician nicks the skin with a scalpel, usually in the upper-outer quadrant of the breast, and the needle is inserted into this incision. From this single incision, five sample cores are removed from the breast (approximately 200mg). A nurse/surgeon’s assistant holds pressure on the incision for 10 full minutes, then applies a pressure bandage. An ice pack is immediately placed on the breast. Within 10 min from collection the tissue cores are fresh frozen in liquid nitrogen

extract_protocol:
Total RNA was extracted using the Allprep DNA/RNA/miRNA Universal Kit (QIAGEN, Germantown, MD).
The concentration and quality of total RNA and DNA samples was first assessed using Agilent 2100 Bioanalyzer. For the RNAsequencing: cDNA library was prepared using the TruSeq Stranded Total RNA Kit (Illumina) and sequenced using Illumina HiSeq4000. For the DNA methylation analysis: Library was generated using MethylCap Library Kit (Diagenode, Denville NJ, US) according to the manufacturer′s protocols followed by single-end 75-bp sequencing on Illumina Nextseq4000

tag: age of menarche

tag: menopausal status

value: Pre

value: No

tag: blood relatives cancer

value: Yes

tag: race

value: WHITE

tag: hispanic

tag: bmi

tag: ever pregnant

tag: life time risk (tyrer-cuzick score)

tag: risk category

value: High


title: GC071398_ATTAGACG-ACTCGCTA

description: smart-seq2 protocol


title: GC071398_ATTAGACG-ACTGAGCG

description: smart-seq2 protocol


title: K109027_RNASeq

description:
transcriptome profile
K109027_RNASeq


title: CD19+/CD20+ B cells 5, scRNA-seq

tag: patient

tag: diagnosis


title: CD19+/CD20+ B cells 4, scRNA-seq

tag: tissue

value: DLBCL

value: ABC DLBCL

tag: coo


title: CD19+/CD20+ B cells 7, scRNA-seq

tag: cell type

value: tFL

tag: age


title: GC071398_ATAGCCTT-TCGACGTC

description: smart-seq2 protocol

tag: timepoint

tag: initially inactive x allele

value: Cast


title: CD19+/CD20+ B cells 6, scRNA-seq

value: B cells

tag: Sex


title: K108978_RNASeq

description:
transcriptome profile
K108978_RNASeq

tag: age of menarche

tag: menopausal status

value: Average


title: GC071398_ATTAGACG-CGATCAGT

description: smart-seq2 protocol

value: iPSCs

value: Mus


title: K108977_RNASeq (second donation from K106845)

description:
transcriptome profile
K108977_RNASeq

value: Post

tag: blood relatives cancer

tag: race


title: GC071398_ATTAGACG-GTAGAGGA

description: smart-seq2 protocol


title: GC071398_ATTAGACG-AAGAGGCA

description: smart-seq2 protocol


title: K108994_RNASeq

description:
transcriptome profile
K108994_RNASeq

tag: hispanic

tag: bmi


title: CD19-/CD20- non-B cells 7, scRNA-seq

value: FL

value: non-B cells

value: M


title: GC071398_ATAGCCTT-CGATCAGT

description: smart-seq2 protocol


title: GC071398_ATTAGACG-ATGCGCAG

description: smart-seq2 protocol


title: CD19-/CD20- non-B cells 2, scRNA-seq

value: GCB DLBCL

value: GCB

value: F


title: K108987_RNASeq

description:
transcriptome profile
K108987_RNASeq

value: No

value: Yes

value: WHITE

tag: ever pregnant

tag: life time risk (tyrer-cuzick score)


title: K109011_RNASeq

description:
transcriptome profile
K109011_RNASeq

tag: risk category

value: High


title: GC071398_ATAGCCTT-ATGCGCAG

description: smart-seq2 protocol


title: GC071398_ATTAGACG-CTCTCTAC

description: smart-seq2 protocol


title: GC071398_ATAGCCTT-GGAGCTAC

description: smart-seq2 protocol


title: GC071398_ATAGCCTT-TAGCGCTC

description: smart-seq2 protocol


title: CD19-/CD20- non-B cells 4, scRNA-seq

tag: patient

value: DLBCL

tag: diagnosis

value: ABC DLBCL

value: ABC


title: K108958_RNASeq

description:
transcriptome profile
K108958_RNASeq

value: Pre

value: AFRNAMER


title: shEZH2_rep1_C4-2.smallRNA

city: Boston

first: Yanqiang

state: MA

address: 300 Longwood Ave.

department: Cardiology Department

institute: Boston Children's Hospital

data_processing:
RNA-seq reads were mapped to the human reference genome hg19 using topHat[45]. Read counts of the annotated genes were obtained by the Python software HTSeq-count[46]. The edgeR package was used to identify differentially expressed genes (DEGs) from RNA-seq with two biological replicates[47]. Genes with at least 1.5-fold change in expression levels and false discovery rate (FDR) less than 0.05 were considered to be differentially expressed. The adaptor sequences in raw data were removed using cutadapt, then an all-in-one small noncoding RNA annotation pipeline AASRA was applied to process the mapping and count the raw count for each small noncoding RNA.
Genome_build: hg19
Supplementary_files_format_and_content: Tab-delimited text file include Reads Per Millinon(RPM) for 4 Samples of RNA-seq and smallRNA-seq seprately.

source_name: PCa cell lines C4-2

growth_protocol: Human PCa cell lines C4-2, was purchased from ATCC. The C4-2, shCTRL, shEZH2 and shCDCA8 cells were grown in RPMI 1640 medium supplemented with 10% FBS, while VCaP cells were grown in DMEM medium supplemented with 10% FBS and used within 20 passages after receipt. The cells were cultured in a 37°C incubator and a humidified atmosphere with 5% CO2.

extract_protocol:
Total RNA was isolated from cells using the RNA MiniPrep kit (Direct-zol, R2052, ZYMO Research) with the procedure provided by the manufacturer.  RNA libraries were prepared for sequencing using standard Illumina protocols
For RNA-seq, total RNA was isolated from cells using RNeasy Plus Mini Kit (Qiagen) and subjected to BGI for library preparation and sequencing using the DNBseq platform.For small RNA-seq, small RNA was extracted from cells using miRNeasy Mini Kit (Qiagen) and subjected to BGI for library preparation and sequencing using the DNBseq platform.

treatment_protocol: no

tag: transfection

tag: cell line


title: shCTRL_rep2_C4-2.smallRNA

value: shCTRL


title: GC071398_ATAGCCTT-CCTAAGAC

description: smart-seq2 protocol

value: Cast


title: GC071398_ATAGCCTT-GCGTAGTA

description: smart-seq2 protocol


title: shCTRL_rep1_C4-2.smallRNA


title: K108919_RNASeq

description:
transcriptome profile
K108919_RNASeq

tag: age

value: Post

value: Average


title: K108899_RNASeq (second donation from K106157)

description:
transcriptome profile
K108899_RNASeq

value: Don‚Äôt know


title: GC071398_ATAGCCTT-TGCAGCTA

description: smart-seq2 protocol

tag: timepoint


title: K108959_RNASeq

description:
transcriptome profile
K108959_RNASeq


title: shCDCA8_rep1_C4-2_RNA


title: shCTRL_rep2_C4-2_RNA


title: GC071398_ATAGAGAG-TGCAGCTA

description: smart-seq2 protocol

value: iPSCs

tag: initially inactive x allele

value: Mus


title: K108921_RNASeq (second donation from K106801)

description:
transcriptome profile
K108921_RNASeq


title: shCTRL_rep1_C4-2_RNA


title: K108912_RNASeq (second donation from K106507)

description:
transcriptome profile
K108912_RNASeq


title: LPS+ tlr4f/f-lysM-cre BMDM3

city: Hanghzou

first: Fuye

last: Yang

state: Zhejiang

address: 88 Jiefang Road

department: Nephrology

country: China

institute: Second Affiliated Hospital of Zhejiang University School of Medicine

data_processing:
Raw fastq sequences were treated with Trimmomatic tools(v 0.36) using the following options: : TRAILING: 20, MINLEN:235 and CROP:235, to remove trailing sequences below a phred quality score of 20 and to achieve uniform sequence lengths for downstream clustering processes.
Sequencing read quality was inspected using the FastQC software. Adapter removal and read trimming were performed using Trimmomatic. Sequencing reads were trimmed from the end (base quality less than Q20) and filtered by length (less than 25).
Paired-end reads were aligned to the mouse reference genome mm10 with HISAT2. HTSeq v0. 6.0 was used to count the reads numbers mapped to each gene. The whole samples expression levels were presented as RPKM (expected number of Reads PerKilobase of transcript sequence per Million base pairs sequenced), which is the recommended and most common method to estimate the level of gene expression.
Genome_build: mm10
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: LPS treated tlr4f/f-lysM-cre  bone marrow-derived macrophages

growth_protocol: The macrophages were differentiated from bone marrow cells by 50ng/ml M-CSF in DMEM/F12 medium with 10% FBS for 7 days.

extract_protocol:
Total RNA was isolated from BMDMs using the Trizol (invitrogen) according to the manufacturer’s protocol. RNA integrity was evaluated using the Agilent 2200 TapeStation (Agilent Technologies, USA) and each sample had the RIN above 7.0.Then, rRNAs were removed from total RNA using EpicentreRibo-Zero rRNA Removal Kit (illumina, USA) and fragmented to approximately 200bp. Subsequently, the purified RNAs were subjected to first strand and second strand cDNA synthesis following by adaptor ligation and enrichment with a low-cycle according to instructions of NEBNext® Ultra™ RNA Library Prep Kit for Illumina (NEB, USA).
The purified  library products were diluted to 10 pM for cluster generation in situ on the pair-end flow cell followed by sequencing (2×150 bp) using Illumina HiSeq  3000 platform.
PolyA RNA-Seq

treatment_protocol: The bone marrow-derived macrophages were further stimulated with 1µg/mL of LPS for additional 6 hours.

tag: strain

tag: cell type

value: primary bone marrow-derived macrophages

tag: genotype

tag: treatment

value: treated with LPS for 6 hours


title: K108895_RNASeq

description:
transcriptome profile
K108895_RNASeq

tag: age of menarche

tag: menopausal status

value: No

value: Yes

tag: blood relatives cancer

tag: race


title: GC071398_ATAGCCTT-ACTGAGCG

description: smart-seq2 protocol


title: GC071398_ATAGCCTT-ACTCGCTA

description: smart-seq2 protocol


title: GC071398_ATAGCCTT-TACGCTGC

description: smart-seq2 protocol


title: shEZH2_rep2_C4-2.smallRNA


title: K108928_RNASeq (second donation from K106620)

description:
transcriptome profile
K108928_RNASeq

tag: hispanic

tag: bmi

tag: ever pregnant

tag: life time risk (tyrer-cuzick score)


title: K108890_RNASeq (second donation from K105810)

description:
transcriptome profile
K108890_RNASeq

value: WHITE

tag: risk category


title: LPS+ tlr4f/f BMDM3

source_name: LPS treated tlr4f/f bone marrow-derived macrophages


title: LPS+ tlr4f/f BMDM2


title: K108874_RNASeq

description:
transcriptome profile
K108874_RNASeq


title: GC071398_ATAGAGAG-TAGCGCTC

description: smart-seq2 protocol


title: GC071398_ATAGAGAG-TCGACGTC

description: smart-seq2 protocol


title: K108883_RNASeq

description:
transcriptome profile
K108883_RNASeq

value: High


title: LPS- tlr4f/f-lysM-cre BMDM2

source_name: tlr4f/f-lysM-cre  bone marrow-derived macrophages

value: untreated


title: K108885_RNASeq

description:
transcriptome profile
K108885_RNASeq


title: shCDCA8_rep2_C4-2_RNA

tag: transfection

tag: cell line


title: LPS- tlr4f/f-lysM-cre BMDM1


title: GC071398_ATAGAGAG-TAAGGCGA

description: smart-seq2 protocol

tag: timepoint


title: LPS- tlr4f/f BMDM2

source_name: tlr4f/f bone marrow-derived macrophages


title: GC071398_ATAGAGAG-TCCTGAGC

description: smart-seq2 protocol

tag: initially inactive x allele


title: K108859_RNASeq (second donation from K106609)

description:
transcriptome profile
K108859_RNASeq

tag: age


title: K108865_RNASeq

description:
transcriptome profile
K108865_RNASeq


title: GC071398_ATAGCCTT-CGGAGCCT

description: smart-seq2 protocol


title: K108860_RNASeq (second donation from K105906)

description:
transcriptome profile
K108860_RNASeq


title: K108838_RNASeq

description:
transcriptome profile
K108838_RNASeq


title: K108879_RNASeq

description:
transcriptome profile
K108879_RNASeq


title: GC071398_ATAGAGAG-GGACTCCT

description: smart-seq2 protocol


title: GC071398_ATAGAGAG-GGAGCTAC

description: smart-seq2 protocol


title: K108587_RNASeq

description:
transcriptome profile
K108587_RNASeq

value: ASIAN


title: LPS+ tlr4f/f BMDM1

tag: strain

tag: cell type


title: GC071398_ATAGAGAG-GCTCATGA

description: smart-seq2 protocol


title: GSCLC_16_W4_1

city: Kyoto

first: Yukihiro

last: Yabuta

state: Kyoto

address: Yoshida-Konoe-cho, Sakyo-ku

department: Anatomy and Cell Biology

country: Japan

institute: Kyoto University, Graduate school of medicine

description: 3'-RNA-seq amplified from 1ng RNA

data_processing:
The processing of the 3-prime-sequencing data for calculating the gene-expression levels was performed as described previously (Nakamura et al., 2015).  In brief, all reads were processed with cutadapt v1.9.1 to remove adaptors and poly-A sequences.
The reads of 30-bp or longer were mapped onto a mouse transcript reference, ref_GRCm38.p6, using Tophat v2.0.11/Bowtie2 v2.2.7.  Read counts per gene were calculated using HTSeq v0.9.1 with the default settings.  Read counts were converted to read counts per million mapped reads (RPM) and used for the analysis.
Genome_build: GRCm38.p6
Supplementary_files_format_and_content: Tab-delimited text files include RPM values for each sample.

source_name: GSC-like cells

growth_protocol: Generation and Culture of Reconstituted Testes (rTestis)  To isolate E12.5 mouse male gonads (fetal testes), pregnant ICR females were sacrificed by cervical dislocation, and the embryos were isolated in chilled Dulbecco's Modified Eagle Medium (DMEM) (GIBCO, #10313-021) containing 10% FCS (Hyclone), 2 mM GlutaMAX (GIBCO, #35050-061), 10 mM HEPES (GIBCO, #15630-106), 100 U/mL penicillin, and 0.1 mg/mL streptomycin (GIBCO, 15070).  Fetal testes were identified by their appearance, and the mesonephroi were dissected out with tungsten needles.  The isolated fetal testes were dissociated into single cells, and endogenous mouse germ cells were selected out by magnetic-activated cell sorting (MACS).  Compared to FACS, MACS requires much less time and less physical stress to collect the cells for the rTestis formation.  The mPGCLCs (10,000 cells/well) and the fetal testes somatic cells (when using frozen stocks, 20,000 cells/well) (total 30,000 cells/well) were mixed and plated on the wells of a Nunclon Sphera 96-well Microplate (#174925; Thermo Fisher Scientific) and cultured under a floating condition in GK10+FR10 medium (GK10, 10 μM forskolin and 10 μM rolipram).  After a period of 2 days for the floating culture, using a glass capillary, the rTestes were transferred onto ThinCert™Cell Culture Inserts for 24-Well Plates (Greiner #662610) soaked in alpha-Minimum Essential Medium (GIBCO, #32561-037) containing 10% FCS (Hyclone), 55 μM 2-mercaptoethanol (GIBCO, 21985-023), 100 U/mL penicillin, and 0.1 mg/mL streptomycin (GIBCO, 15070).  Half the medium was changed every two days.  All rTestes were cultured for a gas-liquid interphase culture at 37℃ under an atmosphere of 5% CO2 in air.    Derivation of GSCLCs from rTestis  For the derivation of GSCLCs, VR+; CD9-APC+ cells in rTestes (m14) were sorted with a flow cytometer (BD Biosciences, FACS Aria Ⅲ).  For deriving GSCLCs from all VR+; CD9-APC+ cells/rTestis, 24-well culture dishes (Falcon, #353047) were coated with PBS supplemented with 0.1% gelatin for at least 30 min, seeded with mouse embryonic feeders (MEF) for at least 6 h prior to the plating of mPGCLC-derived cells, and then VR+; CD9-APC+ cells (derived from 1 rTestis)/well were seeded and cultured with GSCs/GSCLCs medium.  For deriving GSCLCs from single VR+; CD9-APC+ cells, 96-well culture dishes (Falcon, #353072) were coated with PBS supplemented with 0.1% gelatin for at least 30 min, then seeded with MMC-treated MEF for at least 6 h prior to the plating of an mPGCLC-derived cell.  A single VR+; CD9-APC+ cell was then seeded using a FACS Automated Cell Deposition Unit (ACDU) system and cultured with GSCs/GSCLCs medium.The GSC/GSCLC medium was as described previously (Kanatsu-Shinohara et al., 2003), with some modifications (Ishikura et al., 2016).  StemPro-34 SFM (GIBCO, #10639011) was supplemented with StemPro supplement (GIBCO, #10639011), 0.1 mM 2-mercaptoethanol (GIBCO, 21985-023), 1% FCS (Hyclone), 1 × minimal essential medium (MEM) Vitamin Solution (GIBCO, # 11120-052), 5.0 mg/mL AlbuMAXⅠ (GIBCO, #11020-021), 0.1 mM NEAA (GIBCO, #11140-050), 1 mM sodium pyruvate (GIBCO, 11360-070), 100 U/mL penicillin, 0.1 mg/mL streptomycin (GIBCO, #15070), 2 mM GlutaMAX (GIBCO, #35050-061), 1 × Insulin-Transferrin-Selenium (ITS-G) (GIBCO, #41400045), 10 ng/mL bFGF Recombinant Human Protein (Life Technologies, #13256029), 20 ng/mL GDNF Rat Recombinant (RSD, #512GF050), 20 ng/mL EGF Mouse Recombinant Carrier-free (RSD, #2028EG200), and 1000 U/mL LIF (Merk, ESG1107).  Half the medium was changed every two or three days.  All GSCs/GSCLCs were cultured at 37℃ under an atmosphere of 5% CO2 in air.

extract_protocol:
The cells were lysed and the total RNAs were purified using a NucleoSpin RNA XS (Takara Bio, #U0902A) according to the manufacturer’s instructions.  1 ng of total RNAs from each sample was used for the synthesis and amplification of cDNAs.
The cDNA synthesis was performed according to the single-cell 3 prime RNA-seq (SC3-seq) method described previously (Nakamura et al., 2015).  The cDNA libraries for Nextseq500 (Illumina) were constructed as described previously (Ishikura et al., 2016).The sequencing was performed on an Illumina Nextseq500/550 platform with a Nextseq500/550 Hiqh output kit (Illumina).

treatment_protocol: Isolation of Germ Cells  To isolate germ cells for the RNA-seq analysis, ICR females were crossed with C57BL/6N; mvh-RFPTg/Tg males.  The embryonic gonads/postnatal testis fragments at E12.5–P7.5 were dissociated into single cells by incubating with 0.05% Trypsin-EDTA (GIBCO, #15400-054) for 10 min at 37℃, and were quenched with an equal volume of DMEM medium (GIBCO, #10313-021) containing 10% FCS (Hyclone), 2 mM GlutaMAX (GIBCO, #35050-061), 100 U/mL penicillin, and 0.1 mg/mL streptomycin (GIBCO, #15070).  Large clumps of cells were removed using a nylon cell strainer (FALCON, #352350), and cells were centrifuged at 1,200 rpm for 5 min.  The cell pellet was re-suspended with DMEM/F12 medium (GIBCO, 1130-082) containing 0.1% BSA fraction V (Life Technologies, # 15260037), and sorted with a flow cytometer (BD Biosciences, FACS Aria Ⅲ)    Fluorescence-activated Cell Sorting (FACS)  The d4 floating aggregates of EpiLCs and d4c5 mPGCLCs were incubated in TrypLE express for 10 min at 37℃, with periodical pipetting, and the dissociates were quenched with a 5 × volume of DMEM/F12 medium (GIBCO, #1130-082) containing 0.1% BSA fraction V (Life Technologies, # 15260037) and DNase I (Sigma, DN25), followed by pipetting to generate a single cell suspension.  After centrifugation at 1,200 rpm for 5 min, the supernatant was discarded.  The cell pellet was re-suspended with DMEM/F12 medium (GIBCO, #1130-082) containing 0.1% BSA fraction V (Life Technologies, #15260037), the cell suspension was filtered through a nylon cell strainer (FALCON, #352350), and BV+ d4 mPGCLCs or BV+; SC+ d4c5 mPGCLCs were sorted by a flow cytometer (BD Biosciences, FACSAria III) and collected in the GK10+FR10 medium.  The rTestes at various culture periods were peeled off from the cell insert membrane using a P1000 pipette tip and incubated in 0.25% Trypsin-EDTA in PBS (GIBCO, #15400-054) for 5~15 min, with periodical intermittent pipetting, and the dissociates were quenched by an equal volume of DMEM medium (GIBCO, #10313-021) containing 10% FCS (Hyclone), 2 mM GlutaMAX (GIBCO, 35050-061), 100 U/mL penicillin, and 0.1 mg/mL streptomycin (GIBCO, 15070).  The resultant cell pellet was resuspended with PBS containing 0.1% BSA fraction V (Life Technologies, # 15260037), and large clumps of cells were removed using a nylon cell strainer (FALCON, #352350).  The BV+; SC+ and Ddx4/mvh-RFP-positive (BV+; SC+; VR+) cells (mPGCLC-derived cells in rTestes: m0, m3, m5, m7, m10), VR+ and CD9-APC-positive (VR+; CD9-APC+) cells (mPGCLC-derived cells in rTestes: m12, m14), and VR+ cells in embryonic gonads/postnatal testes were sorted by the FACSAria III (BD Biosciences) cell sorter, and were collected in CELLOTION (Nippon Zenyaku Kogyo, CB051).  For RNA/DNA extraction, the sorted cells were centrifuged at 500G for 10 min, and the cell pellets were frozen down by liquid N2, and preserved at −80℃.

tag: genotype

value: Acr-EGFPTg/0; Actin-EGFPTg/0

value: Germ cells derived from ESCs

tag: strtain

value: 129/SvJcl  x  C57BL/6


title: GC071398_ATAGAGAG-GTAGAGGA

description: smart-seq2 protocol

data_processing:
For non-allele resulotion analyses, reads were mapped to the mouse reference genome (mm10) using STAR 2.5.3a (Dobin et al. 2013) and GENCODE vM16 annotation file. Alignment was performed with default parameters and --sjdbOverhang set to 74 and output to sorted BAM files. Uniquely aligned reads were quantified using the featureCounts function from the R Bioconductor package “Rsubread” (version 1.5.2) (Liao et al. 2019).
For allele resolution analyses, reads processed as previously described in (Janiszewski, talon et al). Briefly, reads were mapped to the same reference genome release in which SNP positions were substituted by N base (referred to as N-masked mm10). N-masking was performed with SNPsplit software (Version 0.3.2 released (29-03-2017)) (Krueger and Andrews 2016) supplied with the list of strain-specific SNPs (129S1_SvImJ and CAST_EiJ) from Sanger Mouse Genomes project database (mgp.v5.merged.snps_all.dbSNP142.vcf.gz). N-masking was done in dual hybrid mode and resulted in the identification throughout the entire genome of 20,563,466 SNP positions unique for either strain, of which 634,730 on the X Chromosome. Next, reads were aligned to the N-masked mm10 genome using STAR 2.5.3a with parameters disabling soft-clipping of incompletely aligned reads (--alignEndsType EndToEnd --outSAMattributes NH HI NM MD). Reads aligned to the N-masked reference genome were then split into two BAM files containing only strain-specific reads (on average 10.95% for Mus and 10.25% for Cast of total mapped reads) using SNPsplit (version 0.3.4). Unclassified reads were not used for subsequent allele-specific analysis. Using the allelic BAM files, variant calling files (VCF) were generated using samtools’ mpilup command (version 1.7) (ref), and merged using bcftools (ref)(version 1.5). An allelic count matrix was created by retaining counts from SNP positions and annotating these positions with their respective genes, where only genes covered by 4 SNPs or more are kept. Allelic data was size factor normalised by dividing allele-specific gene counts by total counts of that cell, this was then multiplied by 10000 and log transformed.
Genome_build: mm10
Supplementary_files_format_and_content: smartseq_norm_counts.csv: text file containing normalized read counts
Supplementary_files_format_and_content: smartseq_annotation.xlsx: spreadsheet containing additional metadata information
Supplementary_files_format_and_content: loom_XCR_5runs.loom: loom file containing both expression and gene regulatory network data together with tSNE embeddings

extract_protocol:
For the isolation of Day 0 time point of single-cell transcriptome analysis, 96 Xi-GFP cells were sorted into a 96-well multiwell plate with 2 µl lysis buffer, followed by initial steps of smart-seq2 protocol (see below). Remaining cells were plated for reprogramming directly after sorting, 50.000 cells per one well of a 12 well plate. Reprogramming was induced by doxycycline (2 μg/ml final) in mouse ESC medium in the presence of ascorbic acid (50 μg/ml final). The medium together with doxycycline and ascorbic acid was replaced every two days and maintained throughout entire reprogramming experiments. To derive iPSCs from picked colonies, the same conditions were used with dox and AA withdrawal after picking. Next, FUT4+ reprogramming intermediates were sorted into single wells, each with 2 µl of the lysis buffer [0,2% Triton X100, 1:20 RRI (Recombinant RNase Inhibitor Takara)] and snap-frozen in -80°C until cells from all timepoints were collected.
All samples were processed following the smart-seq2 protocol (Picelli et al). cDNA synthesis was done starting from 500 pg of input RNA, followed by library preparation from 80 pg of cDNA using the Nextera XT kit (Illumina, FC-131-1096). Indexing was performed with the Nextera XT index Kit V2 (Illumina, FC-131-2003). The quality of cDNA and individual libraries was assessed using an Agilent 2100 Bioanalyzer system.


title: LPS+ tlr4f/f-lysM-cre BMDM1

tag: treatment


title: LPS+ tlr4f/f-lysM-cre BMDM2


title: GC071398_ATAGAGAG-GCGTAGTA

description: smart-seq2 protocol


title: LPS- tlr4f/f BMDM1


title: GSCLC_16_W1_2

description: 3'-RNA-seq amplified from 1ng RNA


title: GC071398_ATAGAGAG-TAGGCATG

description: smart-seq2 protocol


title: GSCLC_16_W1_1

description: 3'-RNA-seq amplified from 1ng RNA


title: LPS- tlr4f/f BMDM3


title: GC071398_ATAGAGAG-CGTACTAG

description: smart-seq2 protocol


title: LPS- tlr4f/f-lysM-cre BMDM3


title: K108518_RNASeq

description:
transcriptome profile
K108518_RNASeq

tag: age of menarche

tag: menopausal status

value: Pre

tag: blood relatives cancer

value: AFRNAMER


title: GC071398_ATAGAGAG-TACGCTGC

description: smart-seq2 protocol


title: K108501_RNASeq (second donation from K107244)

description:
transcriptome profile
K108501_RNASeq

tag: race

tag: hispanic

tag: bmi

value: Average


title: GSCLC_16_W2_1

description: 3'-RNA-seq amplified from 1ng RNA


title: GSCLC_S3_1

description: 3'-RNA-seq amplified from 1ng RNA


title: GSCLC_S3_2

description: 3'-RNA-seq amplified from 1ng RNA


title: K108206_RNASeq

description:
transcriptome profile
K108206_RNASeq

value: Post

tag: ever pregnant

tag: life time risk (tyrer-cuzick score)

tag: risk category


title: K108839_RNASeq

description:
transcriptome profile
K108839_RNASeq


title: GSCLC_S2_1

description: 3'-RNA-seq amplified from 1ng RNA


title: GSCLC_S4_2

description: 3'-RNA-seq amplified from 1ng RNA


title: K108433_RNASeq

description:
transcriptome profile
K108433_RNASeq


title: GSCLC_S1_2

description: 3'-RNA-seq amplified from 1ng RNA


title: GC071398_ATAGAGAG-CTCTCTAC

description: smart-seq2 protocol

tag: timepoint


title: GSCLC_16_W4_2

description: 3'-RNA-seq amplified from 1ng RNA


title: GSCLC_16_W2_2

description: 3'-RNA-seq amplified from 1ng RNA


title: K108482_RNASeq

description:
transcriptome profile
K108482_RNASeq


title: K108168_RNASeq

description:
transcriptome profile
K108168_RNASeq


title: K108301_RNASeq

description:
transcriptome profile
K108301_RNASeq

value: AMINALNA


title: GC071398_ATAGAGAG-ATGCGCAG

description: smart-seq2 protocol

value: iPSCs

tag: initially inactive x allele

value: Mus


title: K108158_RNASeq

description:
transcriptome profile
K108158_RNASeq

tag: age


title: GC071398_ATAGAGAG-ATCTCAGG

description: smart-seq2 protocol


title: GC071398_ATAGAGAG-CGGAGCCT

description: smart-seq2 protocol


title: GSCLC_S2_2

description: 3'-RNA-seq amplified from 1ng RNA


title: K108194_RNASeq

description:
transcriptome profile
K108194_RNASeq


title: GSCLC_W1_2

description: 3'-RNA-seq amplified from 1ng RNA


title: GC071398_ATAGAGAG-CGAGGCTG

description: smart-seq2 protocol


title: GSCLC_W1_1

description: 3'-RNA-seq amplified from 1ng RNA


title: GSCLC_S4_1

description: 3'-RNA-seq amplified from 1ng RNA


title: GC071398_ATAGAGAG-AGGCAGAA

description: smart-seq2 protocol


title: GSC1_1

description: 3'-RNA-seq amplified from 1ng RNA

source_name: GSCs

value: Germ cells


title: GSCLC_W4_1

description: 3'-RNA-seq amplified from 1ng RNA


title: GSCLC_W2_2

description: 3'-RNA-seq amplified from 1ng RNA


title: GSCLC_S1_1

description: 3'-RNA-seq amplified from 1ng RNA


title: GC071398_ATAGAGAG-CGATCAGT

description: smart-seq2 protocol


title: K108059_RNASeq (second donation from K107241)

description:
transcriptome profile
K108059_RNASeq

value: No


title: K108129_RNASeq

description:
transcriptome profile
K108129_RNASeq

value: Yes


title: GSCLC_W3_2

description: 3'-RNA-seq amplified from 1ng RNA


title: GSCLC_W2_1

description: 3'-RNA-seq amplified from 1ng RNA


title: m10_1

description: 3'-RNA-seq amplified from 1ng RNA

source_name: Spermatogonia like cells

value: B6C3(Cg) × C57BL/6


title: K108105_RNASeq

description:
transcriptome profile
K108105_RNASeq

value: High


title: GC071398_AGGCTTAG-TGCAGCTA

description: smart-seq2 protocol


title: GSCLC_W3_1

description: 3'-RNA-seq amplified from 1ng RNA


title: K108074_RNASeq

description:
transcriptome profile
K108074_RNASeq


title: GSC1_2

description: 3'-RNA-seq amplified from 1ng RNA


title: m14_2

description: 3'-RNA-seq amplified from 1ng RNA


title: GSCLC_W4_2

description: 3'-RNA-seq amplified from 1ng RNA


title: m7_2

description: 3'-RNA-seq amplified from 1ng RNA

source_name: Prospermatogonia like cells


title: m10_2

description: 3'-RNA-seq amplified from 1ng RNA


title: m14_1

description: 3'-RNA-seq amplified from 1ng RNA


title: GC071398_ATAGAGAG-CCTAAGAC

description: smart-seq2 protocol


title: GC071398_ATAGAGAG-ACTCGCTA

description: smart-seq2 protocol


title: GC071398_ATAGAGAG-ACTGAGCG

description: smart-seq2 protocol


title: K108015_RNASeq

description:
transcriptome profile
K108015_RNASeq

value: WHITE


title: GC071398_AGGCTTAG-TCCTGAGC

description: smart-seq2 protocol


title: K108035_RNASeq

description:
transcriptome profile
K108035_RNASeq


title: K108078_RNASeq

description:
transcriptome profile
K108078_RNASeq


title: m3_2

description: 3'-RNA-seq amplified from 1ng RNA


title: m12_1

description: 3'-RNA-seq amplified from 1ng RNA


title: GC071398_AGGCTTAG-TCGACGTC

description: smart-seq2 protocol


title: K107980_RNASeq

description:
transcriptome profile
K107980_RNASeq

value: ASIAN


title: m0_2

description: 3'-RNA-seq amplified from 1ng RNA


title: m0_1

description: 3'-RNA-seq amplified from 1ng RNA


title: m5_2

description: 3'-RNA-seq amplified from 1ng RNA


title: m7_1

description: 3'-RNA-seq amplified from 1ng RNA


title: d4c5_1

description: 3'-RNA-seq amplified from 1ng RNA

source_name: PGC like cells


title: K107928_RNASeq

description:
transcriptome profile
K107928_RNASeq


title: d4c5_2

description: 3'-RNA-seq amplified from 1ng RNA


title: GC071398_AGGCTTAG-TAGCGCTC

description: smart-seq2 protocol


title: K108029_RNASeq

description:
transcriptome profile
K108029_RNASeq


title: GC071398_ATAGAGAG-AAGAGGCA

description: smart-seq2 protocol


title: m12_2

description: 3'-RNA-seq amplified from 1ng RNA


title: K107894_RNASeq (second donation from K107266)

description:
transcriptome profile
K107894_RNASeq

value: Don‚Äôt know


title: m5_1

description: 3'-RNA-seq amplified from 1ng RNA

value: Germ cells derived from ESCs


title: GC071398_AGGCTTAG-TACGCTGC

description: smart-seq2 protocol


title: m3_1

description: 3'-RNA-seq amplified from 1ng RNA


title: K107981_RNASeq

description:
transcriptome profile
K107981_RNASeq


title: GC071398_AGGCTTAG-TAGGCATG

description: smart-seq2 protocol


title: GC071398_AGGCTTAG-TAAGGCGA

description: smart-seq2 protocol


title: d4_2

description: 3'-RNA-seq amplified from 1ng RNA


title: P3_2

description: 3'-RNA-seq amplified from 1ng RNA

source_name: Spermatogonia

value: ICR x B6C3(Cg)B6F1(5N)


title: P3_1

description: 3'-RNA-seq amplified from 1ng RNA


title: P7_2

description: 3'-RNA-seq amplified from 1ng RNA


title: P1_1

description: 3'-RNA-seq amplified from 1ng RNA


title: GC071398_AGGCTTAG-GGAGCTAC

description: smart-seq2 protocol


title: d4_1

description: 3'-RNA-seq amplified from 1ng RNA


title: P7_1

description: 3'-RNA-seq amplified from 1ng RNA


title: K107962_RNASeq

description:
transcriptome profile
K107962_RNASeq

value: Pre


title: K107964_RNASeq

description:
transcriptome profile
K107964_RNASeq


title: GC071398_AGGCTTAG-GTAGAGGA

description: smart-seq2 protocol


title: GC071398_AGGCTTAG-CGTACTAG

description: smart-seq2 protocol


title: K107863_RNASeq (second donation from K105898)

description:
transcriptome profile
K107863_RNASeq