title: B1a Cic KO rep1 (IgKL)

city: Pohang-Si

first: Hyebeen

last: Hong

address: Cheongam-Ro, 77

department: Department of Life Science

institute: POSTECH

data_processing:
1) Sequence reads were de-multiplexed according to the barcode sequences.
2) Pooled sequence reads were trimmed according to their base qualities with a 2-base sliding window. If either quality value in this window is lower than 20, this sequence stretches from the window to 3’ end were trimmed out from the original read.
3) Trimmed pair-end reads were joined together through overlapping alignment with a modified Needleman-Wunsch algorithm.
4) Using a Smith-Waterman algorithm, the merged reads were mapped to germline V, D, and J reference sequences downloaded from the IMGT database.
Genome_build: Reference sequences downloaded from the IMGT database (http://www.imgt.org/).
Supplementary_files_format_and_content: Non-templated (N) nucleotide addition distributions from each sample are shown in (5 digits)_1_Naddition files. V usages and their distributions from each sample are shown in (5 digits)_V_1_usage files. The first 5 digits of the file name are the unique number of the sample, and the sample for each number is as follows: 85699: Heavy chain of B1a Control rep1, 85669: k chain of B1a Control rep1, 85665: l of B1a Control rep1, 85698: Heavy chain of B1a Control rep2, 85668: k chain of B1a Control rep2, 85664: l of B1a Control rep2, 85697: Heavy chain of B1a Cic KO rep1, 85675: k chain of B1a Cic KO rep1, 85667: l of B1a Cic KO rep1, 85696: Heavy chain of B1a Cic KO rep2, 85670: k chain of B1a Cic KO rep2, 85666: l of B1a Cic KO rep2.

source_name: B-1a cell

extract_protocol:
Peritoneal cavity B-1a cells (IgM+, CD19+, CD5+, CD43+) were isolated by FACS-sorting using a MoFlo-XDP (Beckman Coulter). Total RNA was extracted using TRIzol Reagent (GeneAll, Seoul, Republic of Korea) according to the manufacturer's protocol.
Long Read iR-Profile Reagent System (iRepertoire) was used to generate NGS libraries covering BCR chains including Igh, Igk, and Igl. Briefly, nested inside and outside primers selectively amplified all V- and C- regions and incorporated communal adaptors. Following clean up, only target amplicons, which contain 5’ and 3’ communal adaptors, were exponentially amplified.

value: Peritoneal cavity B-1a cells

tag: age

value: 12 weeks


title: B1a Cic KO rep2 (IgH)

status: Public on Dec 16 2021

type: SRA

country: South Korea

library_source: transcriptomic

molecule: total RNA

organism: Mus musculus

tag: strain

tag: genotype

tag: cell type


title: 170kb Enhancers + SynHoxA assemblon in HoxA -/- mESCs, 48h of RA differentiation, Hi-C

city: Seattle

first: Sudarshan

last: Pinglay

state: WA

address: 3720 15th Ave NE

country: USA

institute: University of Washington

library_source: genomic

data_processing:
Basecalling was performed by the NovaSeq 6000 instrument (RTA Version 3.4.4) and the fastq files were generated using the bcl2fastq2 Conversion software (v2.20).
Alignment: Hi-C data was aligned against the custom mm10_synHoxA_delHoxA genome using BWA mem (version 0.7.17) using parameters -M -t 4 and aligning each mate pair independently. Samtools (version 1.11) was used to sort mapped reads by read name, and the pair_reads.py script in mHiC was used to join mate-pairs into a paired-end SAM file. Paired-end read counts were then binned at 10kbp resolution to create the genome-wide contact matrix.
The TAD calls displayed were produced using HiCseg (version 1.1). The HiCseg_linkC_R function in HiCseg was provided with the segment of the 10kbp-resolution contact matrix corresponding to coordinates chrX:43000000-63000000 (mm10_synHoxA_delHoxA custom genome), and the following parameters: nb_change_max=100, distrib="G", model="D". The heatmap was then plotted at coordinates chrX:52400000-53600000 and chrX:52800000-53300000, with maximum color intensity set at a contact frequency of 40.
Genome_build: mm10_synHoxA_delHoxA custom genome

molecule: genomic DNA

source_name: ES-derived embryoid bodies with variant synthetic Hox clusters

growth_protocol: mESCs were cultured on plastic tissue culture plates coated with 0.1% gelatin (EMD Millipore ES-006-B) at 37°C and 5% CO2 in ‘80/20’ medium comprising 80% 2i medium and 20% mESC medium. mESCs were grown at 37°C and 8% CO2 before differentiation experiments.  2i medium was made from a 1:1 mix of Advanced DMEM/F12 (Gibco 12634010) and Neurobasal-A (Gibco 10888022), containing 1X N-2 supplement (Gibco 17502048), 1X B-27 supplement (Gibco 17504044), 2mM Glutamax (Gibco 35050061), 0.1mM Beta-Mercaptoethanol (Gibco 31350010), 103 units/mL LIF (Millipore, ESG1107), 1 μM MEK1/2 inhibitor (Stemgent, PD0325901), and 3 μM GSK3 inhibitor (R&D Systems, CHIR99021). mESC medium was made from Knockout DMEM (Gibco 10829018), containing 15% Fetal Bovine Serum (Gemini), 0.1 mM Beta-Mercaptoethanol (Gibco 31350010), 1X MEM Non Essential Amino Acids (Gibco 11140050), Glutamax (Gibco 35050061), 1X Nucleosides (Millipore ES-008-D) and LIF (Millipore ESG1107).

extract_protocol:
Cells were collected at 0h and 48h after RA treatment. Cells were divided into ~1x106 aliquots and crosslinked in a final concentration of 2% FA (vol/vol) in 1 × PBS for 10 min at room temperature. After quenching with Glycine, cells incubated on ice for 15 min, pelleted by centrifugation at 500 g, and frozen at -80°C.
Hi-C was performed using the Arima-HiC workflow (Arima Genomics, San Diego, CA) by NYU Langone's Genome Technology Center (RRID: SCR_017929).

treatment_protocol: Trypsinized (Gibco) mESCs were plated in AK medium (Advanced DMEM/F12:Neurobasal (1:1) medium (Gibco), 7% KnockOut SR (vol/vol) (Gibco), 2 mM L-glutamine, 0.1 mM ß-mercaptoethanol and penicillin–streptomycin (Gibco)) to induce formation of embryoid bodies (EBs), at 37°C, 5% CO2. 3.5x105 cells were plated in 100 mm suspension plates (Corning) for RNA-seq experiments, while 3.5x106 cells were plated in 245 mm x 245 mm square plates (Corning) for ChIP-seq experiments. After 2 days (0h timepoint), the EBs were split 1:2 and plated in fresh AK medium supplemented with 1 μM all-trans retinoic acid (RA) and 0.5 μM smoothened agonist (SAG) (Millipore 566660).

tag: treatment

value: 48h of RA differentiation

value: Embryoid Bodies


title: B1a Cic KO rep1 (IgH)


title: GK3R91-GIL2: Wt_Small Intestine_GFPlo_2

city: Vari

first: Vasiliki

last: Koliaraki

state: Attiki

address: 34 Fleming street

country: Greece

institute: BSRC "Alexander Fleming"

description:
processed data file: metaseqr_all_out_TI_vs_GIL.txt
processed data file: metaseqr_all_out_UI_vs_GIL.txt
processed data file: metaseqr_all_out_GIH_vs_GIL.txt

data_processing:
The sample GK3R96-UI1 was excluded from analysis, because it did not match the quality control criteria.
The RNA-Seq FASTQ files obtained after Ion Proton sequencing were mapped using TopHat2 [Kim2013], with default settings and using additional transcript annotation data for the mm10 genome from Illumina iGenomes (https://support.illumina.com/sequencing/sequencing_software/igenome.html). According to the Ion Proton manufacturers recommendation, the reads which remained unmapped were submitted to a second round of mapping using Bowtie2 [Langmead2012] against the mm10 genome with the --very-sensitive switch turned on and merged with the initial mappings.
The raw bam files were summarized to read counts table using the Bioconductor package GenomicRanges.
The gene counts table was normalized for inherent systematic or experimental biases using the Bioconductor package DESeq after removing genes that had zero counts over all the RNA-Seq samples.
The resulting gene counts table was subjected to differential expression analysis using the Bioconductor package DESeq.
All the above were performed through the Bioconductor package metaseqr.
Differential expression analysis files were subjected to additional filtering by removing the genes that had less than three natural normalized read counts in more than four samples.
Genome_build: mm10
Supplementary_files_format_and_content: txt (tab separated) files containing all the results from metaseqr analysis including expression per replicate, fold change compared to control and p-values.

source_name: Intestinal Mesenchymal Cells

extract_protocol:
Intestinal mesenchymal cells were isolated as previously described (Koliaraki et al., 2015) and total RNA was extracted using RNAeasy Mini kit (QIAGEN), according to the manufacturer's instructions.
The quantity and quality of RNA samples from sorted cells were analyzed using the bioanalyzer form Agilent in combination with the Agilent RNA 6000 Nano. RNA samples with RNA Integrity Number (RIN) > 7 were further used for library preparation using the 3’ mRNA-Seq Library Prep Kit Protocol for Ion Torrent (QuantSeq-LEXOGEN™) according to manufacturer’s instructions. The quantity and quality of libraries were assessed using the DNA High Sensitivity Kit in the bioanalyzer, according to the manufacturer’s instructions (Agilent Technologies). Libraries were subsequently pooled and templated using the Ion PI IC200 Chef Kit (ThermoFisher Scientific) on an Ion Proton Chef instrument or Ion OneTouch System. Sequencing was performed using the Ion PI™ Sequencing 200 V3 Kit and Ion Proton PI™ V2 chips (ThermoFisher Scientific) on an Ion Proton™ System, according to the manufacturer's instructions.
3’ RNA-Seq (QuantSeq)

treatment_protocol: DSS-induced colitis was performed as previously described (Wirtz et al., 2017)

value: ColVI-cre, Rosa mTmG

tag: tissue

value: Small Intestine

value: Intestinal Mesenchymal Cells

tag: cell isolation

value: Fresh isolation

tag: disease model


title: 170kb Enhancers + SynHoxA assemblon in HoxA -/- mESCs, 0h of RA differentiation, Hi-C

value: 0h of differentiation


title: B1a Control rep2 (IgKL)


title: B1a Control rep2 (IgH)


title: GK3R90-GIL1: Wt_Small Intestine_GFPlo_1


title: GK3R89-GIH3: Wt_Small Intestine_GFPhi_3

description:
processed data file: metaseqr_all_out_TI_vs_GIH.txt
processed data file: metaseqr_all_out_UI_vs_GIH.txt
processed data file: metaseqr_all_out_GIH_vs_GIL.txt


title: 134kb SynHoxA assemblon in HoxA -/- mESCs, 48h of RA differentiation, Hi-C


title: 130kb RARE∆ SynHoxA assemblon in WT mESCs, 24h of RA+SAG differentiation, replicate 1, RNA-Seq

description:
pSP0328_WT_#C4_24hRA/SAG_rep1
featurecounts_WTlines_synHoxAWTaligned.txt
HKLHFDRXX_n01_mb309

data_processing:
Basecall conversion to fastq files was performed using Picard
Alignment: Fastq files were aligned to the genome (mm10_synHoxA or mm10_synHoxA_delHoxA custom genomes) using HISAT2, using options: -p 20 -q --rna-strandness F.
Computing Abundance: Mapped reads were assigned to annotated genes using the featureCount function in Rsubread, using options -s 2.
Differential gene expression analysis: Read counts were normalized using the ‘rlog’ or regularized log transformation in DESeq2 and used as inputs for the Principal Component Analysis (PCA). The log2 fold change (FC) and adjusted p-value in gene expression levels between 24h, 48h, and 96h vs. 0h was estimated using DESeq2 and plotted using ggplot. Normalized counts from DESeq2 were used to generate transgene/endogenous ratio plots, with the counts from endogenous locus being reduced by half to normalize the copy number between HoxA clusters. RNAseq track visualization was performed using combine tracks tool in IGV on bigwigs generated with deeptools bamCoverage and subsequent editing in Adobe Illustrator.
Genome_build: mm10_synHoxA or mm10_synHoxA_delHoxA custom genomes
Supplementary_files_format_and_content: Tab Separated Text File: Unnormalized Read Counts at annotated genes

molecule: polyA RNA

extract_protocol:
Cells were collected at 0h or 24h, 48h, or 96h after RA/SAG treatment. RNA was extracted with the TRIzol LS Reagent (Life Technologies) followed by purification with the RNAeasy mini kit (Qiagen). RNA integrity was checked with the Agilent High Sensitivity RNA Screentape (Agilent, 5067-5579).
500 ng of RNA was used to prepare libraries and spiked-in with ERCC Exfold Spike-in mixes (Thermo Fisher 4456739). The TruSeq Stranded mRNA Library Preparation kit (Illumina 20020594) was used to prepare RNA-seq libraries. Library size was checked on the High Sensitivity DNA ScreenTape (Agilent 5067-5584). The KAPA library amplification kit was used to quantify libraries on the Bio-Rad CFX96 or the Roche Lightcycler 480 before pooling libraries. Libraries were sequenced on the Illumina NextSeq 500 using V2.5 chemistry (75 cycles, single-end 75 bp) or on the Illumina NovaSeq 6000 using the SP Reagent Kit (100 cycles, single-end 100bp) at the Genomics Core Facility at NYU.

treatment_protocol: Trypsinized (Gibco) mESCs were plated in AK medium (Advanced DMEM/F12:Neurobasal (1:1) medium (Gibco), 7% KnockOut SR (vol/vol) (Gibco), 2 mM L-glutamine, 0.1 mM ß-mercaptoethanol and penicillin–streptomycin (Gibco)) to induce formation of embryoid bodies (EBs), at 37°C, 5% CO2. 3.5x105 cells were plated in 100 mm suspension plates (Corning) for RNA-seq experiments, while 3.5x106 cells were plated in 245 mm x 245 mm square plates (Corning) for ChIP-seq experiments. After 2 days (0h timepoint), the EBs were split 1:2 and plated in fresh AK medium supplemented with 1 μM all-trans retinoic acid (RA) and 0.5 μM smoothened agonist (SAG) (Millipore 566660). For CHIR differentiation, in place of RA/SAG, CHIR99021 was added at 3 µM concentration

value: 130kb RARE{delta} SynHoxA assemblon in WT mESCs

value: 24h of RA+SAG differentiation


title: B1a Control rep1 (IgH)


title: GK3R92-GIL3: Wt_Small Intestine_GFPlo_3


title: B1a Control rep1 (IgKL)


title: 5-6h wt embryos RNA-seq replicate 1

city: Beijing

first: Guoqiang

last: Zhang

address: 1 Beichen West Road, Chaoyang District

country: China

institute: INSTITUTE OF ZOOLOGY, CHINESE ACADEMY OF SCIENCES

data_processing:
For RNA-seq amd  Fmr1 RIP-seq, the reads were mapped to the reference genome of Drosophila melanogaster (Release 6/dm6) with TopHat version 2.0.Differential expression analysis was carried out by cuffdiff.
For MeRIP (m6A)-seq, reads were processed using Cutadapt software with the parameter "cutadapt -m 20 -q 15 -a AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC -A AGATCGGAAGAGCA -U 3", then the  clean reads were aligned to the Drosophila genome (version dm6) using HISAT2. MACS2 software was used for m6A peak calling with the default options except for "-no modle".
Genome_build: dm6
Supplementary_files_format_and_content: bed file of the callpeak result. Txt files for the FPKM value of RNA-seq and FMR1 RIP-seq

organism: Drosophila melanogaster

source_name: w1118 embryo

extract_protocol:
Total RNAs were isolated from embryos at the indicated stages using TRIzol reagent (Thermo Fisher). The mRNAs were purified using a NEBNext Poly(A) mRNA Magnetic Isolation kit (NEB) according to the user manual. The MeRIP-Seq was performed by Cloudseq Biotech Inc. (Shanghai, China) . Briefly, 5 ug of fragmented mRNAs were incubated with 5 ug of anti m6A polyclonal antibody (millipore) in IP buffer (150 mM NaCl, 10 mM Tris–HCl, 0.1% NP-40, pH 7.4) for 2 h at 4°C. The mixture was then immunoprecipitated by incubation with protein-A beads (Thermo Fisher) at 4◦C for an additional 2 h. Beads with captured RNA fragments were then immediately washed 3 times with 500 μl of ice-cold IP buffer. Bound mRNAs were eluted from the beads with N6-methyladenosine (BERRY & ASSOCIATES, PR3732) in IP buffer and then extracted with Trizol reagent (Thermo Fisher).
To RNA-seq and RIP-seq,  Illumina Truseq libraries were constructed according to the manufacturer’s instructions and sequenced using NovaSeq platform. with paired end read length of 150 bp. RNA-seq library generation with NEBNext® Ultra II Directional RNA Library Prep Kit (New England Biolabs, Inc., USA). MeRIP-Seq Library sequencing was performed on an illumina Hiseq instrument with 150bp paired-end reads.

tag: background strain

value: wildtype

value: embryo


title: 5-6h M-,Z+ fmr1 mutant embryos RNA-seq replicate 2

source_name: w1118 embryo  M-,Z+ Fmr1 mutant

value: w1118, M-,Z+ Fmr1 mutant


title: B1a Cic KO rep2 (IgKL)


title: 5-6h M-,Z+ fmr1 mutant embryos RNA-seq replicate 1


title: 166kb Enhancers + RARE∆ SynHoxA assemblon in HoxA -/- mESCs, 96h of RA+SAG differentiation, replicate 1, H3K27ac ChIP

data_processing:
Basecall conversion to fastq files was performed using Picard
Alignment: Fastq files were aligned to the mm10_synHoxA_delHoxA custom genome using Bowtie 2, using options -p 20. Samtools was used to create sorted bam files for inputs into the bamCoverage tool from deeptools to create bigWig files, using options: --binSize 1 --scaleFactor 0.001 --normalizeUsingRPKM --ignoreForNormalization chrX -p max --extendReads 100.
Sliding windows: To generate sliding window plots of ChIP-seq signal, bedtools makewindows was used to generate bins of 3kb sliding 300 bp. Bedtools coverage was then used to compute the mean coverage in each bin from the sorted bam files. Coverage was normalized across samples using RPKM that was calculated as: reads-per-bin/(number of mapped reads (in millions) * bin length (kb)). Mean value and standard deviation of replicates was then plotted using Python matplotlib.
Genome_build: mm10_synHoxA_delHoxA custom genome

extract_protocol:
Cells were collected at 0h or 24h, 48h, or 96h after RA/SAG treatment. Cells were crosslinked at room temperature in 1 mM DSG (ProteoChem) for 15 min, followed by the addition of 1% FA (vol/vol) for 15 min. The reaction was quenched with Glycine and cells were washed with 1 × PBS. Samples were divided into ~25-30x106 cell aliquots, pelleted by centrifugation at 275 g, and frozen at -80°C. Cell aliquots were thawed on ice and lysis was performed in 5 mL of 50 mM HEPES-KOH pH 7.5, 140 mM NaCl, 1 mM EDTA pH 8.0, 10% glycerol (vol/vol), 0.5% Igepal (vol/vol), 0.25% Triton X-100 (vol/vol) with 1 × protease inhibitors (Roche, 11697498001) for 10 min at 4°C. Cells were pelleted by centrifugation for 5 min at 1200 g, resuspended in 5 mL of 10 mM Tris-HCl pH 8.0, 200 mM NaCl, 1 mM EDTA pH 8.0, 0.5 mM EGTA pH 8.0 with 1 × protease inhibitors, and incubated for 10 min at 4°C on a rotating platform. Cells were centrifuged for 5 min at 1200 g and resuspended in 2 mL of Sonication Buffer (50 mM Hepes pH 7.5, 140 mM NaCl, 1 mM EDTA pH 8.0, 1 mM EGTA pH 8.0, 1% Triton X-100 (vol/vol), 0.1% sodium deoxycholate (wt/vol), 0.1% SDS (vol/vol) with 1 × protease inhibitors). For sonication, each sample was split in two Bioruptor tubes with added sonication beads. Sonication was performed using the Bioruptor Pico (Diagenode) for 18 cycles of 30 sec on and 30 sec off to sheer DNA into an average size of approximately 200bp. Immunoprecipitation was performed for 16h at 4°C on a rotating platform by incubating with Dynabeads protein-G (Thermo Fisher Scientific) conjugated with antibodies. For histone modifications, half of each original cell aliquot was incubated with Dynabeads protein-G conjugated with 5 µg of rabbit polyclonal to Histone H3K27me3 (Active motif 39155) or rabbit polyclonal to Histone H3 (acetyl K27) (Abcam ab4729) antibodies. For CTCF, the entire cell aliquot was incubated with Dynabeads protein-G conjugated with 5 µl of rabbit polyclonal to CTCF (EMD 07-729) antibody. After the immunoprecipitation, washes were performed with the following ice-cold buffers: sonication buffer, sonication buffer with 500 mM NaCl, LiCl wash buffer (20 mM Tris-HCl pH 8.0, 1 mM EDTA pH 8.0, 250 mM LiCl, 0.5% Igepal (vol/vol), 0.5% sodium deoxycholate (wt/vol)), and TE buffer (10 mM Tris-HCl pH 8.0, 1 mM EDTA pH 8). Elution was performed in elution buffer (50 mM Tris-HCl pH 8.0, 10 mM EDTA pH 8.0, 1% SDS (vol/vol)) by incubating for 45 min at 65°C with occasional flicking of the tube. Samples were incubating for 16h at 65°C to perform reversal of crosslinks. 200 μL of TE and RNase A (Sigma) at a final concentration of 0.2 mg/mL was added to digest RNA by and incubating for 2h at 37°C. Proteins were digested by adding Proteinase K (Invitrogen) at a final concentration of 0.2 mg/mL, supplemented with CaCl2, at 55°C for 30 min. DNA was purified with phenol:chloroform:isoamyl alcohol (25:24:1; vol/vol) (Invitrogen) followed by an ethanol precipitation. DNA pellets were resuspended in 70 μL of water.
lllumina DNA sequencing libraries were prepared with approximately one third of the ChIP sample (24 μL) or a 1:100 dilution of the input sample in water. Library preparation was performed by end repair, A-tailing and ligating Illumina-compatible Bioo Scientific multiplexed adapters. Agencourt AmpureXP beads (Beckman Coulter) were used to remove unligated adapters. PCR amplification was performed with Phusion polymerase (New England Biolabs) and TruSeq primers (Sigma). Libraries were gel purified (Qiagen) between 250 and 550bp in size. Libraries were quantified before pooling using the KAPA library amplification kit on the Roche Lightcycler 480 or the Bio-Rad CFX96. The libraries were sequenced on Illumina NextSeq 500 using V2.5 chemistry (75 cycles, single-end 75bp) or on Illumina NovaSeq 6000 using the SP Reagent Kit (100 cycles, single-end 100bp) at the Genomics Core Facility at NYU.

value: 166kb Enhancers + RARE{delta} SynHoxA assemblon in HoxA -/- mESCs

tag: chip target

tag: chip antibody

value: abcam, #ab4729

value: 96h of RA+SAG differentiation


title: 2-3h wt embryos RNA-seq replicate 2


title: 166kb Enhancers + RARE∆ SynHoxA assemblon in HoxA -/- mESCs, 96h of RA+SAG differentiation, replicate 2, H3K27ac ChIP


title: GK3R87-GIH1: Wt_Small Intestine_GFPhi_1


title: 5-6h wt embryos RNA-seq replicate 2


title: 2-3h wt embryos RNA-seq replicate 1


title: 2-3h M-,Z+ fmr1 mutant embryos RNA-seq replicate 1


title: 2-3h M-,Z+ fmr1 mutant embryos RNA-seq replicate 2


title: 166kb Enhancers + RARE∆ SynHoxA assemblon in HoxA -/- mESCs, 96h of RA+SAG differentiation, replicate 2, H3K27me3 ChIP

description: pSP0394_A-/-_#G1_96hRA/SAG_H3K27me3_rep2

value: activemotif, #39155


title: 134kb SynHoxA assemblon in HoxA -/- mESCs, 0h of RA differentiation, Hi-C


title: GK3R9-G3: Wt_Colon_GFP_3

description:
processed data file: metaseqr_all_out_T_vs_G.txt
processed data file: metaseqr_all_out_U_vs_G.txt
processed data file: metaseqr_all_out_G_vs_GDS.txt

value: Colon


title: 1-2h M-,Z+ fmr1 mutant embryos RNA-seq replicate 2


title: 1-2h wt embryos RNA-seq replicate 1


title: 166kb Enhancers + RARE∆ SynHoxA assemblon in HoxA -/- mESCs, 96h of RA+SAG differentiation, replicate 1, H3K27me3 ChIP

description: pSP0394_A-/-_#G1_96hRA/SAG_H3K27me3_rep1


title: 1-2h wt embryos RNA-seq replicate 2


title: 166kb Enhancers + RARE∆ SynHoxA assemblon in HoxA -/- mESCs, 48h of RA+SAG differentiation, replicate 2, H3K27ac ChIP

value: 48h of RA+SAG differentiation


title: GK3R7-G1: Wt_Colon_GFP_1


title: 1-2h M-,Z+ fmr1 mutant embryos RNA-seq replicate 1


title: GK3R8-G2: Wt_Colon_GFP_2


title: 166kb Enhancers + RARE∆ SynHoxA assemblon in HoxA -/- mESCs, 48h of RA+SAG differentiation, replicate 1, H3K27ac ChIP

value: Embryoid Bodies


title: GK3R88-GIH2: Wt_Small Intestine_GFPhi_2

value: ColVI-cre, Rosa mTmG


title: GK3R6-U3: Wt_Colon_Unsorted_3

description:
processed data file: metaseqr_all_out_U_vs_G.txt
processed data file: metaseqr_all_out_U_vs_T.txt

source_name: Intestinal Cells

value: Intestinal Cells


title: 0.5-1h wt embryos RNA-seq replicate 2


title: GK3R5-U2: Wt_Colon_Unsorted_2


title: Pancreatic Islets Replicate 1

type: RNA

city: Toronto

first: Eldad

last: Zacksenhaus

state: Ontario

address: 101 College Street

country: Canada

institute: University Health Network

description: Biological replicate 1 of 2.

hyb_protocol: 300 ng of the corresponding Cy3- and Cy5-labeled fragmented cRNA were combined and hybridized overnight (65oC) to Agilent Whole Mouse Genome Oligo Microarrays 8x60K

scan_protocol: Fluorescence signals of the hybridized Agilent OligoMicroarrays were detected using Agilent’s DNA microarray scanner (Agilent Technologies Scanner G2505C US22502695)

data_processing: The scanned images were analyzed with Feature Extraction Software 10.7.3.1 (Agilent) using default parameters (protocol GE2_107_Sep09) to obtain background subtracted and quantile normalized median signal intensities

source_name: Pancreatic Islets

label_protocol: 15 ng of each total RNA sample was used to produce Cy3(control samples)- and Cy5(experimental samples)-labeled cRNA, the RNA samples were amplified and labeled using Agilent Low Input Quick Amp Labeling Kit (Agilent Technologies

growth_protocol: Pancreatic islets were isolated from mice as previously described (Choi et al., 2010; Liadis et al., 2005), using 3 ml of 3 mg/ml collagenase (Sigma-Aldrich) injected into the common bile duct for pancreatic digestion, and islets were picked up under dissecting microscope in RPMI 1640 supplemented with 10% fetal bovine serum, 100 U/ml penicillin, and 100 μg/ml streptomycin, and frozen immediately.

extract_protocol: RNA was extracted using NucleoSpin® RNA II, Macherey-Nagel

treatment_protocol: Pancreatic islets were isolated from control and phosphorylation-resistant RbΔK7 knockin mice.

tag: genotype/variation

value: control sample

value: experimental sample (Rb[delta]K7 mutant)


title: 166kb Enhancers + RARE∆ SynHoxA assemblon in HoxA -/- mESCs, 48h of RA+SAG differentiation, replicate 2, H3K27me3 ChIP

description: pSP0394_A-/-_#G1_48hRA/SAG_H3K27me3_rep2


title: 0.5-1h wt embryos RNA-seq replicate 1


title: 0.5-1h M-,Z+ fmr1 mutant embryos RNA-seq replicate 2

description: 0.5-1h_M-,Z+_fmr1_mutant_embryos_FPKM.txt


title: 0.5-1h M-,Z+ fmr1 mutant embryos RNA-seq replicate 1


title: 0-0.5h wt embryos RNA-seq replicate 2


title: GK3R4-U1: Wt_Colon_Unsorted_1

value: Fresh isolation


title: 0-0.5h wt embryos RNA-seq replicate 1


title: 166kb Enhancers + RARE∆ SynHoxA assemblon in HoxA -/- mESCs, 48h of RA+SAG differentiation, replicate 2, CTCF ChIP

value: CTCF


title: Pancreatic Islets Replicate 2

description: Biological replicate 2 of 2.


title: 0-0.5h M-,Z+ fmr1 mutant embryos RNA-seq replicate 2

description: 0-0.5h_M-,Z+_fmr1_mutant_embryos_FPKM.txt


title: 166kb Enhancers + RARE∆ SynHoxA assemblon in HoxA -/- mESCs, 48h of RA+SAG differentiation, replicate 1, CTCF ChIP


title: GK3R3-T3: Wt_Colon_Tomato_3

description:
processed data file: metaseqr_all_out_T_vs_G.txt
processed data file: metaseqr_all_out_U_vs_T.txt
processed data file: metaseqr_all_out_T_vs_TDS.txt

value: Intestinal Mesenchymal Cells


title: 5-6h wild type embryos RNA-seq replicate 1

value: wildtype


title: GK3R2-T2: Wt_Colon_Tomato_2


title: 130kb RARE∆ SynHoxA assemblon in HoxA -/- mESCs, 48h of RA+SAG differentiation, replicate 2, H3K27Ac ChIP

value: 130kb RARE{delta} SynHoxA assemblon in HoxA -/- mESCs


title: 5-6h M-,Z+ mettl3 and mettl14 double mutant embryos RNA-seq replicate 2

description: 5-6h_M-,Z+_mettl3_and_mettl14_double_mutant_embryos_FPKM.txt

source_name: w1118 embryo  M-,Z+ mettl3 and mettl14 double mutant

value: w1118, M-,Z+ mettl3 and mettl14 double mutant

value: embryo


title: GK3R1-T1: Wt_Colon_Tomato_1


title: 5-6h wild type embryos RNA-seq replicate 2


title: 5-6h M-,Z+ mettl3 and mettl14 double mutant embryos RNA-seq replicate 1


title: 2-3h wild type embryos RNA-seq replicate 1


title: D5

city: Melbourne

first: Andrew

middle: Ian

last: Jobling

state: Victoria

address: Medical Building, Cnr Grattan St and Royal Pde

department: Anatomy & Physiology

country: Australia

institute: University of Melbourne

data_processing:
Image analysis was performed in real time by the HiSeq Control Software (HCS) v2.2.68 and Real Time Analysis (RTA) v1.18.66.3, running on the instrument computer. RTA performs real-time base calling on the HiSeq instrument computer. Then the Illumina bcl2fastq 2.18.0.12 pipeline was used to generate the sequence data.
The reads were also screened for the presence of any Illumina adaptor/overrepresented sequences and cross-species contamination. The cleaned sequence reads were then aligned against the genome of Rattus norvegicus (Ensemble verison Rnor_6.0 (GCA_000001895.4)).
Tophat aligner (v2.0.14) was used to map reads to the genomic sequences and are in the compressed BAM format
The transcripts were assembled with the Stringtie tool v1.2.4 utilising the reads alignment and reference annotation based assembly option (RABT).
Differential expression analysis was carried out using the bioconductor package edgeR. Default normalisation method (TMM) was used.
Genome_build: Rnor_6.0
Supplementary_files_format_and_content: gene counts, transcript assemblies with TPM/FPKM values, differential expression analysis table

organism: Rattus norvegicus

source_name: STZ-treated_isolated retinal microglia

growth_protocol: Rats were rendered diabetic at 8-10 weeks of age

extract_protocol:
Whole retina from control and 4 week STZ-treated rats (n = 5 control, n = 4 STZ) were isolated, papain digested (Worthington Biochemical, NJ, USA), and labelled with CD11b-FITC conjugate (Miltenyi Biotec, Bergisch Gladbach, Germany) and microglia were isolated via FACS. RNA was extracted from isolated populations (RNeasy Micro Kit, Qiagen, Hilden, Germany) and purity analysed (Agilent Technologies, Santa Clara, CA, USA). A SmartSeq v4 kit (Clontech Laboratories, Mountain View, CA, USA) was used for a preamplification step.
RNA libraries were prepared for sequencing using standard Illumina protocols - NexteraXT

treatment_protocol: Rats received a dose of steptozotocin (STZ, 55mg/kg) or citrate buffer control at 10am after 12 hours of fasting. Blood glcuose levels were measured 24 hours later to check for hyperglycaemia. After 1 week blood glucose was measured bi-weekly and diabetic rats were treated with 2 Units of Protaphane (insulin) if blood glucose reaadings were >30mmol/l. Animals were taken out to 4 weeks post STZ-treatment.

value: Dark Agouti

value: 55mg/kg Steptozotocin

tag: blood glucose

value: hyperglycaemic

value: isolated retinal microglia


title: 130kb RARE∆ SynHoxA assemblon in HoxA -/- mESCs, 0h of RA+SAG differentiation, replicate 2, H3K27Ac ChIP

description: pSP0328_A-/-_#A2_t=0_2D_EBs_H3K27Ac_rep2

value: abcam, #ab4729

value: 0h of RA+SAG differentiation


title: 130kb RARE∆ SynHoxA assemblon in HoxA -/- mESCs, 48h of RA+SAG differentiation, replicate 1, H3K27Ac ChIP

value: 48h of RA+SAG differentiation

value: Embryoid Bodies


title: 2-3h wild type embryos RNA-seq replicate 2


title: 2-3h M-,Z+ mettl3 and mettl14 double mutant embryos RNA-seq replicate 1

description: 2-3h_M-,Z+_mettl3_and_mettl14_double_mutant_embryos_FPKM.txt


title: 2-3h M-,Z+ mettl3 and mettl14 double mutant embryos RNA-seq replicate 2

source_name: w1118 embryo  mettl3 and mettl14 double mutant

value: w1118, mettl3 and mettl14 double mutant


title: 130kb RARE∆ SynHoxA assemblon in HoxA -/- mESCs, 0h of RA+SAG differentiation, replicate 1, H3K27Ac ChIP

description: pSP0328_A-/-_#A2_t=0_2D_EBs_H3K27Ac_rep1


title: 166kb Enhancers + RARE∆ SynHoxA assemblon in HoxA -/- mESCs, 48h of RA+SAG differentiation, replicate 1, H3K27me3 ChIP

description: pSP0394_A-/-_#G1_48hRA/SAG_H3K27me3_rep1

value: 166kb Enhancers + RARE{delta} SynHoxA assemblon in HoxA -/- mESCs

value: activemotif, #39155


title: D4


title: 1-2h wild type embryos RNA-seq replicate 2


title: D2


title: 130kb RARE∆ SynHoxA assemblon in HoxA -/- mESCs, 96h of RA+SAG differentiation, replicate 2, H3K27me3 ChIP

description: pSP0328_A-/-_#A2_96hRA/SAG_H3K27me3_rep2

value: 96h of RA+SAG differentiation


title: D1


title: 0-0.5h M-,Z+ fmr1 mutant embryos RNA-seq replicate 1

value: w1118, M-,Z+ Fmr1 mutant


title: 1-2h wild type embryos RNA-seq replicate 1

value: wildtype


title: 1-2h M-,Z+ mettl3 and mettl14 double mutant embryos RNA-seq replicate 2

description: 1-2h_M-,Z+_mettl3_and_mettl14_double_mutant_embryos_FPKM.txt


title: 130kb RARE∆ SynHoxA assemblon in HoxA -/- mESCs, 96h of RA+SAG differentiation, replicate 1, H3K27me3 ChIP

description: pSP0328_A-/-_#A2_96hRA/SAG_H3K27me3_rep1

value: 130kb RARE{delta} SynHoxA assemblon in HoxA -/- mESCs


title: 0.5-1h wild type embryos RNA-seq replicate 2


title: C6

source_name: control_isolated retinal microglia

value: citrate buffer control

value: normal


title: 0.5-1h wild type embryos RNA-seq replicate 1

value: embryo


title: 0.5-1h M-,Z+ mettl3 and mettl14 double mutant embryos RNA-seq replicate 2

description: 0.5-1h_M-,Z+_mettl3_and_mettl14_double_mutant_embryos_FPKM.txt

value: w1118, M-,Z+ mettl3 and mettl14 double mutant


title: C5

value: Dark Agouti


title: 0-0.5h wild type embryos RNA-seq replicate 2


title: 0.5-1h M-,Z+ mettl3 and mettl14 double mutant embryos RNA-seq replicate 1


title: 130kb RARE∆ SynHoxA assemblon in HoxA -/- mESCs, 48h of RA+SAG differentiation, replicate 1, H3K27me3 ChIP

description: pSP0328_A-/-_#A2_48hRA/SAG_H3K27me3_rep1


title: 0-0.5h wild type embryos RNA-seq replicate 1


title: 130kb RARE∆ SynHoxA assemblon in HoxA -/- mESCs, 24h of RA+SAG differentiation, replicate 2, H3K27me3 ChIP

description: pSP0328_A-/-_#A2_24hRA/SAG_H3K27me3_rep2

value: 24h of RA+SAG differentiation


title: 0-0.5h M-,Z+ mettl3 and mettl14 double mutant embryos RNA-seq replicate 2

description: 0-0.5h_M-,Z+_mettl3_and_mettl14_double_mutant_embryos_FPKM.txt


title: C3

value: isolated retinal microglia


title: C4


title: GLC12_LN_CD4

city: Gothenburg

first: Eric

last: Malmhäll-Bah

address: Bruna stråket 16

department: Laboratory Medicine

country: Sweden

institute: University of Gothenburg

data_processing:
Aligned: STAR,  Ref. genome: Primary Assembly (C57BL/6J) (GCF_000001635.20 )
quantification: featureCounts
Genome_build: mm10
Supplementary_files_format_and_content: matrix with ENS number and samples in each one column

source_name: Lymph node CD4+ cells

growth_protocol: At termination, spleen, paws, and joint draining LN from the inguinal and axillary areas were collected. Splenocytes and LNs were mashed through a 70μm cell strainer. Erythrocytes were lysed in NH4Cl solution (0.83%, pH 7.29) and cell pellets was washed with PBS. CD4+ cells were isolated with Dynabeads™ Untouched™ Mouse CD4 Cells Kit (Cat.no.11415D), resuspended in the Iscove’s complete medium (10% FBS, 4mM L-glutamine, 50 μM β-mercaptoethanol, 50 μg/ml gentamycin sulphate) and cultured in the presence of concanavalin A (1.25 μg/ml) for 2 h.

extract_protocol: RNA from splenocytes and CD4+ cells was prepared using the Norgen Total RNA kit (Norgen, Ontario, Canada)

value: LN from the inguinal and axillary areas

tag: cells

value: activated CD4+ cells

tag: stimulation

value: Concanavalin A


title: 130kb RARE∆ SynHoxA assemblon in HoxA -/- mESCs, 24h of RA+SAG differentiation, replicate 1, H3K27me3 ChIP

description: pSP0328_A-/-_#A2_24hRA/SAG_H3K27me3_rep1

value: Embryoid Bodies


title: 0-0.5h M-,Z+ mettl3 and mettl14 double mutant embryos RNA-seq replicate 1


title: GLC11_LN_CD4


title: 1-2h M-,Z+ mettl3 and mettl14 double mutant embryos RNA-seq replicate 1


title: 130kb RARE∆ SynHoxA assemblon in HoxA -/- mESCs, 0h of RA+SAG differentiation, replicate 2, H3K27me3 ChIP

description: pSP0328_A-/-_#A2_t=0_2D_EBs_H3K27me3_rep2

value: 0h of RA+SAG differentiation


title: C1


title: GLC10_LN_CD4


title: 130kb RARE∆ SynHoxA assemblon in HoxA -/- mESCs, 0h of RA+SAG differentiation, replicate 1, H3K27me3 ChIP

description: pSP0328_A-/-_#A2_t=0_2D_EBs_H3K27me3_rep1

value: activemotif, #39155


title: DNA sequencing of 166kb Enhancers + RARE∆ SynHoxA assemblon purified from E.coli

description: Hoxa_RnHoxa_CompoundEnhancer_allRAREdelta_pSP0394_BAC

data_processing:
Library strategy: DNA-seq
Illumina adapter trimming with trimmomatic v0.39
Reads mapped using bowtie2 v2.2.9
Sort bam files using samtools
Make bigwig files using deeptools bamCoverage v3.2.1
Genome_build: mm10_synHoxA custom genome or mm10_synHoxA_delHoxA custom genome, mm10 or rn6
Supplementary_files_format_and_content: bigwig files to normalize coverage

source_name: E.coli strain bearing synthetic Hox construct

growth_protocol: Plasmids were purified from bacterial cultures in Luria Broth (LB) supplemented with the appropriate antibiotic (12.5 µg/mL Chloramphenicol for source BACs, and 25 µg/mL Kanamycin for all assemblons. mESCs were cultured on plastic tissue culture plates coated with 0.1% gelatin (EMD Millipore ES-006-B) at 37°C and 5% CO2 in ‘80/20’ medium comprising 80% 2i medium and 20% mESC medium. mESCs were grown at 37°C and 8% CO2 before differentiation experiments.  2i medium was made from a 1:1 mix of Advanced DMEM/F12 (Gibco 12634010) and Neurobasal-A (Gibco 10888022), containing 1X N-2 supplement (Gibco 17502048), 1X B-27 supplement (Gibco 17504044), 2mM Glutamax (Gibco 35050061), 0.1mM Beta-Mercaptoethanol (Gibco 31350010), 103 units/mL LIF (Millipore, ESG1107), 1 μM MEK1/2 inhibitor (Stemgent, PD0325901), and 3 μM GSK3 inhibitor (R&D Systems, CHIR99021). mESC medium was made from Knockout DMEM (Gibco 10829018), containing 15% Fetal Bovine Serum (Gemini), 0.1 mM Beta-Mercaptoethanol (Gibco 31350010), 1X MEM Non Essential Amino Acids (Gibco 11140050), Glutamax (Gibco 35050061), 1X Nucleosides (Millipore ES-008-D) and LIF (Millipore ESG1107).

extract_protocol:
Plasmids were purified from small scale bacterial cultures (5-10 mL) using alkaline lysis. gDNA was extracted from mESC cell pellets using Qiagen DNA mini kit.
Illumina sequencing libraries for BACs were generated from 100-200 ng BAC DNA using NEBNext Ultra II FS DNA Library Prep Kit (New England Biolabs E7805S) according to the manufacturer’s protocol. Whole genome sequencing and capture sequencing libraries were prepared as follows: 1 µg of DNA was sheared to ∼500 to 900 bp in a 96-well microplate using the Covaris LE220 (450 W, 10% Duty Factor, 200 cycles per burst, and 90-s treatment time). Sheared DNA was purified using the DNA Clean and Concentrate-5 Kit (Zymo Research D4013), and the concentration was measured on a NanoDrop instrument (Invitrogen). DNA fragments were end-repaired with T4 DNA polymerase, Klenow DNA polymerase, and T4 polynucleotide kinase (New England Biolabs M0203S, M0210S and M0201S, respectively), and A-tailed using Klenow (3′-5′ exo-; New England Biolabs M0212L). Illumina-compatible adapters were subsequently ligated to DNA ends, and DNA libraries were amplified with KAPA 2X Hi-Fi Hotstart Readymix (Roche). Biotinylated baits for capture sequencing were prepared from assemblon BACs using nick translation

value: 166kb Enhancers + RARE{delta} SynHoxA assemblon purified from E.coli

tag: capture bait

value: E. coli


title: Monocytes, normal control 3

city: nanjing

first: Juan

last: Wu

state: jiangsu

address: Nanjing Stomatological Hospital, Gulou District, ZhongYang Road.

department: Department of Periodontology

institute: Nanjing Stomatological Hospital

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence using Trim Galore version: 0.6.7. with parameters -j 4 -e 0.1 -q 25 -O 3 -a CTGTCTCTTATA
read counts and TPM were calculated using Salmon (version 1.5.2) with the prebuilt version of full-decoy salmon indice provided by Salmon.
Genome_build: hg38
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample generated by DESeq2
Supplementary_files_format_and_content: abundance measurements generated by Salmon

organism: Homo sapiens

source_name: monocytes

extract_protocol:
Blood (10 mL) was collected from 2 pEDS patients and 3 healthy controls. Blood samples were collected to extract peripheral blood mononuclear cells (PBMCs) using the Ficoll density gradient method. According to the manufacturer’s instructions, total RNA was extracted by TRIzol reagent for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: monocytes

tag: disease state

value: control


title: Monocytes, normal control 2


title: DNA sequencing of 130kb RARE∆ SynHoxA assemblon purified from E.coli

value: 130kb RARE{delta} SynHoxA assemblon purified from E.coli


title: GLC9_LN_CD4


title: 130kb RARE∆ SynHoxA assemblon in HoxA -/- mESCs, 48h of RA+SAG differentiation, replicate 2, CTCF ChIP

value: 130kb RARE{delta} SynHoxA assemblon in HoxA -/- mESCs

value: CTCF

value: 48h of RA+SAG differentiation


title: Monocytes, normal control 1


title: 130kb RARE∆ SynHoxA assemblon in HoxA -/- mESCs, 48h of RA+SAG differentiation, replicate 2, H3K27me3 ChIP

description: pSP0328_A-/-_#A2_48hRA/SAG_H3K27me3_rep2


title: DNA sequencing of 170kb Enhancers + SynHoxA assemblon purified from E.coli

description: Hoxa_RnHoxa_CompoundEnhancer_pSP0242_BAC

value: 170kb Enhancers+SynHoxA assemblon purified from E.coli


title: GLC78_LN_CD4

description: mRNA from 2 mice were pooled in this sample


title: DNA sequencing of 134kb SynHoxA assemblon purified from E.coli


title: 130kb RARE∆ SynHoxA assemblon in HoxA -/- mESCs, 48h of RA+SAG differentiation, replicate 1, CTCF ChIP


title: DNA sequencing of Source BAC CH230-454G2 purified from E.coli


title: GLC6_LN_CD4


title: WT5_LN_CD4

value: WT


title: 130kb RARE∆ SynHoxA assemblon in HoxA -/- mESCs, 0h of RA+SAG differentiation, replicate 1, CTCF ChIP


title: DNA sequencing of Source BAC CH230-79B14 purified from E.coli


title: WT4_LN_CD4


title: MM.P20190322

first: Shishang

last: Qin

address: No.5 Yiheyuan Road, Haidian District

institute: Peking university

description:
processed data file:
MM_10X.CD4.counts.txt.gz
MM_10X.CD8.counts.txt.gz
metadata.txt.gz
10X_VDJ.merge.txt.gz
bulk_RNA.counts.txt.gz
bulk_Exome.mutation.txt.gz

data_processing:
For 10X data, Cell Ranger 3.0.0 was used to quantify gene expression level and to identify TCR sequences.
For Smart-seq2 data, HTSeqGenie pipeline (R package version 4.8) was used to quantify gene expression level.
For bulk RNAseq data, UCSC Xena Toil RNAseq pipeline was used to quantify gene expression level.
For bulk exome data, BWA-MEM algorithm was used to align the reads to genome, PICARD was used to sorted and de-duplicated the bam files, GATK 3.7 was used to realign reads around INDEL region and re-calibrate base quality, and finally strelka 1.0.14 was used to call somatic mutations (SNV and INDEL).
Genome_build: GRCh38 for RNA expression and TCR data, and b37 for DNA mutation calling.
Supplementary_files_format_and_content: text files for expression matrices, cell metadata, TCR summary, and mutation summary.

source_name: MM

extract_protocol:
Tumors and adjacent normal tissues were cut into approximately 1-2 mm3 pieces in the RPMI-1640 medium (Gibco) with 10% fetal bovine serum (FBS, Gibco), and enzymatically digested with gentleMACS (Miltenyi) for 60 min on a rotor at 37°C, according to manufacturer’s instruction. The dissociated cells were subsequently passed through a 100 µm SmartStrainer and centrifuged at 400 g for 5 min. After the supernatant was removed, the pelleted cells were suspended in red blood cell lysis buffer (TIANDZ) and incubated on ice for 1-2 min to lyse red blood cells. After washing twice with 1× PBS (Gibco), the cell pellets were re-suspended in sorting buffer (PBS supplemented with 1% FBS).
Single cell suspensions were stained with antibodies against CD45 and 7AAD for FACS sorting, performed on a BD Aria SORP instrument. Based on FACS analysis, single cells were sorted into 1.5 ml tubes (Eppendorf) and counted manually under the microscope. The concentration of single cell suspensions was adjusted to 500-1200 cells/ul. Cells were loaded between 7,000 and 15,000 cells/chip position using the 10x Chromium Single cell 5’ Library, Gel Bead & Multiplex Kit and Chip Kit (10x Genomics, V3 barcoding chemistry) according to the manufacturer’s instructions. All the subsequent steps were performed following the standard manufacturer’s protocols. Purified libraries were analyzed by an Illumina Hiseq X Ten sequencer with 150-bp paired-end reads.
10x Chromium Single cell 5’ + VDJ Library, and Smart-seq2 Library (only for one CHOL sample)

value: Tumor, Blood

tag: platform


title: 170kb Enhancers + SynHoxA assemblon in HoxA -/- mESCs, 96h of RA+SAG differentiation, replicate 2, H3K27Ac ChIP

description: C1_A-/-_compE_RnHoxA_96hRA/SAG_rep2_H3K27Ac

tag: strain

value: abcam, #ab4729

value: 96h of RA+SAG differentiation


title: MM.P20190122


title: DNA sequencing of 134kb SynHoxA 15-28 half assemblon purified from E.coli

value: 134kb SynHoxA assemblon 15-28 half construct purified from E.coli


title: MM.P20181219

value: Tumor


title: WT3_LN_CD4

value: LN from the inguinal and axillary areas

value: activated CD4+ cells

tag: genotype

value: Concanavalin A


title: 170kb Enhancers + SynHoxA assemblon in HoxA -/- mESCs, 96h of RA+SAG differentiation, replicate 1, H3K27Ac ChIP

description: C1_A-/-_compE_RnHoxA_96hRA/SAG_rep1_H3K27Ac

tag: cell type

value: Embryoid Bodies


title: WT2_LN_CD4


title: 170kb Enhancers + SynHoxA assemblon in HoxA -/- mESCs, 96h of RA+SAG differentiation, replicate 2, H3K27me3 ChIP

description: C1_A-/-_compE_RnHoxA_96hRA/SAG_rep2_H3K27me3

value: activemotif, #39155

tag: treatment


title: DNA sequencing of 134kb SynHoxA 1-14 half assemblon purified from E.coli

value: 134kb SynHoxA assemblon 1-14 half construct purified from E.coli

value: E. coli


title: L.P20181123

description:
processed data file:
BCL_10X.CD4.counts.txt.gz
BCL_10X.CD8.counts.txt.gz
metadata.txt.gz
10X_VDJ.merge.txt.gz
bulk_RNA.counts.txt.gz
bulk_Exome.mutation.txt.gz

source_name: BCL

tag: tissue


title: WT1_LN_CD4


title: 170kb Enhancers + SynHoxA assemblon in HoxA -/- mESCs, 96h of RA+SAG differentiation, replicate 1, H3K27me3 ChIP

description: C1_A-/-_compE_RnHoxA_96hRA/SAG_rep1_H3K27me3


title: Control T06

first: yang

last: niuzi

department: College of  Plant Protection

institute: jaas

data_processing:
Illumina Casava1.8 software used for basecalling.
Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts. In this step, clean data(clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data.
bowtie  1.1.1 software used for read alignment,paramter set as follows:  -q --phred33-quals -n 2 -e 99999999 -l 25 -I 1 -X 1000 -p 4 -a -m 200
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample and tab-delimited fasta file are assembled sequences from all the samples.

organism: Tetranychus truncatus

source_name: From laboratory breeding

extract_protocol:
Total RNA was extracted from each sample using Trizol reagent ( Sigmae Aldrich ) according to the manufacturer’s instructions.A total amount of 3 μg RNA per sample was used as input material for the RNA sample preparations
RNA libraries were prepared for sequencing using standard Illumina protocols

value: 27.5% acetone water (control)

value: body

tag: developmental stage

value: adult


title: Control T05


title: 134kb SynHoxA assemblon in HoxA -/- mESCs, 96h of RA+SAG differentiation, replicate 2, H3K27Ac ChIP


title: OV.P20181225

description:
processed data file:
FTC_10X.CD4.counts.txt.gz
FTC_10X.CD8.counts.txt.gz
metadata.txt.gz
10X_VDJ.merge.txt.gz
bulk_RNA.counts.txt.gz
bulk_Exome.mutation.txt.gz

source_name: FTC


title: PanC1 expressing Cas9 with ARID1A KO (C2) infected with VSV, R2

city: Ottawa

first: Adrian

last: Pelin

address: 501 Smyth Rd.

institute: Ottawa Hospital Research Institute

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, then mapped to ensembl_release-95/Homo_sapiens.GRCh38.dna_sm.toplevel.fa whole genome using HISAT2 using default paramters
Tags per million (TPM) were calculated using StringTie (M Pertea et al,  2015) from mapped reads
Genome_build: ensembl_release-95/Homo_sapiens.GRCh38.dna_sm.toplevel.fa
Supplementary_files_format_and_content: tab-delimited text files include TPM (tags over million) values for each Sample

extract_protocol:
Total RNA was extracted from 1 million cells cultured in vitro using Qiagen's RNAeasy kit
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: cell line

value: PanC1 ATCC

value: Pancreatic cancer

tag: age

value: Unknown

value: wild type

value: ARID1A KO (C2)

tag: infection

value: VSV


title: 130kb RARE∆ SynHoxA assemblon in HoxA -/- mESCs, 0h of RA+SAG differentiation, replicate 2, CTCF ChIP

source_name: ES-derived embryoid bodies with variant synthetic Hox clusters

value: 130kb RARE{delta} SynHoxA assemblon in HoxA -/- mESCs

tag: chip target

value: CTCF

tag: chip antibody

value: 0h of RA+SAG differentiation


title: PanC1 expressing Cas9 with ARID1A KO (C2) infected with VSV, R1


title: Monocytes, pEDS patient 2

value: monocytes

value: Periodontal Ehlers–Danlos Syndrome


title: Monocytes, pEDS patient 1


title: Control T04


title: Abamectin T03

value: sublethal concentration abamectin (LC30)


title: 134kb SynHoxA assemblon in HoxA -/- mESCs, 96h of RA+SAG differentiation, replicate 1, H3K27Ac ChIP

value: abcam, #ab4729

value: 96h of RA+SAG differentiation

value: Embryoid Bodies


title: 134kb SynHoxA assemblon in HoxA -/- mESCs, 96h of RA+SAG differentiation, replicate 2, H3K27me3 ChIP

value: activemotif, #39155


title: PanC1 expressing Cas9 with ARID1A KO (C2), R2


title: Abamectin T02

value: body

value: adult


title: UCEC.P20190910

description:
processed data file:
UCEC_10X.CD4.counts.txt.gz
UCEC_10X.CD8.counts.txt.gz
metadata.txt.gz
10X_VDJ.merge.txt.gz
bulk_RNA.counts.txt.gz
bulk_Exome.mutation.txt.gz

source_name: UCEC

value: Tumor, Adjacent-normal


title: UCEC.P20190717


title: 134kb SynHoxA assemblon in HoxA -/- mESCs, 96h of RA+SAG differentiation, replicate 1, H3K27me3 ChIP


title: Abamectin T01


title: PanC1 expressing Cas9 with ARID1A KO (C1) infected with VSV, R2

value: PanC1 ATCC

value: Pancreatic cancer

value: Unknown

value: ARID1A KO (C1)


title: L.P20190404

value: Tumor, Blood


title: UCEC.P20190625


title: undifferentiated HPEK, stimulated with TGF-beta

city: Tokyo

first: Daizo

last: Koinuma

address: Hongo 7-3-1, Bunkyo-ku

department: Pathology

country: Japan

institute: University of Tokyo

description: column q4_FPKM in FPKM_call.xlsx

data_processing:
Reference files of the human genome hg19 (NCBI build 37, Feb. 2009) and GTF annotation file were obtained from iGenomes (http://support.illumina.com/sequencing/sequencing_software/igenome.html).
RNA-seq reads were aligned and gene expression levels in fragments per kilobase of exon per million fragments mapped (FPKM) were estimated using Tophat2 (2.0.8)/Cufflinks with the default parameter settings (Trapnell et al., 2012).
BAM files were sorted using Picard SortSam (http://picard.sourceforge.net/) ver 1.76.
Genome_build: hg19
Supplementary_files_format_and_content: An Excel file includes FPKM values of genes for each sample, which was generated by Cufflinks. Columns q1_FPKM, q2_FPKM, q3_FPKM, and q4_FPKM correspond to s_4_export.fastq, s_5_export.fastq, s_6_export.fastq, and s_7_export.fastq, respectively.

source_name: A human progenitor epidermal keratinocyte

growth_protocol: HPEK cells were obtained from CELLnTEC (Bern, Switzerland) and cultured in Progenitor Cell Targeting (PCT) medium (CnT-57) (CELLnTEC) supplemented with 50 U/ml penicillin G and 50 µg/ml streptomycin to maintain progenitor state.

extract_protocol:
RNA was extracted using Tripure (Roche diagnostics).
The libraries were constructed as described (Morikawa et al, Nuc Acids Res 2011).

treatment_protocol: For induction of differentiation, cells were cultured in CnT-02 supplemented with 1.5 mM CaCl2 for 7 days, following the protocols provided by the manufacturer (CELLnTEC). Cells were then treated with 1 ng/ml of TGF-beta for 24 h.

tag: differentiation

value: Undifferentiated HPEK cells were maintained with CnT-57 medium.

tag: sample type

value: differentiated keratinocyte, with TGF-beta

value: TGF-beta, 1ng/ml, 24 h


title: undifferentiated HPEK, unstimulated control

description: column q3_FPKM in FPKM_call.xlsx

value: differentiated keratinocyte, no TGF-beta

tag: stimulation

value: no


title: PanC1 expressing Cas9 with ARID1A KO (C1) infected with VSV, R1

value: wild type

value: VSV


title: PanC1 expressing Cas9 with ARID1A KO (C1), R2


title: PanC1 expressing Cas9 with ARID1A KO (C1), R1


title: diffrentiated HPEK, stimulated with TGF-beta

description: column q2_FPKM in FPKM_call.xlsx

value: Differentiation was induced by 7-day culture with CnT-02 medium supplemented with 1.5 mM CaCl2.

value: progenitor state, with TGF-beta


title: UCEC.P20190213


title: PanC1 expressing Cas9 infected with VSV, R2

value: wildtype


title: UCEC.P20190911


title: differentiated HPEK, unstimulated control

description: column q1_FPKM in FPKM_call.xlsx

value: progenitor state, no TGF-beta


title: UCEC.P20181122

value: Tumor, Adjacent-normal


title: control genomic data in HPEK cells

description: control genomic DNA data

data_processing:
Reference files of the human reference sequence assembly (hg19) were obtained from iGenomes (http://support.illumina.com/sequencing/sequencing_software/igenome.html)
ChIP-seq reads were aligned using Bowtie2 (Langmead et al., 2009).
Smad3 binding peak summits were identified using MACS2 software (Model based analysis of ChIP-seq) (Zhang et al, 2008) with the command "callpeak --bdg --call-summits" and a q-value threshold of 0.0001 (two sample analysis using control genomic data).
bam files were sorted and bai index files were generated using tools of IGV.
Genome_build: hg19
Supplementary_files_format_and_content: BED and bam files were generated using MACS2 and samtools.

extract_protocol:
ChIP of HPEK cells were performed using 10 μg of anti-Smad3 antibody (Isogaya et al, Cell Res 2011) as described previously (Koinuma D et al, Mol cell biol, 2009).
The libraries were constructed as described (Morikawa et al, Nuc Acids Res 2011). Adaptor-ligated samples were amplified by 15 cycles of PCR.

treatment_protocol: For induction of differentiation, cells were cultured in CnT-02 supplemented with 1.5 mM CaCl2 for 8 days, following the protocols provided by the manufacturer (CELLnTEC). Cells were then treated with 1 ng/ml of TGF-beta for 1.5 h before fixation.

value: Undifferentiated HPEK cells were used to obtain control genomic DNA for library construction.

tag: ChIP

value: control genome

value: no treatment


title: PanC1 expressing Cas9 infected with VSV, R1

value: PanC1 ATCC

value: Pancreatic cancer

value: Unknown


title: PM2.5-treated [PM_100_3]

city: Chongqing

first: Fuquan

last: Shi

address: 30 Gaotanyan Street

institute: Army Medical University

data_processing:
Illumina Casava1.8 software used for basecalling.
Clean data (clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data.
Index of the reference genome was built using Hisat2 v2.0.5 and paired-end clean reads were aligned to the reference genome using Hisat2 v2.0.5.
FeatureCounts v1.5.0-p3 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene.
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample.

source_name: spermatocyte

growth_protocol: The GC-2spd cell line was purchased from American type culture collection (ATCC, CRL-2196) and cultured in Dulbecco's modified Eagle's medium (DMEM), supplemented with 10% FBS, 100 U/mL penicillin, and 100 μg/mL streptomycin at 37 ℃, 5% CO2.

extract_protocol:
The total RNA from the GC-2spd cells was isolated using TRIzol reagent. A total amount of 1 µg RNA per sample was used for the RNA sample preparations, and Sequencing libraries were structured with NEBNext® UltraTM RNA Library Prep Kit for Illumina® (NEB, USA)
PCR products were purified (AMPure XP system) and library quality was assessed on the Agilent Bioanalyzer 2100 system. The clustering of the index-coded samples was performed on a cBot Cluster Generation System using TruSeq PE Cluster Kit v3-cBot-HS (Illumia). After cluster generation, the library preparations were sequenced on an Illumina Novaseq platform and 150 bp paired-end reads were generated.

treatment_protocol: The GC-2spd cells were treated with 100 μg/mL PM2.5 for 48 h, and the normal culture medium was regarded as the control group.

tag: strain background

value: BALB/c

value: spermatocyte-derived GC-2spd cells


title: UCEC.P20190312

tag: platform


title: PM2.5-treated [PM_100_2]


title: PanC1 expressing Cas9 with ARID1A KO (C2), R1

value: ARID1A KO (C2)


title: PanC1 expressing Cas9, R2


title: Smad3 binding region in differentiated HPEK cells stimulated with TGF-beta

description: anti-Smad3 ChIP-seq data

value: Differentiation was induced by 8-day culture with CnT-02 medium supplemented with 1.5 mM CaCl2.

value: anti-Smad3 ChIP

value: TGF-beta, X ng/ml, 1.5h


title: PM2.5-treated [PM_100_1]


title: THCA.P20190816

description:
processed data file:
THCA_10X.CD4.counts.txt.gz
THCA_10X.CD8.counts.txt.gz
metadata.txt.gz
10X_VDJ.merge.txt.gz
bulk_RNA.counts.txt.gz
bulk_Exome.mutation.txt.gz

source_name: THCA


title: untreated [PM_0_3]

value: untreated


title: IR_4

city: Hangzhou

first: Xin

last: Shao

state: Zhejiang

address: #866 Yuhangtang Rd.

institute: Zhejiang University

data_processing:
Raw sequenced files were processed with CellRanger 3.0.2 based on the GRCh38 reference for read alignment to generate the raw counts data, which were then processed in accordance with the pipeline detailed in the Satija Lab tutorial, using Seurat 3.0, wherein cells with more than 4,000 unique features or with mitochondrial counts greater than 25% were filtered out to exclude the possible doublets and dead cells.
Gene symbols were revised in accordance with NCBI gene data (https://www.ncbi.nlm.nih.gov/gene/) updated on April. 28, 2020, wherein unmatched genes and duplicated genes were removed.
The raw data were normalized via the global-scaling normalization method LogNormalize. Principal component analyses (PCAs) were performed, followed by t-Distributed Stochastic Neighbor Embedding (t-SNE) analysis for dimensional reduction and clustering analysis.
Genome_build: GRCh38
Supplementary_files_format_and_content: Matrix table with counts for every gene and every cell

source_name: Liver

extract_protocol:
Liver tissues were cut into pieces and placed into a pre-prepared gentleMACSTM C tubes with dissociation enzyme mix. Then, perform an appropriate gentleMACSTM program (37C_h_TDK_1) to dissociate tissues for I h using the gentleMACSTM Octo dissociator with heaters. Subsequently, the cell suspension was filtered by 40 μm nylon cell strainer (Falcon, Cat#352340) and transferred to a 50 ml centrifuge tube. The erythrocytes were lysed by using 5 mL ACK lysing buffer (Gibco, Cat#A1049201). Dead cells were removed by the Dead Cell Removal Kit (Miltenyi Biotec, Cat#130090101) according to the manufacturer’s recommendations. Finally, the cell pellet was washed twice and resuspended in PBS, and the cell viability was calculated by trypan blue (Gibco, Cat#15250-061), and then placed on ice for later use. The Chromium Single Cell 3′ Library & Gel Bead Kit v3 (10x Genomics; Pleasanton, CA, USA) was used for the construction of sequencing libraries.
Liver single cell suspensions were loaded onto the 10x Genomics Chromium chip (10x Genomics; Pleasanton, CA, USA) to generate droplets. The obtained Gel Beads-in-emulsion (GEMs) were followed by reverse transcription using ProFlex PCR System (Thermo Fisher, MA, USA). Then the resulting cDNA was purified, amplified. According to the cDNA concentration quantified by Qubit (Thermo Fisher, MA, USA), libraries were constructed by the Chromium Single Cell 3′ Library & Gel Bead Kit v3 (10x Genomics; Pleasanton, CA, USA) according to the manufacturer’s instructions.

tag: condition

value: after LT

tag: Sex

value: Male


title: THCA.P20190730


title: UCEC.P20190305


title: PanC1 expressing Cas9, R1

tag: genotype

value: wild type

value: wildtype


title: IR_3

value: Female


title: THCA.P20190703

value: Tumor


title: untreated [PM_0_2]

tag: cell type

tag: treatment


title: UCEC.P20181211

tag: tissue


title: untreated [PM_0_1]


title: IR_2


title: THCA.P20190621


title: IR_1


title: N2_5chol_2

city: Worcester

first: Read

last: Pukkila-Worley

state: Massachusetts

address: 55 N Lake Ave

department: Medicine

institute: University of Massachusetts Medical School

data_processing:
Raw fastq reads were evaluated by FastQC (version 0.11.5), clean reads were aligned to the C. elegans reference genome (WBcel235) and quantified using Kallisto (version 0.45.0). Differentially expressed genes were identified using Sleuth (version 0.30.0).
Genome_build: WBcel235
Supplementary_files_format_and_content: tsv files include TPM transcript abundance values for each sample

organism: Caenorhabditis elegans

source_name: Whole animal

extract_protocol:
RNA was isolated using TriReagent (Molecular Research Center, Inc.) and purified with RNeasy columns (Qiagen)
Oligo (dT) magnetic beads are used to select mRNA with polyA tail. Fragment the target RNA and reverse transcription to double-strand cDNA (dscDNA) by N6 random primer. End repair the dscDNA with phosphate at 5' end and stickiness 'A' at 3' end, then ligate and adaptor with stickiness 'T' at 3' end to the dscDNA. Two specific primers were used to amplify the ligation product. Denature the PCR product by heat and the single strand DNA is cyclized by splint oligo and DNA ligase.

treatment_protocol: C. elegans wild-type (N2) animals were grown for two generations on nematode growth medium (NGM) supplemented with either 0 μg/mL or 5 cholesterol μg/mL cholesterol. Animals were  harvested at the L4 growth stage for RNA isolation.

tag: developmental stage

tag: exposure

value: 5 μg/ml cholesterol (0.1% ethanol)


title: LIN_neg_DAY7

city: Guangzhou

first: Jinyong

last: Wang

state: GuangDong

address: 190 Kai Yuan Avenue, Science Park, Guangzhou, China

institute: Guangzhou Institutes of Biomedicine and Health (GIBH)

data_processing:
Droplet-based scRNA-seq datasets were aligned and quantified using the CellRanger software package (version 4.0.0)
Datasets were subjected to Seurat3(version 3.2.3) for further analysis
To pass quality control, cells were required to have less than 60000 raw reads mapping to nuclear genes, at least 2000 genes detected, less than 10% of mapped reads mapping to mitochondrial genes
Genome_build: mm10

source_name: bone marrow

growth_protocol: We identified that the coordinated expression of exogenous transcription factors(XXX), efficiently guides PSC-derived hematopoietic progenitors (iHPC) preferentially towards B cell lineage commitment, which successfully regenerate B lymphopoiesis in B-cell deficient animals

treatment_protocol: At day 7.5 after iHPC transplantation, we sorted the GFP+CD45+ Lin- cells from the bone marrow of recipients for Droplet-based scRNA-seq.  Droplet-based scRNA-seq datasets were produced using a Chromium system (10x Genomics, PN120263) following manufacture’s instruction.

value: GFP+CD45+ Lin- cells


title: N2_5chol_3


title: N2_5chol_1


title: Con_3

value: before LT

tag: age


title: N2_0chol_2

value: 0 μg/ml cholesterol (0.1% ethanol)


title: THCA.P20190612

value: Tumor, Adjacent-normal


title: THCA.P20190125


title: Con_2


title: THCA.P20190122


title: RNLSKO-CKD

city: New Haven

first: Leyuan

last: Xu

state: CT

address: 300 Cedar Street, Ste S255B

department: Internal Medicine/Section of Nephrology

institute: Yale University

description:
rnlsko_ckd
Single cell RNA

data_processing:
Cell Ranger version 3.0.0 was used to process Chromium single cell 3’ RNA-seq output and align the Read to the mouse reference transcriptome (mm10).
A downstream data analysis was performed using Seurat v4.1 R package.
Red blood cells, cells with transcriptome <200 (likely cell fragments) or >3,500 (potentially cell duplets), cells with reads <650 (poor-quality cells), and cells with mitochondrial gene percentage >50% were excluded.
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: Tab-delimited text files include gene counts, data, and scaled data for each cell and each sample.
Supplementary_files_format_and_content: wt_ctrl_counts.txt: WT control counts
Supplementary_files_format_and_content: wt_ctrl_data.txt: WT control normalized data
Supplementary_files_format_and_content: wt_ctrl_scale_data.txt: WT control scaled data
Supplementary_files_format_and_content: wt_ckd_counts.txt: WT CKD counts
Supplementary_files_format_and_content: wt_ckd_data.txt: WT CKD normalized data
Supplementary_files_format_and_content: wt_ckd_scale_data.txt: WT CKD scaled data
Supplementary_files_format_and_content: rnlsko_ctrl_counts.txt: RNLSKO control counts
Supplementary_files_format_and_content: rnlsko_ctrl_data.txt: RNLSKO control normalized data
Supplementary_files_format_and_content: rnlsko_ctrl_scale_data.txt: RNLSKO control scaled data
Supplementary_files_format_and_content: rnlsko_ckd_counts.txt: RNLSKO CKD counts
Supplementary_files_format_and_content: rnlsko_ckd_data.txt: RNLSKO CKD normalized data
Supplementary_files_format_and_content: rnlsko_ckd_scale_data.txt: RNLSKO CKD scaled data
Supplementary_files_format_and_content: models_counts.txt: combined counts
Supplementary_files_format_and_content: models_data.txt: combined normalized data
Supplementary_files_format_and_content: models_scale_data.txt: combined scaled data

source_name: Kidney

extract_protocol:
Kidneys were collected from each experimental animal and weighed, then dissected into small pieces using a razor blade. The dissected tissue was incubated in 1.48 U/mL Liberase DL enzyme mixture (Roche) and 200 U/mL DNase I (Roche) at 37°C for 45 minutes on a rocker. Cell suspension was filtered through 40 μm filters then pelleted by centrifugation at 500 × g for 10 minutes. Cells were resuspended in ACK Lysing Buffer (ThermoFischer) for 3 minutes at room temperature, followed by subsequently wash in DMEM-2% FBS. Cell debris was removed using the Miltenyi Debris Removal Solution. Live and dead cells were counted by Trypan Blue staining (Gibco) using a TC20 Cell Counter (Bio-Rad). Cells were diluted to a concentration of 10^6 cells/mL. We then proceeded to single cell library preparation.
The scRNA-seq library and sequencing were performed at the Yale Center for Genome Analysis (YCGA).

tag: strain

value: Kidney

value: 4 months

value: Rnls knockout

value: cisplatin, 15mg/kg, 2 dose, 2 weeks apart

tag: diagnosis

value: CKD


title: THCA.P20190118


title: CHOL.P0216

description:
processed data file:
CHOL_SS2.CD4.counts.txt.gz
CHOL_SS2.CD8.counts.txt.gz
metadata.txt.gz
bulk_RNA.counts.txt.gz
bulk_Exome.mutation.txt.gz

source_name: CHOL

value: Tumor, Adjacent-normal, Blood


title: Con_1


title: THCA.P20190108


title: RP81MNP

description:
Single cell RNA
Named "rp81mnp" in the combined processed data files

data_processing:
Cell Ranger version 3.0.0 was used to process Chromium single cell 3’ RNA-seq output and align the Read to the mouse reference transcriptome (mm10).
A downstream data analysis was performed using Seurat v4.1 R package.
Red blood cells, cells with transcriptome <200 (likely cell fragments) or >3,500 (potentially cell duplets), cells with reads < 650 (poor-quality cells), and cells with mitochondrial gene percentage >50% were excluded.
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: Tab-delimited text files include gene counts, data, and scaled data for each cell and each sample.
Supplementary_files_format_and_content: models_counts.txt: combined counts
Supplementary_files_format_and_content: models_data.txt: combined normalized data
Supplementary_files_format_and_content: models_scale_data.txt: combined scaled data

extract_protocol:
Kidneys were collected from each experimental animal and weighed, then dissected into small pieces using a razor blade. The dissected tissue was incubated in 1.48 U/mL Liberase DL enzyme mixture (Roche) and 200 U/mL DNase I (Roche) at 37°C for 45 minutes on a rocker. Cell suspension was filtered through 40 μm filters then pelleted by centrifugation at 500 × g for 10 minutes. Cells were resuspended in ACK Lysing Buffer (ThermoFischer) for 3 minutes at room temperature, followed by subsequently wash in DMEM-2% FBS. Cell debris was removed using the Miltenyi Debris Removal Solution. Live and dead cells were counted by Trypan Blue staining (Gibco) using a TC20 Cell Counter (Bio-Rad). Cells were diluted to a concentration of 106 cells/mL. We then proceeded to single cell library preparation.
The scRNA-seq library and sequencing were performed at the Yale Center for Genome Analysis (YCGA).

value: RNLS-/-

tag: treatment 1

value: RP81MNP, 70 mg/Kg, once a week for 4 weeks

tag: treatment 2


title: THCA.P20181226


title: WT-CTRL

description:
wt_ctrl
Single cell RNA

value: Wild-type

value: saline, 0.1ml/kg, 2 dose, 2 weeks apart

value: Healthy


title: SMK-2m-1

city: Biberach

first: Meshal

last: Ansari

address: Birkendorfer Straße 65

country: Germany

institute: Boehringer Ingelheim

description:
Drop-seq
muc13944

data_processing:
For preprocessing of the single cell data of mouse lung tissue cells, the Dropseq computational pipeline was used (version 2.3.0) as previously described (Pubmed ID: 26000488). Briefly, STAR (version 2.5.3a) was used for mapping. Reads were aligned to the mm10 reference genome (GSE63269). For barcode filtering, we excluded barcodes with less than 200 genes detected. A high proportion (> 20%) of transcript counts derived from mitochondria-encoded genes may indicate low cell quality, and we removed these unqualified cells from the downstream analysis.
Genome_build: mm10
Supplementary_files_format_and_content: Raw count matrix (MonocyteExtravasation_raw_counts.mtx) from Drop-seq experiments with 27780 genes and 68256 cells in market matrix format and corresponding column (MonocyteExtravasation_genes.txt) and row (MonocyteExtravasation_barcodes.txt) labels. Cell-level metadata (MonocyteExtravasxation_cells_metadata.txt).

source_name: Lung tissue

extract_protocol:
Single cells were diluted in PBS, supplemented with 0.04% bovine serum albumin up to a final concentration of 100 cells/µl. Using a microfluidic PDMS device (Nanoshift), single cells were co-encapsulated in droplets with barcoded beads (Chemgenes Corporation, Wilmington, MA) at a final concentration of 120 beads/uL. Droplets were collected for 15 min/sample. After droplet breakage, beads were harvested, washed, and prepared for on bead mRNA reverse transcription (Maxima RT, Thermo Fisher). Following an exonuclease I (New England Biolabs) treatment for the removal of unused primers, beads were treated with Klenow enzyme to improve single cell transcript quality; thereafter, beads were counted, aliquoted (2000 beads/reaction, equals ~100 cells/reaction), and pre-amplified by 12 PCR cycles (primers, chemistry, and cycle conditions identical to those previously described in Macosko et al., 2015).
PCR products were pooled and purified twice using 0.6x clean-up beads (CleanNA). Prior to tagmentation, cDNA samples were loaded on a DNA High Sensitivity Chip on the 2100 Bioanalyzer (Agilent) to ensure transcript integrity, purity, and amount. For each sample, 1 ng of pre-amplified cDNA from an estimated 1500 cells was tagmented by Nextera XT (Illumina) with a custom P5 primer (Integrated DNA Technologies). Single cell libraries were sequenced in a 100 bp paired-end run on the Illumina HiSeq4000 using 0.2 nM denatured sample and 5% PhiX spike-in. For priming of read 1, 0.5 µM Read1CustSeqB was used (primer sequence: GCCTGTCCGCGGAAGCAGTGGTATCAACGCAGAGTAC).

treatment_protocol: Cigarette smoke (CS) was generated from 3R4F Research Cigarettes, with the filters removed. Mice were whole body exposed to active 100% mainstream CS of 500 mg/m3 total particulate matter for 50 min twice per day for either 2 or 4 months in a manner mimicking natural human smoking habits. Control mice were kept in a filtered air (FA) environment, but exposed to the same stress as CS-exposed animals.

value: Lung tissue

tag: air exposure

value: cigarette smoke

tag: time point

value: 2 months

tag: number of cells


title: FA-4m-3

description:
Drop-seq
muc13929

value: filtered air


title: D124PrFcol

city: Dallas

first: Gervaise

middle: H.

last: Henry

state: Texas

address: 5323 Harry Hines Blvd, Mail Code:9110

department: Urology

institute: UT Southwestern Medical Center

data_processing:
Illumina's RTA version 1.18.66.3 was used for basecalling
10x Genomics’ cellranger mkfastq version 4.0.0 was used to demultiplex fastqs using default settings
10x Genomics’ cellranger count version 4.0.0 was used to generate mapped bam files using default settings
Genome_build: GRCh38
Supplementary_files_format_and_content: Genes-by-cells matrix in Hierarchical Data Format 5 File (H5)

source_name: Viable human prostate

extract_protocol:
Single-cell suspensions containing ~17400 cells were loaded on 10x Genomics Chromium single-cell Controller with 3’ library and gel bead kit v3 according to manufacture’s recommendations
According to 10x Genomics’ protocol, sequenced PE150 on NovaSeq 6000

treatment_protocol: Single-cells were dissociated (5mg/mL collaginase I) from health disected lower urinary tracts from an organ donor

tag: patient phenotype

value: Donor (Normal)

tag: tissue type

value: Prostate

tag: digestion enzyme

value: 5mg/mL Collagenase I 4hr

tag: 10x library type


title: D124VMFcol

source_name: Viable human verumontanum

value: Verumontanum


title: RC.P20190925

description:
processed data file:
RC_10X.CD4.counts.txt.gz
RC_10X.CD8.counts.txt.gz
metadata.txt.gz
10X_VDJ.merge.txt.gz
bulk_RNA.counts.txt.gz
bulk_Exome.mutation.txt.gz

source_name: RC

value: Tumor, Adjacent-normal

tag: platform


title: Control

description:
Single cell RNA
Named "ctrl" in the combined processed data files

value: Kidney

value: 4 months

tag: genotype

value: empty MNP, 70 mg/Kg, once a week for 4 weeks

value: cisplatin, 15mg/kg, 2 dose, 2 weeks apart


title: N2_0chol_3

value: 0 μg/ml cholesterol (0.1% ethanol)


title: FA-4m-2

description:
Drop-seq
muc13926

tag: tissue


title: RC.P20190923


title: Con_4

tag: condition

value: before LT

tag: Sex

value: Male


title: N2_0chol_1

tag: developmental stage

tag: exposure


title: SHP099_2_scRNA-seq

city: Nanjing

first: Dijun

last: Chen

state: Jiangsu

address: Xianlin

department: Life Sciences

institute: Nanjing University

data_processing:
Sample demultiplexing, barcode processing, and single cell 3’ gene counting were performed by the Cell Ranger pipelines (v3.1.0,10X Genomics).
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: TSV files with genes and barcode sequences corresponding to row and column indices, respectively.
Supplementary_files_format_and_content: matrix.mtx: Filtered gene-barcode matrix file (demultiplexed)

source_name: skin

growth_protocol: Eight- to ten-week-old female C57BL/6J mice were treated with a daily topical dose of 62.5 mg of IMQ cream (5%) (Aldara; 3M Pharmaceuticals) on the shaved dorsal skin for 4 consecutive days. Mice were sacrificed 1 day later after the last treatment.

extract_protocol:
Mouse skin were excised and mechanically dissociated into single cells using skin digestive enzymes
Single cells were captured in the 10×Genomics Chromium Single Cell 3′ Solution, and RNA-seq libraries were prepared following the manufacturer’s protocol (10×Genomics). The libraries were subjected to high-throughput sequencing on an Illumina Hiseq X Ten PE150 platform, and 150-bp paired-end reads were generated.

treatment_protocol: Mice were treated with SHP099 hydrochloride (10 mg/kg, i.g, every day) for an additional 4 days.

tag: mice

tag: mouse model

value: IMQ-induced psoriasis model

tag: treatment

value: Treated with 62.5 mg IMQ and 10 mg/kg SHP099


title: FA-4m-1

description:
Drop-seq
muc13925

value: Lung tissue

tag: air exposure


title: RNLSKO-CTRL

description:
rnlsko_ctrl
Single cell RNA

tag: strain

tag: age

value: Rnls knockout

value: saline, 0.1ml/kg, 2 dose, 2 weeks apart

tag: diagnosis

value: Healthy


title: SHP099_1_scRNA-seq


title: BPH553PrF

data_processing:
Illumina's RTA version 1.18.66.3 was used for basecalling
10x Genomics’ spaceranger mkfastq version 1.2.0 was used to demultiplex fastqs using default settings
10x Genomics’ spaceranger count version 1.2.0 was used to generate mapped bam files using default settings combining fastq's from NovaSeq 6000
Genome_build: GRCh38
Supplementary_files_format_and_content: Genes-by-cells matrix in Hierarchical Data Format 5 File (H5) and H&E image files (png)

source_name: OCT Frozen BPH Tissue

extract_protocol:
Slides were processed using 10x Genomics Visium Fresh-Frozen Spatial Gene Expression protocol (3' v1 with H&E).
According to 10x Genomics’ protocol, sequenced PE150 on a NovaSeq 6000
spatialRNA-seq

treatment_protocol: Tissues obtained fresh from simple prostatectomies on BPH patients were embedded in OCT.

tag: patient phenotype

value: BPH

tag: prostatic zone

value: Transition Zone

value: prostate


title: BPH559PrF


title: WT-CKD

description:
wt_ckd
Single cell RNA

value: Wild-type

value: CKD


title: SMK-4m-5

description:
Drop-seq
muc13924

value: cigarette smoke

tag: time point

value: 4 months

tag: number of cells


title: IMQ_2_scRNA-seq

value: Treated with 62.5 mg IMQ


title: RC.P20190919

value: Tumor, Adjacent-normal

tag: platform


title: RC.P20190918

tag: tissue


title: BPH186PrRpF


title: SMK-4m-4

description:
Drop-seq
muc13923


title: RC.P20181224


title: SMK-4m-3

description:
Drop-seq
muc13922


title: IMQ_1_scRNA-seq


title: BPH186PrRtF


title: Normal_2_scRNA-seq

value: Untreated


title: RC.P20181217


title: BPH560PrF


title: PACA.P20190909

description:
processed data file:
PACA_10X.CD4.counts.txt.gz
PACA_10X.CD8.counts.txt.gz
metadata.txt.gz
10X_VDJ.merge.txt.gz
bulk_RNA.counts.txt.gz
bulk_Exome.mutation.txt.gz

source_name: PACA

value: Tumor


title: BPH185RpF


title: Normal_1_scRNA-seq

value: IMQ-induced psoriasis model


title: SMK-4m-2

description:
Drop-seq
muc13921


title: SMK-4m-1

description:
Drop-seq
muc13920


title: BPH185RtF


title: PACA.P20190515


title: FA-2m-3

description:
Drop-seq
muc13919

value: filtered air

value: 2 months


title: BPH20PrF


title: PACA.P20190306


title: PACA.P20190225


title: FA-2m-2

description:
Drop-seq
muc13918

value: Lung tissue


title: FA-2m-1

description:
Drop-seq
muc13917


title: KR04

city: Aachen

first: Ivan

middle: Gesteira

last: Costa

state: Northrhine-Westphalia

address: Pauwelsstr. 19

department: Joint Research Center for Computational Biomedicine

institute: UKA RWTH Aachen

data_processing:
The Cell Ranger Software Suite (version 3.1.0) was used for processing sequencing information and single cell barcodes.
Seurat (version 3.2.2) was used to integrate the scRNA-seq data and predict cell labels.
Genome_build: GRCh38
Supplementary_files_format_and_content: barcodes: barcodes present in input data
Supplementary_files_format_and_content: matrix: a count matrix with Market Exchange Format (MEX). The first line contains the type code and the second line includes format and cell-ranger versions. Number of peaks, barcodes, and non-zero entries can be found in the third line.  The rest of the lines represent  nonzero entries with the first two numbers corresponding to peak and barcode indices and the last one corresponding to  the number of cut sites.
Supplementary_files_format_and_content: genes: a bed file contains genes corresponding to row indices. For each gene, its gene ID and name are stored in the first and second column of the gene.tsv file, respectively

source_name: SARS-CoV-2 infected iPSC-derived kidney organoids

growth_protocol: To generate human induced pluripotent stem cell (iPSC) derived kidney organoids, iPSCs were seeded using a density of 18,000 cells/cm2 on Geltrex (Thermo Fisher, Breda, the Netherlands) coated 6-well plates (Greiner Bio-one, Alphen aan de Rijn, the Netherlands). The differentiation protocol was modified from Takasato et al. (Takasato et al. 2016). On day 0 (d 0), differentiation was initiated using CHIR-99021 (6 µM, R&D systems, Abingdon, United Kingdom) in Essential 6 medium (E6, Thermo Fisher). CHIR treatment was maintained for 3 or 5 days and medium was replaced sequentially for E6 supplemented with fibroblast growth factor 9 (FGF9), 200 ng/ml, R&D systems) and heparin (1 µg/ml, Sigma-Aldrich, Zwijndrecht, Netherlands) up to d 7. Cell layers were trypsinized and suspensions were counted on d 7. One part 3 days CHIR-differentiated cells was mixed with two parts 5 days CHIR-differentiated cells. To generate cell aggregates, cells were aliquoted using 300,000 cells per 1.5 ml tube and centrifuged. Cell aggregates were plated on Costar Transwell filters (type 3450, Corning, Sigma-Aldrich). One hour CHIR pulse (5 µM) in E6 was used to stimulate self-organizing nephrogenesis and the medium was replaced for E6 supplemented with FGF9 and heparin for additional 5 days. As of d 7+5, organoids were cultured using E6 media supplemented with human epidermal growth factor (hEGF, 10 ng/ml, Sigma-Aldrich), bone morphogenetic protein-7 (BMP7, 50 ng/ml, R&D systems), stromal derived factor 1 beta (SDF1β, 10 ng/ml, R&D systems), vasopressin (10 nM, Sigma-Aldrich) and aldosterone (10 nM, Sigma-Aldrich) until viral infection at d 7+18.

extract_protocol: All protocols to generate scRNA-seq data on the 10x Chromium platform, including sample prep, library prep, instrument and sequencing settings, are available here: https://support.10xgenomics.com/single-cell-gene-expression

treatment_protocol: To study direct effects of the virus on kidney cells independent of systemic effects we chose human induced pluripotent stem cell (iPSC)-derived kidney organoids to model SARS-CoV-2 infection in vitro, using the Bavarian strain of the virus (MT270101.1). iPSC-derived kidney organoids were infected with SARS-CoV-2 at an MOI of 1.0 at d7+18. Virus incubation lastet 4h until changing the medium back to E6 without virus and incubating the organoids for five more days.

value: Kidney organoid

tag: condition

value: COVID


title: KR03


title: SMK-2m-5

description:
Drop-seq
muc13916


title: PACA.P20181128


title: PACA.P20181121


title: KR01

source_name: iPSC-derived kidney organoids without SARS-CoV-2 infection

value: CTR


title: SMK-2m-3

description:
Drop-seq
muc13914


title: OV.P20190304

description:
processed data file:
OV_10X.CD4.counts.txt.gz
OV_10X.CD8.counts.txt.gz
metadata.txt.gz
10X_VDJ.merge.txt.gz
bulk_RNA.counts.txt.gz
bulk_Exome.mutation.txt.gz

source_name: OV


title: Capture Sequencing of 166kb Enhancers + RARE∆ SynHoxA assemblon delivered to WT mESC

city: Seattle

first: Sudarshan

last: Pinglay

address: 3720 15th Ave NE

institute: University of Washington

description: mESC_WT_CompoundEnhancer_allRAREdelta_cloneA10

data_processing:
Library strategy: DNA-seq
Illumina adapter trimming with trimmomatic v0.39
Reads mapped using bowtie2 v2.2.9
Sort bam files using samtools
Make bigwig files using deeptools bamCoverage v3.2.1
Genome_build: mm10_synHoxA custom genome or mm10_synHoxA_delHoxA custom genome, mm10 or rn6
Supplementary_files_format_and_content: bigwig files to normalize coverage

organism:
Mus musculus
Rattus norvegicus

source_name: Mouse ES cells with variant synthetic Hox clusters

extract_protocol:
Plasmids were purified from small scale bacterial cultures (5-10 mL) using alkaline lysis. gDNA was extracted from mESC cell pellets using Qiagen DNA mini kit.
Illumina sequencing libraries for BACs were generated from 100-200 ng BAC DNA using NEBNext Ultra II FS DNA Library Prep Kit (New England Biolabs E7805S) according to the manufacturer’s protocol. Whole genome sequencing and capture sequencing libraries were prepared as follows: 1 µg of DNA was sheared to ∼500 to 900 bp in a 96-well microplate using the Covaris LE220 (450 W, 10% Duty Factor, 200 cycles per burst, and 90-s treatment time). Sheared DNA was purified using the DNA Clean and Concentrate-5 Kit (Zymo Research D4013), and the concentration was measured on a NanoDrop instrument (Invitrogen). DNA fragments were end-repaired with T4 DNA polymerase, Klenow DNA polymerase, and T4 polynucleotide kinase (New England Biolabs M0203S, M0210S and M0201S, respectively), and A-tailed using Klenow (3′-5′ exo-; New England Biolabs M0212L). Illumina-compatible adapters were subsequently ligated to DNA ends, and DNA libraries were amplified with KAPA 2X Hi-Fi Hotstart Readymix (Roche). Biotinylated baits for capture sequencing were prepared from assemblon BACs using nick translation

value: 166kb Enhancers + RARE{delta} SynHoxA assemblon in WT mESCs

tag: capture bait

value: 170kb Enhancers + SynHoxA BAC, pLM1103 + ICEFlanking

tag: cell type

value: mESC


title: SMK-2m-2

description:
Drop-seq
muc13913


title: KR02


title: ESCA.P20190916

city: Beijing

description:
processed data file:
ESCA_10X.CD4.counts.txt.gz
ESCA_10X.CD8.counts.txt.gz
metadata.txt.gz
10X_VDJ.merge.txt.gz
bulk_RNA.counts.txt.gz
bulk_Exome.mutation.txt.gz

data_processing:
For 10X data, Cell Ranger 3.0.0 was used to quantify gene expression level and to identify TCR sequences.
For Smart-seq2 data, HTSeqGenie pipeline (R package version 4.8) was used to quantify gene expression level.
For bulk RNAseq data, UCSC Xena Toil RNAseq pipeline was used to quantify gene expression level.
For bulk exome data, BWA-MEM algorithm was used to align the reads to genome, PICARD was used to sorted and de-duplicated the bam files, GATK 3.7 was used to realign reads around INDEL region and re-calibrate base quality, and finally strelka 1.0.14 was used to call somatic mutations (SNV and INDEL).
Genome_build: GRCh38 for RNA expression and TCR data, and b37 for DNA mutation calling.
Supplementary_files_format_and_content: text files for expression matrices, cell metadata, TCR summary, and mutation summary.

source_name: ESCA


title: Capture Sequencing of 166kb Enhancers + RARE∆ SynHoxA assemblon delivered to Hoxa -/- mESC

description: mESC_dHoxa_CompoundEnhancer_allRAREdelta_cloneG1

value: 166kb Enhancers + RARE{delta} SynHoxA assemblon in HoxA -/- mESCs


title: ESCA.P20190613


title: Capture Sequencing of 130kb RARE∆ SynHoxA assemblon delivered to WT mESC

value: 130kb RARE{delta} SynHoxA assemblon in WT mESCs


title: 5-6h wild type embryo m6A MeRIP-seq replicate 2

first: Guoqiang

last: Zhang

address: 1 Beichen West Road, Chaoyang District

institute: INSTITUTE OF ZOOLOGY, CHINESE ACADEMY OF SCIENCES

description: 5-6h_wt_embryos_mRNA_m6A_replicate_2.bed

data_processing:
Library strategy: meRIP-seq
For RNA-seq amd  Fmr1 RIP-seq, the reads were mapped to the reference genome of Drosophila melanogaster (Release 6/dm6) with TopHat version 2.0.Differential expression analysis was carried out by cuffdiff.
For MeRIP (m6A)-seq, reads were processed using Cutadapt software with the parameter "cutadapt -m 20 -q 15 -a AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC -A AGATCGGAAGAGCA -U 3", then the  clean reads were aligned to the Drosophila genome (version dm6) using HISAT2. MACS2 software was used for m6A peak calling with the default options except for "-no modle".
Genome_build: dm6
Supplementary_files_format_and_content: bed file of the callpeak result. Txt files for the FPKM value of RNA-seq and FMR1 RIP-seq

source_name: w1118 embryo

extract_protocol:
Total RNAs were isolated from embryos at the indicated stages using TRIzol reagent (Thermo Fisher). The mRNAs were purified using a NEBNext Poly(A) mRNA Magnetic Isolation kit (NEB) according to the user manual. The MeRIP-Seq was performed by Cloudseq Biotech Inc. (Shanghai, China) . Briefly, 5 ug of fragmented mRNAs were incubated with 5 ug of anti m6A polyclonal antibody (millipore) in IP buffer (150 mM NaCl, 10 mM Tris–HCl, 0.1% NP-40, pH 7.4) for 2 h at 4°C. The mixture was then immunoprecipitated by incubation with protein-A beads (Thermo Fisher) at 4◦C for an additional 2 h. Beads with captured RNA fragments were then immediately washed 3 times with 500 μl of ice-cold IP buffer. Bound mRNAs were eluted from the beads with N6-methyladenosine (BERRY & ASSOCIATES, PR3732) in IP buffer and then extracted with Trizol reagent (Thermo Fisher).
To RNA-seq and RIP-seq,  Illumina Truseq libraries were constructed according to the manufacturer’s instructions and sequenced using NovaSeq platform. with paired end read length of 150 bp. RNA-seq library generation with NEBNext® Ultra II Directional RNA Library Prep Kit (New England Biolabs, Inc., USA). MeRIP-Seq Library sequencing was performed on an illumina Hiseq instrument with 150bp paired-end reads.

tag: background strain

tag: genotype

value: wildtype

value: embryo


title: FoB Cic KO rep2

city: Pohang-Si

first: Hyebeen

last: Hong

address: Cheongam-Ro, 77

institute: POSTECH

description:
Spleen
Table_S2.xlsx

data_processing:
1) Quality control analysis of the raw sequenced reads was performed to examine overall reads' quality, total bases, total reads, and GC (%).
2) Artifacts such as low quality reads, adaptor sequences, contaminant DNAs, or PCR duplicates were removed to reduce biases.
3) Trimmed reads were mapped to mouse reference genome with HISAT2, a splice-aware aligner.
4) Transcripts were assembled with aligned reads by StringTie. It provides information of known transcripts, novel transcripts, and alternatively spliced transcripts.
5) Expression profiles were represented as read counts and normalization values, based on the transcript length and depth of coverage. The FPKM (Fragments Per Kilobase of transcript per Million Mapped reads) value was used as a normalization value.
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: The differentially expressed genes (DEGs) in Cic-null B-1a and Fo B cells are presented in Table_S1_DEG.xlsx and Table_S2_DEG.xlsx file, respectively. KO versus Control fold changes, p-values, read counts and FPKM values for each sample are also shown in Table S1_DEG.xlsx and Table S2_DEG.xlsx files.

source_name: Follicular B cell

extract_protocol:
B-1a (IgM+, CD19+, CD5+, CD43+) and Fo B (B220+, CD93-, CD23+, CD21lo-mid) cells were isolated from the spleen by FACS-sorting using a MoFlo-XDP (Beckman Coulter). Total RNA was extracted using TRIzol Reagent (GeneAll, Seoul, Republic of Korea) according to the manufacturer's protocol.
DNA library for mRNA sequencing was prepared using a SMART-seq v4 Ultra Input RNA Kit (Clontech, for B-1a cells) and TruSeq RNA Sample Prep Kit v2 (Illumina, for Fo B cells), according to the manufacturer’s protocols. Libraries were sequenced on the Illumina Hiseq 4000 sequencer.

value: Splenic follicular B cells

value: 12 weeks


title: FoB Cic KO rep1

description:
Spleen
Table_S2.xlsx


title: Capture Sequencing of 130kb RARE∆ SynHoxA assemblon delivered to Hoxa -/- mESC

value: 130kb RARE{delta} SynHoxA assemblon in HoxA -/- mESCs


title: 5-6h wild type embryo m6A MeRIP-seq replicate 1

description: 5-6h_wt_embryos_mRNA_m6A_replicate_1.bed


title: Capture Sequencing of Parental WT A17iCre mESCs

value: Parental WT A17iCre mESCs


title: ESCA.P20181114

extract_protocol:
Tumors and adjacent normal tissues were cut into approximately 1-2 mm3 pieces in the RPMI-1640 medium (Gibco) with 10% fetal bovine serum (FBS, Gibco), and enzymatically digested with gentleMACS (Miltenyi) for 60 min on a rotor at 37°C, according to manufacturer’s instruction. The dissociated cells were subsequently passed through a 100 µm SmartStrainer and centrifuged at 400 g for 5 min. After the supernatant was removed, the pelleted cells were suspended in red blood cell lysis buffer (TIANDZ) and incubated on ice for 1-2 min to lyse red blood cells. After washing twice with 1× PBS (Gibco), the cell pellets were re-suspended in sorting buffer (PBS supplemented with 1% FBS).
Single cell suspensions were stained with antibodies against CD45 and 7AAD for FACS sorting, performed on a BD Aria SORP instrument. Based on FACS analysis, single cells were sorted into 1.5 ml tubes (Eppendorf) and counted manually under the microscope. The concentration of single cell suspensions was adjusted to 500-1200 cells/ul. Cells were loaded between 7,000 and 15,000 cells/chip position using the 10x Chromium Single cell 5’ Library, Gel Bead & Multiplex Kit and Chip Kit (10x Genomics, V3 barcoding chemistry) according to the manufacturer’s instructions. All the subsequent steps were performed following the standard manufacturer’s protocols. Purified libraries were analyzed by an Illumina Hiseq X Ten sequencer with 150-bp paired-end reads.
10x Chromium Single cell 5’ + VDJ Library, and Smart-seq2 Library (only for one CHOL sample)

value: Tumor, Adjacent-normal


title: ESCA.P20181123


title: Atrial Fibrillation 10

city: Seoul

first: Hyewon

last: Park

address: Gangseo-gu

institute: Ewha Womans University College of Medicine

hyb_protocol: A hybridization mixture with controls, including control oligo B2, 20 X hybridization controls (bioB, bioC, bioD, cre), 27.5% Formamide, DMSO, 2 X hybridization buffer and water, was added to all eight samples. 110.5 μl of this mixture was injected into GeneChip miRNA 4.0 arrays (Affymetrix, Santa Clara, California, USA) and placed in the Affymetrix GeneChip Hybridization Oven 640 at 48 °C and 60 rpm for 16 h overnight. Stain cocktails (stain cocktail 1 and stain cocktail 2) were added to amplify signal intensities.

scan_protocol: Arrays were stained and washed in the Affymetrix GeneChip Fluidics Station 450 using the FS450_0002 fluidics protocol. All arrays were scanned with the Affymetrix GeneChip Scanner 3000

data_processing:
The raw analysis performed with Transcriptome Analysis ConsoleTM(TAC) software. The raw data images produced from the scanner were processed into CEL files, which contained measure intensities for each probe on the array
CEL files were imported into the Gene Expression Workflow in GeneSpring GX version 14.9.1 (Agilent Technologies Inc.,). The RMA algorithm (Background correction, log2 transformation, and probeset summarization) was performed using default settings in GeneSpring software. A Principal Component Analysis (PCA), which reduces the dimensionality of a data set consisting of a large number of interrelated variables, was performed using a covariance dispersion matrix as part of the quality control of the data.

label: biotin

source_name: urine

label_protocol: The RNA was labeled using the FlashTag Biotin RNA Labeling Kit (Affymetrix Inc., Santa Clara, CA, USA) and hybridized to GeneChip miRNA 4.0 microarrays (Affymetrix Inc., Santa Clara, CA, USA). Briefly, 800 ng of RNA was poly-A tailed and a proprietary biotin-labeled dendramer molecule was joined to the 3′ end using DNA ligase.

extract_protocol: The miRNeasy kit from Qiagen requires the addition of 100 µl of urine to 700 µl of Qiazol.  The minimum volume that we have tested is 12 µl of urine and we have been able to generate amplifiable cDNA from RNA extracted with volumes ranging from 12 to 100 µls of urine. The use of the lowest recommended volume of RNase-free water to elute the RNA from the column (30 µls) is used in order to keep the extracted RNA as concentrated as possible.

tag: status after 5 years

value: Alive

tag: disease state

value: Atrial Fibrillation

tag: Sex

value: Male


title: SMK-2m-4

description:
Drop-seq
muc13915

value: Lung tissue

tag: air exposure

value: cigarette smoke

value: 2 months


title: FoB Control rep2

description:
Spleen
Table_S2.xlsx

tag: strain

tag: age


title: 5-6h wild type embryo Input for MeRIP-seq replicate 2


title: Atrial Fibrillation 7

value: Female


title: ESCA.P20190411

first: Shishang

last: Qin

institute: Peking university


title: Capture Sequencing of HoxA -/- A17iCre mESCs

value: Parental HoxA -/- A17iCre mESCs

value: 170kb Enhancers + SynHoxA BAC, pLM1103 + ICEFlanking

value: mESC


title: FoB Control rep1

description:
Spleen
Table_S2.xlsx


title: paroxysmal supraventricular tachycardia 2

value: paroxysmal supraventricular tachycardia


title: paroxysmal supraventricular tachycardia 5


title: ESCA.P20190410


title: Capture Sequencing of 170kb Enhancers + SynHoxA assemblon delivered to Hoxa -/- mESC

value: 170kb Enhancers + SynHoxA assemblon in HoxA -/- mESCs

value: 170kb Enhancers + SynHoxA BAC


title: B1a Cic KO rep2

description:
Spleen
Table_S1.xlsx

source_name: B-1a cell

value: Splenic B-1a cells

value: 12 weeks


title: 0-1h wild type embryo m6A MeRIP-seq replicate 2

description: 0-1h_wt_embryos_mRNA_m6A_replicate_2.bed

value: wildtype

value: embryo


title: B1a Cic KO rep1

description:
Spleen
Table_S1.xlsx


title: Atrial Fibrillation 8

value: Alive


title: 0-1h wild type embryo m6A MeRIP-seq replicate 1

description: 0-1h_wt_embryos_mRNA_m6A_replicate_1.bed


title: BC.P20190123

description:
processed data file:
BC_10X.CD4.counts.txt.gz
BC_10X.CD8.counts.txt.gz
metadata.txt.gz
10X_VDJ.merge.txt.gz
bulk_RNA.counts.txt.gz
bulk_Exome.mutation.txt.gz

source_name: BC

value: Tumor, Adjacent-normal


title: Atrial Fibrillation 9

value: Atrial Fibrillation

value: Male


title: 0-1h wild type embryo Input replicate 2


title: Atrial Fibrillation 6


title: Capture Sequencing of 134kb SynHoxA assemblon delivered to WT mESC

value: 134kb SynHoxA assemblon in WT mESCs

value: 134kb SynHoxA BAC


title: BC.P20190403


title: paroxysmal supraventricular tachycardia 3

value: Female


title: B1a Control rep1

description:
Spleen
Table_S1.xlsx


title: 0-1h wild type embryo Input replicate 1


title: 5-6h wild type embryo Input for MeRIP-seq replicate 1