title: RNA-seq_Microglia, SALL1 Enhancer Heterozygous KO, Rep3

value: Sall1 Enhancer Heterozygous


title: SAMPLE 23_prime/boost challengeFluB-RANS/IGIPd14 dpc

status: Public on May 01 2023

type: protein

city: Athens

first: Daniel

middle: Roberto

last: Perez

state: GA

address: 953 College Station Road

country: USA

institute: University of Georgia

description:
Fig. 5, 6 and 7
UGA#3 IBV-IGIP array

hyb_protocol: Serum and NW samples were diluted 1:100 in a protein array blocking buffer (GVS, Sanford,  ME, USA), supplemented with E. coli lysate (GenScript, Piscataway, NJ, USA) to a final  concentration of 10 mg/mL, and preincubated at room temperature (RT) for 30 min. Concurrently,  arrays were rehydrated in blocking buffer (without lysate) for 30 min. Blocking  buffer was removed, and arrays were probed with preincubated serum samples using  sealed chambers to prevent cross-contamination of samples between the pads. Arrays were  incubated overnight at 4  C with gentle agitation. They were then washed at RT three  times with Tris-buffered saline (TBS) containing 0.05% Tween 20 (T-TBS), biotin-conjugated  goat anti-mouse IgA and Biotin-conjugated anti-mouse IgG (Jackson Immuno Research  Laboratories, Inc., West Grove, PA, USA) were diluted 1:400 in blocking buffer and applied  to separate arrays for 1 h, RT with gentle agitation. Arrays were washed three times  with T-TBS, followed by incubation with streptavidin-conjugated Qdot655 (Thermo Fisher  Scientific, Waltham, MA, USA) diluted 1:200 in blocking buffer for 1 h, RT. Arrays were  washed three times with T-TBS and once with water. Arrays were air dried by centrifugation  at 500 g for 5 min. Images were acquired using the ArrayCAM imaging system from  Grace Bio-Labs (Bend, OR, USA). Spot and background intensities were measured using  an annotated grid (.gal) file. Mean fluorescence across antigens grouped by isotypes were  used for subsequent analysis. The different antigens were acquired from Sino biological  (Wayne, PA, USA).

scan_protocol: Images were acquired using the ArrayCAM imaging system from Grace Bio-Labs (Bend, OR) with gain and exposure times of 50 and 400-1000ms, respectively.

data_processing: Spot and background intensities were measured using an annotated grid (.gal) file.  Signal intensities (SI) for each antigen on the array were first background corrected by subtracting sample-specific T-PBS buffer signals from purified protein spot signals. For statistical analysis,   A two-way ANOVA was performed. A P value below 0.05 was considered significan. All data analyses and graphs were performed using GraphPad Prism software version 9 (GraphPad Software Inc., San Diego, CA, USA).

molecule: protein

organism: Mus musculus

source_name: Serum

extract_protocol: Blood and nasal wash samples were collected at 14 dpc for serology and to determine antigen-specific IgG and IgA responses

tag: tissue

value: Serum

tag: vaccine regimen

value: prime/boost challenge

tag: vaccine

value: FluB-RANS/IGIP

tag: time point

value: d14 dpc

tag: mouse id

tag: extracted molecule

value: IgG


title: SJ_PQRXLF-3

type: SRA

city: New York

first: Yimeng

last: Zhu

state: NY

address: 1130 ST NICHOLAS AVE.

department: Institute for Cancer Genetics

institute: Columbia University

description: Signal Join junctions on the chromosomal V(D)J recombination substrate pMX-INV

library_source: genomic

data_processing:
Basecalls performed using Illumina RTA version 1.18.54.
Miseq reads were first de-multiplexed by fastq-multx tool from ea-util, then adaptor sequence was further trimmed with SeqPrep utility.
Pre-processed reads were then mapped to customized mm9 (for CSR) or mm10 (for chromosomal V(D)J recombination) genome using Bowtie2. The best-path searching algorithm (related to YAHA; G. G. Faust, et al. Bioinformatics 28, 2417-2424 (2012)) was used to identify optimal sequence alignments from Bowtie2-reported top alignments (alignment score > 50).
The reads were then filtered to exclude mis-priming events, germline (unmodified) sequence, sequential joints, and duplicated reads. A “duplicate read” is defined by bait and prey alignment coordinates within 2 nt of another read’s bait and prey alignments. Since signal joint reads number was very low after applying deduplication filter, this filter was not used for SJ analysis. For SJ and CJ deletion analyses, the deletion size was capped at 1,000 bp. Since some switch region sequences are very repetitive, the alignments in those regions were filtered out by the mappability filter. But they do unequivocally map to an individual switch region, so to plot all the switch region junctions, we added the ones filtered out by the mappability filter back after deduplication (J. Dong, et al. Nature 525, 134-139 (2015)). MHs are defined as regions of 100% homology between the bait and prey-break site. Insertions are defined as regions containing nucleotides that map to neither the bait nor prey-break site. Blunt junctions are considered to have no MHs or insertions.
To specifically study the DNA repair junctions on the pMX-INV substrate we added the substrate sequence as an additional chromosome (chrP) on top of the mm10 genome during the alignment process.
Supplementary files format and content: .xlsx files generated from tab-delimited text files after analysis for reads distribution.

molecule: genomic DNA

source_name: Bone marrow

growth_protocol: V-abl transformed B cells from mice were cultured in DMEM medium.

extract_protocol:
Genomic DNA was extracted from treated B cells on day 4.
Sonicated DNA was linearly amplified with primer (/5Bios/GGCAGCCTACCAAGAACAAC) and nested amplified with primer (5′-CGGTGGTACCTCACCCTTA-3′). Germline sequence was removed with EcoRI (NEB) digestion.
High-throughput genome translocation sequencing (HTGTS). Sequenced with MiSeq 500v.

treatment_protocol: V-abl transformed B cells with integrated pMX-INV substrate were treated with STI571 (3 µM; Novartis Pharmaceuticals) for 4 days to arrest cells in G1 phase and induce RAG recombinase expression, generating breaks for V(D)J recombination of the substrate. Cells were analyzed via flow cytometry before DNA extraction.

value: Bone marrow

tag: cell line

value: v-abl transformed B cell

tag: cell type

value: B cells

tag: genotype

value: DNA-PKcsPQR/PQRXlf-/-

tag: treatment

value: STI571 for 4 days


title: RNA-seq_Microglia, SALL1 Enhancer Heterozygous KO, Rep2

city: La Jolla

first: Christopher

last: Glass

state: CA

address: 9500 Gilman Dr.

department: CMM

institute: University of California, San Diego

library_source: transcriptomic

data_processing:
FASTQ files from sequencing experiments were mapped to mm10. RNA-seq files were mapped using STAR with default parameters. The gene expression raw counts were quantified by HOMER's (Heinz et al., 2020) analyzeRepeats command with the option “-condenseGenes -count exons -noadj”. Differential gene expression was calculated using the HOMER command “getDiffExpression.pl”. TPM (transcript per kilobase million) were quantified for all genes matching accession number to raw counts. Differentially expressed genes were assessed with DESeq2 (Love et al., 2014) at p-adj (adjusted pvalue) < 0.05 and FC (fold change) > 2 where indicated. Genes with TPM < 4 in all conditions were removed from analysis. Gene ontology enrichment analyses were performed using Metascape (Zhou et al., 2019)).
Assembly: mm10
Supplementary files format and content: SALL1SMAD4_RNAseq_RAW.txt, tab-delimited text file containing table of unnormalized read counts ffor all RNA-seq samples
Supplementary files format and content: SALL1SMAD4_RNAseq_TPM.txt, tab-delimited text file containing table of TPM counts for all RNA-seq samples

molecule: polyA RNA

source_name: Brain

extract_protocol:
Mouse brains were homogenized as previously described by gentle mechanical dissociation (Gosselin et al, 2014) and stained with anti-mouse anti-CD11b-APC (BioLegend 101212), anti-CD45-Alexa488 (BioLegend 103122), and anti-CX3CR1-PE (BioLegend 149006). Microglia were sorted as DAPI negative, singlets, and CD11b+CD45lowCX3CR1+. Total RNA was extracted from sorted cells using the Direct-zol RNA MicroPrep Kit (Zymo Research R2052) and stored at -80°C until library preparation.
RNA-seq libraries were prepared as previously described (Sakai et al., 2019, Immunity)  with approximately 100,000 sorted live microglia. mRNAs were enriched from total RNA by incubation with Oligo d(T) Magnetic beads (NEB, S1419S) in 2X DTBB buffer (20 mM Tris-HCl pH 7.5, 1 M LiCl, 2mM EDTA, 1% lithium dodecyl sulfate, 0.1% Triton X-100) at 65°C for 2 minutes and were incubated at room temperature while rotating for 15 minutes. The beads were then washed 1x with RNA Wash Buffer 1 (10mM TrisHCl pH 7.5, 0.15M LiCl, 1mM EDTA, 0,1% lithium dodecyl sulfate 0.1% Triton X-100) and 1x with RNA Wash Buffer 3 (10mM Tris-HCl pH 7.5, 0.15 M NaCl, 1mM EDTA) before elution in RNA Elution Buffer (10mM Tris-HCl pH 7.5, 1mM EDTA) at 80°C for 2 minutes. PolyA selection was performed a second time, and samples were washed 1x with Wash Buffer 1, 1x with Wash Buffer 3, and 1x with 1x SuperScript III first-strand buffer. Beads were then resuspended in 10 µL 2x SuperScript III buffer plus 10 mM DTT, and RNA was fragmented at 94°C for 9 minutes and immediately chilled on ice before the next step. For first-strand synthesis, 10 µL of fragmented mRNA, 0.5 µL Random primers (50 µM)(Thermo Fisher), 0.5 µL SUPERase-In (Ambion), 1µL dNTPs (10mM), and 1µL of DTT (10mM) were heated for 50°C for one minute. At the end of incubation, 5.8 µL of water, 1 µL of DTT (100mM), 0.1 µL Actinomycin D (2µg/uL), 0.2uL of 1% Tween-20 (Sigma) and 0.5µL of SuperScript III (Thermo Fisher Scientific) were added and incubated in a PCR machine using the following conditions: 25°C for 10 minutes, 50°C for 50 minutes, and a 4°C hold. The product was then purified with RNAClean XP beads (Beckman Coulter) according to manufacturer’s instruction and eluted with 10 µL nuclease-free wate. The RNA/cDNA double-stranded hybrid was then added to 1.5 µL Blue Buffer (Enzymatics), 1.1 µL of dUTP mix (10mM dATP, dCTP, dGTP and 20 mM dUTP), 0.2 µL RNase H (5U/uL), 1.05 µL of water, 1µL of DNA Polymerase I (Enzymatics) and 0.15 µL of 1% Tween-20. The mixture was incubated at 16°C overnight. The following day, the dUTP marked dsDNA was purified using 28 µL of SpeedBeads (GE Healthcare), diluted with 20% PEG8000, 2.5M NaCl to a final concentration of 13% PEG, eluted with 40 µL elution buffer (DNA elution buffer from Zymo ChIP Clean and Concentrator Kit). The purified dsDNA underwent end repair by blunting, A-tailing, and adaptor ligation as previously described 14 using barcoded adapters (NextFlex, Bioo Scientific). Libraries were PCR amplified for 16 cycles, size for 200-500bp size range, quantified using a Qubit dsDNA HS Assay Kit (Thermo Fisher Scientific) and sequenced on a HiSeq 4000 for 51 cycles according to the manufacturer’s instructions.

value: Brain

tag: strain

value: whole cell Microglia (CD45+ CD11b+ CX3CR1+)


title: SAMPLE 22_prime/boost challengeFluB-RANS/IGIPd14 dpc

description:
Fig. 5, 6 and 7
UGA#3 IBV-IGIP array


title: 110721_1_S52

city: Aurora

first: Lauren

last: Vanderlinden

state: Colorado

address: 13001 E. 17th Place, Mail Stop B119

department: Department of Biostatistics and Informatics

institute: Colorado School of Public Health

data_processing:
FASTQ files for the two runs for each sample were concatenated. Reads were trimmed to remove adapters and low-quality base calls with Cutadapt (13). Reads were aligned to the reference human genome (hg19) with use of TopHat2 (14). Individual samples were quantified against the most up-to-date Ensembl reference transcriptome with the RSEM (RNA-Seq by Expectation-Maximization) algorithm (15). The expected counts were used for further processing and normalization. For removal of any technical variation, the data first were quantile normalized with DESeq2 (16) and then normalized with removal of unwanted variation (17). Based on scree plots, we adjusted for one factor, as it explained the most variability in the data. The data were then transformed with the regularized log function (16). The transformed data were used in all subsequent analyses. We filtered out genes if ≥20% of the samples did not have a read mapped to the gene (transcripts per million value of 0) or the average transcripts per million value across all samples was <1. A total of 12,477 genes passed the filtering criteria.
Assembly: hg19/Ensembl.v87
Supplementary files format and content: RSEM.RUVs.k1.rlog.Dec2020.csv  Final normalized and cleaned dataset used in analyses, each row a gene and column a sample.
Supplementary files format and content: RSEM.estCounts.geneLevel.csv Estimated counts per gene from the RSEM output.  Not normalized or cleaned.

molecule: total RNA

organism: Homo sapiens

source_name: blood

extract_protocol:
In DAISY, venous blood samples are collected at 9, 15, and 24 months and yearly thereafter. Beginning in November of 2007, RNA samples were collected from all DAISY participants with Tempus tubes (Applied Biosystems). We selected samples from two visits (termed IA-1 and IA-2) that occurred after the onset of IA for mRNA sequencing. The IA-1 visit was selected as the first available visit after the onset of IA for all groups. In the progressor group, the visit that preceded clinical onset of T1D was selected as the IA-2 visit. In the maintainer and reverter groups, the IA-2 visit was selected as the visit where age was closest to median age in the progressor group at the IA-2 visit.
Total RNA was isolated and purified from frozen (−80°C), peripheral whole blood samples ofn= 138 subjects meeting the inclusion criteria (Supplementary Material). We also included 12 control samples and 12 technical replicates. NuGEN library preparation kits were used to construct the strand-specific total RNA libraries. The Globin AnyDeplete kit was used to remove globin transcripts. RNA integrity number (RIN) scores for all samples were quantitated with use of the TapeStation (Agilent). Paired-end 150-cycle 2 × 150 sequencing was performed with the Illumina NovaSeq 6000 system. Samples were pooled together in a single flow cell and were sequenced twice to obtain the desired read depth, resulting in a median read depth of 90 million paired end reads across the samples (range 54–128 million).

value: blood

tag: ID

tag: tr n

tag: visit

value: RNA 2

tag: group

value: Progressor

tag: female yn

tag: nhw yn

tag: dr34 yn

tag: fdr yn

tag: age

tag: age ia


title: SAMPLE 21_prime/boost challengeFluB-RANS/IGIPd14 dpc

description:
Fig. 5, 6 and 7
UGA#3 IBV-IGIP array

tag: tissue

tag: vaccine regimen

tag: vaccine

tag: time point

tag: mouse id


title: SJ_PQRXLF-2

tag: cell line

tag: cell type

tag: genotype

tag: treatment


title: RNA-seq_Microglia, SALL1 Enhancer Heterozygous KO, Rep1

tag: strain


title: 110638_1_S44

tag: ID

tag: tr n

tag: visit

value: RNA 1

tag: group


title: 110585_2_S84

value: Reverter

tag: female yn

tag: nhw yn

tag: dr34 yn

tag: fdr yn


title: SJ_PQRXLF-1

tag: tissue


title: RNA-seq_Microglia, SALL1 Enhancer WT, Rep3

value: Wild type


title: 110506_2_S92

tag: age

tag: age ia


title: SAMPLE 20_prime/boost challengeFluB-RANS/IGIPd14 dpc

description:
Fig. 5, 6 and 7
UGA#3 IBV-IGIP array

value: Serum

tag: vaccine regimen

value: prime/boost challenge

tag: vaccine

tag: time point

tag: mouse id

tag: extracted molecule


title: SAMPLE 19_prime/boost challengeFluB-RAM/IGIPd14 dpc

description:
Fig. 5, 6 and 7
UGA#3 IBV-IGIP array

value: FluB-RAM/IGIP

value: d14 dpc


title: SJ_XLF-2

value: Bone marrow

tag: cell line

tag: cell type

tag: genotype

value: Xlf-/-

tag: treatment


title: RNA-seq_Microglia, SALL1 Enhancer WT, Rep2

tag: strain


title: 110494_1_S18

tag: ID

tag: tr n

tag: visit

tag: group

value: Maintainer

tag: female yn


title: RNA-seq_Microglia, SALL1 Enhancer WT, Rep1

tag: tissue


title: 110473_1_S10

tag: nhw yn

tag: dr34 yn

tag: fdr yn

tag: age

tag: age ia


title: SJ_XLF-1

value: v-abl transformed B cell

value: B cells


title: SJ_PQR-3

value: DNA-PKcsPQR/PQR

value: STI571 for 4 days


title: SAMPLE 18_prime/boost challengeFluB-RAM/IGIPd14 dpc

description:
Fig. 5, 6 and 7
UGA#3 IBV-IGIP array

tag: vaccine regimen

tag: vaccine

tag: time point

tag: mouse id

tag: extracted molecule

value: IgG


title: SAMPLE 17_prime/boost challengeFluB-RAM/IGIPd14 dpc

description:
Fig. 5, 6 and 7
UGA#3 IBV-IGIP array


title: 110584_2_S83

value: blood


title: EKO_SMAD4_Input_Rep2

description: Input used for: Microglia, SMAD4 ChIPseq Input, SMAD4-conditional KO, Rep2  Microglia, SALL1 ChIPseq Input, SALL1 Enhancer KO, Rep2

data_processing:
FASTQ files were mapped to the mouse mm10 genome using Bowtie2 with default parameters (Langmead and Salzberg, 2012). After mapping, tag directories were created using the HOMER command makeTagDirectory (Heinz et la., 2010). To quantify the TF binding and chromatin accessibility between conditions, raw and normalized tag counts at merged IDR peaks identified by HOMER’s mergePeaks were identified using HOMER’s annotatePeaks with “-noadj,” “-size 500” for TF ChIP-seq peaks and “-size 1000” for ATAC peaks annotated with H3K27ac reads. DESeq2 was used to identify differentially bound TF binding distal sites or differential distal chromatin accessibility (p-adj. < 0.05 and FC >2 or <-2).  Super-enhancers were defined using the HOMER ‘findPeaks -style super’ command.
Supplementary files format and content: Tab delimited text file containing IDR peaks for P300, SALL1 and SMAD4
Supplementary files format and content: Tab delimited text file containing Microglia H3K27ac peaks centered on ATAC peaks
Supplementary files format and content: Tab delimited text file containing peak files for H3K27ac for NeuN, PU1, and Olig2 nuclei

extract_protocol:
Mouse brains were homogenized as previously described (Gosselin et al. 2014)  by gentle mechanical dissociation. Cells were then incubated in staining buffer on ice with anti-CD16/32 blocking antibody (BioLegend 101319) for 15 minutes, and then with anti-mouse anti-CD11b-APC (BioLegend 101212), anti-CD45-Alexa488 (BioLegend 103122), and anti-CX3CR1-PE (BioLegend 149006) for 25 minutes. Cell preparations for H3K27ac ChIP-seq were fixed with 1% formaldehyde for 10 minutes and quenched with 0.125M glycine for 5 minutes after staining, and subsequently washed three times. Cells were washed once and filtered through a 40 M cell strainer. Sorting was performed on a Sony MA900 or MoFlo Astrios EQ cell sorter. Microglia were defined as events that were DAPI negative, singlets, and CD11b+CD45lowCX3CR1+. Sorted microglia were pelleted at 800xg for 5 minutes, pellets were then snap frozen and stored at -80°C prior to library preparation. Brain nuclei were isolated as previously described (Nott et al., 2019), with initial homogenization performed with either 1% formaldehyde in Dulbecco’s phosphate buffered saline or 2mM DSG (Proteochem) in Dulbecco’s phosphate buffered saline. Nuclei were stained overnight with PU.1-PE (Cell Signaling 81886S), OLIG2-AF488 (Abcam 225099) or SALL1 AF647 (Thermo, clone NRNSTNX 51-9279-82) or NEUN-AF488 (Millipore MAB 377X). Nuclei were washed the following day with 4 mL FACs buffer, passed through a 40 uM strainer, and stained with 0.5 ug/mL DAPI. Nuclei for each cell type were sorted with a Beckman Coulter MoFlo Astrio EQ cell sorter and pelleted at 1600xg for 5 minutes at 4°C in FACs buffer. Nuclei pellets were snap frozen and stored at -80°C prior to library preparation.
Chromatin immunoprecipitation was performed as previously described (Heinz et al., 2018). For H3K27ac ChIP, 500,000-1,000,000 fixed sorted cells or nuclei were thawed on ice and resuspended in ice-cold LB3 (10mM Tris-HCl pH 7.5, 100mM NaCl, 1 mM EDTA, 0.5mM EGTA, 0.1% Na-Deoxycholate, 0.5% N-lauroylsarcosine), 1x protease inhibitor cocktail (Sigma). Chromatin was sheared by sonication. Samples were sonicated in a 96 Place microtube Rack (Covaris cat#500282) using a Covaris E220 for 12 cycles with the following setting: time 60 seconds, duty cycle 5.0, PIP 175, cycles, 200, amplitude 0.0, velocity 0.0, dwell 0.0. Samples were recovered and spun down at max speed, 4°C for 10 minutes. The supernatant was then diluted 1.1-fold with ice-cold 10% Triton X-100. One percent of the lysate was kept as ChIP input. 25 uL of Dynabeads Protein A were added per sample, in addition to 1ug of a specific antibody for H3K27ac (Active Motif 39685). The samples were rotated overnight at 4°C and were washed as follows the next day: 3x with Wash Buffer I (20mM Tris-HCl pH 7.5, 150 mM NaCl, 2mM EDTA, 0.1% SDS, 1% Triton X-100) + protease inhibitor cocktail, 3x with Wash Buffer III (10mM Tris-HCl pH 7.5, 250 mM LiCl, 1% Triton X-100, 1mM EDTA, 0.7% Sodium Deoxycholate)+ protease inhibitor cocktail, 2x with TET (0.2% Tween-20/TE) + 1/3 protease inhibitor cocktail, 1x with TE-NaCl (50mM NaCl + TE), and 1x with IDTET (0.2% Tween-20, 10mM Tris pH8, 0,1mM EDTA). Samples were finally resuspended in TT buffer (10mM Tris pH 8 + 0.05% Tween 20) prior to on-bead library preparation. For SALL1, SMAD4, and P300 ChIPs, 500,0000-2million nuclei were thawed on ice and resuspended in ice-cold RLNR1 buffer (20mM Tris HCl pH 7.5, 150 mM NaCl, 1 mM EDTA, 0.5 mM EGTA, 0.4% sodium deoxycholate, 1% NP-40, 0,1% SDS, 0.5mM DTT) + 1x protease inhibitor cocktail/PMSF. Samples were sonicated in a 96 Place microtube Rack (Covaris cat#500282) using a Covaris E220 for 20 cycles with the following setting: time 60 seconds, duty cycle 5.0, PIP 175, cycles, 200, amplitude 0.0, velocity 0.0, dwell 0.0. Samples were recovered and spun down at max speed, 4°C for 10 minutes. One percent of the lysate was kept as ChIP input. 10 uL of Dynabead Protein A and 10 uL of Dynabead Protein G beads per sample were coupled to either 4 ug of SALL1 antibody (Abcam, ab41974), SMAD4 antibody (1 μg each of Cell Signaling technology 46535 and 38454), or P300 antibody (1 ug each of EMD Millipore RW128  and Diagenode C15200211). Beads/antibody was added to each sample, which were then rotated overnight at 4°C. The samples were washed with the following buffers: 3x RLNR1 + PIC/PMSF/DTT, 6x LWB-RCNR1 (10mM Tris HCl pH 7.5, 1mM EDTA, 0.7% sodium deoxycholate, 1% NP-40, 250mM LiCl)+ PIC/PMSF, 3x TET, 2x IDTET, and then resuspended in TT for on-bead library preparation. Libraries for ChIP and input samples were prepared with NEBNext Ultra II DNA library prep kit (NEB) reagents according to the manufacturer’s protocol on the beads suspended in 25 μL TT (10mM Tris/HCl pH7.5, 0.05% Tween-20), with reagent volumes reduced by half. DNA was eluted and crosslinks reversed by adding 4 μl 10% SDS, 4.5 μl 5 M NaCl, 3 μl EDTA, 4 μl EGTA, 1 μl proteinase K (20 mg/ml), 16 μl water, incubating for 1 h at 55°C, then 30 minutes to overnight at 65°C. DNA was purified using 2 μL of SpeedBeads (GE Healthcare), diluted with 20% PEG8000, 1.5M NaCl to final of 12% PEG, eluted with 25 μl TT.  DNA contained in the eluate was then amplified for 12-14 cycles in 25 μl PCR reactions using NEBNext High-Fidelity 2X PCR Master Mix (NEB) and 0.5 mM each of primers Solexa 1GA and Solexa 1GB. Resulting libraries were size selected by gel excision to 200-500 bp, purified, and single-end sequenced using a HiSeq 4000 or paired end on a NovaSeq 6000.

value: Brain

tag: strain

tag: cell type

value: whole cell Microglia (CD45+ CD11b+ CX3CR1+)

tag: genotype

value: SMAD4-conditional deletion

tag: antibody

value: Input


title: SJ_PQR-1

tag: cell line

tag: treatment


title: SAMPLE 15_prime/boost challengeFluB-RAM/IGIPd14 dpc

description:
Fig. 5, 6 and 7
UGA#3 IBV-IGIP array

tag: tissue

value: Serum


title: SJ_PQR-2


title: EKO_SMAD4_Input_Rep1

description: Input used for: Microglia, SMAD4 ChIPseq Input, SMAD4-conditional KO, Rep1  Microglia, SALL1 ChIPseq Input, SALL1 Enhancer KO, Rep2


title: Microglia, SMAD4 ChIPseq, SMAD4-conditional KO, Rep2


title: SJ_WT-2

value: WT


title: SAMPLE 14_prime/boost challengeFluB-RAM/IGIPd14 dpc

description:
Fig. 5, 6 and 7
UGA#3 IBV-IGIP array

value: prime/boost challenge

value: FluB-RAM/IGIP


title: 110538_1_S23

tag: ID

tag: tr n

tag: visit

value: RNA 2

tag: group

tag: female yn

tag: nhw yn


title: 110538_3_S24

tag: dr34 yn

tag: fdr yn

tag: age

tag: age ia


title: 110480_1_S31

value: RNA 1


title: Microglia, SMAD4 ChIPseq, SMAD4-conditional KO, Rep1

tag: strain


title: Microglia, SMAD4 ChIPseq Input, SMAD4 WT, Rep2

tag: cell type


title: SJ_WT-1

value: Bone marrow

tag: genotype


title: SAMPLE 13_prime/boost challengeFluB-RAM/IGIPd14 dpc

description:
Fig. 5, 6 and 7
UGA#3 IBV-IGIP array

tag: vaccine regimen

tag: vaccine

tag: time point

value: d14 dpc

tag: mouse id

tag: extracted molecule


title: SAMPLE 12_prime/boost challengeFluB-RAM/IGIPd14 dpc

description:
Fig. 5, 6 and 7
UGA#3 IBV-IGIP array

tag: tissue


title: Microglia, SMAD4 ChIPseq, SMAD4 WT, Rep2

tag: antibody


title: SAMPLE 11_prime/boostFluB-att/IGIPd19 dpb

description:
Fig. 3 and 5
UGA#3 IBV-IGIP array

value: prime/boost

value: FluB-att/IGIP

value: d19 dpb


title: 110644_2_S91

tag: ID

tag: tr n

tag: visit

tag: group

value: Maintainer


title: CJ_PQRXLF-1

description: Coding Join junctions on the chromosomal V(D)J recombination substrate pMX-INV

extract_protocol:
Genomic DNA was extracted from treated B cells on day 4.
Sonicated DNA was linearly amplified with biotinylated primer (/5Bios/ACAACCACTACCTGAGCACC) and nested amplified with (5’-CAAAGACCCCAACGAGAAGC-3’) primer. Germline sequence was removed with BstBI (NEB) digestion.
High-throughput genome translocation sequencing (HTGTS). Sequenced with MiSeq 500v.

tag: cell line

value: v-abl transformed B cell

value: B cells

value: DNA-PKcsPQR/PQRXlf-/-

tag: treatment

value: STI571 for 4 days


title: 110527_1_S89

value: blood

tag: female yn

tag: nhw yn

tag: dr34 yn

tag: fdr yn

tag: age

tag: age ia


title: SAMPLE 16_prime/boost challengeFluB-RAM/IGIPd14 dpc

description:
Fig. 5, 6 and 7
UGA#3 IBV-IGIP array

value: Serum

tag: vaccine regimen

tag: vaccine

tag: time point

value: IgG


title: 110488_1_S2

tag: tissue


title: SAMPLE 10_prime/boostFluB-att/IGIPd19 dpb

description:
Fig. 3 and 5
UGA#3 IBV-IGIP array

tag: mouse id

tag: extracted molecule


title: Microglia, SALL1 ChIPseq Input, Spret, Rep2

value: Brain

tag: strain

value: Spret

tag: cell type

value: whole cell Microglia (CD45+ CD11b+ CX3CR1+)

tag: genotype

value: Wild type

tag: antibody

value: Input


title: 110543_4_S61

tag: ID

tag: tr n

tag: visit

value: RNA 2

tag: group

value: Reverter


title: CJ_XLF-1

value: Bone marrow

tag: cell line

value: Xlf-/-

tag: treatment


title: CJ_PQR-3

value: DNA-PKcsPQR/PQR


title: 110523_4_S60

value: RNA 1

tag: female yn

tag: nhw yn

tag: dr34 yn

tag: fdr yn

tag: age

tag: age ia


title: SAMPLE 9_prime/boostFluB-att/IGIPd19 dpb

description:
Fig. 3 and 5
UGA#3 IBV-IGIP array

tag: tissue

tag: vaccine regimen

value: prime/boost

tag: vaccine

value: FluB-att/IGIP

tag: time point

value: d19 dpb

tag: mouse id

tag: extracted molecule


title: Microglia, SALL1 ChIPseq Input, Spret, Rep1

tag: strain

tag: cell type

tag: genotype

tag: antibody


title: SAMPLE 8_prime/boostFluB-RANS/IGIPd19 dpb

description:
Fig. 3 and 5
UGA#3 IBV-IGIP array

value: FluB-RANS/IGIP


title: 110720_1_S86

value: blood

tag: ID

tag: tr n

tag: visit

tag: group

value: Progressor


title: SAMPLE 7_prime/boostFluB-RANS/IGIPd19 dpb

description:
Fig. 3 and 5
UGA#3 IBV-IGIP array

value: Serum

value: IgG


title: CJ_PQR-2

tag: cell line

value: v-abl transformed B cell

value: B cells

tag: treatment

value: STI571 for 4 days


title: Microglia, SALL1 ChIPseq, Spret, Rep2

value: Brain

value: Spret

value: whole cell Microglia (CD45+ CD11b+ CX3CR1+)

value: Wild type


title: CJ_PQRXLF-2

value: Bone marrow

value: DNA-PKcsPQR/PQRXlf-/-


title: Microglia, SALL1 ChIPseq, Spret, Rep1


title: 110429_1_S94

value: RNA 1

tag: female yn

tag: nhw yn

tag: dr34 yn

tag: fdr yn

tag: age

tag: age ia


title: SAMPLE 6_prime/boostFluB-RANS/IGIPd19 dpb

description:
Fig. 3 and 5
UGA#3 IBV-IGIP array

tag: tissue

tag: vaccine regimen

value: prime/boost

tag: vaccine

tag: time point

tag: mouse id

tag: extracted molecule


title: Microglia, SALL1 ChIPseq Input, PWK, Rep2

tag: strain

value: PWK

tag: cell type

tag: genotype

tag: antibody

value: Input


title: 110551_1_S16

value: blood

tag: ID

tag: tr n

tag: visit

value: RNA 2

tag: group

value: Maintainer


title: Microglia, SMAD4 ChIPseq, SMAD4 WT, Rep1


title: CJ_WT-2

tag: cell line

value: WT

tag: treatment


title: CJ_XLF-2

value: v-abl transformed B cell

value: Xlf-/-


title: Microglia, SALL1 ChIPseq Input, PWK, Rep1


title: SAMPLE 5_prime/boostFluB-RANS/IGIPd19 dpb

description:
Fig. 3 and 5
UGA#3 IBV-IGIP array

value: Serum

value: FluB-RANS/IGIP

value: d19 dpb

value: IgG


title: CJ_WT-1

value: B cells

value: STI571 for 4 days


title: Microglia, SALL1 ChIPseq, PWK, Rep2

value: Brain

value: whole cell Microglia (CD45+ CD11b+ CX3CR1+)

value: Wild type


title: SAMPLE 4_prime/boostFluB-RAM/IGIPd19 dpb

description:
Fig. 3 and 5
UGA#3 IBV-IGIP array

value: prime/boost

value: FluB-RAM/IGIP


title: SAMPLE 3_prime/boostFluB-RAM/IGIPd19 dpb

description:
Fig. 3 and 5
UGA#3 IBV-IGIP array


title: 110608_3_S37

value: blood

value: Reverter

tag: female yn

tag: nhw yn

tag: dr34 yn

tag: fdr yn

tag: age

tag: age ia


title: 110604_3_S29

tag: tissue

value: RNA 1


title: 129713

city: Vienna

first: Moritz

middle: M

last: Gaidt

address: Campus-Vienna-Biocenter 1

country: Austria

institute: IMP

data_processing:
VDJ-Seq: The bioinformatic analysis of the VDJ-seq data was performed as described in detail in Chovanec et al., Nat. Protoc. 13, 2018. using the BabrahamLinkON pipeline: (1) preclean.py (default parameters), Includes trimming and alignment steps (BabrahamLinkOn pipeline) deduplicate.py (default parameters), based on UMI  (BabrahamLinkOn pipeline) (2) assemble_clones.py (default parameters)  (BabrahamLinkOn pipeline) (3) The resulting counts were summarized using customized scripts based on the statistical language R version 3.3.3. The relative usage of each VH gene is shown as percentage of all VDJH recombination events determined.
ChIP-Seq:  Reads were aligned against the Mus musculus genome version of July 2007 (NCBI37/mm9) with the Bowtie program version 0.12.5. Genome-wide read coverages were normalized to the number of aligned reads, per million (=RPM)., using 'bedtools' and 'kent source utilities'.
RNA-Seq: The number of reads per gene was counted using the featureCounts version 1.5.0 with default settings. Transcripts per million (TPM) values were calculated as described previously.
total RNA-Seq: Reads were aligned with STAR version 2.4.2 to the Mus musculus genome version of July 2007 (NCBI37/mm9). Read coverages were calculated with the BEDTool program, were normalized to reads per millions (RPM) using the SAMTools as well as the KentTools.
Assembly: mm9 (total RNA-Seq, RNA-Seq,ChIP-Seq), mm10 (VDJ-Seq)
Supplementary files format and content: tab-delimited text files include RPM values for each VDJ-Seq sample and TPM values for RNA-Seq samples. bigWig files include read coverage for total RNA-Seq and ChIP-Seq samples.

source_name: Igh VDJ-Seq Pro-B cell Igh(P4_delta_CtftGV/P4_delta_CtftGV)

extract_protocol:
DNA was sheared using the Bioruptor sonicator (Diagenode) and subjected to end-repair and A-tailing, followed by ligation of adapters containing 12 UMI sequences using the NEBNext Ultra II DNA library prep kit for Illumina (NEB). A primer extension step with biotinylated JH-specific primers generated the single-stranded DNA products that were captured using Dynabeads MyOne streptavidin T1 beads (Thermo Fisher Scientific) and PCR-amplified with nested JH-specific and adapter-binding primers. The llumina sequencing adapter primers including the indexes for multiplexing of libraries were added to the PCR products in a final PCR amplification step.
genomic DNA was extracted using isopropanol / ethanol purification

value: bone marrow

tag: chip antibody

value: Pro-B cell

value: Ex-vivo FACS sorted from bone marrow


title: Microglia, SALL1 ChIPseq Input, SALL1 Enhancer KO, Rep2

tag: strain

tag: cell type

value: Sall1 Enhancer Knockout

value: Input


title: SAMPLE 2_prime/boostFluB-RAM/IGIPd19 dpb

description:
Fig. 3 and 5
UGA#3 IBV-IGIP array

value: Serum

tag: vaccine regimen

tag: vaccine

tag: time point

value: d19 dpb

tag: mouse id

tag: extracted molecule


title: Microglia, SALL1 ChIPseq, PWK, Rep1

value: PWK

tag: genotype

tag: antibody


title: 129712

tag: treatment


title: Microglia, SALL1 ChIPseq Input, SALL1 Enhancer KO, Rep1


title: CJ_PQR-1

value: Bone marrow

tag: cell line

value: v-abl transformed B cell

value: B cells

value: DNA-PKcsPQR/PQR

value: STI571 for 4 days


title: 110497_2_S18

tag: ID

tag: tr n

tag: visit

tag: group

tag: female yn

tag: nhw yn

tag: dr34 yn


title: 129709

source_name: Igh VDJ-Seq Pro-B cell Igh(P4_delta_Pax5GV/P4_delta_Pax5GV)

tag: tissue

tag: chip antibody

tag: cell type


title: WT_2

city: Beijing

first: Zi-Qian

last: Wang

address: NO.1 Beichen West  Road, Chaoyang District

country: China

institute: Institute of Microbiology, Chinese Academy of Sciences

data_processing:
The reads matched to rRNA were removed by SOAP v2.21 (parameters: -m 0 -x 1000 -s 28 -l 32 -v 5 -r 1 -p 3).
The adapter sequences and low-quality reads (those with more than 5% unknown bases or more than 20% of bases of which the quality scores were lower than 10) were discarded.
Trimmed sequence reads were mapped to Nostoc sp. PCC 7120 = FACHB-418 using  Bowite2 v2.2.5 (parameters: -q–phred64 –sensitive –dpad 0 –gbar 99,999,999 –mp 1,1 –np 1 –score-min L,0, -0.1 -I 1 -X 1000 –no-mixed –no-discordant -p 1 -k 200)
Read count extraction and normalizaiton were performed using RSEM v1.2.12 (parameters: --forward-prob=0.0).
Assembly: Nostoc sp. PCC 7120 = FACHB-418
Supplementary files format and content: tab-delimited excel files include FPKM values for each Sample

organism: Nostoc sp. PCC 7120 = FACHB-418

source_name: cyanobacterial cells

growth_protocol: Nostoc sp. PCC 7120 and its derivative Mall0854 were incubated with constant illumination (light density of 30 μmol·m-2·s-1) in BG11 medium. Cultures in flasks were shaken at 180 rpm.

extract_protocol:
Total RNA was extracted using the hot phenol procedure. The quality of RNA samples was examined by Agilent 2100 Bioanalyzer (Agilent Technologies, PaloAlto, CA, USA), and the RNA integrity numbers (RIN) of all the samples were between 7.9–8.3.
RNA libraries for RNA-seq were prepared using Illumina TruSeq Stranded Kit (Illumine, San Diego, CA, USA) following manufacturer's protocols.

value: cyanobacterial cells

value: wild type

value: normal laboratory culture conditions

tag: growth phase

value: logarithmic phase


title: WT_3


title: 110552_2_S26

value: blood

value: RNA 2

value: Reverter

tag: fdr yn

tag: age

tag: age ia


title: SAMPLE 1_prime/boostFluB-RAM/IGIPd19 dpb

description:
Fig. 3 and 5
UGA#3 IBV-IGIP array

tag: vaccine regimen

value: prime/boost

tag: vaccine

value: FluB-RAM/IGIP

tag: time point

tag: mouse id

tag: extracted molecule

value: IgG


title: 110525_1_S8

tag: ID

tag: tr n

tag: visit

value: RNA 1

value: Maintainer


title: 110464_3_S36

tag: group

tag: female yn

tag: nhw yn


title: Microglia, SALL1 ChIPseq, SALL1 Enhancer KO, Rep2

tag: tissue

value: Brain

tag: strain

value: whole cell Microglia (CD45+ CD11b+ CX3CR1+)

tag: genotype

value: Sall1 Enhancer Knockout

tag: antibody


title: 129708

value: bone marrow

tag: chip antibody

tag: cell type

value: Pro-B cell

tag: treatment

value: Ex-vivo FACS sorted from bone marrow


title: WT_1

value: cyanobacterial cells

value: wild type

tag: growth phase


title: Microglia, SALL1 ChIPseq, SALL1 Enhancer KO, Rep1


title: 110423_3_S28

tag: dr34 yn

tag: fdr yn

tag: age

tag: age ia


title: 129714


title: Mall0854_3

value: all0854 knockout

value: normal laboratory culture conditions

value: logarithmic phase


title: Mall0854_2


title: 129710

source_name: Igh VDJ-Seq Pro-B cell Igh(+/+)


title: 129707


title: 129711


title: Microglia, SALL1 ChIPseq Input, SALL1 Enhancer WT, Rep1

value: Wild type

value: Input


title: Microglia, SALL1 ChIPseq, SALL1 Enhancer WT, Rep2


title: Microglia, SALL1 ChIPseq Input, SALL1 Enhancer WT, Rep2


title: Mall0854_1


title: 129706


title: rad9D_4h_bio rep 2

city: Emeryville

first: Pei-Ching

last: Huang

address: 1545 Park Ave

institute: Metagenomi

data_processing:
Mapping of the reads onto the S288c reference genome (SacCer2) was performed using the SHRiMP mapper50 (gmapper-ls) with arguments: -E -U -n 1 -Q --sam-unaligned --strata -o 10001 -N 20 Before mapping, adaptor sequences were removed using fastx_clipper (http://hannonlab.cshl.edu/fastx_toolkit/) and a custom script. Code used for read processing and mapping is available online at https://github.com/soccin/S1Seq. After mapping, the reads were separated into unique and multiple-mapping sets, but only uniquely mapping reads were analyzed in this study. Analyses were performed using the R package (RStudio version 0.99.879, R version 3.1.2).
Maps were curated by masking (set to NA) 500 bp at the ends of each chromosome, because telomeres represent naturally occurring resected DNA ends and therefore give a high frequency of reads.
We masked regions that gave a high frequency of meiotic DSB-independent reads, defined as positions with more than 10 reads in the high-depth biological replicates and/or more than 5 reads in the lower depth biological replicates from the 0-h maps from wild type, spo11-Y135F, dmc1 null, and exo1-D173A plus the 4-h map from spo11-Y135F. A table of mask coordinates is provided at https://github.com/soccin/S1Seq.
Reads mapping to mitochondrial DNA or the 2 μ plasmid were excluded.
Each map was normalized to reads per million remaining mapped reads (provided here as processed data files) and biological replicates were averaged.
Assembly: Reads were mapped to the SGD assembly released in June 2008, called "SacCer2" by UCSC.
Supplementary files format and content: txt files include RPM (reads per million mapped) for each genotype and biological replicate over the experimental meiotic time points examined. Column names: letter "w" or "c" denotes watson (top) or crick (bottom) strand respectively, followed by a number indicating meiotic  time point.
Library strategy: S1-seq

organism: Saccharomyces cerevisiae

source_name: diploids

growth_protocol: Cells were grown in YPA (1% yeast extract, 2% Bacto Peptone, 1% potassium acetate) for 14 hr at 30°C, harvested, resuspended to OD600=6.0 in 2% potassium acetate and sporulated at 30°C.

extract_protocol:
Genomic DNA was extracted in low-melting point (LMP) agarose to yield intact high molecular weight DNA. Each cell pellet was resuspended in 150 μl 50 mM EDTA pH 8.0 and allowed to thaw at 40°C. 498 μl LMP agarose (2% in 50 mM EDTA pH 8.0) was mixed with 102 μl Solution 1 (SCE (1 M sorbitol, 0.1 M sodium citrate, 60 mM EDTA pH 7.0) plus 5% β- mercaptoethanol and 1 mg/ml zymolyase 100T) and the mix was prewarmed at 40°C before adding to the cells. The resuspended cells were pipetted into plug molds and chilled at 4°C for 30 min. Once solidified, the agarose plugs (three at a time) were expressed into 3 ml of Solution 2 (0.45 M EDTA pH 8.0, 0.01 M Tris-HCl pH 7.5, 7.5 % β-mercaptoethanol, 10 μg/ml RNase A) and incubated at 37°C for 1 h. Solution 2 was then replaced with Solution 3 (0.25 M EDTA pH 8.0, 0.01 M Tris-HCl pH 7.5, 1% SDS, 1 mg/ml proteinase K) and plugs were incubated at 50°C overnight. Plugs were finally washed three times with 3 ml 50 mM EDTA pH 8 and stored in plug storage solution (0.05 M EDTA pH 8.0, 50% glycerol) at -20°C until all plugs were ready to be processed for library preparation.
Ten plugs of each sample to be analyzed were equilibrated in 500 μl 1× S1 buffer (50 mM sodium acetate pH 4.5, 0.28 M NaCl, 4.5 mM ZnSO4) per plug in 2 ml conical tubes for 30 min and this was repeated three times. Fresh 1× S1 buffer (500 ul) containing 9 U of S1 nuclease (Promega) was added to each tube and the plugs were incubated on ice for 15 min to allow the enzyme diffuse into the plugs, followed by 20 min incubation at 37°C. S1 nuclease was inactivated by addition of EDTA pH 8.0 to a final concentration 10 mM and incubation on ice for 15 min. Plugs were rinsed with 1× TE and further equilibrated in 500 μl T4 polymerase buffer (1× T4 DNA ligase buffer (NEB), 1× BSA, 100 μM dNTPs), four times for 30 min each. Fresh T4 polymerase buffer (500 μl) containing 30 U of T4 DNA polymerase (NEB) was added to each tube and the plugs were incubated on ice for 15 min, followed by 30 min incubation at 12°C. T4 polymerase was inactivated by addition of EDTA pH 8.0 to a final concentration of 10 mM and incubation on ice for 15 min. At this point all buffer was aspirated,the plugs were rinsed with 1× TE and incubated at 75°C for 20 min to fully inactivate T4 polymerase. Plugs were allowed to gradually cool and solidify, before equilibrating in 250 μl 1× T4 ligase buffer (NEB), four times for 15 min each. After the last equilibration step, 200 μl of the buffer were removed leaving each plug immersed in 50 μl 1× T4 DNA ligase buffer, to which 1 μl of 50 μM adaptor and 1 μl of 2000 U/μl T4 DNA ligase were added. Ligation took place at 4°C for ≥18 h. The adaptor was prepared the day of the experiment by mixing oligos P5-top (5BiosG/ACACTCTTTCCCTACACGACGCTCTTCCGATCT, biotin attached to the 5′- end of the oligo) and P5-bottom (5Phos/AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT/3InvdT, 5′- end phosphorylated with inverted dT incorporated at the 3′-end to block ligation) at equimolar concentration, boiling for 5 min and cooling down at room temperature for at least 1 h.  To retrieve the DNA from the agarose plugs, the Epicentre GELase Enzyme Digestion protocol was used, followed by phenol extraction and ethanol precipitation. During this process plugs of DNA from a single culture and time point were pooled. The purified DNA was then subjected to size selection by electrophoresis through a 1% LMP 1× TAE agarose gel at 80 V/cm for 2 h to separate the high-molecular-weight genomic DNA from the excess unligated adaptor. The genomic DNA was excised and extracted from the gel using the Epicentre GELase enzyme protocol, phenol extraction and ethanol precipitation; then the DNA was dissolved in 100 μl 1× TE. To ensure complete removal of unligated adaptor, each sample was further purified by passing three times through Chroma Spin-1000 (Clontech) columns. The eluates were then subjected to shearing according to the Covaris instrument protocol to DNA fragment sizes ranging between 200-500 bp.  Following shearing, fragments containing the biotinylated adaptor were enriched by affinity purification with streptavidin. For each sample, 50 μl of streptavidin M-280 beads (Roche) were used, prewashed twice with 1× TE and twice with 1× B&W (binding and washing buffer, 10 mM Tris-HCl pH 7.5, 1 mM EDTA, 2 M NaCl), according to the manufacturer’s instructions. Binding was carried out at 20°C for 30 min, followed by two washes with 500 μl 1x B&W buffer and two washes with 500 μl 10 mM Tris-HCl pH 7.5. The remaining steps were performed with the DNA fragments still bound to the streptavidin beads. Because sheared ends are not always readily ligatable, an end-repair step was included according to Epicentre’s End-it DNA Repair kit protocol. The beads for each sample were incubated in 100 μl of reaction mix according to manufacturer’s instructions and incubated at 20°C for 45 min. Following washes with 500 μl 1× B&W buffer (twice) and 500 μl 10 mM Tris-HCl pH 7.5 (twice), the beads were incubated in 100 μl of 1× T4 DNA ligase buffer containing 400 U T4 ligase and 1 μM P7 adaptor. The adaptor was prepared by annealing oligos P7 top (5Phos/GATCGGAAGAGCACACGTCTGAACTCCAGTCAC/3InvdT) and P7 bottom (GTGACTGGAGTTCAGACGTGTGCTCTTCCGATC) at equimolar concentration, boiling for 5 min and allowing to cool down at room temperature for at least one hour. Ligation of the P7 adaptor was allowed at 20°C for 4 h and was followed by washes with 500 μl 1× TE and 500 μl 10 mM Tris-HCl pH 7.5 (three times each). Beads of each sample were resuspended in 20 μl 10 mM Tris-HCl pH 7.5.  Each sample of beads was split into two PCR reactions in a total of 50 μl containing 10 μl of the resuspended beads, 1× Phusion HF buffer, 0.2 mM dNTP, 1 U Phusion HF polymerase (Thermo Scientific), 0.4 μM P5 universal primer (AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATC T) and 0.4 μM P7 indexed primer (CAAGCAGAAGACGGCATACGAGATCGTGATGTGACTGGAGTTCAGACGTGTG, shown here with Illumina TruSeq index 1 underlined). PCR was initiated by a denaturation step at 98°C for 30 sec, followed by 16 cycles of amplification (98°C for 10 sec, 65°C for 20 sec, and 72°C for 20 sec). PCR products were pooled, and the DNA was precipitated by adding ammonium acetate to 2.5 M and 2.5 volumes of ice-cold 100% ethanol. Following an overnight incubation at -20°C, the samples were spun at 16000 g for 30 min, washed with ice-cold 70% ethanol, air-dried and dissolved in 20 μl 10 mM Tris, pH 7.5. PCRs from each sample were pooled and separated on a 5% non-denaturing polyacrylamide gel in 1× TBE. The gel piece between 200–600 bp was excised, crushed, and eluted in 300 μl 10 mM Tris pH 8.0 at 37°C overnight. The elution mixture was spun through a SPIN-X column, and DNA was precipitated with ammonium acetate and ethanol as above. The DNA pellet was dissolved in 20 μl 10 mM Tris pH 7.5 and sequenced on the Illumina HiSeq platform (50 bp single-end) in the Integrated Genomics Operation at Memorial Sloan Kettering Cancer Center.

value: diploids

tag: developmental stage

value: time = 4 hr in meiosis

tag: index

value: GTTTCC


title: 129705


title: Microglia, SALL1 ChIPseq, SALL1 Enhancer WT, Rep1


title: 75648

source_name: Igh VDJ-Seq Pro-B cell Igh(P4GV/P4GV)


title: 129716


title: 75649


title: PU1+ nuclei, P300 Input, SALL1 Enhancer WT, Rep3

value: PU1+ nuclei


title: PU1+ nuclei, P300 Input, SALL1 Enhancer WT, Rep2

value: Brain


title: swr1D_4h_bio rep 2

value: AGTTCC


title: Microglia, P300 Input, SALL1 Enhancer WT, Rep1

value: whole cell Microglia (CD45+ CD11b+ CX3CR1+)


title: swr1D_4h_bio rep 1

value: CAGATC


title: PU1+ nuclei, P300 ChIPseq, SALL1 Enhancer WT, Rep2


title: 129715

value: bone marrow

value: Pro-B cell


title: PU1+ nuclei, P300 ChIPseq, SALL1 Enhancer WT, Rep3


title: 75647

value: Ex-vivo FACS sorted from bone marrow


title: fun30Dsae2D_4h_bio rep 1

value: ATGTCA


title: fun30Dsae2D_4h_bio rep 2

value: CCGTCC


title: sae2D_4h

value: AGTCAA


title: Microglia, P300 ChIPseq, SALL1 Enhancer WT, Rep1


title: 75645


title: 75646


title: PU1+ nuclei, H3K27ac ChIPseq, SALL1 Enhancer KO, Rep2

value: Sall1 Enhancer Knockout


title: PU1+ nuclei, H3K27ac ChIPseq, SALL1 Enhancer KO, Rep1


title: rad9D_4h_bio rep 1

value: GTGGCC


title: fun30Dexo1nd_4h_bio rep 2

value: TGACCA


title: Olig2+ nuclei, H3K27ac ChIPseq, SALL1 Enhancer KO, Rep2

value: Olig2+ nuclei


title: fun30Dexo1nd_4h_bio rep 1

value: diploids

value: time = 4 hr in meiosis

value: TTAGGC


title: fun30D_4h_bio rep 2

value: CGATGT


title: 75644


title: 126447

source_name: Igh VDJ-Seq Pro-B cell Igh(EmG/EmG)

value: Igh(EmG/EmG)


title: Olig2+ nuclei, H3K27ac ChIPseq, SALL1 Enhancer KO, Rep1

value: Brain


title: fun30D_4h_bio rep 1

value: ATCACG


title: 126445

value: bone marrow


title: NeuN+ nuclei, H3K27ac ChIPseq, SALL1 Enhancer KO, Rep1

value: NeuN+ nuclei


title: NeuN+ nuclei, H3K27ac ChIPseq, SALL1 Enhancer KO, Rep2


title: exo1nd_4h_bio rep 2

value: GCCAAT


title: KYSE 510 cells, MAGEA6-KO, DDP, 3

city: Guangzhou

first: Yujing

last: He

state: guangdong

address: No.1023-1063 South Shatai Road, Baiyun District, Guangzhou City, Guangdong Province

department: thoracic

institute: nanfang hospital

data_processing:
The original image data file obtained by high-throughput sequencing is converted into the original data of sequencing sequence (Raw) through CASAVA base calling analysis Data), the results are stored in FASTQ (abbreviated as fq) file format, which contains sequence information of sequencing data and its corresponding sequencing quality information
Quality Score or Q-score is obtained based on the Phred mass value formula, an integer mapping is used to determine the probability of base calling errors
AT and GC separation was checked in the distribution of base types
Based on the sequencing characteristics of the Illumina platform, datas from dual end sequencing were used and taken Q30 with an average proportion of over 85%
Sequencing align Clean Reads with the reference genome was used Hisat2 to obtain positional information on the reference genome or gene, as well as sequence characteristic information unique to the sequencing sample
The quality of transcriptome library is assessed by evaluating the randomness of mRNA fragmentation, the dispersion of inserted fragment length, and the adequacy of library capacity and mapped Data
Gene expression quantification was used with network flow algorithms and optional denovo assembly to assemble complex datasets into transcripts. FPKM (Fragments Per Kilobase of script per Million fragments mapped) was an indicator to measure transcript or gene expression levels
Assembly: mm10
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

source_name: KYSE 510

growth_protocol: KYSE 150 and KYSE 510 cells were maintained in RPMI1640 supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
Total RNA was harvested using Tiangen DP411, CLB+Adlai RN40, CTAB+Adlai RN40, Tiangen DP762-T1C reagent kit/TRIzol reagent. 1.3 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using SMARTER mRNA-Seq Library Prep Kit following manufacturer's protocols.

treatment_protocol: KYSE 150 cells were treated with cisplatin in 40μM, 2 days; KYSE 150 cells were treated with cisplatin in 8μM, 2 days.

value: KYSE 510

tag: cell line

value: esophageal squamous carcinoma cells

value: MAGEA6 knockout and treatment of cisplatin


title: exo1nd_4h_bio rep 1

value: ACAGTG


title: 126452

source_name: Igh VDJ-Seq Pro-B cell Igh(P4StopG/P4StopG)

value: Pro-B cell

value: Ex-vivo FACS sorted from bone marrow


title: KYSE 510 cells, MAGEA6-KO, 3

value: MAGEA6 knockout


title: Wild type_4h_bio rep 2

value: diploids

value: Wild type


title: 126451


title: Wild type_4h_bio rep 1

value: time = 4 hr in meiosis


title: PU1+ nuclei, H3K27ac ChIPseq, SALL1 Enhancer WT, Rep1

value: PU1+ nuclei


title: Olig2+ nuclei, H3K27ac ChIPseq, SALL1 Enhancer WT, Rep1

value: Olig2+ nuclei


title: KYSE 510 cells, MAGEA6-KO, 2


title: 126450


title: NeuN+ nuclei, H3K27ac ChIPseq, SALL1 Enhancer WT, Rep1

value: Brain


title: 126446

value: Igh(EmG/EmG)


title: 126457

source_name: Igh VDJ-Seq Pro-B cell Igh(P4inv/P4inv)

value: bone marrow


title: KYSE 510 cells, DDP, 2

value: Cisplatin


title: 126456


title: Fun30-Myc spo11yf sae2D_ip_bio rep1

data_processing:
Reads were mapped to the S. cerevisiae sacCer2 genome assembly using BWA mem (version 0.7.5a-r405) to generate coverage maps for each data set.
Assembly: The SGD assembly released in June 2008, called "sacCer2" by UCSC: http://genome.ucsc.edu/cgi-bin/hgGateway?hgsid=340067645
Supplementary files format and content: Text files of coverage maps

growth_protocol: Cells were grown in YPA (1% yeast extract, 2% Bacto Peptone, 1% potassium acetate) for 13.5–14 hr at 30ºC, harvested, resuspended in 2% potassium acetate, and sporulated at 30ºC.

extract_protocol: ChIP was performed as described (Murakami et al., 2014). Cells were sporulated and 50 mL of meiotic culture (2 x 109 cells) was collected at 4h and crosslinked with 1% formaldehyde for 30 min at room temperature. Crosslinking was terminated by 5 min incubation with 131 mM glycine. Cells were washed twice with ice-cold TBS, flash frozen with liquid nitrogen and stored at -80°C. Cells were suspended in 1 mL of Lysis buffer (50 mM HEPES-KOH pH 7.5, 140 mM NaCl, 1 mM EDTA, 1% Triton X-100, 0.1% Na-deoxycholate, 1 mM PMSF, 7 ug/mL aprotinin, 1% protease inhibitor cocktail (Sigma), 1x Complete Protease Inhibitor Cocktail (Roche)) with ca. 900 uL of 0.5 mm zirconia/silica beads (BioSpec Products) in 2 mL screw-cap tubes. Cells were disrupted by vigorous shaking 3 min x 6 times in Mini-beadbeater-16 (BioSpec Products) or at 6.5 m/s for 1 min x 8 times in FastPrep24 (MP Biomedicals). 1 mL of Lysis buffer was added after cell disruption. Subsequently, chromatin in the whole cell extracts (WCE) was sheared by sonication with "M" intensity, 30 sec ON/ 30 sec OFF for 15 min x 2 times in Bioruptor Sonication System UCD200 (Diagenode) in 15 mL polystyrene conical tubes. Insoluble fraction (cell debris) was removed by centrifugation at 21,130 g, 5 min, 4°C. WCE was further sonicated with the same conditions 1-3 times to yield average DNA size less than 500 bp. WCE was flash frozen and stored at -80°C.

value: Fun30-Myc spo11yf sae2D

value: epitope tag:Fun30-Myc; ChIP antibody:anti-Myc antibody (9E10)

value: TTCGAACC/AGGTGACA


title: KYSE 510 cells, MAGEA6-KO, DDP, 2

value: KYSE 510

value: esophageal squamous carcinoma cells

value: MAGEA6 knockout and treatment of cisplatin


title: Fun30-Myc spo11yf sae2D_ip_bio rep2

value: CAGACCAC/GCCGAAGC


title: Fun30-Myc spo11yf sae2D_input_bio rep2

value: CATGATGA/CCTCTAAC


title: Microglia, H3K27ac ChIPseq Input, SALL1 Enhancer KO, Rep4

value: whole cell Microglia (CD45+ CD11b+ CX3CR1+)

value: Sall1 Enhancer Knockout

value: Input


title: Microglia, H3K27ac ChIPseq Input, SALL1 Enhancer KO, Rep3


title: Fun30-Myc spo11yf sae2D_input_bio rep1

value: diploids

value: time = 4 hr in meiosis

value: CAACTGCT/ATACTACT


title: KYSE 510 cells, MAGEA6-KO, DDP, 1


title: 126455

value: Pro-B cell

value: Ex-vivo FACS sorted from bone marrow


title: KYSE 510 cells, DDP, 1

value: Cisplatin


title: 126454

value: bone marrow


title: fun30K603R sae2D_ip_bio rep 2

value: fun30K603R sae2D

value: epitope tag:Fun30-Myc; ChIP antibody:anti-Myc antibody (9E10)

value: GGACAACG/GGCCATCA


title: KYSE 510 cells, NC, 3

value: KYSE 510

value: esophageal squamous carcinoma cells

value: WT

value: sgNC


title: 126453


title: fun30K603R sae2D_input_bio rep 2

value: GTACAGCT/ACCGATCA


title: Microglia, H3K27ac ChIPseq Input, SALL1 Enhancer WT, Rep4

value: Brain

value: whole cell Microglia (CD45+ CD11b+ CX3CR1+)

value: Wild type


title: KYSE 510 cells, NC, 2


title: KYSE 510 cells, MAGEA6-KO, 1

value: MAGEA6 knockout


title: fun30K603R sae2D_ip_bio rep 1

value: diploids

value: time = 4 hr in meiosis

value: AAGTTGGA/CCTGTATT


title: Microglia, H3K27ac ChIPseq Input, SALL1 Enhancer WT, Rep3

value: Input


title: KYSE 510 cells, DDP, 3

value: Cisplatin


title: KYSE  510 cells, NC, 1


title: 126448

value: bone marrow

value: Pro-B cell

value: Ex-vivo FACS sorted from bone marrow


title: KYSE 150 cells, MAGEA6-KO, DDP, 3

source_name: KYSE 150

value: KYSE 150

value: MAGEA6 knockout and treatment of cisplatin


title: Microglia, H3K27ac ChIPseq, SALL1 Enhancer WT, Rep2


title: 126444


title: fun30K603R sae2D_input_bio rep 1

value: fun30K603R sae2D

value: epitope tag:Fun30-Myc; ChIP antibody:anti-Myc antibody (9E10)

value: AAGTTATC/TTGCTATT


title: Fun30-Myc sae2D_ip_bio rep 2

value: Fun30-Myc sae2D

value: CAGGTTCC/GGTGTTCG


title: Microglia, H3K27ac ChIPseq, SALL1 Enhancer WT, Rep1

value: Brain

value: whole cell Microglia (CD45+ CD11b+ CX3CR1+)

value: Wild type


title: KYSE 150 cells, MAGEA6-KO, DDP, 2

value: esophageal squamous carcinoma cells


title: ATAC-Microglia, SALL1 Enhancer KO, Rep5

data_processing:
ATAC-seq files were trimmed to 30 bp and then mapped to the mouse mm10 genome using Bowtie2 with default parameters (Langmead and Salzberg, 2012). After mapping, tag directories were created using the HOMER command makeTagDirectory (Heinz et la., 2010). For IDR analysis (Brown et al., 2011) to test for reproducibility between replicates, peaks were called with HOMER for each tag directory with relaxed peak finding parameters “-L 0 -C 0 -fdr 0.9 -minDist 200 -size 200”. Only peaks with an IDR < 0.05 were used for downstream analyses. For sample groups with > 2 libraries, peak sets from all pairwise IDR comparisons were merged into a final set of peaks for further analysis.
Assembly: mm10
Supplementary files format and content: *_idr.txt; tab-delimited text files including IDR peaks per each indicated genotype

extract_protocol:
Mouse brains were homogenized as previously described by gentle mechanical dissociation (Gosselin et al, 2014) and stained with anti-mouse anti-CD11b-APC (BioLegend 101212), anti-CD45-Alexa488 (BioLegend 103122), and anti-CX3CR1-PE (BioLegend 149006). Microglia were sorted as DAPI negative, singlets, and CD11b+CD45lowCX3CR1+.
Approximately 50,000 sorted microglia were prepped for ATAC-seq as previously described (Buenrostro et al., 2013). Briefly, cells were lysed in 150 uL lysis buffer (10mM Tris-HCl pH 7.5, 10 mM NaCl, 3 mM MgCl2, 0.1% IGEPAL, CA-630 in water). Resulting nuclei were centrifuged at 500 rcf for 10 minutes. Pelleted nuclei were resuspended in 50 uL transposase reaction mix (1x Tagment DNA Buffer (Illumina 15027866), 2.5 uL DNA enzyme I (Illumina 15027865), and incubated at 37°C for 30 minutes. DNA was purified with Zymo ChIP DNA concentrator columns (Zymo Research D5205), eludated with 11 uL of elution buffer, and amplified using NebNext High-fidelity 2x PCR MasterMix (New England BioLabs M0541) with the Nextera primer Ad1 (1.25 uM) and a unique Ad2.n barcoding primer (1.25 uM) for 8-12 cycles  Resulting libraries were size selected by gel excision to 155-250 bp, purified, and single end sequenced using a HiSeq 4000 (Illumina) for 51 cycles according to the manufacturer’s instructions.

value: Sall1 Enhancer Knockout


title: Fun30-Myc sae2D_input_bio rep 2

value: diploids

value: time = 4 hr in meiosis

value: TGGTGCAC/GTGATTCC


title: 72363

source_name: Igh VDJ-Seq Pro-B cell Igh(P4/P4)

value: bone marrow

value: Pro-B cell


title: Microglia, H3K27ac ChIPseq, SALL1 Enhancer KO, Rep1


title: Microglia, H3K27ac ChIPseq, SALL1 Enhancer KO, Rep2


title: KYSE 150 cells, MAGEA6-KO, 3

value: KYSE 150

value: MAGEA6 knockout


title: KYSE 150 cells, MAGEA6-KO, DDP, 1

value: MAGEA6 knockout and treatment of cisplatin


title: KYSE 150 cells, MAGEA6-KO, 2


title: 126449

value: Ex-vivo FACS sorted from bone marrow


title: KYSE 150 cells, MAGEA6-KO, 1


title: Fun30-Myc sae2D_input_bio rep 1

value: epitope tag:Fun30-Myc; ChIP antibody:anti-Myc antibody (9E10)

value: CAACCGTG/CGTGAGAG


title: ATAC-Microglia, SALL1 Enhancer KO, Rep2


title: 126443


title: ATAC-Microglia, SALL1 Enhancer KO, Rep1


title: untagged_input_bio rep 2

value: TGGTCATT/CCATCTGC


title: ATAC-Microglia, SALL1 Enhancer KO, Rep3

value: Brain


title: untagged_ip_bio rep 2

value: CAGAAGAT/CAATGTAC


title: 72360

source_name: Igh VDJ-Seq Pro-B cell Igh(P4V/P4V)


title: KYSE 150 cells, DDP, 3

value: Cisplatin


title: ATAC-Microglia, SALL1 Enhancer KO, Rep4

value: whole cell Microglia (CD45+ CD11b+ CX3CR1+)


title: Fun30-Myc sae2D_ip_bio rep 1

value: Fun30-Myc sae2D

value: TGAGGCGC/TGGTCTCC


title: 72362


title: 72359


title: untagged_ip_bio rep 1

value: diploids

value: time = 4 hr in meiosis

value: Wild type

value: TGACTACT/CTGTAAGG


title: ATAC-Microglia, SALL1 Enhancer WT, Rep4


title: KYSE 150 cells, DDP, 2

value: KYSE 150

value: esophageal squamous carcinoma cells


title: ATAC-Microglia, SALL1 Enhancer WT, Rep5


title: 72357

value: bone marrow

value: Pro-B cell


title: untagged_input_bio rep 1

value: epitope tag:Fun30-Myc; ChIP antibody:anti-Myc antibody (9E10)

value: CACAGTAA/CTCTAGTG


title: KYSE 150 cells, NC, 3

value: WT

value: sgNC


title: 72356

value: Ex-vivo FACS sorted from bone marrow


title: ATAC-Microglia, SALL1 Enhancer WT, Rep3

value: Brain


title: 72361


title: ATAC-Microglia, SALL1 Enhancer WT, Rep2

value: whole cell Microglia (CD45+ CD11b+ CX3CR1+)


title: KYSE 150 cells, NC, 2


title: ATAC-Microglia, SALL1 Enhancer WT, Rep1


title: KYSE 150 cells, NC, 1


title: 72355


title: 70500

source_name: Igh VDJ-Seq Pro-B cell Igh(_delta_890/_delta_890)


title: 72358


title: KYSE 150 cells, DDP, 1

value: Cisplatin


title: 70499


title: 70498


title: Microglia, H3K4me3 ChIPseq Input, SALL1 Enhancer WT, Rep4

data_processing:
Hi-C fastq files were trimmed at DpnII recognition sites (GATC) and then mapped to using Bowtie2 (Langmead & Salzberg, et a;., 2012). Hi-C interaction matrices were generated using juicertools (Durand et al., 2016)  and were visualized using juicebox (Durand et al., 2016). PC1 values for each sample were calculated using HOMER’s runHiCpca.pl with -res 50000 30and were visualized using the UCSC genome browser. Differential PC1 compartments were determined using the command ‘getHiCCorrDiff.pl”. TADs and loops were called using HOMER’s findTADsAndLoops.pl find with parameters -res 3000 and -window 15000. To compare TADs and loops between groups, TADs and loops were merged using merge2Dbed.pl -tad and -loop, respectively. Differential enrichment of these features was then calculated using Homer’s getDiffExpression.pl.
H3K4me3 ChIP-seqs from purified ex-vivo microglia were performed in duplicate with input controls. Alignment, QC and peak calling were performed with the official ENCODE-ChIP-seq pipeline as previously described (Nott et al., 2019). PLAC-seq fastq-files were processed with MAPS 33 at 5000-bp resolution as previously described (Nott et al., 2019); the H3K4me3-ChIP-seq peak files from the ENCODE pipeline were used as a template.
Assembly: mm10

extract_protocol:
Mouse brains were homogenized as previously described (Gosselin et al. 2014)  by gentle mechanical dissociation. Cells were then incubated in staining buffer on ice with anti-CD16/32 blocking antibody (BioLegend 101319) for 15 minutes, and then with anti-mouse anti-CD11b-APC (BioLegend 101212), anti-CD45-Alexa488 (BioLegend 103122), and anti-CX3CR1-PE (BioLegend 149006) for 25 minutes. Cell preparations for H3K27ac ChIP-seq were fixed with 1% formaldehyde for 10 minutes and quenched with 0.125M glycine for 5 minutes after staining, and subsequently washed three times. Cells were washed once and filtered through a 40 M cell strainer. Sorting was performed on a Sony MA900 or MoFlo Astrios EQ cell sorter. Microglia were defined as events that were DAPI negative, singlets, and CD11b+CD45lowCX3CR1+. Sorted microglia were pelleted at 800xg for 5 minutes, pellets were then snap frozen and stored at -80°C prior to library preparation. Brain nuclei were isolated as previously described (Nott et al., 2019), with initial homogenization performed with either 1% formaldehyde in Dulbecco’s phosphate buffered saline or 2mM DSG (Proteochem) in Dulbecco’s phosphate buffered saline. Nuclei were stained overnight with PU.1-PE (Cell Signaling 81886S), OLIG2-AF488 (Abcam 225099) or SALL1 AF647 (Thermo, clone NRNSTNX 51-9279-82) or NEUN-AF488 (Millipore MAB 377X). Nuclei were washed the following day with 4 mL FACs buffer, passed through a 40 uM strainer, and stained with 0.5 ug/mL DAPI. Nuclei for each cell type were sorted with a Beckman Coulter MoFlo Astrio EQ cell sorter and pelleted at 1600xg for 5 minutes at 4°C in FACs buffer. Nuclei pellets were snap frozen and stored at -80°C prior to library preparation.
PLAC-seq libraries were prepared for ex vivo microglia as previously described with minor modifications (Nott et al., 2019; Fang et al., 2016). In situ Hi-C was performed as described previously, with minor modifications (Heinz et al., 2018).

value: none (input)


title: Microglia, PLACseq, SALL1 Enhancer WT, Rep2

data_processing:
Hi-C fastq files were trimmed at DpnII recognition sites (GATC) and then mapped to using Bowtie2 (Langmead & Salzberg, et a;., 2012). Hi-C interaction matrices were generated using juicertools (Durand et al., 2016)  and were visualized using juicebox (Durand et al., 2016). PC1 values for each sample were calculated using HOMER’s runHiCpca.pl with -res 50000 30and were visualized using the UCSC genome browser. Differential PC1 compartments were determined using the command ‘getHiCCorrDiff.pl”. TADs and loops were called using HOMER’s findTADsAndLoops.pl find with parameters -res 3000 and -window 15000. To compare TADs and loops between groups, TADs and loops were merged using merge2Dbed.pl -tad and -loop, respectively. Differential enrichment of these features was then calculated using Homer’s getDiffExpression.pl.
H3K4me3 ChIP-seqs from purified ex-vivo microglia were performed in duplicate with input controls. Alignment, QC and peak calling were performed with the official ENCODE-ChIP-seq pipeline as previously described (Nott et al., 2019). PLAC-seq fastq-files were processed with MAPS 33 at 5000-bp resolution as previously described (Nott et al., 2019); the H3K4me3-ChIP-seq peak files from the ENCODE pipeline were used as a template.
Assembly: mm10
Library strategy: PLAC-seq


title: 70497


title: Microglia, H3K4me3 ChIPseq, SALL1 Enhancer WT, Rep2


title: TNF-α presence and differentiation of human adipose stem cells, biological rep1

type: RNA

city: Guiyang

first: ZHEN

last: YANG

state: Guizhou

address: Jiaxiu South Road； Baoshan South Road

institute: Medical College of Guizhou University/Guizhou Provincial People's Hospital (People's Hospital of Guizhou University)

description:
Gene expression data from fourth generation human adipose stem cells differentiated into cartilage in the presence of TNF-α (10 ng/ml) for 7 days.
Adipose stem cells in the differentiation stage

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Rat Gene 2.0. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using the Hewlett-Packard GeneArray Scanner G3000 7G.

data_processing: The data were analyzed with RMA using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100.

label: biotin

source_name: In the presence of TNF-α (10 ng/ml), the fourth passage of human adipose stem cells were chondrogenic differentiated for 7 days

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: Induction of adipose stem cells into chondrogenic differentiation by different differentiation media.

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions.

treatment_protocol: After the cells were cultured, they were collected in enzyme-free 2 ml EP tubes, rinsed with PBS containing 0.7% NaCl and 0.04% triton-X100 and placed in Trizol solution (Invitrogen) on ice.

tag: differentiation

value: differentiation


title: Human adipose stem cell differentiation, biological rep1

description:
Gene expression data from fourth generation human adipose stem cells at 7 days of chondrogenic differentiation.
Adipose stem cells in the differentiation stage

source_name: The fourth generation of human adipose stem cells were chondrogenic for 7 days


title: Infected-Jurkat-Pool_scATAC-seq

city: New Haven

first: Ya-Chi

last: Ho

state: Connecticut

address: 295 Congress Avenue,BCMM 354E

institute: Yale University

description:
Infected-Jurkat_atac_fragments.tsv.gz
Infected-Jurkat_barcodes.tsv.gz
Infected-Jurkat_features.tsv.gz
Infected-Jurkat_matrix.mtx.gz

data_processing:
Raw reads were processed using the Cellranger arc pipeline (version 2.0.1) with default parameters, CITE reads were processed with CITE-seq-Count (version 1.4.5).
Assembly: Hg38 + NL4-3
Supplementary files format and content: Matrix files and fragments.tsv files from the cellranger pipeline or CITE-seq-Count, hashkey ~ 1 = 8B10, 2=5F9, 3= 1G2, 4=1D7
Library strategy: Single cell multiome

source_name: Blood

growth_protocol: Jurkat T cells were grown in R10 (RPMI + 10% FBS) at high viability, passaged 1:10 twice weekly.

extract_protocol:
cDNA, transposed cDNA, and CITE cDNA were extracted according to the 10X multiome protocol with th emodifications described in Mimitou et al.Nat. Biotechnol. 2021.
Libraries were constructed using the 10X multiome protocol with the modificaitons described in Mimitou et al. Nat. Biotechnol. 2021.

treatment_protocol: Dead cells were removed using a bead based kit (STEMCELL Technologies #17899), and hashed using TotalSeq-A antibodies. Each clone was pooled in equal ratios and then lysed on ice with DIG lysis buffer for 5 minutes before washing. Cells werethen loaded into the 10X Chromium controller (10x Genomics) according to the manufacturer protocol.

value: Blood

value: Jurkat Cm6

value: CD4 T cell lymphoma


title: Uninfected-Jurkat_scATAC-seq

description:
Uninfected-Jurkat_atac_fragments.tsv.gz
Uninfected-Jurkat_barcodes.tsv.gz
Uninfected-Jurkat_features.tsv.gz
Uninfected-Jurkat_matrix.mtx.gz


title: Infected-Jurkat-Pool_hashtags

description:
Infected-Jurkat_atac_fragments.tsv.gz
Mix_CITE_barcodes.tsv.gz
Mix_CITE_features.tsv.gz
Mix_CITE_matrix.mtx.gz

library_source: other

tag: library type

value: ADT


title: Microglia, PLACseq, SALL1 Enhancer WT, Rep1

source_name: Brain

tag: tissue

value: Wild type


title: 70496

value: bone marrow


title: Infected-Jurkat-Pool_mRNA-derived-cDNA

value: mRNA


title: Uninfected-Jurkat_mRNA-derived-cDNA


title: 70495

value: Pro-B cell


title: Human adipose stem cells undifferentiated, biological rep1

description:
Gene expression data from fourth generation human adipose stem cells.
Human adipose stem cells

source_name: The fourth generation of human adipose stem cells

value: Undifferentiated


title: HMDM_Donor-4_LPS+NAM

city: bethesda

first: abdel

last: elkahloun

state: MD

address: 50 south dr

institute: nih

hyb_protocol: Protocols were followed for the GeneChip hybridization Wash and Stain kit (ThermoFisher #900720)

scan_protocol: GeneChip Scanner 3000 7G with a carousel, two Fluidics Station 450, one Hybridization Oven 640, and a computer workstation with dual Xeon processors loaded with Affymetrix GeneChip Command Console (AGCC) and GTYPE

data_processing:
Microarray signal intensity values were assessed using ThermoFisher Transcriptome Analysis Console (Version 4.0.1.36) and they were normalized and log2 transformed using the Robust Multiarray Average (RMA) method. Probe set IDs were annotated using PrimeView Human Gene Expression Array annotation file version 36 (release date 03/30/16).
Data are log2 transformed using the Robust Multiarray Average (RMA) method

label: Biotin

source_name: Human elutriated monocytes Donor 4

label_protocol: Biotin-labeled cRNA was generated with the GeneChip 3” IVT Plus Reagent kit (ThermoFisher  #902416)

growth_protocol: Human elutriated monocytes from 4 male donors were differentiated 6 days with 30ng/ml macrophage colony-stimulating factor (M-CSF) in IMDM (Iscove's Modified Dulbecco's Medium) supplemented with 10% heat-inactivated fetal bovine serum (media). Human monocyte-derived macrophages (HMDMs) were lifted by treating with 0.25% trypsin (0.5mL) for 3m, quenching with 0.5mL media and scraping with a cell scraper. HMDMs were resuspended at 1x10^6 cells/2mL media in 6-well plates and allowed to adhere 24h.

extract_protocol: Total RNA was extracted using the RNeasy kit (Qiagen) with processing through QIAshredder columns (Qiagen)

treatment_protocol: HMDMs were treated with vehicle control (media), 10ng/ml lipopolysaccharide (LPS), or 10mM nicotinamide (NAM) for 4h.

tag: subject id

value: Donor 4

tag: gender

value: Male

value: 55 years old

value: human monocyte-derived macrophages (HMDMs)

value: LPS+NAM


title: HMDM_Donor-4_LPS

value: LPS


title: Microglia, H3K4me3 ChIPseq, SALL1 Enhancer WT, Rep1

value: Brain

tag: strain

value: whole cell Microglia (CD45+ CD11b+ CX3CR1+)

tag: genotype

tag: antibody


title: ATAC_CRISPR_i_sgNT_8B10_Rep3

data_processing:
Raw reads were timmed of the Nextera adpter using cutadapt (version 3.5), mapped using Bowtie2 (version 2.4.4), and used to call peaks with Genrich (version 0.6.1) with options -j -y -r -e chrM -v.
Peaks from all samples were appended, sorted, and merged with bedtools (verison 2.30.0).
DeepTools (version 3.5.1) was used to make bigwig files with bamCoverage (options --binSize 10 --normalizeUsing CPM --ignoreDuplicates)
Assembly: Hg38 + NL4-3
Supplementary files format and content: .bw, bigwig files of genome tracks for ATAC-seq signal from a given sample, resolution of 10bp

extract_protocol:
DNA was isolated using a MinElute PCR cleanup kit (Qiagen #28004) and eluted in 10 L twice. The resulting
The resulting DNA was amplified using NEBNext ULTRA II Q5 master mix (New England Biolabs #M0544X) and Nextera indexing primers for 72°C for 5 minutes, then 98°C for 1 minute, followed by 5 cycles of 98°C for 15 seconds, 63°C for 30 seconds, and 72°C for 1 minute, with a final extension at 72°C for 5 minutes. Additional cycles were added based on qPCR measurements of library amplification for a total of 8–20 cycles per library.

treatment_protocol: cells were lysed on ice for 3 minutes in 50 L ATAC-lysis buffer (10 mM Tris-HCl pH 7.4, 10 mM NaCl, 3 mM MgCl2, 0.1% Tween 20, 0.1% NP40, 0.01% digitonin) before the addition of 1mL of ATAC-wash buffer (10 mM Tris-HCl pH 7.4, 10  mM NaCl, 3 mM MgCl2, 0.1% Tween-20). Cells were pelleted at 4°C and then transposed with ATAC-transposition mix (1X TD buffer with 33% PBS, 0.1% Tween-20, 0.01% digitonin, 2.5 L TDE1) at 37°C for 30 minutes.

value: Blood

tag: cell type


title: HMDM_Donor-4_control

tag: treatment

value: control


title: HMDM_Donor-4_NAM

value: NAM


title: Microglia, H3K4me3 ChIPseq Input, SALL1 Enhancer WT, Rep3

value: none (input)


title: ATAC_CRISPR_i_sgNT_8B10_Rep2

value: Jurkat Cm6

value: CD4 T cell lymphoma


title: 3069-6-brainWT rep4

city: Houston

first: Yuan

last: Qi

state: TX

address: 1400 Pressler St

department: Bioinformatics & Computational Biology

institute: University of Texas M.D. Anderson Cancer Center

data_processing:
Quality control checks on raw sequencing reads using FastQC (0.11.5)
Sequence reads were trimmed for adaptor sequence using Trim Galore (0.6.5)
alignment and gene count by STAR (2.6.0b)
gene annotation using GENCODE M19 (Ensembl 94)
differential expression analysis carried out in R (4.0.2) using Bioconductor package DESeq2
Assembly: GRCm38
Supplementary files format and content: gene raw count matrix
Supplementary files format and content: tab-delimited text file

source_name: embryonic brain

extract_protocol:
Embryonic livers, lungs and brains were collected, flash frozen on dry ice, and RNA was harvested using Trizol reagent.
RNA libraries were prepared for sequencing using standard Illumina protocols.

value: embryonic brain

value: WT


title: 2974-1-brainWT rep3


title: ATAC_CRISPR_i_sgNT_8B10_Rep1


title: 2851-4-brainWT rep2


title: 2848-4-brainWT rep1


title: 3069-7-brainY130A rep4


title: ATAC_CRISPR_i_sgNT_5F9_Rep3


title: ATAC_CRISPR_i_sgNT_5F9_Rep1


title: ATAC_CRISPR_i_sgNT_5F9_Rep2


title: 2974-7-brainY130A rep3


title: ATAC_CRISPR_i_sgNT_1G2_Rep3


title: 2851-5-brainY130A rep2


title: ATAC_CRISPR_i_sgNT_1G2_Rep2


title: HMDM_Donor-2_LPS

source_name: Human elutriated monocytes Donor 2

value: Donor 2

value: 32 years old


title: 2848-1-brainY130A rep1


title: differentiated_neurosphere_mosaic_wild_type-Pcdh19_knockout_2

city: Adelaide

first: Mark

middle: A

last: Corbett

state: South Australia

address: Adelaide Health and Medical Sciences, University of Adelaide, North Tce

department: Adelaide Medical School

country: Australia

institute: University of Adelaide

hyb_protocol: Service provided by the Australian Genome Research Facility as per manufacturer's instruction

data_processing:
As per Homan, CC, et al. Am. J. Hum. Genet., 94 (2014), pp. 470-478.  Core probesets only are displayed in the data matrix
probe group file: MoGene-2_0-st.pgf
meta-probeset file: MoGene-2_0-st.mps

source_name: differentiated mouse neurospheres

extract_protocol: Trizol extraction followed by purification with QIAGEN Rneasy columns

value: female

value: mosaic

value: differentiated


title: differentiated_neurosphere_Pcdh19_knockout_3

scan_protocol: Service provided by the Australian Genome Research Facility as per manufacturer's instruction

growth_protocol: As per Homan, CC, et al. Am. J. Hum. Genet., 94 (2014), pp. 470-478

value: knockout


title: HMDM_Donor-3_NAM

source_name: Human elutriated monocytes Donor 3

value: Donor 3

value: Male

value: 54 years old

value: human monocyte-derived macrophages (HMDMs)


title: differentiated_neurosphere_mosaic_wild_type-Pcdh19_knockout_3

label_protocol: Service provided by the Australian Genome Research Facility as per manufacturer's instruction

treatment_protocol: As per Homan, CC, et al. Am. J. Hum. Genet., 94 (2014), pp. 470-478


title: differentiated_neurosphere_Pcdh19_knockout_1


title: HMDM_Donor-2_LPS+NAM

value: LPS+NAM


title: HMDM_Donor-2_control

value: control


title: differentiated_neurosphere_mosaic_wild_type-Pcdh19_knockout_1


title: differentiated_neurosphere_Pcdh19_knockout_2


title: differentiated_neurosphere_wild_type_3


title: HMDM_Donor-1_LPS+NAM

source_name: Human elutriated monocytes Donor 1

value: Donor 1

value: 66 years olld


title: HMDM_Donor-2_NAM

value: NAM


title: differentiated_neurosphere_wild_type_2


title: HMDM_Donor-1_LPS

value: 66 years old

value: LPS


title: 2974-1-lungWT rep3

source_name: embryonic lung

value: embryonic lung

value: WT


title: HMDM_Donor-3_LPS


title: HMDM_Donor-3_control


title: ATAC_CRISPR_i_sgNT_1D7_Rep3

value: Blood

value: Jurkat Cm6

value: CD4 T cell lymphoma


title: ATAC_CRISPR_i_sgNT_1D7_Rep2


title: 2851-4-lungWT rep2


title: 2848-4-lungWT rep1


title: ATAC_CRISPR_i_sgNT_1G2_Rep1


title: ATAC_CRISPR_i_sgNT_1D7_Rep1


title: differentiated_neurosphere_wild_type_1

value: female

value: differentiated


title: ATAC_CRISPR_i_sgHIV_8B10_Rep3


title: HMDM_Donor-1_control

value: Male


title: 3069-7-lungY130A rep4


title: ATAC_CRISPR_i_sgHIV_8B10_Rep1


title: HMDM_Donor-1_NAM


title: 2851-5-lungY130A rep2


title: 3069-6-liverWT rep3

source_name: embryonic liver

value: embryonic liver


title: 2848-4-liverWT rep4


title: neurosphere_mosaic_wild_type-Pcdh19_knockout_3

source_name: cultured mouse neurospheres

value: mosaic

value: neurosphere


title: neurosphere_Pcdh19_knockout_3

value: knockout


title: ATAC_CRISPR_i_sgHIV_5F9_Rep2


title: ATAC_CRISPR_i_sgHIV_5F9_Rep1


title: ATAC_CRISPR_i_sgHIV_1G2_Rep3


title: 2851-4-liverWT rep1


title: ATAC_CRISPR_i_sgHIV_1G2_Rep2


title: 2974-7-lungY130A rep3


title: 2974-1-liverWT rep2


title: ATAC_CRISPR_i_sgHIV_8B10_Rep2


title: neurosphere_mosaic_wild_type-Pcdh19_knockout_1


title: neurosphere_wild_type_3


title: 3069-7-liverY130A rep4


title: neurosphere_Pcdh19_knockout_1


title: neurosphere_wild_type_2


title: 2848-1-lungY130A rep1


title: ATAC_CRISPR_i_sgHIV_5F9_Rep3


title: 2974-7-liverY130A rep3


title: neurosphere_mosaic_wild_type-Pcdh19_knockout_2


title: neurosphere_wild_type_1


title: neurosphere_Pcdh19_knockout_2


title: 2851-5-liverY130A rep2


title: ATAC_CRISPR_i_sgHIV_1D7_Rep3


title: ATAC_CRISPR_i_sgHIV_1D7_Rep2


title: 2848-1-liverY130A rep1


title: CD3 T cells, ConA + PLL 24 h

city: Gwangju

first: Changduk

last: Jun

state: Not US or Canada

address: Bukgu oryongdong GIST

department: life science

country: South Korea

institute: Gwangju institute of science and technology(GIST)

description: gene expression data from mouse CD3 T cell for 24 h activation via conA treatment on PLL coated plate

hyb_protocol: Approximately 5.5 μg of labeled DNA target was hybridized to the Affymetrix GeneChip Array at 45°C for 16hour

scan_protocol: Hybridized arrays were washed and stained on a GeneChip Fluidics Station 450 and scanned on a GCS3000 Scanner (Affymetrix).

data_processing: The probe cell intensity data computation and a CEL file generation was performed using Affymetrix® GeneChip Command Console® Software (AGCC).

source_name: mouse CD3 T cell

label_protocol: The sense cDNA was then fragmented and biotin-labeled with TdT (terminal deoxynucleotidyl transferase) using the GeneChip WT Terminal labeling kit

growth_protocol: Mouse primary CD3 T cells were incubated in MTM (Mouse T cell Media, RPMI + 10% FBS + penicylin/streptomycin + b-mercaptoethanol + sodium pyruvate + MEM-NEAA)

extract_protocol: total RNA were isolated using Rneasy Plus mini kit (Qiagen)

treatment_protocol: Cells were activated for 3 h under the indicated conditions and washed for additional culture

value: CD3 T cell

tag: time


title: 2875-2-brainS226A rep3

value: embryonic brain


title: ATAC_CRISPR_a_sgNT_8B10_Rep3


title: CD3 T cells, ConA 24 h

description: gene expression data from mouse CD3 T cell for 24 h activation via conA treatment

value: activation via conA treatment


title: CD3 T cells, Naïve (NT) 24 h

description: gene expression data from mouse CD3 T cell in steady state for 24 h

value: steady state


title: ATAC_CRISPR_a_sgNT_8B10_Rep1


title: ATAC_CRISPR_a_sgNT_8B10_Rep2


title: CD3 T cells, ConA + PLL 3 h

description: gene expression data from mouse CD3 T cell for 3 h activation via conA treatment on PLL coated plate

value: 3 h


title: 2875-5-brainWT rep3


title: CD3 T cells, PLL 24 h

description: gene expression data from mouse CD3 T cell in steady state on PLL coated plate for 24 h

value: steady state on PLL coated plate


title: CD3 T cells, PLL 3 h

description: gene expression data from mouse CD3 T cell in steady state on PLL coated plate for 3 h


title: ATAC_CRISPR_a_sgNT_5F9_Rep2


title: CD3 T cells, ConA 3 h

description: gene expression data from mouse CD3 T cell for 3 h activation via conA treatment


title: 2881-6-brainWT rep2

value: WT


title: ATAC_CRISPR_a_sgNT_5F9_Rep3

value: Blood


title: 2881-1-brainS226A rep2


title: ATAC_CRISPR_a_sgNT_1G2_Rep3

value: Jurkat Cm6


title: CD3 T cells, coated 24 h

description: gene expression data from mouse CD3 T cell for 24 h activation via immobilized anti-CD3/28 antibody stimulation

treatment_protocol: Cells were activated for 3 h via iAb of sAb and washed for additional culture


title: 2972-4-brainS226A rep1


title: 2972-1-brainWT rep1


title: ATAC_CRISPR_a_sgNT_1G2_Rep2

value: CD4 T cell lymphoma


title: 2970-2-brainWT rep4


title: 2970-7-lungS226A rep4

value: embryonic lung


title: ATAC_CRISPR_a_sgNT_5F9_Rep1


title: 2970-7-brainS226A rep4


title: CD3 T cells, Naive (NT)

description: gene expression data from mouse CD3 T cell in steady state

value: control


title: mammary gland p8 p11 p14 hashing

city: Zurich

first: Genome

last: Informatics

address: Winterthurerstrasse 190

department: Functional Genomics Center Zurich (FGCZ)

country: Switzerland

institute: ETH ZURICH / University of Zurich

description: cell-hashing library

library_source: transcriptomic single cell

data_processing:
Demultiplexing performed using the Cell Ranger software
For p7 samples, CellRanger 3.1.0 was used to generate count matrices; for p8p11p14 samples, CellRanger 6.0.2 was used to demultiplex the samples and generate count matrices
Assembly: p7 lactating and naive samples: GRCm38.p6 GENCODE Release M23; for p8p11p14 samples: GRCm39 GENCODE Release M26
Supplementary files format and content: tab-delimited matrix, features, and barcodes

source_name: mammary gland

growth_protocol: All mice were kept in individually ventilated cages under specific-pathogen-free conditions.

extract_protocol:
Mice were sacrificed by CO2 inhalation and intracardially perfused with phosphate buffered saline. After perfusion, left and right abdominal mammary glands were dissected, and inguinal lymph nodes were removed. All the samples were cut into small pieces in an Eppendorf tube, followed by digestion in 0.4 mg/ml collagenase type IV and 0.04 mg/ml DNase I in Ca2+/Mg2+ HBSS supplemented with 10% FCS for 40 mins at 37°C, while shaking. Samples were homogenized with a 18G needle and a syringe and filtered through a 100 µm cell strainer to obtain a homogeneous cell suspension. Cells were once washed in PBS, resuspended in red blood cell lysis and incubated on ice for 5 min, then filtered through 100 μm cell strainer and washed with PBS. Then cells were first incubated with a-CD16/32 antibody to block FcR receptors, and stained with an antibody mix as specified in the "Methods" section of the paper. Following staining, populations of interest were sorted on BD FACS Aria III or BD S6 equipped with a 100 µm nozzle (the gating strategies are specified in the paper). The sorted populations were then washed, resuspended in PBS and ready for scRNAseq sample preparation steps. Human milk samples were collected at the University Hospital Zurich from healthy women, aged 20 to 40 years [mean (SD) 32.0 (5.0)], within 4 to 63 days after delivery. For isolation of milk cells, milk was diluted in a 1:1 ratio with PBS and centrifuged at 800 g for 20 minutes at 15°C. The lipid layer and skim milk were removed, and the cell pellet was washed twice in PBS by centrifugation at 400 g for 5 minutes and resuspension in PBS.
for p8p11p14 samples, libraries were constructed using 10X 3' scRNA-seq v3.1 with Hashtags with dual-indexing; for the p7 samples, libraries were prepared using the 10X Genomcis GEX 3`v3.1 Single index kit

value: mammary gland


title: CD3 T cells, sol + LatA 3 h

description: gene expression data from mouse CD3 T cell for 3 h activation via soluble anti-CD3/28 antibody stimulation with treatment of latrunculin A


title: CD3 T cells, coated 3 h

description: gene expression data from mouse CD3 T cell for 3 h activation via immobilized anti-CD3/28 antibody stimulation


title: ATAC_CRISPR_a_sgNT_1G2_Rep1


title: CD3 T cells, sol 24 h

description: gene expression data from mouse CD3 T cell for 24 h activation via soluble anti-CD3/28 antibody stimulation


title: CD3 T cells, sol + LatA 24 h

description: gene expression data from mouse CD3 T cell for 24 h activation via soluble anti-CD3/28 antibody stimulation with treatment of latrunculin A


title: 2881-1-lungS226A rep2


title: naive mammary gland p7

description: 3' mRNA library


title: mammary gland p8 p11 p14

description: 3' mRNA library


title: ATAC_CRISPR_a_sgNT_1D7_Rep1


title: CD3 T cells, Naïve_LatA

description: gene expression data from mouse CD3 T cell in steady state with treatment of latrunculin A


title: ATAC_CRISPR_a_sgNT_1D7_Rep2


title: lactating mammary gland p7 2

description: 3' mRNA library


title: 2972-4-lungS226A rep1


title: 2970-9-lungWT rep4


title: ATAC_CRISPR_a_sgHIV_8B10_Rep3


title: 2875-5-lungWT rep3


title: lactating mammary gland p7 1

description: 3' mRNA library


title: ATAC_CRISPR_a_sgHIV_8B10_Rep2


title: CD3 T cells, sol 3 h

description: gene expression data from mouse CD3 T cell for 3 h activation via soluble anti-CD3/28 antibody stimulation


title: 2875-2-lungS226A rep3


title: 2881-6-lungWT rep2


title: ATAC_CRISPR_a_sgNT_1D7_Rep3


title: KCNR-SM3

city: Birmingham

first: Han-Fei

last: Ding

state: Alabama

address: WTI 602D, 1824 6th Avenue South

department: Pathology

institute: University of Alabama at Birmingham

description: RNA expression value

hyb_protocol: Standard Affymetrix hybridization protocol

scan_protocol: Standard Affymetrix scanning protocol

data_processing: Data were normalized from CEL files using R/Bioconductor and gcRMA algorithm (http://homer.ucsd.edu/homer/basicTutorial/affymetrix.html).

label_protocol: TdT-labled cRNA were prepared with an Affymetrix GeneChip WT Terminal labeling kit.

growth_protocol: SMS-KCNR cells were cultured in RPMI 1640 (HyClone SH30027) supplemented with 10% FBS (Fisher Scientific, FB12999102).

extract_protocol: Total RNA was isolated from the cell samples using Trizol (Invitrogen), and RNA quality and quantity was assessed using a Agilent BioAnalyzer and a Nanodrop Spectrophotometer.

treatment_protocol: SMS-KCNR cells were treated with DMSO, simvastatin at 5 µM or simvastatin at 5 µM plus mevalonate at 2 mM for 30 hours.

value: SMS-KCNR

value: Neuroblastoma

value: simvastatin+mevalonate


title: 2972-1-lungWT rep1


title: C IgG, scRNAseq

city: los angeles

first: Sandra

last: Orsulic

state: california

address: 10833 Le conte ave

department: OBGYN

institute: UCLA

description: 10x Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v7.0.1 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Peritoneal wall

extract_protocol:
Tumors collected from the site of peritoneal abrasion from mice treated with Activin A neutralizing antibody or control IgG were pooled and minced into 1mm pieces. Tissue was further dissociated by enzymatic digestion by rotating at 37°C for 30 minutes with 1 mg/ml Collagenase/Hyaluronidase (STEMCELL), DNAse and trypsin (0.01%). After dissociation, the suspension was strained (70 micron strainer) followed by centrifugation (8 minutes at 300g). Red blood lysis buffer (Thermo Fisher) was used followed by dead cell removal (STEMCELL) to deplete the samples of erythrocytes and dead cells, respectively according to the manufacturer’s instructions. Finally, cells were resuspended in 0.04% BSA-PBS solution at a concentration of 700-1000 cells/microliter without selection for specific cell types.
Library construction was performed according to the manufacturer’s instructions (single cell 3’ v2 protocol, 10x Genomics). Briefly, GCs were resuspended in the master mix and loaded together with partitioning oil and gel beads into the chip to generate the gel bead-in-emulsion (GEM). The poly-A RNA from the cell lysate contained in every single GEM was retrotranscripted to cDNA, which contains an Ilumina R1 primer sequence, Unique Molecular Identifier (UMI), and the 10x Barcode. The pooled barcoded cDNA was then cleaned up with Silane DynaBeads, amplified by PCR, and the appropriate-sized fragments were selected with SPRIselect reagent for subsequent library construction. During the library construction Ilumina R2 primer sequence, single-end constructs were added

value: Ovarian tumor

tag: Sex

value: Female

value: 6-8 weeks old


title: Activin, scRNAseq

description: 10x Genomics

tag: age


title: DAAO_B6Cdh5_Cre

city: Boston

first: Thomas

last: Michel

state: MA

address: 75 Francis Street

institute: BWH/HMS

data_processing:
Reads (Fastq files) obtained from paired-end sequencing were aligned were to the mouse genome (GRCm38 - mm10) using hisat2(v2.0.5)
Quality control was performed on raw reads and alignment results using fastQC and Qualimap, respectively. Sample clustering was visualized using principal component analysis.
Differential expression analysis was performed using DESeq2 (v1.20.0) using standard parameters, comparing DAAO mouse with their controls
Assembly: Mus Musculus(GRCm38/mm10)
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample

source_name: DRGs

extract_protocol:
DRGs were removed, snap frozen in liquid nitrogen, and RNA was harvested using Trizol reagent. RNA quantification and sample integrity were then analyzed using a Nanodrop spectrophotometer and an Agilent 2100 bioanalyzer, respectively.
Library preparation and sequencing were performed by Novogene (Sacramento, CA) using an Illumina Platform PE150.

value: DRGs

value: D-Alanine


title: CD3 T cells, Naïve (NT)

value: CD3 T cell

value: steady state


title: ATAC_CRISPR_a_sgHIV_5F9_Rep2


title: 2970-7-liverS226A rep4

value: embryonic liver


title: ATAC_CRISPR_a_sgHIV_5F9_Rep3

value: Blood


title: DAAO_B5Cdh5_Cre


title: 2875-2-liverS226A rep3


title: KCNR-SM1

description: RNA expression value


title: KCNR-S3

description: RNA expression value

value: simvastatin


title: ATAC_CRISPR_a_sgHIV_5F9_Rep1

value: Jurkat Cm6

value: CD4 T cell lymphoma


title: DAAO_B4Cdh5_Cre


title: ATAC_CRISPR_a_sgHIV_1G2_Rep3


title: ATAC_CRISPR_a_sgHIV_8B10_Rep1


title: KCNR-SM2

description: RNA expression value


title: DAAO_B3Cdh5_Cre


title: KCNR-S2

description: RNA expression value


title: 2972-4-liverS226A rep1


title: ATAC_CRISPR_a_sgHIV_1G2_Rep2


title: KCNR-S1

description: RNA expression value


title: KCNR-D3

description: RNA expression value

value: DMSO


title: KCNR-D2

description: RNA expression value


title: DAAO_B2Cdh5_Cre


title: 2970-2-liverWT  rep4

value: WT


title: ATAC_CRISPR_a_sgHIV_1G2_Rep1


title: 2875-5-liverWT  rep3


title: DAAO_B1Cdh5_Cre


title: KCNR-D1

description: RNA expression value

value: SMS-KCNR


title: Control_A6Cdh5_Cre


title: valvular interstitial cells OIM induced calcification  added BFGF rep1 [BFGF_1]

city: shanghai

first: YUAN

last: GAO

address: No. 168, Changhai Road, Yangpu District, Shanghai

department: Cardiovascular surgery

institute: Changhai Hospital

data_processing:
Raw reads generated during high-throughput sequencing were fastq format sequences.
In order to get high-quality reads that could be used for later analysis, raw reads needed to be further quality filtered.
Trimmomatic software was first used for adpter removing, And then low-quality bases and N-bases or low-quality reads were filtered out. Finally, we got high-quality clean reads.
Using hisat2  to align clean reads to the reference genome of the experimental specie, the sample should be assessed by genomic and gene alignment.
Using the Stringtie software to assemble the reads, the new transcript was spliced. Then the candidate lncRNA transcripts were selected by comparing the gene annotation information of the reference sequence produced by Cuffcompare  software. Finally, transcripts with coding potential were screened out by CPC , CNCI , Pfam and PLEK to obtain lncRNA predicted sequences.
Assembly: sscrofa11.1
Supplementary files format and content: tab-delimited text files include counts values for each Sample

organism: Sus scrofa

source_name: aortic valve

growth_protocol: Porcine aortic VICs were harvested and isolated from pigs aged 4–5 months (Wufeng, Shanghai). The porcine hearts were collected in an icebox after sacrifice and immediately taken back to the laboratory. Aortic valve leaflets were cut and immersed in precooled phosphate- buffered saline (PBS) solution. The valve leaflets were digested in 2 mg/mL type II collagenase for 15 min and the valve endothelial cells on the surface were gently scraped off with a sterile cotton swab. The valve leaflets were cut into pieces and then digested in type II collagenase for another 2 hours. Undigested tissue was removed by a filtrating screen. The harvested VICs were collected by centrifugation and then seeded on culture dish in DMEM containing 10% fetal bovine serum, and the medium was changed every 2–3 days.

extract_protocol:
Total RNA was extracted using the mirVana miRNA Isolation Kit (Ambion) following the manufacturer’s protocol.
The libraries were constructed using TruSeq Stranded Total RNA with Ribo-Zero Gold according to the manufacturer’s instructions.
Then these libraries were sequenced on the Illumina sequencing platform (HiSeqTM 2500 ) and 150 bp/125bp paired-end reads were generated

treatment_protocol: The porcine valvular interstitial cells (PVIC) as the model. We used OIM differentiation medium containing 2 mmol/L sodium dihydrogen phosphate, 50 µg/mL ascorbic acid, and 10−7mol/L insulin to induce calcification as well as bFGF  (50 ng/ml, peprotech) treatment to inhibit the calcification for 3 days.

value: aortic valve

value: valvular interstitial cell

value: wild type

value: OIM induce calcification with BFGF for three days


title: ATAC_CRISPR_a_sgHIV_1D7_Rep3

source_name: Blood


title: ATAC_CRISPR_a_sgHIV_1D7_Rep2


title: Control_A5Cdh5_Cre


title: valvular interstitial cells OIM induced calcification  added BFGF rep2 [BFGF_2]


title: valvular interstitial cells OIM induced calcification rep3 [OIM_3]

value: OIM induce calcification for three days


title: 2881-1-liverS226A rep2


title: 2972-1-liverWT  rep1


title: ATAC_CRISPR_a_sgHIV_1D7_Rep1


title: valvular interstitial cells OIM induced calcification rep2 [OIM_2]


title: 58492

data_processing:
VDJ-Seq: The bioinformatic analysis of the VDJ-seq data was performed as described in detail in Chovanec et al., Nat. Protoc. 13, 2018. using the BabrahamLinkON pipeline: (1) preclean.py (default parameters), Includes trimming and alignment steps (BabrahamLinkOn pipeline) deduplicate.py (default parameters), based on UMI  (BabrahamLinkOn pipeline) (2) assemble_clones.py (default parameters)  (BabrahamLinkOn pipeline) (3) The resulting counts were summarized using customized scripts based on the statistical language R version 3.3.3. The relative usage of each VH gene is shown as percentage of all VDJH recombination events determined.
ChIP-Seq:  Reads were aligned against the Mus musculus genome version of July 2007 (NCBI37/mm9) with the Bowtie program version 0.12.5. Genome-wide read coverages were normalized to the number of aligned reads, per million (=RPM)., using 'bedtools' and 'kent source utilities'.
RNA-Seq: The number of reads per gene was counted using the featureCounts version 1.5.0 with default settings. Transcripts per million (TPM) values were calculated as described previously.
total RNA-Seq: Reads were aligned with STAR version 2.4.2 to the Mus musculus genome version of July 2007 (NCBI37/mm9). Read coverages were calculated with the BEDTool program, were normalized to reads per millions (RPM) using the SAMTools as well as the KentTools.
Assembly: mm9 (total RNA-Seq, RNA-Seq,ChIP-Seq), mm10 (VDJ-Seq)
Supplementary files format and content: tab-delimited text files include RPM values for each VDJ-Seq sample and TPM values for RNA-Seq samples. bigWig files include read coverage for total RNA-Seq and ChIP-Seq samples.

source_name: mRNA-Seq IgMb immature B cell Igh(P4V/P4V)

extract_protocol:
RNA libraries were prepared for sequencing using standard Illumina protocols
Rneasy Plus Mini Kit, Dynabeads mRNA purification kit

value: bone marrow

tag: chip antibody

value: IgMb immature B cell

value: Ex-vivo FACS sorted from bone marrow


title: valvular interstitial cells OIM induced calcification  added BFGF rep3 [BFGF_3]


title: ATAC_Jurkat_Rep3


title: Control_A3Cdh5_Cre

value: DRGs

value: D-Alanine


title: Control_A4Cdh5_Cre


title: valvular interstitial cells rep3 [NC_3]

value: DMEM cultivation for three days


title: ATAC_Jurkat_Rep2

value: Blood