title: GSCLC_S3

city: Kyoto

description: PBAT

treatment_protocol: The rTestes at various culture periods were peeled off from the cell insert membrane using a P1000 pipette tip and incubated in 0.25% Trypsin-EDTA in PBS (GIBCO, #15400-054) for 5~15 min, with periodical intermittent pipetting, and the dissociates were quenched by an equal volume of DMEM medium (GIBCO, #10313-021) containing 10% FCS (Hyclone), 2 mM GlutaMAX (GIBCO, 35050-061), 100 U/mL penicillin, and 0.1 mg/mL streptomycin (GIBCO, 15070).  The resultant cell pellet was resuspended with PBS containing 0.1% BSA fraction V (Life Technologies, # 15260037), and large clumps of cells were removed using a nylon cell strainer (FALCON, #352350).  The BV+; SC+ and Ddx4/mvh-RFP-positive (BV+; SC+; VR+) cells (mPGCLC-derived cells in rTestes: m0, m3, m5, m7, m10), VR+ and CD9-APC-positive (VR+; CD9-APC+) cells (mPGCLC-derived cells in rTestes: m12, m14), and VR+ cells in embryonic gonads/postnatal testes were sorted by the FACSAria III (BD Biosciences) cell sorter, and were collected in CELLOTION (Nippon Zenyaku Kogyo, CB051).  For RNA/DNA extraction, the sorted cells were centrifuged at 500G for 10 min, and the cell pellets were frozen down by liquid N2, and preserved at −80℃.

tag: cell type


title: GSCLC_S1

status: Public on Sep 30 2021

type: SRA

first: Yukihiro

last: Yabuta

state: Kyoto

address: Yoshida-Konoe-cho, Sakyo-ku

department: Anatomy and Cell Biology

country: Japan

institute: Kyoto University, Graduate school of medicine

description: PBAT

library_source: genomic

data_processing:
The genome sequences of the pseudo-autosomal region (PAR) on the chromosome Y in GRCm38.p6, chrY:90745845-91644698 were replaced with Ns and the genes in this region were deleted from the reference to avoid a “mapped multi” call at the mapping step.
Read data processing of the methylation levels was performed as described previously (Shirane et al., 2016).  In brief, all reads were processed with Trim-Galore v0.4.1 (https://www.bioinformatics.babraham.ac.uk/projects/trim_galore/)/cutadapt v1.9.1 (http://cutadapt.readthedocs.io/en/stable/guide.html) with the “--clip_R1 4”, “--trim1” and “-a AGATCGGAAGAGC” options.
Output reads were mapped onto the mouse genome, GRCm38.p6, using Bismark v0.22.1/Bowtie2 v2.3.4.1 with the "--pbat" option.   All CpG sites with a read depth of between 4 and 200 were used for the bigWig files.
Genome_build: GRCm38.p6

molecule: genomic DNA

organism: Mus musculus

source_name: GSC-like cells

growth_protocol: Generation and Culture of Reconstituted Testes (rTestis)  To isolate E12.5 mouse male gonads (fetal testes), pregnant ICR females were sacrificed by cervical dislocation, and the embryos were isolated in chilled Dulbecco's Modified Eagle Medium (DMEM) (GIBCO, #10313-021) containing 10% FCS (Hyclone), 2 mM GlutaMAX (GIBCO, #35050-061), 10 mM HEPES (GIBCO, #15630-106), 100 U/mL penicillin, and 0.1 mg/mL streptomycin (GIBCO, 15070).  Fetal testes were identified by their appearance, and the mesonephroi were dissected out with tungsten needles.  The isolated fetal testes were dissociated into single cells, and endogenous mouse germ cells were selected out by magnetic-activated cell sorting (MACS).  Compared to FACS, MACS requires much less time and less physical stress to collect the cells for the rTestis formation.  The mPGCLCs (10,000 cells/well) and the fetal testes somatic cells (when using frozen stocks, 20,000 cells/well) (total 30,000 cells/well) were mixed and plated on the wells of a Nunclon Sphera 96-well Microplate (#174925; Thermo Fisher Scientific) and cultured under a floating condition in GK10+FR10 medium (GK10, 10 μM forskolin and 10 μM rolipram).  After a period of 2 days for the floating culture, using a glass capillary, the rTestes were transferred onto ThinCert™Cell Culture Inserts for 24-Well Plates (Greiner #662610) soaked in alpha-Minimum Essential Medium (GIBCO, #32561-037) containing 10% FCS (Hyclone), 55 μM 2-mercaptoethanol (GIBCO, 21985-023), 100 U/mL penicillin, and 0.1 mg/mL streptomycin (GIBCO, 15070).  Half the medium was changed every two days.  All rTestes were cultured for a gas-liquid interphase culture at 37℃ under an atmosphere of 5% CO2 in air.    Derivation of GSCLCs from rTestis  For the derivation of GSCLCs, VR+; CD9-APC+ cells in rTestes (m14) were sorted with a flow cytometer (BD Biosciences, FACS Aria Ⅲ).  For deriving GSCLCs from all VR+; CD9-APC+ cells/rTestis, 24-well culture dishes (Falcon, #353047) were coated with PBS supplemented with 0.1% gelatin for at least 30 min, seeded with mouse embryonic feeders (MEF) for at least 6 h prior to the plating of mPGCLC-derived cells, and then VR+; CD9-APC+ cells (derived from 1 rTestis)/well were seeded and cultured with GSCs/GSCLCs medium.  For deriving GSCLCs from single VR+; CD9-APC+ cells, 96-well culture dishes (Falcon, #353072) were coated with PBS supplemented with 0.1% gelatin for at least 30 min, then seeded with MMC-treated MEF for at least 6 h prior to the plating of an mPGCLC-derived cell.  A single VR+; CD9-APC+ cell was then seeded using a FACS Automated Cell Deposition Unit (ACDU) system and cultured with GSCs/GSCLCs medium.The GSC/GSCLC medium was as described previously (Kanatsu-Shinohara et al., 2003), with some modifications (Ishikura et al., 2016).  StemPro-34 SFM (GIBCO, #10639011) was supplemented with StemPro supplement (GIBCO, #10639011), 0.1 mM 2-mercaptoethanol (GIBCO, 21985-023), 1% FCS (Hyclone), 1 × minimal essential medium (MEM) Vitamin Solution (GIBCO, # 11120-052), 5.0 mg/mL AlbuMAXⅠ (GIBCO, #11020-021), 0.1 mM NEAA (GIBCO, #11140-050), 1 mM sodium pyruvate (GIBCO, 11360-070), 100 U/mL penicillin, 0.1 mg/mL streptomycin (GIBCO, #15070), 2 mM GlutaMAX (GIBCO, #35050-061), 1 × Insulin-Transferrin-Selenium (ITS-G) (GIBCO, #41400045), 10 ng/mL bFGF Recombinant Human Protein (Life Technologies, #13256029), 20 ng/mL GDNF Rat Recombinant (RSD, #512GF050), 20 ng/mL EGF Mouse Recombinant Carrier-free (RSD, #2028EG200), and 1000 U/mL LIF (Merk, ESG1107).  Half the medium was changed every two or three days.  All GSCs/GSCLCs were cultured at 37℃ under an atmosphere of 5% CO2 in air."  "Isolation of Germ Cells  To isolate germ cells for the RNA-seq analysis, ICR females were crossed with C57BL/6N; mvh-RFPTg/Tg males.  The embryonic gonads/postnatal testis fragments at E12.5–P7.5 were dissociated into single cells by incubating with 0.05% Trypsin-EDTA (GIBCO, #15400-054) for 10 min at 37℃, and were quenched with an equal volume of DMEM medium (GIBCO, #10313-021) containing 10% FCS (Hyclone), 2 mM GlutaMAX (GIBCO, #35050-061), 100 U/mL penicillin, and 0.1 mg/mL streptomycin (GIBCO, #15070).  Large clumps of cells were removed using a nylon cell strainer (FALCON, #352350), and cells were centrifuged at 1,200 rpm for 5 min.  The cell pellet was re-suspended with DMEM/F12 medium (GIBCO, 1130-082) containing 0.1% BSA fraction V (Life Technologies, # 15260037), and sorted with a flow cytometer (BD Biosciences, FACS Aria Ⅲ)    Fluorescence-activated Cell Sorting (FACS)  The d4 floating aggregates of EpiLCs and d4c5 mPGCLCs were incubated in TrypLE express for 10 min at 37℃, with periodical pipetting, and the dissociates were quenched with a 5 × volume of DMEM/F12 medium (GIBCO, #1130-082) containing 0.1% BSA fraction V (Life Technologies, # 15260037) and DNase I (Sigma, DN25), followed by pipetting to generate a single cell suspension.  After centrifugation at 1,200 rpm for 5 min, the supernatant was discarded.  The cell pellet was re-suspended with DMEM/F12 medium (GIBCO, #1130-082) containing 0.1% BSA fraction V (Life Technologies, #15260037), the cell suspension was filtered through a nylon cell strainer (FALCON, #352350), and BV+ d4 mPGCLCs or BV+; SC+ d4c5 mPGCLCs were sorted by a flow cytometer (BD Biosciences, FACSAria III) and collected in the GK10+FR10 medium.  The rTestes at various culture periods were peeled off from the cell insert membrane using a P1000 pipette tip and incubated in 0.25% Trypsin-EDTA in PBS (GIBCO, #15400-054) for 5~15 min, with periodical intermittent pipetting, and the dissociates were quenched by an equal volume of DMEM medium (GIBCO, #10313-021) containing 10% FCS (Hyclone), 2 mM GlutaMAX (GIBCO, 35050-061), 100 U/mL penicillin, and 0.1 mg/mL streptomycin (GIBCO, 15070).  The resultant cell pellet was resuspended with PBS containing 0.1% BSA fraction V (Life Technologies, # 15260037), and large clumps of cells were removed using a nylon cell strainer (FALCON, #352350).  The BV+; SC+ and Ddx4/mvh-RFP-positive (BV+; SC+; VR+) cells (mPGCLC-derived cells in rTestes: m0, m3, m5, m7, m10), VR+ and CD9-APC-positive (VR+; CD9-APC+) cells (mPGCLC-derived cells in rTestes: m12, m14), and VR+ cells in embryonic gonads/postnatal testes were sorted by the FACSAria III (BD Biosciences) cell sorter, and were collected in CELLOTION (Nippon Zenyaku Kogyo, CB051).  For RNA/DNA extraction, the sorted cells were centrifuged at 500G for 10 min, and the cell pellets were frozen down by liquid N2, and preserved at −80℃.

extract_protocol:
The sample preparations from GSCLCs were performed essentially as described previously (Ishikura et al., 2016) (see Fluorescence-activated Cell Sorting (FACS)).  15,000 cells of GSCLCs (GSCLC_S1, GSCLC_S2, GSCLC_S3, GSCLC_S4) were sorted and the genomic DNA was extracted with NucleoSpin ® Tissue XS (MACHEREY-NAGEL, U0901).  For the bisulfite treatment, the whole elute of the genomic DNA extraction containing 0.45 ng of unmethylated λ phage DNA was treated with an EZ DNA Methylation‐Gold Kit (ZYMO RESEARCH,  D5005) according to the manufacturer's instructions.
Sequence libraries were generated with a post-bisulfite adaptor tagging method (http://www.crest-ihec.jp/english/epigenome/index.html; Miura et al., 2012; Shirane et al., 2016).  Some reagents were replaced as follows: Phusion Hot Start High‐Fidelity DNA Polymerase (Thermo Fisher Scientific, F540S) was replaced with Phusion Hot Start II DNA Polymerase (Thermo Fisher Scientific, F549S); Agencourt AMPure XP was replaced with an AxyPrep MAG PCR Clean‐Up Kit (Corning, MAG‐PCR‐CL‐250).  The sequencing was performed on an Illumina HiSeq 2500 platform with the TruSeq SR Cluster Kit ‐cBot‐HS and TruSeq SBS Kit ‐HS (Illumina).
library strategy: Post-bisulfite adaptor-tagging (PBAT)

tag: genotype

value: Germ cells derived from ESCs

tag: strain

value: B6C3(Cg) x C57BL/6


title: TAFwtK9

city: Cambridge

first: Sergio

last: Martínez Cuesta

address: 1 Francis Crick Avenue

department: Data Sciences and Quantitative Biology, Discovery Sciences

country: United Kingdom

institute: AstraZeneca

description: WT H3K9me3

data_processing:
The data was processed as described in the methods section of the associated manuscript. Details about the analysis are available in https://github.com/semacu/hush
Genome_build: GRCh38
Supplementary_files_format_and_content: txt files contain quantification of signal in genes of interest, bed files contain peaks calculated with a tailored peak calling strategy and bigwig capture genomic signal. Data was processed jointly with RNA-seq and ChIP-seq data available in GSE95374

organism: Homo sapiens

source_name: HeLa cells

growth_protocol: HEK293T were obtained from ATCC and HeLa were obtained from ECACC. All cell lines were cultured at 37°C and 5% CO2 in Iscove's Modified Dulbecco's Medium (IMDM, Sigma-Aldrich) supplemented with 10% fetal calf serum (FCS, Gibco), 1x GlutaMAX (Gibco), and 100 U/mL penicillin/streptomycin (Gibco).

extract_protocol:
RIPseq:  Lysates from UV-treated cells were clarified from sonicated nuclei and RNA-protein complexes were isolated with anti-HA magnetic beads. ChIPseq: Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with H3K9me3 antibody.
RIPseq: Immunoprecipitated RNA was subjected to DNA library preparation using SMARTer Stranded Total RNA-Seq Kit V3 – Pico Input Mammalian (Takara Bio, USA) kit according to the manufacturer’s instructions and following conditions: initial fragmentation at 94°C for 3-4 min, ribosomal RNA depletion step included, 5 PCR cycles for PCR adding adapters and indexes and 12 for final library amplification). The library quality was determined using Bioanalyzer, and sequenced using Illumina MiniSeq System with the following specifications: 32 bp (R1) and 43 bp (R2), paired-end reads were sequenced using MiniSeq High-Output 75 cycles kit. ChIPseq: ChIP DNA and input DNA were subjected to library preparation with NEBNext Ultra II DNA Library Prep Kit for Illumina according to manufacturer's instructions. Libraries were purified, quantified, multiplexed (with NEBNext Multiplex Oligos for Illumina) and sequenced with 2× 50-bp pair-end reads on Illumina Novaseq platform (Genomics Core, Cancer Research UK Cambridge Institute).

value: HeLa

value: wild type

tag: antibody


title: GSCLC_S2

description: PBAT


title: Hippocampus microvessels, LDL-R -/- mice fed with western diet (WD)

type: RNA

city: Davis

first: Saivageethi

last: Nuthikattu

state: CA

address: 550 Hutchison Dr

department: Internal Medicine, Cardiovascular division

country: USA

institute: University of California Davis

description:
Gene expression data of hippocampus microvessels from male LDL-R -/- mice fed with western diet (WD)
LDLR KO WD

hyb_protocol: Following fragmentation and labeling, 5.5 ug of sscDNA were hybridized for 16 hr at 45C on the Mouse Gene 2.0 ST Array using Affymetrix WT array hybridization protocol. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the GeneChip Scanner 3000 7G.

data_processing: Analyses of gene expression levels were performed with Transcriptome Analysis Console software version 3.1.0.5.

label: biotin

molecule: total RNA

source_name: Male Mice brain hippocampus microvessels

label_protocol: 125 pg of total RNA was used to prepare cRNA according to Affymetrix's GeneChip® WT Pico Kit protocol. Biotinylated sscDNA (5.5 ug) were prepared from 20 ug of cRNA.

growth_protocol: Male mice were housed in single cages in a temperature- and humidity-controlled environment with a 12 h light/dark cycle.

extract_protocol: Total RNA was extracted from the laser-captured hippocampal brain microvessels from each of the four experimental groups using an Arcturus PicoPure™ RNA Isolation Kit according to the manufacturer’s instructions.

treatment_protocol: Five-week-old LDL-R-/- and wild type (WT) male mice were fed a chow (control diet, CD) or western diet (WD) for 8 weeks.

tag: gender

value: male

value: B6.129S7-Ldlr tm1Her/J

value: LDL-R -/-

tag: diet

value: western diet

tag: tissue

value: brain hippocampus microvessels


title: Embryonic Stem Cell dervived Hypothalamus-like Neurons  (ATAC-Seq) Replicate 5

status: Public on Oct 01 2021

city: Philadelphia

first: Matthew

middle: C

last: Pahl

state: PA

address: 3615 Civic Center Blvd

institute: Children's Hospital of Philadelphia

description:
HNvsHP.DE_atacseq_edgeR.txt
HNvsESC.DE_atacseq_edgeR.txt
HypothalamusESC_atac_counts_fpkm.txt

data_processing:
Bases were called using Illumina bcl2fastq2 conversion v2.29
Reads were aligned using bowtie2 implimented in the ENCODE pipeline. Reads alignment by offsetting +4bp for all the reads aligned to the forward strand, and -5bp for all the reads aligned to the reverse strand
Open chromatin regions (OCRs) were called using MACS2 implimented in the ENCODE pipeline with the following parameters -p 0.01 --nomodel --shift -75 --extsize 150 -B --SPMR --keep-dup all --call-summits. The encode blacklist regions (wgEncodeDacMapabilityConsensusExcludable.bed.gz) were removed from called peaks.
Prior to differential analysis peaks were filtered to remove peaks not identified in at least half of replicates using bedtools intersect (v2.25.0). A consensus set of peaks was generated by taking the union of peaks defined in the three stages of differentiation
Read counts for the consensus set of peaks were normalized using csaw v1.8.1. OCRs with maximium median value of less than 1.2 CPM (~10-50 reads per OCR) across all replicates were filtered prior to differential analysis.
Differential analysis was performed using the glmQLFit implmented in edgeR v 3.16.5 using the normalization factors calculated with csaw. Differential OCRs were identified with thresholds of FDR < 0.05 and log2 fold change > 1.
FPKM values were calculated from reads mapped to consensus OCRs and bigWig files were generated from the duplicate filtered bam files using the R packages GenomicAlignments (v1.10.1) & rtracklayer(1.34.2)
Genome_build: hg19
Supplementary_files_format_and_content: bigwig files for each replicate as well as a tab-deliminated file containing OCR locations, raw counts and fpkm, as well as results from each differential comparison

source_name: WiCell

growth_protocol: Human ESC H9 (W09; WiCell) were seeded on Matrigel plates (16 million cells/148 cm2) in DMEM KO medium supplemented with 15% KnockOut Serum Replacement, 0.1mM MEM Non-Essential Amino Acids, 2mM GlutaMAX, 0.06 mM 2-Mercaptoethanol) with FGF-Basic (20 ng/ml media), and 10 mM Rock inhibitor.

extract_protocol:
A total of 50,000 cells were centrifuged at 550g for 5 min at 4°C. The cell pellet was washed with cold PBS and resuspended in 50 μL cold lysis buffer (10 mM Tris-HCl, pH 7.4, 10 mM NaCl, 3 mM MgCl2, 0.1% NP-40/IGEPAL CA-630) and immediately centrifuged at 550 g for 10 min at 4°C. The tagmented DNA was then purified using the Qiagen MinElute kit and eluted in 10.5 μL Elution Buffer.
Ten microliters of purified tagmented DNA was PCR amplified using the Nextera Indexing Kit for 12 cycles to generate each library. The PCR reaction was subsequently purified using 1.8x AMPure XP beads, and concentrations were measured by Qubit Fluorometer.  Quality of completed libraries was assessed on a Bioanalyzer 2100 high sensitivity DNA Chip.  Libraries were paired-end sequenced at the Center for Spatial and Functional Genomics on the Novaseq 6000 platform (50 bp read length).

treatment_protocol: ESC were untreated. Upon confluency, cells were cultured in ESC medium without FGF-Basic and Y-27632, but supplemented with Shh (100 ng/ml), Purmorphamine (2 μM), 10 μM SB431542, and 2.5 μM LDN193289. From days 5 to 8, ESC medium was gradually replaced with neuroprogenitor medium (DMEM/F-12 supplemented with 0.1 mM MEM Non-Essential Amino Acids, N-2 Supplement, 0.2 μM ascorbic acid, 0.16% glucose). At day 9, cells were switched into neuronal differentiation medium (DMEM/F-12 supplemented with 0.1 mM MEM Non-Essential Amino Acids, N-2 Supplement, B-27 Supplement minus Vitamin A, 0.2 μM ascorbic acid, 0.16% glucose containing 10 μM DAPT). On day 12, cells were collected with TrypLE Express Enzyme at 37°C for 7 min and washed twice including filtration through pre-wetted 40 μm Corning Sterile Cell Strainer. The hypothalamic progenitor cell pellet was then resuspended with neuronal differentiation medium containing 10 μM Y-27632 for plating on 148 cm2 dishes coated with Poly-L-Ornithine solution (0.01%) and laminin (4 μg/ml) at a seeding density of 16 million cells/148 cm2. After 4 hours (once the cells had completely attached to the plate), the medium was changed to neuronal differentiation medium supplemented with 10 μM DAPT. On day 15, the neuronal differentiation medium was supplemented with 20 ng/ml BDNF (Peprotech Cat # 450-02) until collection on day 27.

tag: cell stage

value: Hypothalamic Neuron

tag: age (differentiation protocol)

tag: esc line

value: human ESC H9


title: TAFkoK9

description: TASOR KO H3K9me3

value: TASOR KO


title: TAF5IN

description: TAF7_promoter mutant INPUT

value: TAF7 mutant


title: TAFkoIN

description: TASOR KO INPUT


title: TAFwtIN

description: WT INPUT


title: L1kosffvK9

description: L1 promoterless L1 TASOR KO H3K9me3

value: TASOR KO + L1 reporter


title: L1kosffvIN

description: L1 promoterless L1 TASOR KO INPUT


title: L1wtIN

description: L1 WT INPUT

value: wild type + L1 reporter


title: Hippocampus microvessels, WT mice fed with western diet (WD)

description:
Gene expression data of hippocampus microvessels from male WT mice fed with western diet (WD)
WT WD

value: WT


title: L1wtsffvIN

description: L1 promoterless WT INPUT


title: Knock-out at 10 days

status: Public on Sep 22 2021

city: Parkville

first: Gordon

middle: K

last: Smyth

state: Vic

address: 1G Royal Pde

department: Bioinformatics

country: Australia

institute: Walter and Eliza Hall Institute of Medical Research

library_source: transcriptomic

data_processing:
Libraries were sequenced on an Illumina HiSeq 2000 to produce 100bp single-end reads. Image analysis was performed in real time by the HiSeq Control Software (HCS)  v1.4.8 and Real Time Analysis (RTA) v1.12.4.2, running on the instrument computer. Then the Illumina CASAVA 1.8.2 pipeline was used to generate the sequence data.
Reads were aligned to the mouse genome mm10 by Rsubread version 1.30.5.
Read counts were summarized by Entrez Gene ID using the Rsubread featureCounts function and Rsubread's inbuilt RefSeq annotation. At least 31 million reads were generated for each sample. Read counts from the two lanes of sequencing were summed together for each sample.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files; columns represent Entrez Gene ID, gene length (total base count of all exons) and the number of reads mapped to that gene.

source_name: spleen

extract_protocol:
Total RNA was extracted.
Standard Illumina TruSeq RNA sample preparation protocols were used at the Australian Genome Research Facility.

tag: background strain

value: Il21r KO

tag: days after immunization

value: Germinal center B cells


title: L1wtK9

description: L1 WT H3K9me3


title: Gudjonsson_017_169

city: Ann Arbor

first: Lam

last: Tsoi

state: MI

address: Medical Sciences 1 Bldg. 1301 E. Catherine

institute: University of Michigan

hyb_protocol: Labeled cDNA was hybridized at 48°C to Affymetrix Human Gene ST 2.1 array plates, which were then washed, stained and scanned using the Affymetrix GeneTitan system (software version 3.2.4.1515) with the assistance of the University of Michigan DNA Sequencing Core.

data_processing: R bioconduct was used to process the data, and RMA was used to summarize and normalize the expression values

source_name: Skin

label_protocol: Complementary DNA was prepared and biotinylated using the NuGEN Encore Biotin Module (Encore Biotin Module Manual, P/N M01111 v6).

extract_protocol: RNA was isolated from 10μm sections of formalin-fixed paraffin embedded blocks of identified skin biopsies. RNA was extracted using the E.N.Z.A. FFPE RNA Kit (Omega Bio-tek).

value: Skin

tag: disease state


title: Wild-type at 14 days


title: Wild-type at 10 days


title: Knock-out at 14 days


title: TAF5K9

description: TAF7_promoter mutant H3K9me3

value: HeLa


title: Knock-out at 7 days


title: Hippocampus microvessels, WT mice fed with control diet (CD)

description:
Gene expression data of hippocampus microvessels from male WT mice fed with control diet (CD)
WT CD

value: control


title: Gudjonsson_013_165

scan_protocol: Labeled cDNA was hybridized at 48°C to Affymetrix Human Gene ST 2.1 array plates, which were then washed, stained and scanned using the Affymetrix GeneTitan system (software version 3.2.4.1515) with the assistance of the University of Michigan DNA Sequencing Core.


title: Wild-type at 7 days


title: T47D_Estrogen_rep2

status: Public on Sep 17 2021

city: Farmington

first: Michael

middle: Joseph

last: Guertin

state: CT

address: 400 Farmington Ave

department: Center for Cell Analysis and Modeling

institute: University of Connecticut

data_processing:
Library strategy: PRO-seq
Adapter trimming: cutadapt v1.8.1
UMI trimming and reverse complementing: seqtk v1.3
FASTQ deduplication: https://github.com/guertinlab/fqdedup v1.0.0
FASTQ pairing: fastq_pair v1.0
Alignment: bowtie2 v2.4.4
File manipulation: samtools v1.9
File manipulation: https://github.com/guertinlab/seqOutBias v1.3.1
All details and code: https://github.com/guertinlab/Nascent_RNA_Methods
Genome_build: hg38
Supplementary_files_format_and_content: Stranded bigWig counts files

source_name: T47D cells

growth_protocol: T47D cells from ATCC were were grown in Roswell Park Memorial Institute (RPMI) 1640 medium containing 10% fetal bovine serum (FBS), 100 U/mL penicillin g-sodium, and 100 μg/mL streptomycin sulfate

treatment_protocol: For each sample, 2x10^6 cells were grown for 3 days in phenol red free RPMI 1640 medium containing 10% charcoal stripped FBS, 100 U/mL penicillin g-sodium, and 100 μg/mL streptomycin sulfate. After 3 days, a final concentration of 1nM beta estradiol or 0.1% volume/volume DMSO was added, and the cells were incubated for 1 hour.

tag: cell line

tag: treatment

value: 1nM beta estradiol

tag: molecule subtype

value: nascent RNA


title: L1koIN

description: L1 TASOR KO INPUT


title: T47D_DMSO_rep2

value: 0.1% volume/volume DMSO


title: T47D_Estrogen_rep1


title: T47D_DMSO_rep1


title: L1koK9

description: L1 TASOR KO H3K9me3


title: L1wtsffvK9

description: L1 promoterless WT H3K9me3


title: Sample  27

status: Public on Sep 01 2021

city: Thousand Oaks

first: Abraham

last: Anderson

state: California

address: 1 amgen center drive

institute: Amgen Inc.

hyb_protocol: Total RNA is hybridized with gene-specific fluorescently barcoded label oligos as well as gene-specific capture oligos that constitute Nanostring’s PanCancer Immune Profiling Panel, according to manufacturer’s protocols.

scan_protocol: The capture oligos allow the RNA-oligo complex to be immobilized to the assay cartridge imaging surface. A fluorescent microscope within the nCounter images the assay cartridge and the nCounter software counts the number of immobilized, barcoded RNA transcripts.

data_processing:
Relative gene expression was evaluated on the NanoString nCounter platform and the starting material was 300 ng of total RNA using the PanCancer Immune Profiling Panel.
Endogeous gene expression was normalized to 1 million counts per sample and log2 transformed for analysis.

source_name: Melanoma

extract_protocol: RNA was extracted from melanoma tumor biopsies and resected tumor tissue for gene expression analysis. Formalin-fixed paraffin-embedded (FFPE) curls were deparaffinized using 100% xylene. Deparaffinized samples were washed with 100% ethanol and then dried at 37°C. RNA was extracted from tissues using the QIAgen RNeasy FFPE kit (QIAgen, catalog #73504) on the QIAcube robotic workstation. Nucleic acid concentrations were determined using the NanoDrop 1000 Spectrophotometer (Thermo Fisher Scientific).

tag: subject alias id

tag: scheduled visit (w=week)

tag: tvec injected sample

tag: study arm (surgery only or tvec + surgery)


title: Sample  28

value: SURG


title: Sample  135


title: Sample  134


title: Sample  131


title: Sample  132


title: Sample  133


title: Sample  130


title: Sample  129


title: Sample  127


title: Sample  124


title: Sample  126


title: Sample  128


title: Sample  125


title: Sample  120


title: Sample  123


title: Sample  119


title: Sample  122


title: Sample  118


title: Sample  121


title: Sample  117


title: Sample  115


title: Sample  114


title: Sample  112


title: Sample  111


title: Sample  108


title: Sample  106


title: Sample  107


title: Sample  109


title: Sample  110


title: Sample  105


title: Sample  113


title: Sample  116


title: Sample  95


title: Sample  97


title: Sample  99


title: Sample  90


title: Sample  96


title: Sample  91


title: Sample  89


title: Sample  88


title: Sample  103


title: Sample  93


title: Sample  94


title: Sample  92


title: Sample  98


title: Sample  86


title: Sample  101


title: Sample  102


title: Sample  100


title: Sample  87


title: Sample  85


title: Sample  104


title: Sample  83


title: Sample  81


title: Sample  77


title: Sample  82


title: Sample  78


title: Sample  79


title: Sample  80


title: Sample  76


title: Sample  75


title: Sample  71


title: Sample  72


title: Sample  84

value: UNSCHED


title: Sample  73


title: Sample  70


title: Sample  60


title: Sample  62


title: Sample  59


title: Sample  63


title: Sample  61


title: Sample  64


title: Sample  57


title: Sample  68


title: Sample  69


title: Sample  66


title: Sample  67


title: Sample  56


title: Sample  58


title: Sample  55


title: Sample  53


title: Sample  51


title: Sample  65


title: Sample  48


title: Sample  52


title: Sample  49


title: Sample  47


title: Sample  46


title: Sample  74


title: Sample  45


title: Sample  39


title: Sample  38


title: Sample  43


title: Sample  40


title: Sample  41


title: Sample  50


title: Sample  37


title: Sample  35


title: Sample  54


title: Sample  30


title: Sample  33


title: Sample  32


title: Sample  31


title: Sample  25


title: Sample  24


title: Sample  22


title: Sample  42


title: Sample  23


title: Sample  21


title: Sample  20


title: Sample  19


title: Sample  17


title: Sample  18


title: Sample  44


title: Sample  29


title: Sample  34


title: Sample  16


title: Sample  36


title: Sample  26


title: Sample  12


title: Sample  15


title: Sample  13


title: Sample  9


title: Sample  8


title: Sample  14


title: APP+Clu

city: Palo Alto

first: Nathalie

last: Khoury

state: CA California

address: 3801 Miranda Avenue Blvd. 100 VAPA D3-111 - Neurology

institute: Stanford University

data_processing:
Reads aligned to mm10 transcriptome using Cell Ranger (version 3.1.0)
Resulting filtered gene by cell matrices of UMI counts were subsequently analyzed using Seurat (version 3.1)
Filtering criteria was applied to remove low quality cells and doublets. Cells that have at least 600 features, a maximum of 6000 features, and 10% mitochondrial RNA were included in the downstream analysis
Counts were then log-normalized and variable features were identified using the FindVariableFeatures function
To integrate the samples from the same experiment into one Seurat object we used the FindIntegrationAnchors and IntegrateData functions from Seurat
The highly variable genes were used for Principal Components Analysis and the first 30 components were used for Dimensionality Reduction (tSNE) and Clustering
Differential expression was performed using the MAST statistical test with the FindMarkers function
Genome_build: mm10
Supplementary_files_format_and_content: mtx, barcodes, features

source_name: Hippocampus

extract_protocol:
Brain endothelial cells were isolated by FACS sorting. 4-5 mice per group were anesthetized and perfused. The hippocampi from each group were pooled, minced and digested using the neural dissociation kit according to kit instructions (Miltenyi, 130–092-628). Myelin removal was performed using 0.9M sucrose in dPBS. Cell pellets were resuspended in FACs buffer and blocked for 5 min on ice with Fc preblock. followed by 30 minute staining with anti-CD31-PE/CF594 (1:75, BD 563616), anti-CD45-PE/Cy7 (1:200, BD 103114), and anti-Cd11b-FITC (1:100, BD 101206). Dead cells were excluded by staining with SYTOX™ Blue Dead Cell Stain (1:2000, Thermo S34857). Flow cytometry data and cell sorting were acquired on an ARIA 3.3 (BD Biosciences) with FACSDiva software (BD Biosciences).
single cell suspensions were counted using the Countess automated cell counter (ThermoFisher). After counting, cells were loaded onto the 10x Chromium chip and using the recommended loading volumes and run on the 10x chromium v3 controller. Immediately after running the chip, the samples were reverse transcribed to cDNA according to the manufacturer’s instructions and kept at 4ºC overnight. The following day, sample cleanup and cDNA amplification with 12 PCR cycles were performed according to instructions. The amplified cDNA was then checked for quality on the Agilent Bioanalyzer (HS DNA kit). Libraries were generated according to manufacturer’s instructions using unique barcodes for each sample and the finalized libraries were again checked for quality on the Agilent Bioanalyzer (HS DNA kit). Samples were sent for sequencing to Novogene where they were first assessed for library quality on a single lane of the HiSeq System followed by deep sequencing on a Novaseq S4 flow cell to ensure > 20,000 reads/cell as recommended.
scRNAseq (10x Genomics chromium v3)

tag: strain

value: APP mice (mThy-1-hAPP751V171I, KM670/671NL; T41 line)

value: clusterin

tag: cell type

value: Brain endothelial cells


title: Sample  11


title: Sample  10


title: WT

value: Wild-type littermates of APP mice (mThy-1-hAPP751V171I, KM670/671NL; T41 line)


title: Sal

value: Saline


title: Sample  6


title: Sample  5


title: control-45

status: Public on Aug 19 2021

city: Guangzhou

first: guodong

last: he

address: zhongshan road No.102

country: China

institute: Guangdong Provincial People's Hospital

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to hg38 whole genome using bowtie hisat2 with parameters -p 12 -5 5 -3 5 --rna-strandness RF
HTseq was used to calculate the counts of the Reads mapped the genome.
Genome_build: hg38
Supplementary_files_format_and_content: Matrix table with Htseq-counts

source_name: exosome from plasma

extract_protocol:
2mL of venous blood from patients were collected into Ethylene Diamine Tetraacetic Acid (EDTA) routine blood tubes. Plasma was separated by centrifugation at 3000 rpm for 10 min at 4℃ and collected into cryogenic vials and stored at −80℃. The exoRNeasy Serum/Plasma kit (Qiagen) was applied to extract the exosomal total RNAs.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: exosome from plasma

tag: age

value: 51 years old

value: healthy individual


title: Sample  7


title: control-43

tag: tissue

value: 56 years old


title: Sample  4


title: Sample  3


title: control-42

value: 66 years old


title: control-36

value: 42 years old


title: APP


title: Sample  2


title: APP+ Sal


title: LPS

value: LPS (lipopolysaccharide)


title: Sample  1


title: LPS+Clu

value: LPS (lipopolysaccharide) + clusterin


title: 604-48_2

status: Public on Aug 18 2021

city: West Hollywood

first: AGCT

last: Core

address: 8687 Melrose Ave, PDC B230

department: BMS

institute: Cedars Sinai Medical Center

data_processing:
Raw sequencing data was demultiplexed and converted to fastq format using bcl2fastq v2.20 (Illumina, San Diego, California). Then reads were aligned to the transcriptome using STAR (version 2.6.1) (Dobin A et al., 2013) / RSEM (version 1.2.28) (Li B and Dewey CN, 2011) with default parameters, using a custom human GRCh38 transcriptome reference downloaded from http://www.gencodegenes.org, containing all protein coding and long non-coding RNA genes based on human GENCODE version 33 annotation. DESeq2(version 1.26.0) was used for normalization and principal component analysis. Expression of each gene was fitted into a negative binomial generalized linear model, and the likelihood ratio test was applied to assess the differential expressions among all conditions. Benjamini and Hochberg procedure was applied to adjust for multiple hypothesis testing, and differential expression gene candidates were selected with a false discovery rate less than 0.05. For visualization of coordinated gene expression in samples, a two-way hierarchical clustering with Pearson correlation distance matrix was performed with samples and DEG candidates using the Bioconductor g-plots package (version 3.0.3) in R. Genes were extracted from the identified clusters for GO enrichment analysis by using DAVID v6.8 (Huang DW et al., 2009).
Genome_build: GRCh38
Supplementary_files_format_and_content: Raw counts expression matrix with row represents gene and column represents samples

source_name: Glioma stem cells

growth_protocol: Glioma stem cells were cultured in Neurobasal Medium A supplemented with N2, B27 (without vitamin A), EGF and FGF.

extract_protocol:
Cells were harvested and stored at -80C until extraction. Total RNA was isolated using Qiagen RNeasy Plus Mini Kit. Up to 1 µg of total RNA per sample was used for library construction using the Illumina TruSeq Stranded mRNA library preparation kit.
Total RNA samples were assessed for concentration using a Qubit fluorometer (ThermoFisher Scientific, Waltham, MA) and for quality using the 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).  Up to one µg of total RNA per sample was used for library construction using the Illumina TruSeq Stranded mRNA library preparation kit (Illumina, San Diego, CA).  Library concentration was measured with a Qubit fluorometer and library size on an Agilent 4200 TapeStation (Agilent Technologies). Libraries were multiplexed and sequenced on a NovaSeq 6000 (Illumina, San Diego, CA) using 75bp single-end sequencing. On average, approximately 30 million reads were generated from each sample.

treatment_protocol: Cells were irradiated at 5Gy by X-ray irradiator and cultured for 0, 3 and 14 days.

value: Patient-derived glioma stem cells

tag: transduction

value: ASNS overexpressed

value: control


title: 604-48_3


title: control-41

value: 39 years old


title: control-34

value: 54 years old


title: 604_2

value: Control


title: 604-48_1


title: 604_3


title: control-32

value: 17 years old


title: control-33


title: control-30

value: 35 years old


title: control-31


title: 827_3


title: 604-ASNS48_5Gy_3day

value: 5Gy, cultured for 3days


title: 827_1


title: 604_1


title: 604-ASNS48_5Gy_14day

value: 5Gy, cultured for 14days


title: 827-shASNS_1

value: ASNS knockdown


title: 827_2


title: 827-shASNS_2


title: 604-ASNS48_5Gy_0day

value: 5Gy, cultured for 0days


title: 604-ctrl_5Gy_0day


title: 604-ctrl_5Gy_14day


title: 604-ctrl_5Gy_3day


title: 604-ctrl_0Gy_0day

value: 0Gy, cultured for 0days


title: 604-ASNS48_0Gy_0day


title: 827-CRISPR-shASNS_5Gy_3day


title: 827-CRISPR-shASNS_5Gy_14day


title: 827-CRISPR-shASNS_0Gy_0day


title: 827-CRISPR-ctrl_5Gy_14day


title: Trp treatment

status: Public on Aug 13 2021

city: Coventry

first: Jie

last: Zhang

address: School of Life Sciences, Gibbet Hill Campus, The University of Warwick

department: School of Life Sciences

institute: University of Warwick

data_processing:
Library strategy: PRO-seq
Reads were trimmed with cutadapt version 1.14 to remove the adaptor, command: cutadapt -a TGGAATTCTCGGGTGCCAAGG -m 20 -e 0.05
Trimmed reads were aligned to hg38 genome with Hisat2 version 2.1.0, command: hisat2 -p 4 -k 1 --no-unal
Sam file was modified by custom script Sam_enlong.pl to extand reads to theoretic length
The extanded sam file was transform to bam file and sort by samtools
Sorted bam file was further transformed into bedgraph files, the bedgraph with nascent RNA on plus strand from command: genomeCoverageBed -strand - -5 -bga -ibam; for minus strand reads:: genomeCoverageBed -strand + -5 -bga -ibam
Genome_build: hg38
Supplementary_files_format_and_content: bedgraph, pausing time of peaks

growth_protocol: HEK293 cells were grown to 60% confluency at 37C and 5% CO2 in a 175cm2 flask in DMEM supplemented with 10% FBS. One day before permeabilization of cells, the culture medium was replaced with fresh medium.

extract_protocol: total RNA was isolated using 500μl TRIzol-LS for each sample according to the manufacturer's protocol (Invitrogen Life Technologies)

tag: sarkosyl run-on

value: Yes


title: 827-CRISPR-shASNS_5Gy_0day


title: Sarkosyl free 8min rep1

extract_protocol:
Run on buffer exclude sarkosyl from PRO-seq protocol (Mahat D B,2016), 37C for 8mins
total RNA was isolated using 500 ul TRIzol-LS for each sample according to the manufacturer's protocol (Invitrogen Life Technologies)

tag: run-on time

value: 8 min

value: No


title: Sarkosyl free 8min rep2


title: 827-CRISPR-ctrl_5Gy_3day


title: 827-shASNS_3


title: Sarkosyl free 2min rep1

extract_protocol:
Run on buffer exclude sarkosyl from PRO-seq protocol (Mahat D B,2016), 37C for 2mins
total RNA was isolated using 500 ul TRIzol-LS for each sample according to the manufacturer's protocol (Invitrogen Life Technologies)

value: 2 min


title: Sarkosyl free 2min rep2


title: 827-CRISPR-ctrl_5Gy_0day

value: Patient-derived glioma stem cells


title: 827-CRISPR-ctrl_0Gy_0day


title: Sarkosyl free 32min rep2

extract_protocol:
Run on buffer exclude sarkosyl from PRO-seq protocol (Mahat D B,2016), 37C for 32mins
total RNA was isolated using 500 ul TRIzol-LS for each sample according to the manufacturer's protocol (Invitrogen Life Technologies)

value: 32 min


title: NB_3

status: Public on Aug 03 2021

city: New York

first: Ashley

middle: Stephen

last: Doane

state: NY

address: 1300 York Ave

institute: Weill Cornell Medicine

data_processing:
Complete processing pipeline available at https://github.com/DoaneAS/atacflow
Read adapter trimming using ngtrim
Alignment to GRCh38 using bowtie2
PCR duplicate removeal by piccard tools
Peak calling using genrich
Genome_build: GRCh38
Supplementary_files_format_and_content: NarrowPeak files contain ATAC-seq peaks.
Supplementary_files_format_and_content: bigWig files contain binned ATAC-seq fragments normalized to reads in peaks using a consensus peak atlas.

source_name: tonsil

growth_protocol: lymphocytes isolated from tonsils by ficoll gradient centrifugation

extract_protocol:
Omni-ATAC-seq https://www.nature.com/articles/nmeth.4396
Illumina nextera per protocol https://www.nature.com/articles/nmeth.4396

value: tonsil

tag: facs markers

value: Naive B


title: Sarkosyl free 0.5min rep2

extract_protocol:
Run on buffer exclude sarkosyl from PRO-seq protocol (Mahat D B,2016), 37C for 0.5mins
total RNA was isolated using 500 ul TRIzol-LS for each sample according to the manufacturer's protocol (Invitrogen Life Technologies)

value: 0.5 min


title: Sarkosyl free 0.5min rep1


title: NB_2


title: GCB_CB_6

value: Germinal Center B cell, centroblast


title: PC_2

value: Plasma cell


title: MB_3

value: Memory B


title: GCB_CB_5


title: GCB_CC_3

value: Germinal Center B cell, centrocyte


title: GCB_CC_2


title: Sarkosyl free 32min rep1


title: MB_2


title: PC_1


title: GCB_CB_3


title: GCB_CC_1


title: GCB_CB_4


title: NB_1


title: GCB_CB_1


title: MB_1


title: PC_4


title: NB_6


title: NB_5


title: NB_4


title: GCB_2

value: Germinal Center B cell


title: H2A.Z.2 si

status: Public on Jul 25 2021

city: Uxbridge

first: Paola

last: Vagnarelli

address: Kingstone Lane

institute: Brunel University London

data_processing:
Reads were aligned using the BWA algorithm (mem mode; default settings) (Li & Durbin, 2009)
Duplicate reads were removed, only reads mapping as matched pairs and only uniquely mapped reads (mapping quality >= 1) were used for further analysis
Alignments were extended in silico at their 3’-ends to a length of 200 bp and assigned to 32-nt bins along the genome. The resulting histograms (genomic “signal maps”) were stored in bigWig files
Peaks were identified using the MACS 2.1.0 algorithm at a cutoff of p-value 1e-7, without control file, and with the –nomodel option. Peaks that were on the ENCODE blacklist of known false ChIP-Seq peaks were removed
Signal maps and peak locations were used as input data to Active Motifs proprietary analysis program
Genome_build: hg38
Supplementary_files_format_and_content: Alignments were extended in silico at their 3’-ends to a length of 200 bp and assigned to 32-nt bins along the genome. The resulting histograms (genomic “signal maps”) were stored in bigWig files

growth_protocol: HeLa cells were grown in DMEM supplemented with 10% foetal bovine serum (FBS) and 1% Penicillin–Streptomycin (Invitrogen Gibco) at 37 °C with 5% CO2

extract_protocol:
HeLa cells were harvested and frozen in culture media containing FBS and 5% DMSO. Cryopreserved cells were sent to Active Motif to perform the ATAC-seq assay. The cells were then thawed in a 37oC water bath, pelleted, washed with cold PBS, and tagmented as previously described (Buenrostro, Giresi et al., 2013), with some modifications based on (Corces, Trevino et al., 2017). Briefly, cell pellets were resuspended in lysis buffer, pelleted, and tagmented using the enzyme and buffer provided in the Nextera Library Prep Kit (Illumina).
Tagmented DNA was then purified using the MinElute PCR purification kit (Qiagen), amplified with 10 cycles of PCR, and purified using Agencourt AMPure SPRI beads (Beckman Coulter).  Resulting material was quantified using the KAPA Library Quantification Kit for Illumina platforms (KAPA Biosystems), and sequenced with PE42 sequencing on the NextSeq 500 sequencer (Illumina).

treatment_protocol: For siRNA treatments, HeLa cells were seeded in 6-well plates, transfected using Polyplus JetPrime (PEQLAB, Southampton, UK) with the appropriate siRNA oligonucleotides (50 nM), and analysed after 72 h.

value: HeLa

value: H2A.Z.2 siRNA


title: GCB_1


title: GCB_CB_7


title: H2A.Z.1 si

value: H2A.Z.1 siRNA


title: WT SETDB1 Rep2

city: New Haven

first: Qin

last: Yan

email: qin.yan@yale.edu, craig.wilen@yale.edu

address: 310 Cedar St.

department: Pathology

institute: Yale University

description:
Skin Melanoma Cell line
YR-SETDB1_merge.msd.redup.bam.center.scale.bw
YR-SETDB1_merge.bed

data_processing:
Illumina Casava software used for basecalling.
Sequenced reads were mapped to mm10 whole genome using bowtie2  with default parameters
Reads Per Gene were calculated using FeatureCount of subread package.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include gene expression values normalized with DESeq2 variance stabilizing transformation (VST) for each Sample

source_name: Melanoma cancer cell line

growth_protocol: Cells were grown in monolay in DMEM/F12+5%FBS+1% Penicillin-streptomycin at 37°C, 5% CO2

extract_protocol:
Chromatin was prepared and immunoprecipiated following previously described protocol ( Greer et al, Cell Rep 2015, 13(7):1444-1455). Anti-KDM5B (Abcam # ab50958) was used for KDM5B ChIP experiment.
ChIP libraries were prepared for sequencing using Illumina DNA Library Preparation protocol

treatment_protocol: Cells were fixed in 1% formaldehyde DMEM/F12 for 10 min.

value: YUMMER1.7(Braf V600E, Pten -/- and Cdkn2 -/- with high frequency of stable UV-induced somatic mutations

tag: antibody

value: Skin Melanoma Cell line

tag: genotype

value: Control knockout


title: Control si

tag: cell line

value: Control siRNA


title: WT KDM5B Rep1

description:
Skin Melanoma Cell line
YR-KDM5B_merge.msd.redup.bam.center.scale.bw
YR-KDM5B_merge.bed
YRand4H3-KDM5B_merge.bed.bed


title: WT Input Rep2

description:
Skin Melanoma Cell line
YR-Input_merge.msd.redup.bam.center.bw


title: GCB_CB_2


title: WT SETDB1 Rep1


title: WT Input Rep1


title: WT H3K9me3 Rep2

description:
Skin Melanoma Cell line
YR-H3K9me3_merge.msd.redup.bam.center.scale.bw
YR-H3K9me3_merge.bed


title: Kdm5b KO SETDB1 Rep1

description:
Skin Melanoma Cell line
4H3-SETDB1_merge.msd.redup.bam.center.scale.bw
4H3-SETDB1_merge.bed

value: Kdm5b deletion 1


title: Kdm5b KO SETDB1 Rep2

value: Kdm5b deletion 2


title: WT H3K4me2 Rep1

description:
Skin Melanoma Cell line
YR-H3K4me2_merge.msd.redup.bam.center.scale.bw
YR-H3K4me2_merge.bed


title: Kdm5b KO KDM5B Rep2

description:
Skin Melanoma Cell line
4H3-KDM5B_merge.msd.redup.bam.center.scale.bw
4H3-KDM5B_merge.bed
YRand4H3-KDM5B_merge.bed.bed


title: PC_3

value: tonsil


title: WT H3K4me3 Rep2

description:
Skin Melanoma Cell line
YR-H3K4me3_merge.msd.redup.bam.center.scale.bw
YR-H3K4me3_merge.bed


title: WT H3K4me3 Rep1


title: Kdm5b KO KDM5B Rep1


title: Kdm5b KO H3K4me3 Rep1

description:
Skin Melanoma Cell line
4H3-H3K4me3_merge.msd.redup.bam.center.scale.bw
4H3-H3K4me3_merge.bed


title: Kdm5b KO Input Rep2

description:
Skin Melanoma Cell line
4H3-Input_merge.msd.redup.bam.center.bw


title: WT H3K4me2 Rep2


title: Kdm5b KO H3K9me3 Rep1

description:
Skin Melanoma Cell line
4H3-H3K9me3_merge.msd.redup.bam.center.scale.bw
4H3-H3K9me3_merge.bed


title: Kdm5b KO H3K4me3 Rep2


title: Kdm5b KO Input Rep1


title: Kdm5b KO H3K4me2 Rep1

description:
Skin Melanoma Cell line
4H3-H3K4me2_merge.msd.redup.bam.center.scale.bw
4H3-H3K4me2_merge.bed


title: WT KDM5B Rep2


title: Kdm5b KO H3K4me2 Rep2


title: blood_368

status: Public on Jul 23 2021

type: genomic

first: Anita

last: Oberbauer

address: One Shields Ave.

department: Animal Science Department

institute: University of California, Davis

description:
Bovine genomic DNA extracted from the tail coccygeal vein was genotyped using the BovineHD Beadchip array (Illumina)
Sample name: 146

hyb_protocol: Hybridization was performed according to the Infinium HD Super Assay documentation using the automated protocol.

scan_protocol: Scanning was performed according to the Infinium HD Super Assay documentation using the automated protocol.

data_processing:
The Illumina GenomeStudio Genotyping Module was used to determine genotypes from the intensity data files (IDAT files) outputted from scanning the BeadChip.
The Illumina GenomeStudio Genotyping Module called genotypes and generated SNP statistics.

label: C-Bio, G-Bio, A-DNP, T-DNP

organism: Bos taurus

source_name: blood from coccygeal vein in the tail

label_protocol: According to the Infinium HD Super Assay documentation (https://support.illumina.com/content/dam/illumina-support/documents/documentation/chemistry_documentation/infinium_assays/infinium-hd-super-assay/infinium-hd-super-assay-reference-guide-11322427-03.pdf), labels were added during allele-specific base extension.

extract_protocol: Whole blood sampled from the coccygueal vein of the tail were centrifuged, and the resulting buffy coat layer was stored at 4C until DNA extraction. Genomic DNA was extracted from buffy coat using the QIAGEN QIAamp DNA Blood Mini Kit according to the manufacturer's instructions.

tag: noninfectious claw lesion phenotype

tag: farm

value: D

tag: Sex

value: female


title: blood_369

description:
Bovine genomic DNA extracted from the tail coccygeal vein was genotyped using the BovineHD Beadchip array (Illumina)
Sample name: 147


title: blood_362

description:
Bovine genomic DNA extracted from the tail coccygeal vein was genotyped using the BovineHD Beadchip array (Illumina)
Sample name: 140


title: blood_366

description:
Bovine genomic DNA extracted from the tail coccygeal vein was genotyped using the BovineHD Beadchip array (Illumina)
Sample name: 144


title: blood_363

description:
Bovine genomic DNA extracted from the tail coccygeal vein was genotyped using the BovineHD Beadchip array (Illumina)
Sample name: 141


title: blood_370

description:
Bovine genomic DNA extracted from the tail coccygeal vein was genotyped using the BovineHD Beadchip array (Illumina)
Sample name: 148


title: blood_365

description:
Bovine genomic DNA extracted from the tail coccygeal vein was genotyped using the BovineHD Beadchip array (Illumina)
Sample name: 143


title: blood_367

description:
Bovine genomic DNA extracted from the tail coccygeal vein was genotyped using the BovineHD Beadchip array (Illumina)
Sample name: 145


title: WT H3K9me3 Rep1

description:
Skin Melanoma Cell line
YR-H3K9me3_merge.msd.redup.bam.center.scale.bw
YR-H3K9me3_merge.bed


title: Kdm5b KO H3K9me3 Rep2


title: blood_361

description:
Bovine genomic DNA extracted from the tail coccygeal vein was genotyped using the BovineHD Beadchip array (Illumina)
Sample name: 139


title: blood_360

description:
Bovine genomic DNA extracted from the tail coccygeal vein was genotyped using the BovineHD Beadchip array (Illumina)
Sample name: 138


title: blood_354

description:
Bovine genomic DNA extracted from the tail coccygeal vein was genotyped using the BovineHD Beadchip array (Illumina)
Sample name: 132


title: blood_352

description:
Bovine genomic DNA extracted from the tail coccygeal vein was genotyped using the BovineHD Beadchip array (Illumina)
Sample name: 130


title: blood_357

description:
Bovine genomic DNA extracted from the tail coccygeal vein was genotyped using the BovineHD Beadchip array (Illumina)
Sample name: 135


title: blood_358

description:
Bovine genomic DNA extracted from the tail coccygeal vein was genotyped using the BovineHD Beadchip array (Illumina)
Sample name: 136


title: blood_356

description:
Bovine genomic DNA extracted from the tail coccygeal vein was genotyped using the BovineHD Beadchip array (Illumina)
Sample name: 134


title: blood_351

description:
Bovine genomic DNA extracted from the tail coccygeal vein was genotyped using the BovineHD Beadchip array (Illumina)
Sample name: 129


title: blood_350

description:
Bovine genomic DNA extracted from the tail coccygeal vein was genotyped using the BovineHD Beadchip array (Illumina)
Sample name: 128


title: blood_348

description:
Bovine genomic DNA extracted from the tail coccygeal vein was genotyped using the BovineHD Beadchip array (Illumina)
Sample name: 126


title: blood_349

description:
Bovine genomic DNA extracted from the tail coccygeal vein was genotyped using the BovineHD Beadchip array (Illumina)
Sample name: 127


title: blood_346

description:
Bovine genomic DNA extracted from the tail coccygeal vein was genotyped using the BovineHD Beadchip array (Illumina)
Sample name: 124


title: blood_344

description:
Bovine genomic DNA extracted from the tail coccygeal vein was genotyped using the BovineHD Beadchip array (Illumina)
Sample name: 122


title: blood_353

description:
Bovine genomic DNA extracted from the tail coccygeal vein was genotyped using the BovineHD Beadchip array (Illumina)
Sample name: 131


title: blood_343

description:
Bovine genomic DNA extracted from the tail coccygeal vein was genotyped using the BovineHD Beadchip array (Illumina)
Sample name: 121


title: blood_345

description:
Bovine genomic DNA extracted from the tail coccygeal vein was genotyped using the BovineHD Beadchip array (Illumina)
Sample name: 123


title: blood_364

description:
Bovine genomic DNA extracted from the tail coccygeal vein was genotyped using the BovineHD Beadchip array (Illumina)
Sample name: 142


title: blood_342

description:
Bovine genomic DNA extracted from the tail coccygeal vein was genotyped using the BovineHD Beadchip array (Illumina)
Sample name: 120


title: blood_359

description:
Bovine genomic DNA extracted from the tail coccygeal vein was genotyped using the BovineHD Beadchip array (Illumina)
Sample name: 137


title: blood_340

description:
Bovine genomic DNA extracted from the tail coccygeal vein was genotyped using the BovineHD Beadchip array (Illumina)
Sample name: 118


title: blood_339

description:
Bovine genomic DNA extracted from the tail coccygeal vein was genotyped using the BovineHD Beadchip array (Illumina)
Sample name: 117


title: blood_338

description:
Bovine genomic DNA extracted from the tail coccygeal vein was genotyped using the BovineHD Beadchip array (Illumina)
Sample name: 116

value: E


title: blood_335

description:
Bovine genomic DNA extracted from the tail coccygeal vein was genotyped using the BovineHD Beadchip array (Illumina)
Sample name: 113


title: blood_355

description:
Bovine genomic DNA extracted from the tail coccygeal vein was genotyped using the BovineHD Beadchip array (Illumina)
Sample name: 133


title: blood_337

description:
Bovine genomic DNA extracted from the tail coccygeal vein was genotyped using the BovineHD Beadchip array (Illumina)
Sample name: 115


title: blood_341

description:
Bovine genomic DNA extracted from the tail coccygeal vein was genotyped using the BovineHD Beadchip array (Illumina)
Sample name: 119


title: blood_334

description:
Bovine genomic DNA extracted from the tail coccygeal vein was genotyped using the BovineHD Beadchip array (Illumina)
Sample name: 112


title: blood_347

description:
Bovine genomic DNA extracted from the tail coccygeal vein was genotyped using the BovineHD Beadchip array (Illumina)
Sample name: 125


title: blood_336

description:
Bovine genomic DNA extracted from the tail coccygeal vein was genotyped using the BovineHD Beadchip array (Illumina)
Sample name: 114


title: blood_333

description:
Bovine genomic DNA extracted from the tail coccygeal vein was genotyped using the BovineHD Beadchip array (Illumina)
Sample name: 111


title: blood_330

description:
Bovine genomic DNA extracted from the tail coccygeal vein was genotyped using the BovineHD Beadchip array (Illumina)
Sample name: 108


title: blood_332

description:
Bovine genomic DNA extracted from the tail coccygeal vein was genotyped using the BovineHD Beadchip array (Illumina)
Sample name: 110


title: blood_326

description:
Bovine genomic DNA extracted from the tail coccygeal vein was genotyped using the BovineHD Beadchip array (Illumina)
Sample name: 104


title: blood_328

description:
Bovine genomic DNA extracted from the tail coccygeal vein was genotyped using the BovineHD Beadchip array (Illumina)
Sample name: 106


title: blood_325

description:
Bovine genomic DNA extracted from the tail coccygeal vein was genotyped using the BovineHD Beadchip array (Illumina)
Sample name: 103


title: blood_323

description:
Bovine genomic DNA extracted from the tail coccygeal vein was genotyped using the BovineHD Beadchip array (Illumina)
Sample name: 101


title: blood_329

description:
Bovine genomic DNA extracted from the tail coccygeal vein was genotyped using the BovineHD Beadchip array (Illumina)
Sample name: 107


title: blood_327

description:
Bovine genomic DNA extracted from the tail coccygeal vein was genotyped using the BovineHD Beadchip array (Illumina)
Sample name: 105


title: blood_322

description:
Bovine genomic DNA extracted from the tail coccygeal vein was genotyped using the BovineHD Beadchip array (Illumina)
Sample name: 100


title: blood_324

description:
Bovine genomic DNA extracted from the tail coccygeal vein was genotyped using the BovineHD Beadchip array (Illumina)
Sample name: 102


title: blood_317

description:
Bovine genomic DNA extracted from the tail coccygeal vein was genotyped using the BovineHD Beadchip array (Illumina)
Sample name: 95


title: blood_321

description:
Bovine genomic DNA extracted from the tail coccygeal vein was genotyped using the BovineHD Beadchip array (Illumina)
Sample name: 99


title: blood_318

description:
Bovine genomic DNA extracted from the tail coccygeal vein was genotyped using the BovineHD Beadchip array (Illumina)
Sample name: 96


title: blood_320

description:
Bovine genomic DNA extracted from the tail coccygeal vein was genotyped using the BovineHD Beadchip array (Illumina)
Sample name: 98


title: blood_319

description:
Bovine genomic DNA extracted from the tail coccygeal vein was genotyped using the BovineHD Beadchip array (Illumina)
Sample name: 97


title: blood_314

description:
Bovine genomic DNA extracted from the tail coccygeal vein was genotyped using the BovineHD Beadchip array (Illumina)
Sample name: 92


title: blood_331

description:
Bovine genomic DNA extracted from the tail coccygeal vein was genotyped using the BovineHD Beadchip array (Illumina)
Sample name: 109


title: blood_312

description:
Bovine genomic DNA extracted from the tail coccygeal vein was genotyped using the BovineHD Beadchip array (Illumina)
Sample name: 90

value: A


title: blood_311

description:
Bovine genomic DNA extracted from the tail coccygeal vein was genotyped using the BovineHD Beadchip array (Illumina)
Sample name: 89


title: blood_316

description:
Bovine genomic DNA extracted from the tail coccygeal vein was genotyped using the BovineHD Beadchip array (Illumina)
Sample name: 94


title: blood_308

description:
Bovine genomic DNA extracted from the tail coccygeal vein was genotyped using the BovineHD Beadchip array (Illumina)
Sample name: 86


title: blood_310

description:
Bovine genomic DNA extracted from the tail coccygeal vein was genotyped using the BovineHD Beadchip array (Illumina)
Sample name: 88


title: blood_309

description:
Bovine genomic DNA extracted from the tail coccygeal vein was genotyped using the BovineHD Beadchip array (Illumina)
Sample name: 87


title: blood_307

description:
Bovine genomic DNA extracted from the tail coccygeal vein was genotyped using the BovineHD Beadchip array (Illumina)
Sample name: 85


title: blood_306

description:
Bovine genomic DNA extracted from the tail coccygeal vein was genotyped using the BovineHD Beadchip array (Illumina)
Sample name: 84


title: blood_305

description:
Bovine genomic DNA extracted from the tail coccygeal vein was genotyped using the BovineHD Beadchip array (Illumina)
Sample name: 83


title: blood_303

description:
Bovine genomic DNA extracted from the tail coccygeal vein was genotyped using the BovineHD Beadchip array (Illumina)
Sample name: 81


title: blood_302

description:
Bovine genomic DNA extracted from the tail coccygeal vein was genotyped using the BovineHD Beadchip array (Illumina)
Sample name: 80


title: blood_300

description:
Bovine genomic DNA extracted from the tail coccygeal vein was genotyped using the BovineHD Beadchip array (Illumina)
Sample name: 78


title: blood_299

description:
Bovine genomic DNA extracted from the tail coccygeal vein was genotyped using the BovineHD Beadchip array (Illumina)
Sample name: 77


title: blood_298

description:
Bovine genomic DNA extracted from the tail coccygeal vein was genotyped using the BovineHD Beadchip array (Illumina)
Sample name: 76


title: blood_296

description:
Bovine genomic DNA extracted from the tail coccygeal vein was genotyped using the BovineHD Beadchip array (Illumina)
Sample name: 74


title: blood_315

description:
Bovine genomic DNA extracted from the tail coccygeal vein was genotyped using the BovineHD Beadchip array (Illumina)
Sample name: 93


title: blood_297

description:
Bovine genomic DNA extracted from the tail coccygeal vein was genotyped using the BovineHD Beadchip array (Illumina)
Sample name: 75


title: blood_295

description:
Bovine genomic DNA extracted from the tail coccygeal vein was genotyped using the BovineHD Beadchip array (Illumina)
Sample name: 73


title: blood_294

description:
Bovine genomic DNA extracted from the tail coccygeal vein was genotyped using the BovineHD Beadchip array (Illumina)
Sample name: 72


title: blood_313

description:
Bovine genomic DNA extracted from the tail coccygeal vein was genotyped using the BovineHD Beadchip array (Illumina)
Sample name: 91


title: blood_293

description:
Bovine genomic DNA extracted from the tail coccygeal vein was genotyped using the BovineHD Beadchip array (Illumina)
Sample name: 71


title: blood_290

description:
Bovine genomic DNA extracted from the tail coccygeal vein was genotyped using the BovineHD Beadchip array (Illumina)
Sample name: 68


title: blood_289

description:
Bovine genomic DNA extracted from the tail coccygeal vein was genotyped using the BovineHD Beadchip array (Illumina)
Sample name: 67


title: blood_292

description:
Bovine genomic DNA extracted from the tail coccygeal vein was genotyped using the BovineHD Beadchip array (Illumina)
Sample name: 70


title: blood_288

description:
Bovine genomic DNA extracted from the tail coccygeal vein was genotyped using the BovineHD Beadchip array (Illumina)
Sample name: 66


title: blood_287

description:
Bovine genomic DNA extracted from the tail coccygeal vein was genotyped using the BovineHD Beadchip array (Illumina)
Sample name: 65


title: blood_286

description:
Bovine genomic DNA extracted from the tail coccygeal vein was genotyped using the BovineHD Beadchip array (Illumina)
Sample name: 64


title: blood_304

description:
Bovine genomic DNA extracted from the tail coccygeal vein was genotyped using the BovineHD Beadchip array (Illumina)
Sample name: 82


title: blood_284

description:
Bovine genomic DNA extracted from the tail coccygeal vein was genotyped using the BovineHD Beadchip array (Illumina)
Sample name: 62


title: blood_283

description:
Bovine genomic DNA extracted from the tail coccygeal vein was genotyped using the BovineHD Beadchip array (Illumina)
Sample name: 61


title: blood_280

description:
Bovine genomic DNA extracted from the tail coccygeal vein was genotyped using the BovineHD Beadchip array (Illumina)
Sample name: 58


title: blood_282

description:
Bovine genomic DNA extracted from the tail coccygeal vein was genotyped using the BovineHD Beadchip array (Illumina)
Sample name: 60


title: blood_278

description:
Bovine genomic DNA extracted from the tail coccygeal vein was genotyped using the BovineHD Beadchip array (Illumina)
Sample name: 56


title: blood_281

description:
Bovine genomic DNA extracted from the tail coccygeal vein was genotyped using the BovineHD Beadchip array (Illumina)
Sample name: 59


title: blood_301

description:
Bovine genomic DNA extracted from the tail coccygeal vein was genotyped using the BovineHD Beadchip array (Illumina)
Sample name: 79


title: blood_279

description:
Bovine genomic DNA extracted from the tail coccygeal vein was genotyped using the BovineHD Beadchip array (Illumina)
Sample name: 57


title: blood_291

description:
Bovine genomic DNA extracted from the tail coccygeal vein was genotyped using the BovineHD Beadchip array (Illumina)
Sample name: 69


title: blood_275

description:
Bovine genomic DNA extracted from the tail coccygeal vein was genotyped using the BovineHD Beadchip array (Illumina)
Sample name: 53


title: blood_276

description:
Bovine genomic DNA extracted from the tail coccygeal vein was genotyped using the BovineHD Beadchip array (Illumina)
Sample name: 54


title: blood_277

description:
Bovine genomic DNA extracted from the tail coccygeal vein was genotyped using the BovineHD Beadchip array (Illumina)
Sample name: 55


title: blood_274

description:
Bovine genomic DNA extracted from the tail coccygeal vein was genotyped using the BovineHD Beadchip array (Illumina)
Sample name: 52


title: blood_266

description:
Bovine genomic DNA extracted from the tail coccygeal vein was genotyped using the BovineHD Beadchip array (Illumina)
Sample name: 44


title: blood_269

description:
Bovine genomic DNA extracted from the tail coccygeal vein was genotyped using the BovineHD Beadchip array (Illumina)
Sample name: 47


title: blood_271

description:
Bovine genomic DNA extracted from the tail coccygeal vein was genotyped using the BovineHD Beadchip array (Illumina)
Sample name: 49


title: blood_264

description:
Bovine genomic DNA extracted from the tail coccygeal vein was genotyped using the BovineHD Beadchip array (Illumina)
Sample name: 42

value: B


title: blood_270

description:
Bovine genomic DNA extracted from the tail coccygeal vein was genotyped using the BovineHD Beadchip array (Illumina)
Sample name: 48


title: blood_272

description:
Bovine genomic DNA extracted from the tail coccygeal vein was genotyped using the BovineHD Beadchip array (Illumina)
Sample name: 50


title: blood_265

description:
Bovine genomic DNA extracted from the tail coccygeal vein was genotyped using the BovineHD Beadchip array (Illumina)
Sample name: 43


title: blood_268

description:
Bovine genomic DNA extracted from the tail coccygeal vein was genotyped using the BovineHD Beadchip array (Illumina)
Sample name: 46


title: blood_267

description:
Bovine genomic DNA extracted from the tail coccygeal vein was genotyped using the BovineHD Beadchip array (Illumina)
Sample name: 45


title: blood_285

description:
Bovine genomic DNA extracted from the tail coccygeal vein was genotyped using the BovineHD Beadchip array (Illumina)
Sample name: 63


title: blood_263

description:
Bovine genomic DNA extracted from the tail coccygeal vein was genotyped using the BovineHD Beadchip array (Illumina)
Sample name: 41


title: blood_262

description:
Bovine genomic DNA extracted from the tail coccygeal vein was genotyped using the BovineHD Beadchip array (Illumina)
Sample name: 40


title: blood_259

description:
Bovine genomic DNA extracted from the tail coccygeal vein was genotyped using the BovineHD Beadchip array (Illumina)
Sample name: 37


title: blood_261

description:
Bovine genomic DNA extracted from the tail coccygeal vein was genotyped using the BovineHD Beadchip array (Illumina)
Sample name: 39


title: blood_256

description:
Bovine genomic DNA extracted from the tail coccygeal vein was genotyped using the BovineHD Beadchip array (Illumina)
Sample name: 34


title: blood_254

description:
Bovine genomic DNA extracted from the tail coccygeal vein was genotyped using the BovineHD Beadchip array (Illumina)
Sample name: 32


title: blood_260

description:
Bovine genomic DNA extracted from the tail coccygeal vein was genotyped using the BovineHD Beadchip array (Illumina)
Sample name: 38


title: blood_252

description:
Bovine genomic DNA extracted from the tail coccygeal vein was genotyped using the BovineHD Beadchip array (Illumina)
Sample name: 30


title: blood_253

description:
Bovine genomic DNA extracted from the tail coccygeal vein was genotyped using the BovineHD Beadchip array (Illumina)
Sample name: 31


title: blood_255

description:
Bovine genomic DNA extracted from the tail coccygeal vein was genotyped using the BovineHD Beadchip array (Illumina)
Sample name: 33


title: blood_258

description:
Bovine genomic DNA extracted from the tail coccygeal vein was genotyped using the BovineHD Beadchip array (Illumina)
Sample name: 36


title: blood_257

description:
Bovine genomic DNA extracted from the tail coccygeal vein was genotyped using the BovineHD Beadchip array (Illumina)
Sample name: 35


title: blood_273

description:
Bovine genomic DNA extracted from the tail coccygeal vein was genotyped using the BovineHD Beadchip array (Illumina)
Sample name: 51


title: blood_249

description:
Bovine genomic DNA extracted from the tail coccygeal vein was genotyped using the BovineHD Beadchip array (Illumina)
Sample name: 27


title: blood_247

description:
Bovine genomic DNA extracted from the tail coccygeal vein was genotyped using the BovineHD Beadchip array (Illumina)
Sample name: 25


title: blood_245

description:
Bovine genomic DNA extracted from the tail coccygeal vein was genotyped using the BovineHD Beadchip array (Illumina)
Sample name: 23


title: blood_251

description:
Bovine genomic DNA extracted from the tail coccygeal vein was genotyped using the BovineHD Beadchip array (Illumina)
Sample name: 29


title: blood_248

description:
Bovine genomic DNA extracted from the tail coccygeal vein was genotyped using the BovineHD Beadchip array (Illumina)
Sample name: 26


title: blood_250

description:
Bovine genomic DNA extracted from the tail coccygeal vein was genotyped using the BovineHD Beadchip array (Illumina)
Sample name: 28


title: blood_246

description:
Bovine genomic DNA extracted from the tail coccygeal vein was genotyped using the BovineHD Beadchip array (Illumina)
Sample name: 24


title: blood_243

description:
Bovine genomic DNA extracted from the tail coccygeal vein was genotyped using the BovineHD Beadchip array (Illumina)
Sample name: 21


title: blood_244

description:
Bovine genomic DNA extracted from the tail coccygeal vein was genotyped using the BovineHD Beadchip array (Illumina)
Sample name: 22


title: blood_242

description:
Bovine genomic DNA extracted from the tail coccygeal vein was genotyped using the BovineHD Beadchip array (Illumina)
Sample name: 20


title: blood_241

description:
Bovine genomic DNA extracted from the tail coccygeal vein was genotyped using the BovineHD Beadchip array (Illumina)
Sample name: 19


title: blood_240

description:
Bovine genomic DNA extracted from the tail coccygeal vein was genotyped using the BovineHD Beadchip array (Illumina)
Sample name: 18


title: blood_234

description:
Bovine genomic DNA extracted from the tail coccygeal vein was genotyped using the BovineHD Beadchip array (Illumina)
Sample name: 12


title: blood_239

description:
Bovine genomic DNA extracted from the tail coccygeal vein was genotyped using the BovineHD Beadchip array (Illumina)
Sample name: 17


title: blood_237

description:
Bovine genomic DNA extracted from the tail coccygeal vein was genotyped using the BovineHD Beadchip array (Illumina)
Sample name: 15


title: blood_235

description:
Bovine genomic DNA extracted from the tail coccygeal vein was genotyped using the BovineHD Beadchip array (Illumina)
Sample name: 13


title: blood_236

description:
Bovine genomic DNA extracted from the tail coccygeal vein was genotyped using the BovineHD Beadchip array (Illumina)
Sample name: 14


title: blood_233

description:
Bovine genomic DNA extracted from the tail coccygeal vein was genotyped using the BovineHD Beadchip array (Illumina)
Sample name: 11


title: blood_232

description:
Bovine genomic DNA extracted from the tail coccygeal vein was genotyped using the BovineHD Beadchip array (Illumina)
Sample name: 10


title: blood_227

description:
Bovine genomic DNA extracted from the tail coccygeal vein was genotyped using the BovineHD Beadchip array (Illumina)
Sample name: 5


title: blood_225

description:
Bovine genomic DNA extracted from the tail coccygeal vein was genotyped using the BovineHD Beadchip array (Illumina)
Sample name: 3


title: blood_230

description:
Bovine genomic DNA extracted from the tail coccygeal vein was genotyped using the BovineHD Beadchip array (Illumina)
Sample name: 8


title: blood_226

description:
Bovine genomic DNA extracted from the tail coccygeal vein was genotyped using the BovineHD Beadchip array (Illumina)
Sample name: 4


title: blood_231

description:
Bovine genomic DNA extracted from the tail coccygeal vein was genotyped using the BovineHD Beadchip array (Illumina)
Sample name: 9


title: blood_228

description:
Bovine genomic DNA extracted from the tail coccygeal vein was genotyped using the BovineHD Beadchip array (Illumina)
Sample name: 6


title: blood_224

description:
Bovine genomic DNA extracted from the tail coccygeal vein was genotyped using the BovineHD Beadchip array (Illumina)
Sample name: 2


title: blood_223

description:
Bovine genomic DNA extracted from the tail coccygeal vein was genotyped using the BovineHD Beadchip array (Illumina)
Sample name: 1


title: CD249pos Fibroblasts/mouse 10

status: Public on Jul 01 2021

data_processing:
Raw sequencing data was demultiplexed and converted to fastq format by using bcl2fastq v2.20 (Illumina, San Diego, California). Then reads were aligned to the transcriptome using STAR (version 2.6.1) (Dobin A et al., 2013) / RSEM (version 1.2.28) (Li B and Dewey CN, 2011) with default parameters, using a custom human GRCh38 transcriptome reference downloaded from http://www.gencodegenes.org, containing all protein coding and long non-coding RNA genes based on human GENCODE version 33 annotation. Expression counts for each gene in all samples were normalized by a modified trimmed mean of the M-values normalization method and the unsupervised PC analysis (PCA) was performed with DESeq2 Bioconductor package version 1.26.0 in R version 3.6.3. Each gene was fitted into a negative binomial generalized linear model, and the Wald test was applied to assess the differential expressions between two sample groups by DESeq2. Benjamini and Hochberg procedure was applied to adjust for multiple hypothesis testing, and differential expression gene candidates were selected with a false discovery rate less than 0.05. For visualization of coordinated gene expression in samples, a two-way hierarchical clustering with Pearson correlation distance matrix was performed with samples and DEG candidates using the Bioconductor g-plots package (version 3.0.3) in R.
Genome_build: GRCh38
Supplementary_files_format_and_content: Raw count expression matrix in CSV format

source_name: FACs-purified lung fibroblasts

extract_protocol:
Qiagen Rnease Micro kit: as per manual
The SMART-Seq V4 Ultra Low RNA Input Kit for Sequencing (Takara Bio USA, Inc., Mountain View, CA) was used for reverse transcription and generation of double stranded cDNA for library preparation using the Nextera XT Library Preparation kit (Illumina, San Diego, CA).  Total RNA quality was analyzed via the 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA) and RNA quantified using QubitTM (ThermoFisher Scientific, Waltham, MA) fluorometric quantitation.  An input of 10 ng total RNA was used for oligo(dT)-primed reverse transcription, cDNA amplification, and cDNA cleanup.  The cDNA was analyzed on the 4200 TapeStation (Agilent Technologies).  Quantification of cDNA was performed using Qubit.  cDNA normalized to 30 pg/ul was fragmented and sequencing primers added simultaneously.  A limiting-cycle PCR added Index 1 (i7) adapters, Index 2 (i5) adapters, and sequences required for cluster formation on the sequencing flow cell.  Indexed libraries were cleaned up, library size verification performed on the 4200 TapeStation, and library quantified via Qubit.  Libraries were sequenced on a NextSeq 500 using with a 1x75 bp read length and coverage of ~50M reads/cell.

value: Wild-type

value: Lung

value: CD249+ fibroblasts


title: blood_238

description:
Bovine genomic DNA extracted from the tail coccygeal vein was genotyped using the BovineHD Beadchip array (Illumina)
Sample name: 16


title: Standard_ATAC_on_frozen_kidney_rep1

status: Public on Jul 02 2021

city: Uppsala

first: xingqi

last: chen

address: Uppsala Biomedical Center C10:2, Husargatan 3

department: IGP

country: Sweden

institute: Uppsala University

data_processing:
Reads were aligned to the mm9 genome/hg19 genome using bowtie2
duplicate reads were removed with Picard
MACS2  was used call narrow peak
Genome_build: mm9 or hg19
Supplementary_files_format_and_content: peak text files

source_name: Kidney

extract_protocol:
RNA is synthesized after in vitro transcription from tagmented DNA with T7-Tn5. And cDNA is synthesized after reverse transcription.
dsDNA was tagmented with Tn5, then PCR is performed using primers with barcode.

treatment_protocol: Samples were fixed with 4% paraformaldehyde overnight, and then washed with phosphate-buffered saline (PBS) and kept in 70% ethanol for paraffin embedding.

value: FVBN

tag: treatment

value: frozen


title: CD249pos Fibroblasts/mouse 8


title: CD249neg Fibroblasts/mouse 8

value: CD249 neg fibroblasts


title: CD249neg Fibroblasts/mouse 10


title: CD249pos Fibroblasts/mouse 2


title: sljmj7_rep1

status: Public on Jun 22 2021

city: guangzhou city

first: Ding

last: xiaochun

state: guangdong

address: 723 xingke road, tianhe district

institute: SOUTH CHINA BOTANICAL GARDEN

data_processing:
Illumina PE150 software used for  sequencing analysis
Filtered out low quality data, only clean data were used for the further methylation related statistics. The clean reads were then mapped to reference genome by the BSseeker software.  CGmap Tools software were used to count the depth of sequencing of C bases across the genome.
Methylation level was determined by dividing the number of reads covering each mC by the total number of reads covering that cytosine, which was also equal to the mC/C ratio at each reference cytosine.
CGmap Tools was used to count the average of C-base methylation levels in various types. Recalculate the distribution ratio of methylation C sites (mC) in different types. Based on the methGO software, we give the copy number change of each sample gene
We used the circlize package to plot the distribution of methylated C sites, DMR and CNV on the genome[6], CGmap Tools software (version: 0.1.1) also was used to map the methylation level distribution of the gene region and the 2 kb region upstream and downstream for all sample.The motif feature sequences corresponding to all DMR regions are passed through Homer software (version 3) predict motif
Genome_build: Tomato reference genome (version SL3.0)

organism: Solanum lycopersicum

source_name: Ailsa Craig

growth_protocol: Wild-type tomato and transgenic lines in the Ailsa-Craig background were grown in a greenhouse at 23°C under 16 h light and 8 h dark condition.

extract_protocol:
5 g tomato sample were used to extract DNA. The qualified DNA was fragmented with an ultrasonic disruptor (Bioruptor), with an average size of about 300-500 bp.
Fragmented DNA were end-repaired and ligated to a fully methylated adapter by using NEXTflex™ Bisulfite-Seq Barcodes-6 Kit (51191, Bioo Scientific). Using EZ DNA Methylation-Gold ™ kit (Zymo Research Corp., catalog number D5005) for bisulfite conversion of adapter-linked DNA. After amplification by PCR, the high-quality library has a DNA fragment distribution of about 300 bp

tag: time point

value: At 38 days after anthesis (dpa)

value: Pericarp

tag: genotype/variation


title: CD249neg Fibroblasts/mouse 2

tag: strain


title: CD249neg Fibroblasts/mouse 7

tag: cell type


title: HYR__c21295__20210330_mcf-7_mmel_S5

status: Public on Jun 04 2021

city: Leuven

first: Stein

last: Aerts

state: Vlaams-Brabant

address: O&N4 Herestraat 49 PO Box 602

country: Belgium

institute: KU Leuven

data_processing:
For HyDrop-ATAC samples (prefix HYA):
Barcode reads (read 2) were trimmed to exclude the intersub-barcode PCR adapters MAWK
Barcode reads (read 2) were trimmed using trimgalore (trim_galore -j 2 -o . $R1 $R2 --paired --gzip), corrected to a whitelist allowing 1 mismatch (custom seq script inVSN pipeline version 41df185308 [develop_atac]), and appended to the fastq sequence identifier of the paired-end ATAC-seq reads (read 1 and read 3)
Cell barcodes were written to the bam as a CB SAM tag using SAMtools and AWK (custom VSN pipeline version 41df185308 [develop_atac] script) (samtools view -h HYA__combined__20210323_cortex_phu_dv_etssb_1-5_S5.bwa.out.possorted.bam | mawk '/^@/ {print;next} {N=split($1,n,"_"); NN=split(n[1],nbc,"-"); ucorr_bc=""; corr_bc=""; if(NN==1){ # BioRad data with format {corrected_bc}_qname; corr_bc="CB:Z:" nbc[1];} if(NN==2){ucorr_bc="CR:Z:" nbc[1]; if(length(nbc[2])>0){corr_bc="
Reads were mapped to reference genomes using bwa-mem and duplicate-marked using samtools markdup by the VSN pipeline version 41df185308 [develop_atac] (bwa mem -t 8 genome.fa $R1.fq.gz $R2.fq.gz | samtools fixmate -@ 6 -m -u -O bam - - | samtools sort -@ 6 -u -O bam - | samtools markdup -@ 6 -f markdup.log - bwa.out.possorted.bam).
Fragments files were generated using Sinto (sinto fragments -b $bam -m 30 --barcodetag CB --use_chrom "(?i)^chr" --min_distance 10 --max_distance 5000 --chunksize 5000000 -p 2 -f $fragments.bed)
Per-cluster differentially accessible region were generated using pycistopic '0.1.dev214+gc72ef83.d20210522' (markers_dict = find_diff_features(cistopic_obj, imputed_acc_obj, variable='cell_type_finetuned', var_features=variable_regions, contrasts=None, adjpval_thr=0.05, log2fc_thr=np.log2(1.5), n_cpu=12)) and written to BED format using a custom python script.
Per-cluster coverage bigwigs were generated using pycistopic '0.1.dev214+gc72ef83.d20210522' (bw_paths, bed_paths = export_pseudobulk(input_data = cistopic '0.1.dev214+gc72ef83.d20210522'_obj.cell_data, variable = 'cell_type_finetuned', chromsizes = chromsizes, bed_path = bed_path, bigwig_path = bw_path, path_to_fragments = fragments_dict, n_cpu = nclusters, normalize_bigwig = True, remove_duplicates = True))
Aggregate genome coverage bigwigs were generated using DeepTools 3.5.0 (bamCoverage -b ${file} -o ${file%.bam}.RPGCnormalized.bw -bs 1 -p 4 --normalizeUsing RPGC  --effectiveGenomeSize 2913022398)
For HyDrop-RNA samples (prefix HYR):
For HyDrop-ATAC samples (prefix HYA):
Barcode reads (read 2) were trimmed to exclude the intersub-barcode PCR adapters MAWK
Reads were mapped  to reference genomes and expression matrices were generated using STAR version: 2.7.8a_2021-04-27 in STARsolo mode (STAR --runThreadN 6 --runMode alignReads --outSAMtype BAM SortedByCoordinate --sysShell /bin/bash --genomeDir "${star_reference_dir}" --readFilesIn "${fastq_R1_filename}" "${fastq_R2_filename}" --readFilesCommand 'gzip -c -d' --soloCBwhitelist "${whitelist_part1_filename}" "${whitelist_part2_filename}" "${whitelist_part3_filename}" --soloType CB_UMI_Complex --soloCBposition 0_0_0_9 0_20_0_29 0_40_0_49 --soloUMIposition 0_50_0_57 --sjdbGTFfile $sjdbgtf --soloCellFilter CellRanger2.2 2000 0.99 10 --soloCBmatchWLtype 1MM --outFilterMultimapNmax 1 --outSAMattributes NH HI AS nM CB UB CR CY UR UY --outFileNamePrefix ${bam_filename%bam} --outReadsUnmapped Fastx --quantMode GeneCounts --bamRemoveDuplicatesType UniqueIdentical --soloFeatures Gene GeneFull Velocyto)
For the optimisation samples (HYR__1ec4a0__20200929_Exo_S1 HYR__3ac717__20201006_non-exo_S2 HYR__70afb2__20201006_TSO-LNA_S3 HYR__c6c4b7__20201016_gtp_S4 HYR__d0a5b4__20201023_klenow_S5 HYR__f0eb5a__20201023_bst_S6), FASTQs were downsampled to match the reads per cell depth of the lowest sample and re-mapped using the same STAR parameters to generate the DOWNSAMPLED expression matrices.
Genome_build: For human samples: hg38, for mouse samples: mm10, for hybrid samples: GRCh38_GRCm10 hybrid genome, for fly samples: dm6
Supplementary_files_format_and_content: For HyDrop-ATAC samples (prefix HYA): standard tab-separated fragments files, tar archive with per-cluster differentially accessible region bed files, tar archive with per-cluster genome coverage bigwig
Supplementary_files_format_and_content: For HyDrop-RNA samples (prefix HYR): STARsolo gene expression matrix in MEX format

molecule: cytoplasmic RNA

organism:
Homo sapiens
Mus musculus

source_name: 50:50 mixture of human MM087 cells and mouse melanoma cells

growth_protocol: MCF7 cells were cultured in RPMI1640 medium supplemented with 10% FBS, 1% penicillin/streptomycin, and 10 ug/mL insulin and passaged twice per week. Mouse melanoma cells were cultured in DMEM supplemented with 10% FBS and 1% penicillin/streptomycin and passaged once per week.

extract_protocol: Cells were washed in PBS and dissociated into single cell suspensions using 1.5 mL of 0.05% Trypsin. The single-cell suspension was centrifuged at 500 rcf for 5 min at 4°C and the resulting pellet was resuspended in PBS. This PBS wash was repeated once more.

tag: tissue/cell line

value: Human:breast cancer cell line/mouse:melanoma cell line


title: sljmj7_rep3

tag: tissue


title: ChIP-seq_CTCF_shCTCF

status: Public on Jun 30 2021

city: Shanghai

first: Xuelong

last: Wang

address: No. 100 Banxia Road

institute: Chinese Academy of Sciences

description: THP1 co-cultured with PANC1

data_processing:
ChIP-Seq and ATAC-seq data sets were trimmed and aligned to hg19 genome using Bowtie2. Reads from RNA-seq experiments were aligned to hg19 genome using STAR.
Duplicate reads were removed with SAMtools.
MACS2 was used to identify regions of ChIP-seq and ATAC-seq peaks; The mRNA expression of a gene was quantified by FPKM based on RefSeq gene annotation using Cuffdiff and R packages.
The top 10000 peaks were used for known motif enrichment analysis, which were performed using HOMER (v4.9).
Genome_build: hg19
Supplementary_files_format_and_content: The bw (BigWig) files were generated using deepTools.

source_name: THP1+PANC1 cell lines

extract_protocol: (1) The RNA-Seq assay was performed as previously described. Total RNA product was purified using RNeasy Mini Kit (QIAGEN, Germany) and run-on Agilent Bioanalyzer 4200 to assess RNA integrity. The total RNA‐seq library preparation from 1 μg of total RNA was performed with TruSeq RNA Sample Prep Kit (Illumina, USA) according to the manufacturer's instructions. (2) The ChIP assay was performed as previously described. H3K27ac (ab4729, Abcam, USA), H3K27me3(9733S, CST, USA), CTCF (Millipore, 07-729), H3K9ac (9649, CST, USA), H3K4me (5326, CST, USA), EP300 (ab275378, Abcam, USA) were used for ChIP experiments. For each sample, 100 million crosslinked cells were lysed to prepare nuclear extracts. After chromatin shearing by sonication for 10 min, lysates were incubated on sky wheel overnight at 4°C with protein A Dynabeads (Invitrogen, USA) coupled with 3-6 μg of antibodies. After immunoprecipitation, beads were washed and recovered using magnets. DNA was reverse- cross‐linked at 55°C for 4 hours. After 4 hours, DNA product was purified with QIAquick PCR Purification Kit (QIAGEN, USA). DNA was quantitated using the Qubit dsDNA HS assay and a Qubit 2.0 Fluorimeter (Invitrogen). For ChIP-seq, 5 ng-50ng of purified DNA product were used to generate the DNA library using a VAHTS Universal DNA Library Prep Kit for Illumina V3 (Vazyme Biotech, China) and the Illumina HiSeq X Ten was used to sequence the paired-end module and with 150 bp reads on each end (Novogene Biotech, China). For ChIP-qPCR, ChIP products which were used to RT-PCR were performed to amplify the pcr products for 40 cycles using the following PCR conditions: 95 °C for 3 min; and thermocycling at 95°C for 15 s, 60 °C for 60 s, following by 4 °C forever. (3) The ATAC-seq assay was performed as previously described. 1 million fresh cells (THP-1 co-cultured with PANC-1 treated with PMA, TAMs and monocytes) were lysed in 100μL lysis buffer per sample (10 mM Tris-HCl at pH 7.4, 10 mM NaCl, 3 mM MgCl2 and 0.1% IGEPAL CA-630) for 10 min on ice to prepare the nuclei briefly. Immediately After 10 min, nuclei were spun for 5 min at 500 x g to remove the supernatant. Then nuclei were incubated at 37 °C with the tagmentation buffer and Tn5 transposome (Vazyme Biotech, China) for 30 min. After the 30 min, ended buffer was added directly into the reaction to quit the tagmentation. Products which were inputted to PCR were performed to amplify the library for 11 cycles using the following PCR conditions: 72 °C for 3 min; 98 °C for 30 s; and thermocycling at 98 °C for 15 s, 60 °C for 30 s and 72 °C for 3 min; following by 72 °C 5 min. After the PCR reaction, DNA libraries were purified with DNA Clean Beads (Vazyme Biotech, China) to remove invalid primer dimmers and quantitate used Qubit 2.0 Fluorimeter (Invitrogen, USA) to quantitate. (4) All eligible DNA libraries were sequenced on the Illumina HiSeq X Ten with 150 bp paired-end reads.

value: CTCF

value: shCTCF


title: WT_rep3

value: WT


title: WT_rep2


title: sljmj7_rep2


title: blood_229

city: Davis

description:
Bovine genomic DNA extracted from the tail coccygeal vein was genotyped using the BovineHD Beadchip array (Illumina)
Sample name: 7

value: D


title: WT_7

status: Public on Jun 03 2021

city: Boston

first: Marie

middle: R

last: Siwicki

state: MA

address: Simches Research Building, 185 Cambridge Street

department: Center for Systems Biology

institute: Harvard / MGH

data_processing:
Read trimming with atropos
Pseudoalignments with salmon,0.14.2
Differntial expresison with tximport and DESeq2 1.22.1
Genome_build: mm10
Supplementary_files_format_and_content: rawcounts.csv - un-normalized counts from tximport of Salmon pseudoalignments, genes (by ensembl IDs) in rows, samples in columns

source_name: Liver

growth_protocol: 50:50 bone marrow chimeric mice were generated: wild type mice were irradiated (~1000 cGy) and injected with 50% wild-type CD45.1+ and 50% Ifngr1-/- CD45.2+ bone marrow, and allowed to reconstitute for 8 weeks.

extract_protocol:
Two days following CD40 agonist treatment, mouse livers were isolated and processed to generate single cell suspensions. Cells were stained for CD45.1 and CD45.2 and neutrophil-labeling markers, and sorted directly into Trizol and put on ice. RNA was extracted using TRIzol™ Plus RNA Purification Kit (Thermo Fisher) according to manufacturer's instructions.
The Total-RNA samples were quantified using an Agilent Bioanalyzer 2100 instrument, with a corresponding Agilent Bioanalyzer RNA Pico assay. The resulting RIN (RNA Integrity Number) scores and concentrations were taken into account for qualifying samples to proceed. The samples were normalized to 1ng of input in 9uL (~111 pg/µL), and the mRNA was captured using oligo-dt primers as part of the Takara SMARTseq V4 Ultra Low workflow. The number of PCR cycles was increased to 13 to account for difficulties associated with neutrophil-derived RNA. A Bioanalyzer High Sensitivity DNA assay was run on the cDNA to evaluate success. cDNA synthesis, adapter ligation, and amplification were conducted subsequently with the Illumina NexteraXT Library Prep kit. Following amplification, residual primers were eluted away using Aline PCR CleanDx Beads.

treatment_protocol: Reconstituted mice were injected with MC38 flank tumors, and one week later treated with CD40 agonist immunotherapy.


title: WT_5


title: KO_6


title: KO_8


title: KO_7


title: KO_5


title: WT_6


title: KO_3


title: KO_9


title: WT_3


title: CD249pos Fibroblasts/mouse 7


title: WT_rep1


title: SUDHL4_VORINO_14D

status: Public on Jun 02 2021

city: Bellinzona

first: Luciano

last: Cascione

state: Ticino

address: Via Chiesa 5

department: Lymphoma & Genomics Research Program

country: Switzerland

institute: IOR

description: Sample 21

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to hg38 whole genome using STAR
For each gene, the counts per millions have been normalized (TMM normalization, edgeR) and logged (base 2)
Genome_build: hg38
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample
Supplementary_files_format_and_content: Matrix table with log2 counts per million (CPM) for every gene and every sample

growth_protocol: All cell lines were cultured according to the recommended conditions. All media were supplemented with foetal bovine serum, penicillin-streptomycin-neomycin (5,000 units penicillin, 5 mg streptomycin and 10 mg neomycin/mL, Sigma) and L-glutamine (1%). Cell line identity was authenticated by short tandem repeat (STR) DNA profiling.

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

treatment_protocol: cells treated for 6 hours and 14 days with DMSO, vorinostat or pracinostat

value: VORINOSTAT

value: 14 Days


title: WT_2

value: WT (wild type)


title: KO_4


title: WT_4


title: Cecal Ligation Puncture Model

status: Public on Jun 01 2021

city: Indianapolis

middle: T

last: Eadon

state: IN

address: 950 W Walnut St

institute: Indiana University

data_processing:
Expression counts determined by spaceranger 1.0.0 and reference genomes GRCh38-3.0.0 and mm10-3.0.0
The remaining processing and normalization steps described on the paper were not performed on the provided processed data
Genome_build: Hg38 and mm10
Supplementary_files_format_and_content: position and counts on csv files, images on tiff files.
Supplementary_files_format_and_content: Human_Nephrectomy.tar.gz - Spots position, filtered counts matrix, and images for the Human Nephrectomy, as outputted from SpaceRanger.
Supplementary_files_format_and_content: Sham_Model.tar.gz - Spots position, filtered counts matrix, and images for the Sham murine model, as outputted from SpaceRanger.
Supplementary_files_format_and_content: IRI_Model.tar.gz - Spots position, filtered counts matrix, and images for the Ischemia Reperfusion Injury murine model, as outputted from SpaceRanger.
Supplementary_files_format_and_content: CLP_Model.tar.gz - Spots position, filtered counts matrix, and images for the Cecal Ligation Puncture murine model, as outputted from SpaceRanger.

extract_protocol:
Human Kidney tissue was obtained from a deceased donor nephrectomy intended for transplant. It was frozen on OCT within 24 h. 10 um of tissue was cut on a cryotome and placed on a 10x Visium capture slide. RNA was extracted according to protocol.
Murine Kidney tissue was obtained from a mice upon sacrifice and immediately frozen on OCT. 10 um of cross-sectional tissue was cut on a cryotome and placed on a 10x Visium capture slide. RNA was extracted according to protocol.
CG000239_VisiumSpatialGeneExpression_UserGuide_RevD, 10X Genomics

tag: disease

value: Cecal Ligarion Puncture

tag: tissue source

value: Nephrectomy

tag: storage

value: OCT at -80C

tag: gender

value: Male


title: Smart-seq2: Macrophages8

status: Public on May 04 2021

city: Chicago

first: Hoang Van

last: Phan

state: Illinois

address: 5640 S Ellis Ave

department: Priztker School of Molecular Engineering

institute: The University of Chicago

description: Prox-seq using Smart-seq2 pipeline

data_processing:
Sequencing data was aligned using a custom Java program to identify the Prox-seq probe barcodes.
Count data was analyzed in Python and RStudio. Cells with fewer total UMI count lower than 10 were discarded.
Protein data caclulated from PLA count data was used to cluster the cells in Seurat v3.
Supplementary_files_format_and_content: The file Smart-seq2_rawfiles_and_SRR_IDs.txt.gz is available on the series record and contains the raw file name and associated SRR for each single cell.

source_name: Peripheral macrophages

growth_protocol: PBMCs and macrophages are kept in RPMI media with 10% FBS

extract_protocol:
PLA products were extracted from single cells following plate-based Smart-Seq2 pipeline
Sequencing library was prepared from PLA products using PCR

treatment_protocol: Macrophages are treated with LPS or PAM2CSK4 or both for 5 minutes, 2 hours or 12 hours

value: Primary human macrophages

tag: donor type

value: Healthy donor

value: LPS/PAM 5 minutes


title: WT_8

tag: genotype


title: Smart-seq2: Macrophages10

description: Prox-seq using Smart-seq2 pipeline

value: LPS/PAM 12 hours


title: Smart-seq2: Macrophages7

description: Prox-seq using Smart-seq2 pipeline

data_processing:
Sequencing data was aligned using a custom Java program to identify the Prox-seq probe barcodes.
Count data was analyzed in Python and RStudio. Cells with fewer total UMI count lower than 10 were discarded.
Protein data caclulated from PLA count data was used to cluster the cells in Seurat v3.

value: PAM 12 hours


title: Human Nephrectomy

first: Michael

value: Reference

value: Female


title: Smart-seq2: Macrophages4

description: Prox-seq using Smart-seq2 pipeline

value: LPS 12 hours


title: Sham Model


title: WT_9

value: WT


title: KO_2