title: ACL repair 11, synovium, 52 weeks

city: Boston

first: Martha

last: Murray

state: Massachusetts

address: 300 Longwood Avenue

department: Department of Orthopedic Surgery

institute: Boston Children's Hospital

data_processing:
Fastq files for cartilage and synovium samples were piped into FastQC version 0.11.9 to create individual sample reports that were then compiled using MultiQC version 1.12. All cartilage samples were contained within a Phred score range of 31.80 to 39.36. All synovium samples were contained within a Phred score range of 25.05 to 38.84.
Using Salmon version 1.8.0, reads were quasi-mapped from untrimmed fastq files, and transcript quantification files were generated.
Differential gene expression analysis was performed in R version 4.2.1 using DESeq2 with RUVSeq adjustment on transcript quantification files produced by Salmon mapping.
Assembly: Sscrofa11.1
Supplementary files format and content: For each sample: Salmon transcript quantification file with transcript name, length, effective length, TPM, and number of reads

organism: Sus scrofa

source_name: Synovium

extract_protocol:
Cartilage specimens were homogenized in 2 ml tubes (MP Biomedical) containing 500 ml of frozen TRIzol (Life Technologies) using a sterile drill bit while tubes were submerged in liquid nitrogen. After one round of drilling, tubes received an additional 500 ml of liquid TRIzol, were flash frozen in liquid nitrogen, and again homogenized using the drill bit. Total RNA was extracted using phenol-chloroform and purified using PureLink RNA Mini Kit (Life Technologies).
Synovium specimens were immediately placed in 2 ml lysing matrix S tubes (MP Biomedicals, Santa Ana, CA) and homogenized in 1 ml TRIzol (Life Technologies, Carlsbad,CA) using a Fast Prep-24 Instrument (MP Biomedical). Samples were then flash frozen in liquid nitrogen, transferred to dry ice, and stored at -80 ̊C until RNA isolation. Total RNA was extracted using phenol-chloroform and purified using PureLink RNA Mini Kit (Life Technologies).
All cartilage and synovium RNA isolates were then library-prepped using KAPA mRNA HyperPrep with RiboErase (Roche) and subsequently pooled and sequenced together on a NovaSeq 6000 S2 Flow Cell with 100-bp paired-end reads (Biopolymers Facility, Harvard Medical School, Boston, MA).

tag: breed

value: Yucatan minipig

value: Synovium

value: ACL repair


title: ACL repair 12, synovium, 52 weeks

status: Public on Apr 17 2023

type: SRA

country: USA

library_source: transcriptomic

molecule: total RNA

tag: tissue

tag: treatment


title: ACL repair 10, synovium, 52 weeks


title: Control 12, synovium, 52 weeks

value: Control


title: Pit_T3_ChAP_BirA2

city: Bethesda

first: Hong

last: Liu

state: MD

address: 9000 Rockville Pike

department: NIDDK

institute: NIH

library_source: genomic

data_processing:
Library strategy: ChAP-seq
Libraries were multiplex sequenced in one lane using Illumina HiSeq2500 Sequencer at NIDDK Genomics Facility
ChIP-seq and ChAP-seq reads were aligned to the mm9 genome assembly using bowtie2.
Peaks were called using SICER with following configuration: For ChIP-seq of histone modifications: Windows (200), Gaps (200), FDR (1e-6); For ChIP-Seq of factors: Windows (50), Gaps (50), FDR (1e-3)
Single-end reads of RNA-seq are aligned to the mm9 genome assembly using STAR.
SICER v1.1 was used to calculate the counts/reads per million mapped reads (CPM) on exonic regions as expression measurements for each gene.
ATAC-seq bam files were analyzed with Genomatix programs (Macs2 and edgeR) for the open-chromatin peaks.
Genome_build: mm9
Supplementary_files_format_and_content: comma delimited files include CPM values for each gene; tab-delimited text files include FPKM values for each sites

molecule: genomic DNA

organism: Mus musculus

source_name: pituitary

extract_protocol:
For ChAP-seq assays, pools of 12 pituitaries from mice of the indicated genotypes  (ThrbHAB/HAB;Rosa26BirA/BirA and control Rosa26BirA/BirA) were processed similarly as for ChIP-seq to the supernatant sample stage. The ChAP-seq method was modified from published protocols (50).  A 3 mL sample was incubated with pre-washed Strepavidin T1 beads (Invitrogen Dynabeads, #65601) on a rotator at 4 °C overnight.  All subsequent steps, including bead washing, elution, and DNA measurement were the same as in the ChIP-seq protocol.
ChAP-seq libraries were generated using Illumina Truseq kit (Cat# 15034288).

tag: genotype

value: Rosa26BirA/BirA (BirA) mice

value: pituitary tissue

tag: strain

value: MMI + T3 treatment (hyperthyroid)

tag: antibody


title: ACL repair 9, synovium, 52 weeks


title: ACL repair 8, synovium, 52 weeks


title: Cerebellum Male 26mo 14ID

city: South San Francisco

first: Oliver

last: Hahn

state: CA

address: 1170 Veterans Blvd

institute: Calico Life Sciences, LLC

description:
Unstranded mRNA-seq
sample name:
BulkSeq_cer_14

data_processing:
Raw sequence reads were trimmed to remove adaptor contamination and poor-quality reads using Trim Galore! (v0.3.7, parameters: --paired --length 25). Trimmed sequences were aligned using STAR (v2.5.3a). Multi-mapped reads were filtered. Data visualization and analysis was performed using SeqMonk (http://www.bioinformatics.babraham.ac.uk/projects/seqmonk/), custom RStudio (https://www.rstudio.com/) scripts and the following Bioconductor packages: Deseq2 (Love et al., 2014), topGO (Alexa and Rahnenfuhrer, 2010) and org.Mm.eg.db.
Assembly: GRCm38
Supplementary files format and content: tab-delimited text file including raw counts for each sample

source_name: Cerebellum

extract_protocol:
RNeasy Qiagen RNA isolation from homogenized tissue.
Smart-Seq2 for preparation of cDNA followed by library preparation using Nextera XT. Nextera tagmentation according to the standard protocol for single cell RNA-seq following Smart-Seq2.

value: Cerebellum

tag: Sex

value: Male

tag: age (months)

tag: mouse id number


title: Pit_T3_ChAP_BirA1

value: Strepavidin T1 beads (Invitrogen Dynabeads, #65601)


title: Cerebellum Male 18mo 19ID

description:
Unstranded mRNA-seq
sample name:
BulkSeq_cer_19


title: 293T_3p_hpRNA_top20_mCherry_R6

city: Berlin

first: Gaetano

last: Gargiulo

address: Robert-Rössle-Straße 10

department: Molecular Oncology

country: Germany

institute: Max Delbrück Center for Molecular Medicine

data_processing:
The initial demultiplexing based on Illumina indices was performed using the bcl2fastq conversion software (v2.20.0).
The oligo-dT barcode sequences were extracted from Read 1 reads using cutadapt (v2.1) and utilized for subsequent internal demultiplexing using BRBseqTools-1.6.jar ( http://github.com/DeplanckeLab/BRB-seqTools).
The BRBseqTools demultiplexed data was aligned to a custom genome (COVGT#5-containing GRCh38) using STAR (v2.7.8a).
The count matrices were subsequently generated using HTSeq (v2.0.2).
Assembly: GRCh38.107 + COVGT#5
Supplementary files format and content: Tab-delimited text file with raw counts for each sample
Library strategy: BRB-seq

organism: Homo sapiens

source_name: kidney; Embryo

growth_protocol: 293T and A549 cell lines were cultured in DMEM or RPMI medium (Gibco) respectively, supplemented with 10% fetal bovine serum (FBS; from Gibco) and penicillin and streptomycin (pen/strep; 100 U/ml; Gibco) at 37°C in a 5% CO2 and 95% air.

extract_protocol:
Total RNA was extracted using the TRIzol Reagent (Invitrogen) with subsequent isopropanol precipitation, DNase I treatment and purification with AMPure XP beads (Beckman Coulter). The concentration of the RNA was quantified by Qubit RNA HS Assay Kit (Invitrogen). The integrity of the RNA was determined with the High-Sensitivity RNA ScreenTape System (Agilent).
60 ng of total RNA per sample was used as input for constructing multiplexed 3’-cDNA libraries using barcoded oligo-dT primers (Datlinger et al., 2021) in an adapted version of Bulk RNA barcoding and sequencing (BRB-seq) protocol (Alpern et al., 2019). The final multiplexed library pools were quantified with Qubit dsDNA HS Assay Kit (Invitrogen) and Collibri™ Library Quantification Kit (Invitrogen), and the proper library fragment distribution was assessed by the TapeStation High-Sensitivity D1000 ScreenTapes kit (Agilent).

treatment_protocol: 293T and A549 reporter cells were induced with IFN mix (20ng/ml IFNa-2a, 20ng/ml IFNa-2b, 20ng/ml IFNb, 10ng/ml IL-28, 5ng/ml IFNg) or 3p-hpRNA (0.1ug/ml) followed by TOPi (30nM Topotecan, 100nM Etoposide) or JAKi (100nM Baricitinib, 300nM Tofacitinib) treatement.

value: kidney; Embryo

tag: cell line

value: WT


title: 293T_3p_hpRNA_top20_mCherry_R1


title: Control 11, synovium, 52 weeks


title: Cerebellum Female 12mo 13ID

description:
Unstranded mRNA-seq
sample name:
BulkSeq_cer_13

value: Female


title: Cerebellum Male 12mo 12ID

description:
Unstranded mRNA-seq
sample name:
BulkSeq_cer_12


description: 293T_3p_hpRNA_Bari_Tofa_bottom40_mCherry_R3.count

value: 3p-hpRNA + JAKi


title: Pit_T3_ChAP_TRb_HAB3

value: ThrbHAB/HAB; Rosa26BirA/BirA (HAB) mice


title: ACL repair 7, synovium, 52 weeks


title: Pit_mmi_ChAP_BirA2

value: MMI treatment (hypothyroid)


description: 293T_3p_hpRNA_Bari_Tofa_bottom40_mCherry_R2.count


title: 293T_3p_hpRNA_top20_mCherry_R3


title: ACL repair 6, synovium, 52 weeks


description: 293T_3p_hpRNA_Bari_Tofa_bottom40_mCherry_R1.count


title: Cerebellum Male 26mo 11ID

description:
Unstranded mRNA-seq
sample name:
BulkSeq_cer_11


title: ACL repair 5, synovium, 52 weeks


title: Cerebellum Male 12mo 15ID

description:
Unstranded mRNA-seq
sample name:
BulkSeq_cer_15


title: 293T_3p_hpRNA_top20_mCherry_R2


title: Cerebellum Female 12mo 10ID

description:
Unstranded mRNA-seq
sample name:
BulkSeq_cer_10


title: Cerebellum Female 12mo 1ID

description:
Unstranded mRNA-seq
sample name:
BulkSeq_cer_1


title: Control 10, synovium, 52 weeks


title: ACL repair 4, synovium, 52 weeks


title: Pit_mmi_ChAP_BirA1


title: Pit-mmi-ChAP-TRb-HAB3


title: B cells from ICB patients 5, 6, 7 and 8, mRNA-BCR-derived (VDJ) cDNA

city: Cambridge

first: Zhaleh

last: Hosseini

address: MRC Toxicology Unit, Tennis Ct Rd

country: United Kingdom

institute: University of Cambrdige

description:
VDJ mRNA library: read1 file contains cell barcode and UMI; read2 file contains VDJ transcript
ICB2_VDJ

library_source: transcriptomic single cell

data_processing:
Raw FASTQ files of the VDJ library were analysed using the 10x Genomics Cell Ranger software v7.0.1
The Dandelion package was used for analysis of clonotypes and clonal expansion
Assembly: GRCh38
Supplementary files format and content: fasta files and comma-separated value (csv) files

molecule: polyA RNA

source_name: Peripheral blood mononuclear Cells

extract_protocol:
Frozen PBMCs were thawed, and B cell population was enriched using magnetic separation (Miltenyi 130-101-638). Samples were next labelled with oligonucleotide-tagged antibodies against CD11c, CD21, CD27 and CD85j (TotalSeq, BioLegend) and hashtagged with four different anti-human CD298/b2-microglobulin/ TotalSeq™ Hashtag antibodies. After labelled, cell counts were adjusted to 1,035 cells per microlitre before being loaded onto a Chromium Next GEM chip K (10X Genomics, 2000182).
Libraries’ construction was performed according to Single cell 5’ v2 protocol (CG000330 RevA, 10X Genomics). Briefly, B cells were resuspended in the master mix and loaded together with partitioning oil and gel beads into the chip to generate the gel bead-in-emulsion (GEM). The poly-A RNA from the cell lysate contained in every single GEM was retrotranscripted to cDNA, which contains an Ilumina R1 primer sequence, Unique Molecular Identifier (UMI) and the 10x Barcode. The pooled barcoded full-length cDNA from poly-adenylated mRNA and DNA from protein Feature barcode are amplified and separated by size selection fro generating  5' Gene expression libraries, and cell surface protein libraries, respectively. cDNA is  then cleaned up with Silane DynaBeads, amplified by PCR and the apropiated sized fragments were selected with SPRIselect reagent for subsequent library construction. During the library construction Ilumina R2 primer sequence, paired-end constructs with P5 and P7 sequences and a sample index were added. The library was quality controlled by Agilent 4150 TapeStation and quantified by RT-PCR using the KAPA library quantification kit for Illumina platforms (Roche, KK4824). Samples were sequenced on an Illumina NovaSeq with a sequencing depth of at least 50, 000 reads per cell.

value: Peripheral blood mononuclear Cells

tag: disease state

value: ICB

tag: cell type

value: B cells

tag: library type

value: VDJ

tag: antibodies/tags


title: B cells from IEI patients 1, 2, 3 and 4, mRNA-BCR-derived (VDJ) cDNA

description:
VDJ mRNA library: read1 file contains cell barcode and UMI; read2 file contains VDJ transcript
IEI_VDJ

value: IEI


title: B cells from ICB patients 1, 2, 3 and 4, mRNA-BCR-derived (VDJ) cDNA

description:
VDJ mRNA library: read1 file contains cell barcode and UMI; read2 file contains VDJ transcript
ICB1_VDJ


title: Brain_untreated_ChAP_BirA3

source_name: Cerebral cortex

value: Cerebral cortex

value: no treatment (euthyroid)


title: Pit-mmi-ChAP-TRb-HAB1

value: pituitary tissue


title: B cells from healthy controls 7 and 8, mRNA-BCR-derived (VDJ) cDNA

description:
VDJ mRNA library: read1 file contains cell barcode and UMI; read2 file contains VDJ transcript
HC4_VDJ

value: healthy control


title: Corpus callosum Male 12mo 9ID

description:
Unstranded mRNA-seq
sample name:
BulkSeq_cc_9

source_name: Corpus callosum

value: Corpus callosum

value: Male


title: ACL repair 2, synovium, 52 weeks

value: Yucatan minipig

value: Synovium

value: ACL repair


title: ACL repair 3, synovium, 52 weeks


title: Corpus callosum Male 26mo 8ID

description:
Unstranded mRNA-seq
sample name:
BulkSeq_cc_8


title: Brain_untreated_ChAP_BirA2

value: Strepavidin T1 beads (Invitrogen Dynabeads, #65601)


title: Corpus callosum Female 12mo 7ID

description:
Unstranded mRNA-seq
sample name:
BulkSeq_cc_7

value: Female


title: ACL repair 1, synovium, 52 weeks


title: Corpus callosum Male 12mo 6ID

description:
Unstranded mRNA-seq
sample name:
BulkSeq_cc_6


title: Brain_untreated_ChAP_BirA1

value: ThrbHAB/HAB; Rosa26BirA/BirA (HAB) mice


title: Corpus callosum Male 28mo 59ID

description:
Unstranded mRNA-seq
sample name:
BulkSeq_cc_59


title: Pit_T3_ChAP_TRb_HAB1

value: MMI + T3 treatment (hyperthyroid)


title: B cells from healthy controls 3 and 4, mRNA-BCR-derived (VDJ) cDNA

description:
VDJ mRNA library: read1 file contains cell barcode and UMI; read2 file contains VDJ transcript
HC2_VDJ

value: Peripheral blood mononuclear Cells


title: ACL reconstruction 12, synovium, 52 weeks

value: ACL reconstruction


title: B cells from healthy controls 5 and 6, mRNA-BCR-derived (VDJ) cDNA

description:
VDJ mRNA library: read1 file contains cell barcode and UMI; read2 file contains VDJ transcript
HC3_VDJ

value: B cells

value: VDJ


title: B cells from healthy controls 1 and 2, mRNA-BCR-derived (VDJ) cDNA

description:
VDJ mRNA library: read1 file contains cell barcode and UMI; read2 file contains VDJ transcript
HC1_VDJ


title: Brain_untreated_ChAP_HAB2

description:
Brain_untreated_ChAP_HAB_5164.txt
Brain_untreated_ChAP_HAB_5164.wig

value: Cerebral cortex


title: Control 8, synovium, 52 weeks

value: Control


title: Brain_untreated_ChAP_HAB3

value: no treatment (euthyroid)


title: HT-1080_CLA18:2_Replicate3

city: Seattle

first: Libin

last: Xu

address: 1705 NE Pacific St

institute: University of Washington

data_processing:
Raw RNA sequencing reads in FASTQ format were mapped to the human genome (hg38) using HISAT algorithm and format conversions were performed using Samtools. FeatureCounts algorithm was used to quantify the aligned RNA-seq data as raw counts. DESeq2 R package was used to determine differentially expressed genes (DEGs) from raw counts in different conditions.
Assembly: hg38
Supplementary files format and content: tab-delimited text files include raw-count for each sample.

extract_protocol:
RNA was harvested using RNeasy mini plus kit (Qiagen).
Total isolated RNA was sent to Novogene to perform the cDNA library construction and sequencing using the Illumina NovaSeq 6000 platform (150 base pairs paired-end, with sequencing depth above 20 million reads per sample)

value: Fibrosarcoma

value: WT


title: HT-1080_CLA18:2_Replicate4


title: Brain_untreated_ChAP_HAB1


title: Control 9, synovium, 52 weeks


title: Corpus callosum Male 28mo 57ID

description:
Unstranded mRNA-seq
sample name:
BulkSeq_cc_57

value: Corpus callosum

value: Male


title: ACL reconstruction 11, synovium, 52 weeks

value: Yucatan minipig

value: Synovium


title: Corpus callosum Female 21mo 56ID

description:
Unstranded mRNA-seq
sample name:
BulkSeq_cc_56


title: Corpus callosum Female 18mo 55ID

description:
Unstranded mRNA-seq
sample name:
BulkSeq_cc_55


title: ACL reconstruction 10, synovium, 52 weeks


title: Pit_untreated_ChAP_BirA3

value: pituitary tissue

value: Strepavidin T1 beads (Invitrogen Dynabeads, #65601)


title: Pit_untreated_ChAP_BirA2

value: ThrbHAB/HAB; Rosa26BirA/BirA (HAB) mice


title: ACL reconstruction 9, synovium, 52 weeks


title: Corpus callosum Female 15mo 54ID

description:
Unstranded mRNA-seq
sample name:
BulkSeq_cc_54

value: Female


title: HT-1080_CLA18:2_Replicate2


title: HT-1080_CLA18:2_Replicate1


title: HT-1080_LA_Replicate4

value: 80 mM LA


title: Pit_untreated_ChAP_HAB3

description:
Pit_untreated_ChAP_HAB_8051.txt
Pit_untreated_ChAP_HAB_8051.wig


title: HT-1080_LA_Replicate3


title: Corpus callosum Female 3mo 53ID

description:
Unstranded mRNA-seq
sample name:
BulkSeq_cc_53


title: Corpus callosum Female 21mo 52ID

description:
Unstranded mRNA-seq
sample name:
BulkSeq_cc_52


title: Pit_untreated_ChAP_HAB2


title: Control 7, synovium, 52 weeks


title: HT-1080_LA_Replicate2


title: Corpus callosum Female 18mo 51ID

description:
Unstranded mRNA-seq
sample name:
BulkSeq_cc_51


title: ACL reconstruction 7, synovium, 52 weeks

value: ACL reconstruction


title: Pit_untreated_ChAP_HAB1


title: Corpus callosum Female 15mo 50ID

description:
Unstranded mRNA-seq
sample name:
BulkSeq_cc_50


title: HT-1080_CLA18:3_Replicate4

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen).
Total isolated RNA was sent to Novogene to perform the cDNA library construction and sequencing using the Illumina NovaSeq 6000 platform (150 base pairs paired-end, with sequencing depth above 20 million reads per sample)

value: 5 mM CLA 18:3


title: ACL reconstruction 5, synovium, 52 weeks


title: ACL reconstruction 6, synovium, 52 weeks


title: RNA-T3-ThrbKO4

data_processing:
Libraries were multiplex sequenced in one lane using Illumina HiSeq2500 Sequencer at NIDDK Genomics Facility
ChIP-seq and ChAP-seq reads were aligned to the mm9 genome assembly using bowtie2.
Peaks were called using SICER with following configuration: For ChIP-seq of histone modifications: Windows (200), Gaps (200), FDR (1e-6); For ChIP-Seq of factors: Windows (50), Gaps (50), FDR (1e-3)
Single-end reads of RNA-seq are aligned to the mm9 genome assembly using STAR.
SICER v1.1 was used to calculate the counts/reads per million mapped reads (CPM) on exonic regions as expression measurements for each gene.
ATAC-seq bam files were analyzed with Genomatix programs (Macs2 and edgeR) for the open-chromatin peaks.
Genome_build: mm9
Supplementary_files_format_and_content: comma delimited files include CPM values for each gene; tab-delimited text files include FPKM values for each sites

extract_protocol:
Total RNA was prepared from three frozen pituitaries per library, using TRIzol Reagent (Invitrogen, Cat 15596-026) with mRNA enrichment using Dynabeads mRNA purification Kit (Ambion Cat# 61006) and quantification using Qubit RNA Broad-range assay Kit (Thermo Fischer Scientific). Five μg of total RNA was denatured at 65°C for 5 min, then incubated with oligo(dT)-beads with rotation at room temperature for 5 min. Beads were washed twice in 10 mM Tris-HCl pH7.5, 0.15 M LiCl and 1mM EDTA, then mRNA eluted in 10 mM Tris-HCl pH 7.5 at 80°C for 2 min. Libraries were synthesized using SuperScript Double-Stranded cDNA Synthesis Kit (Invitrogen) and sequencing libraries generated using Illumina Truseq kit (Cat# 15034288) or ThruPLEX DNA-seq kit (Takara, R400428).
Libraries were synthesized using SuperScript Double-Stranded cDNA Synthesis Kit (Invitrogen) and sequencing libraries generated using Illumina Truseq kit (Cat# 15034288) or ThruPLEX DNA-seq kit (Takara, R400428).

value: Thrb-deficient (KO) mice

value: MMI + T3 treatment (hyperthyroid)


title: RNA-T3-ThrbKO5


title: Control 6, synovium, 52 weeks

value: Control


title: RNA-T3-ThrbKO3


title: HT-1080_CLA18:3_Replicate2


title: ACL reconstruction 8, synovium, 52 weeks


title: Pit_untreated_ChAP_BirA1

value: no treatment (euthyroid)


title: ACL reconstruction 4, synovium, 52 weeks


title: HT-1080_CLA18:3_Replicate1

value: Fibrosarcoma


title: RNA-T3-ThrbKO2


title: Corpus callosum Female 21mo 48ID

description:
Unstranded mRNA-seq
sample name:
BulkSeq_cc_48


title: ACL reconstruction 3, synovium, 52 weeks


title: RNA-T3-ThrbKO1


title: HT-1080_RSL3+CLA18:2_Replicate4

value: WT

value: 10 nM RSL3 + 80 mM CLA 18:2


title: ACL reconstruction 2, synovium, 52 weeks


title: Corpus callosum Female 18mo 47ID

description:
Unstranded mRNA-seq
sample name:
BulkSeq_cc_47

value: Corpus callosum


title: Corpus callosum Female 15mo 46ID

description:
Unstranded mRNA-seq
sample name:
BulkSeq_cc_46


title: RNA-mmi-ThrbKO5

value: MMI treatment (hypothyroid)


title: HT-1080_LA_Replicate1


title: Corpus callosum Male 26mo 5ID

description:
Unstranded mRNA-seq
sample name:
BulkSeq_cc_5

value: Male


title: HT-1080_RSL3+CLA18:2_Replicate3


title: Corpus callosum Female 21mo 44ID

description:
Unstranded mRNA-seq
sample name:
BulkSeq_cc_44


title: HT-1080_RSL3+CLA18:2_Replicate2


title: HT-1080_RSL3+CLA18:2_Replicate1


title: ACL reconstruction 1, synovium, 52 weeks

value: Yucatan minipig

value: Synovium


title: Corpus callosum Female 3mo 45ID

description:
Unstranded mRNA-seq
sample name:
BulkSeq_cc_45


title: ACL transection alone 12, synovium, 52 weeks

value: ACL transection alone


title: RNA-mmi-ThrbKO4

value: pituitary tissue


title: HT-1080_CLA18:3_Replicate3


title: Corpus callosum Female 3mo 49ID

description:
Unstranded mRNA-seq
sample name:
BulkSeq_cc_49

value: Female


title: Corpus callosum Female 18mo 43ID

description:
Unstranded mRNA-seq
sample name:
BulkSeq_cc_43


title: Corpus callosum Female 3mo 41ID

description:
Unstranded mRNA-seq
sample name:
BulkSeq_cc_41


title: Corpus callosum Female 15mo 42ID

description:
Unstranded mRNA-seq
sample name:
BulkSeq_cc_42


title: HT-1080_RSL3+LA_Replicate2

value: 10 nM RSL3 + 80 mM LA


title: HT-1080_RSL3+LA_Replicate4


title: RNA-mmi-ThrbKO2


title: Corpus callosum Female 21mo 40ID

description:
Unstranded mRNA-seq
sample name:
BulkSeq_cc_40


title: Control 4, synovium, 52 weeks


title: HT-1080_RSL3+LA_Replicate3


title: RNA-T3-WT4

value: wild type


title: RNA-mmi-ThrbKO1

value: Thrb-deficient (KO) mice


title: RNA-T3-WT3

value: MMI + T3 treatment (hyperthyroid)


title: ACL transection alone 11, synovium, 52 weeks


title: HT-1080_RSL3+LA_Replicate1


title: ACL transection alone 9, synovium, 52 weeks


title: ACL transection alone 8, synovium, 52 weeks


title: ACL transection alone 10, synovium, 52 weeks


title: Control 5, synovium, 52 weeks

value: Control


title: Corpus callosum Female 12mo 4ID

description:
Unstranded mRNA-seq
sample name:
BulkSeq_cc_4


title: HT-1080_RSL3_Replicate3

value: 10 nM RSL3


title: Control 3, synovium, 52 weeks


title: Corpus callosum Female 18mo 39ID

description:
Unstranded mRNA-seq
sample name:
BulkSeq_cc_39


title: RNA-mmi-ThrbKO3


title: RNA-T3-WT1


title: RNA-mmi-WT4


title: Corpus callosum Female 15mo 38ID

description:
Unstranded mRNA-seq
sample name:
BulkSeq_cc_38


title: HT-1080_RSL3_Replicate2

value: Fibrosarcoma


title: HT-1080_RSL3_Replicate1

value: WT


title: RNA-mmi-WT2


title: Corpus callosum Female 3mo 37ID

description:
Unstranded mRNA-seq
sample name:
BulkSeq_cc_37


title: RNA-mmi-WT3


title: HT-1080_DMSO_Replicate3

value: DMSO


title: Corpus callosum Male 21mo 36ID

description:
Unstranded mRNA-seq
sample name:
BulkSeq_cc_36

value: Corpus callosum


title: HT-1080_DMSO_Replicate4


title: ACL transection alone 5, synovium, 52 weeks


title: RNA-mmi-WT1

value: MMI treatment (hypothyroid)


title: HT-1080_RSL3_Replicate4


title: ACL transection alone 6, synovium, 52 weeks


title: Corpus callosum Male 18mo 35ID

description:
Unstranded mRNA-seq
sample name:
BulkSeq_cc_35

value: Male


title: shCTDP1-#2_R3

city: Omaha

first: Nicholas

last: Woods

state: Nebraska

institute: Univeristy of Nebraska Medical Cent

data_processing:
The original fastq format reads were trimmed by fqtirm tool (https://ccb.jhu.edu/software/fqtrim) to remove adapters, terminal unknown bases (Ns) and low quality 3’ regions (Phred score < 30).
The trimmed fastq files were processed by our newly developed standard pipelines utilizing STAR [1] as the aligner and RSEM [2] as the tool for annotation and quantification at both gene and isoform levels. Human genome hg19 was used for the reference genome.
The FPKM (Fragments Per Kilobase of transcript per Million mapped reads) and TPM (Transcripts Per Kilobase Million) values were calculated for each gene/isoform.
Genome_build: Human genome hg19
Supplementary_files_format_and_content: BEDGRAPH. The score signifies the TPM values

growth_protocol: MDA-MB-231 cells were cultured in RPMI 1640 medium (Invitrogen) containing 10% fetal bovine serum (FBS) and 1% penicillin-streptomycin.

extract_protocol:
After puromycin selection, the total RNA was extracted directly from the petri dish using the reagents and procedure in the QIAGEN Rneasy mini-kit.
The library was prepared with the reagents and protocol provided TruSeq RNA Library Prep Kit v2.

treatment_protocol: 293FT cells were transfected with the shRNA vectors and the ViraPower lentivirus packaging vectors using calcium phosphate precipitation method as the manufacturer described. The lentiviral particle produced were harvested by DMEM medium containing 10% FBS and 1% penicillin-streptomycin for 48 hours. The lentivirus containing supernatant was then collected, spun down in 300 × g for 5 min and filtered with 0.45 µm nylon filter. The lentiviral supernatant was then supplemented with fresh media  in 3 : 1 ratio and 10 µg/mL of polybrene (Sigma Aldrich) and incubated with the cells for 48 hours.

tag: shRNA


title: Corpus callosum Male 15mo 34ID

description:
Unstranded mRNA-seq
sample name:
BulkSeq_cc_34


title: HT-1080_DMSO_Replicate2


title: shCTDP1-#2_R2


title: HT-1080_DMSO_Replicate1


title: RNA-T3-WT2


title: ACL transection alone 4, synovium, 52 weeks

value: Yucatan minipig


title: Corpus callosum Male 3mo 33ID

description:
Unstranded mRNA-seq
sample name:
BulkSeq_cc_33


title: ACL transection alone 2, synovium, 52 weeks

value: Synovium


title: ACL transection alone 3, synovium, 52 weeks

value: ACL transection alone


title: shCTDP1-#1_R3


title: ACL transection alone 7, synovium, 52 weeks


title: Corpus callosum Male 21mo 32ID

description:
Unstranded mRNA-seq
sample name:
BulkSeq_cc_32


title: shCTDP1-#2_R1


title: Control 2, synovium, 52 weeks


title: Corpus callosum Male 15mo 30ID

description:
Unstranded mRNA-seq
sample name:
BulkSeq_cc_30


title: H4 cells, VPS35 KO Clone 16 + VPS35-GFP sample 2

city: Santander

first: Lucio

last: Di Filippo

state: Cantabria

address: PCTCAN - Cl. Albert Einstein, 22

country: Spain

institute: IBBTEC

data_processing:
Illumina NovaSeq 6000 base call (BCL) files were converted in fastq file through bcl2fastq
Trimming and cleaning with bbduk
Alignment was performed with STAR 2.6.0a
The expression levels of genes were determined with HTseq-counts 0.9.1
Assembly: hg38
Supplementary files format and content: tab-delimited text files including raw counts

source_name: Brain

growth_protocol: Grown in DMEM media containing 4.5 g/L glucose (Sigma, D5796) supplemented with 10% fetal bovine serum (Sigma, F7524), 100U/mL penicillin and 0.1mg/mL streptomycin

extract_protocol:
RNA extracted from confluent 6-well plates using the Qiagen RNeasy kit (Qiagen, 74134)
NEGEDIA Digital mRNA-seq research grade sequencing service (Next Generation Diagnostic srl)

value: Brain

value: Neuroglioma

value: VPS35 KO Clone 16 + VPS35-GFP


title: H4 cells, VPS35 KO Clone 16 + VPS35-GFP sample 1


title: Corpus callosum Male 12mo 3ID

description:
Unstranded mRNA-seq
sample name:
BulkSeq_cc_3


title: ACL repair 12, cartilage, 52 weeks

source_name: Articular Cartilage

value: Articular Cartilage

value: ACL repair


title: Control 1, synovium, 52 weeks


title: Control 12, cartilage, 52 weeks


title: H4 cells, VPS35 KO Clone 15 + VPS35-GFP sample 2

value: VPS35 KO Clone 15 + VPS35-GFP


title: shCTDP1-#1_R2


title: Corpus callosum Male 3mo 29ID

description:
Unstranded mRNA-seq
sample name:
BulkSeq_cc_29


title: shCTDP1-#1_R1


title: H4 cells, VPS35 KO Clone 15 + VPS35-GFP sample 1


title: Corpus callosum Male 18mo 27ID

description:
Unstranded mRNA-seq
sample name:
BulkSeq_cc_27


title: H4 cells, VPS35 KO Clone 9 + VPS35-GFP sample 2

value: VPS35 KO Clone 9 + VPS35-GFP


title: shScr_R1

value: shScr


title: H4 cells, VPS35 KO Clone 16 sample 2

value: VPS35 KO Clone 16


title: shScr_R3


title: Corpus callosum Male 21mo 28ID

description:
Unstranded mRNA-seq
sample name:
BulkSeq_cc_28


title: ACL repair 10, cartilage, 52 weeks


title: Corpus callosum Male 15mo 26ID

description:
Unstranded mRNA-seq
sample name:
BulkSeq_cc_26


title: Corpus callosum Male 28mo 58ID

description:
Unstranded mRNA-seq
sample name:
BulkSeq_cc_58


title: H4 cells, VPS35 KO Clone 16 sample 1


title: Bo_AV_3

city: Anseong-si, Gyeonggi-do

first: Heewon

last: Moon

address: 4726,Seodong-daero, Daedeok-myeon

country: South Korea

institute: Chung-ang university

data_processing:
Quality of the RNA-seq reads were evaluated using the FastQC software
The raw reads were trimmed and quality-filtered before alignment, and those with more than 90 % threshold (Q>30) were used for mapping. B. rapa reference genome was obtained from Ensembl and were used using the TopHat2 software with default parameters
Aligned reads were converted to digital counts using featureCounts and were analyzed using edgeR.
Differentially expressed genes (DEGs) were identified based on a 0.05 p-value and a cutoff of two-fold difference in expression.
Assembly: B. oleracea reference genome was obtained from BRAD
Supplementary files format and content: tab-delimited text files with raw gene counts for individual samples

organism: Brassica oleracea

source_name: whole plant

extract_protocol:
Total RNA was extracted from whole seedling samples using RNeasy Mini Kit (Qiagen, Germany) and treated with DNase I (New England Biolabs, USA) to remove genomic DNA contamination.
RNA-seq libraries were constructed using TruSeq Stranded mRNA LT Sample Prep Kit (Illumina Inc., USA) according to the manufacturer’s instructions.

value: whole plant


title: Corpus callosum Male 18mo 31ID

description:
Unstranded mRNA-seq
sample name:
BulkSeq_cc_31


title: shScr_R2


title: ACL transection alone 1, synovium, 52 weeks


title: ACL repair 11, cartilage, 52 weeks


title: Bo_AV_1


title: ACL repair 9, cartilage, 52 weeks


title: Corpus callosum Male 3mo 25ID

description:
Unstranded mRNA-seq
sample name:
BulkSeq_cc_25


title: ACL repair 8, cartilage, 52 weeks


title: H4 cells, VPS35 KO Clone 9 + VPS35-GFP sample 1


title: Control 11, cartilage, 52 weeks

value: Control


title: H4 cells, VPS35 KO Clone 15 sample 1

value: VPS35 KO Clone 15


title: Corpus callosum Male 21mo 24ID

description:
Unstranded mRNA-seq
sample name:
BulkSeq_cc_24

value: Corpus callosum


title: Bo_V40_3


title: Corpus callosum Male 15mo 22ID

description:
Unstranded mRNA-seq
sample name:
BulkSeq_cc_22

value: Male


title: Corpus callosum Male 18mo 23ID

description:
Unstranded mRNA-seq
sample name:
BulkSeq_cc_23


title: ACL repair 7, cartilage, 52 weeks

value: Yucatan minipig


title: H4 cells, VPS35 KO Clone 9 sample 2

value: VPS35 KO Clone 9


title: Bo_V40_2


title: ACL repair 6, cartilage, 52 weeks


title: Corpus callosum Male 3mo 21ID

description:
Unstranded mRNA-seq
sample name:
BulkSeq_cc_21


title: Bo_V40_1


title: ACL repair 5, cartilage, 52 weeks


title: Corpus callosum Male 21mo 20ID

description:
Unstranded mRNA-seq
sample name:
BulkSeq_cc_20


title: H4 cells, WT sample 5

value: WT


title: Control 10, cartilage, 52 weeks


title: Bo_AV_2


title: Bo_NV_3


title: H4 cells, VPS35 KO Clone 15 sample 2

value: Brain


title: H4 cells, WT sample 6

value: Neuroglioma


title: Bo_NV_2


title: H4 cells, WT sample 4


title: ACL repair 4, cartilage, 52 weeks


title: ACL repair 3, cartilage, 52 weeks


title: H4 cells, WT sample 3


title: Corpus callosum Male 15mo 18ID

description:
Unstranded mRNA-seq
sample name:
BulkSeq_cc_18


title: Corpus callosum Male 3mo 17ID

description:
Unstranded mRNA-seq
sample name:
BulkSeq_cc_17


title: H4 cells, VPS35 KO Clone 9 sample 1


title: Corpus callosum Male 21mo 16ID

description:
Unstranded mRNA-seq
sample name:
BulkSeq_cc_16


title: Bo_NV_1


title: Corpus callosum Male 18mo 19ID

description:
Unstranded mRNA-seq
sample name:
BulkSeq_cc_19


title: H4 cells, WT sample 2


title: ACL repair 2, cartilage, 52 weeks


title: H4 cells, WT sample 1


title: Corpus callosum Male 12mo 15ID

description:
Unstranded mRNA-seq
sample name:
BulkSeq_cc_15


title: ACL repair 1, cartilage, 52 weeks


title: 10x scATAC-seq on mix of MM050, MM099, MM116, MM001, MM011, MM057 and MM087

city: Leuven

first: Gert

last: Hulselmans

address: Herestraat 49 PO Box 602

department: Center for Brain and Disease Research

country: Belgium

institute: VIB

data_processing:
scATAC-seq runs reads were mapped to GRCh38 and fragments files generated using cellranger-atac count command (v2.0.0) using default parameters. Fragment files  for both libraries can be found under the names: CRM__34940b_fragments.tsv.gz and NML__a56c4b_fragments.tsv.gz. A merged fragment count matrix can be found under the name: "mm_lines_fragment_counts.tsv.gz".
Cell barcodes were demultiplexed based on their cell line identity using demuxlet using cell line specific mutations obtained from bulk ATAC-seq data on individual cell lines. For this, Genotypes of the individual cell lines were called using the bcftools mpileup command (v.1.11; options, --max-depth 8000 and --skip-indels) and bcftools call command (v1.11; options, --multiallelic-caller, -variants-only, --skip-variants indels and --output-type b). Only variants which were SNPs and not homozygous across samples were kept. To run demuxlet the scATAC-seq bam files were filtered to only contains reads covering SNPs and having a cell barcode (based on CB tag), reads were piledup using the popscle dsc-pileup command using default parameters and demuxlet was run using the popscle demuxlet command (using the option –field GT).
Based on the cell barcode to cell line annotation pseudobulk consensus peaks were called and a binary count matrix of chromatin accessibility of cells over consensus peaks was generated using pycisTopic.
Only high quality barcodes corresponding to cells were kept by filtering out cells with less than 3.25 and 3.8 log number of unique fragements per cell, FRIP below 0.5 and TSS enrichment below 4 and 5, respectively for data from NML__a56c4b and CRM__34940b using pycisTopic. Doublets based on Scrublet calls with a threshold of 0.25 were removed.
Using the high quality barcodes and the binary accessibility matrix an imputed accessibility matrix, resolving drop outs, was generated using topic modeling. For this Latent Dirichlet allocation with a collapsed Gibbs samples was used and a model of 30 topics using pycisTopic.
Pseudo multi ome data was generated by bootstrapping 5 cells of the same cell line into multiple meta cells containing both imputed chromatin accessibility data and gene expression data( from GSE134432 ) for the cell lines present in both assays. This data is available in the mm_lines_gene_expression_matrix.tsv and mm_lines_region_accessibility_matrix.tsv.gz file together with meta cell to cell line annotations in mm_lines_cell_metadata.tsv.
hg38
Supplementary files format and content: mm_lines_gene_expression_matrix.tsv:  tab seperated flat text file containing gene expression counts for the pseudo multi ome data (rows are meta cells and columns are genes).
Supplementary files format and content: mm_lines_region_accessibility_matrix.tsv.gz: tab seperated flat text file, compressed using gzip, containing imputed chromatin accessibility data for the pseudo multi ome data (columns are meta cells and rows are genomic region coordinates).
Supplementary files format and content: mm_lines_cell_metadata.tsv.: tab seperated flat text file containing meta cell to cell line annotations.
Supplementary files format and content: mm_lines_fragment_counts.tsv.gz: tab seperated flat text file, compressed using gzip, containing raw fragment counts (columns are cell barcodes and rows are genomic coordinates).
Supplementary files format and content: CRM__34940b_fragments.tsv.gz: tab seperated flat text file, compressed using gzip, containig Tn5 fragments from scATAC-seq library CRM__34940b (first three columns describe genomic region coordinates (chrom, start, end), column four contains the cell barcode identifier, column five contains the total number of read pairs associated with this fragment).
Supplementary files format and content: CRM__34940b_fragments.tsv.gz: tab seperated flat text file, compressed using gzip, containig Tn5 fragments from scATAC-seq library NML__a56c4b (first three columns describe genomic region coordinates (chrom, start, end), column four contains the cell barcode identifier, column five contains the total number of read pairs associated with this fragment).

source_name: melanoma cell lines

growth_protocol: Cells were cultured in Ham’s F10 nutrient mux (Thermo Fisher Scientific, Waltham, MA) supplemented with 10% fetal bovine serum (FBS; Thermo Fisher Scientific) and 100  µg ml−1 penicillin–streptomycin. Cell cultures were kept at 37°C and 5% CO2. The identity of each line has been determined using RNA-seq and ATAC-seq and cell cultures used for experiments providing data to this study were tested for myoplasm contamination and were found to be negative.

extract_protocol:
Nuclei were extracted from the mm lines as follows; Cells were washed with phosphate buffered saline (1x PBS; Thermo Fisher Scienific), detached using trypsin (Thermo Fisher Scientific) and centrifuged at 1,000 r.p.m. for 5 min to remove the medium after this protocol CG000169 (10x Genomics) was followed. Briefly, cells were washed with PBS + 0.04% BSA and cell concentration was determined with the LUNA-FL Dual Fluorescence Cell Counter. For each cell line, 500k cells were resuspended in 100 µl nuclei lysis buffer (10 mM Tris-HCl pH 7.4; 10 mM NaCl; 3 mM MgCl2; 0.1% Tween-20; 0.1% NP40; 0.01% Digitonin and 1% BSA in nuclease-free water). After 5 min incubation on ice, 1 ml chilled wash buffer was added to the lysed cells (10 mM Tris-HCl pH 7.4; 10 mM NaCl; 3 mM MgCl2; 0.1% Tween-20 and 1% BSA in nuclease-free water). The lysed cell suspension was centrifuged at 500 rcf for 5 min at 4°C and the pellet was resuspended in 1x nuclei buffer.
Single-cell libraries were generated using the GemCode Single-Cell Instrument and Single Cell ATAC Library & Gel Bead Kit v1-v1.1 and ChIP Kit (10x Genomics). Briefly, single nuclei suspended in 1x nuclei buffer were incubated for 60 min at 37°C with a transposase that fragments the DNA in open regions of the chromatin and adds adapter sequences to the ends of the DNA fragments. After generation of nanoliter-scale gel-bead-in-emulsions (GEMs), GEMs were incubated in a C1000 Touch Thermal Cycler (Bio-Rad) under the following program: 72°C for 5 min; 98°C for 30 s; 12 cycles of 98°C for 10 s, 59°C for 30 s, 72°C for 1 min; and hold at 15°C. After incubation, single-cell droplets were broken, and the single-strand DNA was isolated and cleaned using Cleanup Mix containing Silane Dynabeads. Illumina P7 sequence and a sample index were added to the single-strand DNA during library construction via PCR: 98°C for 45s; 9-13 cycles of 98°C for 20 s, 67°C for 30 s, 72°C for 20 s; 72°C for 1 min; and hold at 15°C. The sequencing-ready library was cleaned up with SPRIselect beads.

value: melanoma cell lines


title: Corpus callosum Male 26mo 14ID

description:
Unstranded mRNA-seq
sample name:
BulkSeq_cc_14


title: Control 9, cartilage, 52 weeks

value: Articular Cartilage


title: ACL reconstruction 12, cartilage, 52 weeks

value: ACL reconstruction


title: Corpus callosum Female 12mo 13ID

description:
Unstranded mRNA-seq
sample name:
BulkSeq_cc_13

value: Female


title: CCB1243 (RoxS-t15-r3)

city: Paris

first: Sylvain

last: Durand

address: 13 rue Pierre et Marie Curie

country: France

institute: CNRS

data_processing:
Quality control checks were performed before and after trimming by FastQC (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/).
Fifty-nt reads were mapped by Bowtie (Langmead et al, 2009)
The analysis is performed using the R [R Core Team. R: A Language and Environment for Statistical Computing. R Foundation for Statistical Computing, Vienna, Austria, 2013.] software, Bioconductor [R.-C. Gentleman and others. Bioconductor: Open software development for computational biology and bioinformatics. Genome Biology, 5:R80, 2004.] packages including DESeq2.
Moderated estimation of fold change and dispersion for RNA-Seq data with DESeq2 and the PF2tools package (version 1.5.3) developed at PF2 (Institut Pasteur)
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

organism: Bacillus subtilis

source_name: Bacterial cell

growth_protocol: Strains CCB1244 and CCB1243 were grown in 50 ml MD modified supplemented with 0.5 % malate and a limiting concentration of lysine (85.5 µM) with shaking at 37°C. Cultures were grown to OD600 = 0.5 and split in two cultures of 20 mL (For RNaseq and Pulsed SILAc experiment). For the RNaseq sample, 1 % arabinose was added for 15 min before harvesting the cultures (10 mL) for RNAseq

extract_protocol:
Total RNA was isolated from 10 mL culture (pelleted and frozen) by the glass beads/phenol method described previously (Bechhofer DH et al. 2008, Methods Enzymol 447:259–276.). RNA samples were treated with RQ DNase Promega (37°C for 20 min) to remove potential contaminating chromosomal DNA. Ribosomal RNA was removed using the RiboZero kit (Illumina), and ribosomal RNA depletion and overall RNA quality was analysed by Bioanalyser (Agilent).
cDNA libraries were prepared using the Smarter Stranded RNA-Seq Kit (Clontech) with adapters for multiplexing, according to the manufacturer’s instructions. cDNA concentration and quality were checked by Bioanalyser (Agilent). The 6 samples were normalised to 2 nM, multiplexed and denatured at a concentration of 1 nM using 0.1 N NaOH (5 min at room temperature) before dilution to 10 pM and loading on a HiSeq Rapid SE65

value: Bacterial cell

value: [delta]roxS, amyE::pXsa-RoxS


title: CCB1244 (pXsa-t15-r3)

value: [delta]roxS, amyE::pXsa


title: CCB1243 (RoxS-t15-r2)


title: Control 8, cartilage, 52 weeks


title: SUM159 pLV-KRAB + empty vector control, ATAC-seq

city: Clayton

first: Joe

last: Cursons

state: VIC

address: 19 Innovation Walk

department: Biomedicine Discovery Institute

country: Australia

institute: Monash University

data_processing:
ATAC-seq data were adapter and quality trimmed with fastp [10.1093/bioinformatics/bty560] with the standard settings followed by mapping with bowtie2 [10.1038/nmeth.1923] against the human reference genome hg38 in parallel with gnu-parallel [https://www.usenix.org/system/files/login/articles/105438-Tange.pdf].
Reads mapped to the mitochondrial genome and to the ENCODE blacklisted regions (ENCFF001TDO) [10.1038/nature11247] were removed. Duplicate reads were identified by samtools markdup and removed with samtools view [10.1093/bioinformatics/btp352] prior to peak calling with MACS2 (--nomodel --extsize 150 --shift -75 --gsize hs --keep-dup all) [10.1186/gb-2008-9-9-r137].
ATAC-seq peaks were intersected with +/- 4kb of promoter annotations with bedtools intersect [10.1093/bioinformatics/btq033]. Counts in promoter peaks were aggregated with bedtools multicov, followed by library size and peak width normalization.
Assembly: hg38
Supplementary files format and content: bigWig, narrowPeak (except for Input sample)

growth_protocol: F12 Medium supplemented with 0.6% 1M Hepes, 5 µg/mL insulin, 1 µg/mL hydrocortisone, 1% Anti-Anti and 10% heat inactivated FBS

extract_protocol:
Cells were grown to ~80% confluency before being dissociated and counted.  Cells were lysed in ATAC resuspension buffer and nuclei were counted before transposition.
Tagmentation was performed in 1x Tagmentation Buffer (1M Tris-HCl pH 7.6, 1M MgCl2, 10% Dimethyl Formamide) using 2 µL Tn5 transposase (in-house made Tn5, 25 µg/ml final) in 100 µl final volume, at 37°C for 30 min, 1000 rpm. Tagmentation was inactivated with a final concentration of 0.5% SDS (Merck) and subjected to Proteinase K treatment (NEB) at 55 °C for 15 min at 1000 rpm.  Reaction was purified using a Bioline PCR Clean-up kit and eluted in 25 µL of H2O. PCR was performed using NEBNext High Fidelity PCR master mix with the following conditions: 58 °C for 5 min, 72 °C for 5 min, 98 °C for 30 sec; 11 cycles of 98 °C for 10 sec, 63 °C for 30 sec, 72 °C for 1 min and then 72 °C for 2 min and hold at 12 °C. Final clean-up of product was performed using 1.0x Ampure XP beads and visualized on the Agilent D5000 TapeStation.

value: Triple-negative breast cancer

tag: transduction (vector)

value: pLV-KRAB

tag: transduction (grna)

value: No targeting gRNA (aka Empty Vector Control)


title: SUM159 pLV-KRAB + all 4-targeting gRNAs, ATAC-seq

value: All 4 gRNAs (vs ZEB1 promoter)


title: Corpus callosum Male 12mo 12ID

description:
Unstranded mRNA-seq
sample name:
BulkSeq_cc_12

value: Corpus callosum

value: Male


title: SUM159 pLV-KRAB + empty vector control, H3K4me3, abcam Ab8580, biol rep 2

data_processing:
Basecalls were performed using bcl2fastq v2.17 for Novaseq output.
ChIP-seq reads were trimmed from 3' end until the final base had a quality score > 30, using Trimmomatic v0.33, discarding reads left with < 20 bp
ChIP-seq reads were aligned to the UCSC hg38 genome using Bowtie version 1.1.2. Only uniquely mapping reads with at most two mismatches were retained.
To create ChIP-seq coverage plots, the locations of the mapped ChIP-seq reads were extended to 150 bp to represent sequenced fragments, renormalized (to reads per million, rpm) and reformatted in the bigWig file format.
Peaks were called uing MACS v2.1.0 with the significance cut-off q-value <=0.01
bigWig files were generated using the genomicRanges R package. Score represents the normalized coverage of DNA fragments at a given genomic coordinate. narrowPeak files were generated using MACS v2 with default settings.
Assembly: hg38
Supplementary files format and content: bigWig, narrowPeak (except for Input sample)

extract_protocol:
Changes in histone modification were assessed using a modified Native ChIP protocol adapted from Grzybowski et al, 2019 [10.1038/s41596-019-0218-7] with minor changes from the original protocol as follows. Native ChIPs were performed using Anti-Rabbit IgG isotype (negative control, CST #66362), Anti-H3K4me3 (Abcam ab8580), and Anti-H3K9me3 (Abcam ab8898) in SUM159 All gRNA and No gRNA. Per 6 ChIP reactions, 6 x 106 cells were harvested for nuclei preparation. The M220 Focused-ultrasonicator™ (Covaris) was used to sonicate the chromatin for 3 min at 20% duty cycle, 75W, 200 cycles per burst before proceeding to MNase digestion and HAP purification as per original protocol. Fifteen µL of HAP purified chromatin was set aside as input control.
Following incubation in a C1000 Touch Thermal Cycler (Bio-Rad) at 75 °C with a hot lid ≥ 85 °C for 6 min, final clean-up was performed using 1.5x AMpure beads and purified fragment size and quality were determined using High Sensitivity dsDNA Qubit™ and Agilent Tapestation. DNA from ChIP input and pulldown were subjected to ThruPLEX® DNA-Seq (Takara  R400675) library preparation as per manufacturer’s instructions.

value: No targeting gRNA (aka Empty Vector Control; EVC)

tag: chip antibody


title: CCB1244 (pXsa-t15-r2)


title: ACL reconstruction 11, cartilage, 52 weeks

tag: breed

value: Yucatan minipig

tag: tissue


title: CCB1244 (pXsa-t15-r1)

tag: genotype


title: Corpus callosum Male 26mo 11ID

description:
Unstranded mRNA-seq
sample name:
BulkSeq_cc_11

tag: strain


title: SUM159 pLV-KRAB + empty vector control, H3K4me3, abcam Ab8580, biol rep 1


title: 10x scATAC-seq on the Drosophila third instar larvae eye disc

data_processing:
5), and the remaining parameters were used as default. The reference index was built upon the 3rd 2017 FlyBase release (D. melanogaster r6.16). CellRanger identified 7,837 high quality cells.
scATAC-seq annotated cells by Bravo et al. 2020 were used to create pseudobulks from which peaks were called with MACS2 and consensus peaks were derived using the iterative filtering approach (as previously described), resulting in 39,732 regions. In addition, we added additional Drosophila cisTarget regions that did not overlap with these peaks, resulting in a data set with 127,711 regions. cisTarget regions are defined by partitioning the entire non-coding Drosophila genome based on cross-species conservation, resulting in more than 136,000 bins with an average size of 790 bp; and we found that using this region set increases the resolution for rare cell types, in which peak calling is difficult due to low amounts of cells.
dm6
Supplementary files format and content: fragments.tsv.gz:  Tab separated file containing chromosome, start, end, cell barcode and counts for each read.
Supplementary files format and content: scATACseq_Eye_Disc_fragment_counts.tsv: tab seperated flat text file containing regions as rows, cells as columns and fragment counts in each region for each cell as values.

organism: Drosophila melanogaster

source_name: Drosophila third instar larvae eye disc

extract_protocol:
Wandering third instar larvae were collected and a total of ~30 eye-antennal discs were dissected and transferred into a tube containing 200 µL of ice-cold PBS. The sample was centrifuged at 800 g for 5 minutes, and after removing the supernatant, resuspended in 500 µl of nuclei lysis buffer (10 mM Tris-HCl (pH 7.4), 10 mM NaCl, 3mM MgCl2, 0.1% Tween-20, 0.1% Nonidet P40, 0.01% Digitonin, 1% BSA, and water) and transferred to a dounce homogenizer (Sigma-Aldrich-D8938_2mL). After incubating the sample for 5 minutes on ice, 25 strokes were applied with the loose pestle. The sample was incubated for 10 minutes on ice and after applying 25 strokes with the tight pestle, transferred to a 2 mL tube. The homogenizer and the pestle were rinsed with wash buffer (10 mM Tris-HCl (pH 7.4), 10 mM NaCl, 3mM MgCl2, 0.1% Tween-20, 1% BSA and water), and the solution was also transferred to the 2mL tube. The sample was washed once with wash buffer and resuspended on 50 µl of 1X diluted nuclei buffer (10X Genomics). The nuclei were passed through a 10 µm pluriStrainer (ImTec Diagnostics_435001050) and cell viability and nuclei concentration were assessed by the LUNA-FL Dual Fluorescence Cell Counter.
Single-cell libraries were generated using the GemCode Single-Cell instruments and the Single Cell ATAC Library & Gel Bead Kit and ChIP Kit from 10X Genomics, following the protocol provided by the manufacturer. Briefly, the eye-antennal disc nuclei were suspended in 1X diluted nuclei buffer (10X Genomics). About 8,700 nuclei were added in each reaction with a targeted nuclei recovery of 5,000 nuclei. The samples were incubated at 37°C for 1 hour with 10 µl of transposition mix (per reaction, 7 µl ATAC Buffer and 3 µl ATAC Enzyme (10X Genomics)). Following the generation of nanoliter-scale Gel bead-in-EMulsions (GEMs), GEMs were reverse transcribed in a C1000 Touch Thermal Cycler (Bio Rad) programed at 72°C for 5 min, 98°C for 30 sec, 12 cycles of 98°C for 10 sec, 59°C for 30 sec and 72°C for 1 min, and held at 15°C. After reverse transcription, single-cell droplets were broken and the single-strand cDNA was isolated and cleaned with Cleanup Mix containing DynaBeads (Thermo Fisher Scientific). cDNA was then amplified with a C1000 Touch Thermal Cycler programed at 98°C for 3 min, 12 cycles of (98°C for 15 s, 67°C for 20 s, 72°C for 1 min), 72°C for 1 min, and held at 4°C twice. Subsequently, the amplified cDNA was fragmented, end-repaired, A-tailed and index adaptor ligated, with SPRIselect Reagent Kit (Beckman Coulter) with cleanup in between steps. Post-ligation product was amplified with a C1000 Touch Thermal Cycler programed at 98°C for 45 s, 14 cycles of (98°C for 20 s, 54°C for 30 s, 72°C for 20 s), 72°C for 1 min, and hold at 4°C. The sequencing-ready library was cleaned up with SPRIselect beads.
Single-cell ATAC-seq (10X Genomics)

value: Drosophila third instar larvae eye disc

value: Hybrid of DGRP-551, DGRP-360, DGRP-907 and DGRP-913


title: ACL reconstruction 10, cartilage, 52 weeks

tag: treatment


title: ACL reconstruction 9, cartilage, 52 weeks


title: ACL reconstruction 8, cartilage, 52 weeks


title: Corpus callosum Female 12mo 10ID

description:
Unstranded mRNA-seq
sample name:
BulkSeq_cc_10

tag: Sex


title: 10x multiome (RNA) on the mouse cortex using the 'TST' protocol

data_processing:
The generated fastq files were processed with cellranger-arc (v2.0.0) count function, with include introns =True option. Reads were aligned to Mus musculus reference genome (ata-cellranger-arc-mm10-2020-A-2.0.0).
scRNA-seq data was first analyzed using VSN (0.27.0). Briefly, cells with at least 100 genes expressed and less than 1% of mitochondrial reads were kept. Doublets were removed using Scrublet, with default parameters. 50P PCs were used as input for harmony, which was used to correct batch effects due to the sample preparation protocol, and the corrected PCs were used for dimensionality reduction and leiden clustering (resolution 1). This resulted in 41 clusters, that were annotated based on marker gene expression. Cell types not belonging to the cortex (such as medium spiny neurons from the striatum) were removed, and the data set was reanalyzed using Seurat (4.0.3), using 52 PCs as input for harmony, as previously described, which were used for dimensionality reduction. This resulted in a data set with 21,969 high quality cells (based on scRNA-seq). These cell type labels were used to create pseudobulks from which peaks were called with MACS2 and consensus peaks were derived using the iterative filtering approach (as previously described), resulting in 568,403 regions. We further filtered the data set based on the scATAC-seq quality as well, keeping cells with at least 1,000 fragments, FRiP > 0.4 and TSS > 4, resulting in 19,485 cells.
mm10
Supplementary files format and content: 10x_complex_UC_atac_fragments.tsv.gz:  Tab separated file containing chromosome, start, end, cell barcode and counts for each read for the sample in which the '10x complex UC' protocol was used
Supplementary files format and content: 10x_complex_atac_fragments.tsv.gz:  Tab separated file containing chromosome, start, end, cell barcode and counts for each read for the sample in which the '10x complex' protocol was used
Supplementary files format and content: 10x_no_perm_atac_fragments.tsv.gz:  Tab separated file containing chromosome, start, end, cell barcode and counts for each read for the sample in which the 'no permeabilization' protocol was used
Supplementary files format and content: TST_NP40_004_atac_fragments.tsv.gz:  Tab separated file containing chromosome, start, end, cell barcode and counts for each read for the sample in which the 'TST NP40 004' protocol was used
Supplementary files format and content: 10x_TST_atac_fragments.tsv.gz:  Tab separated file containing chromosome, start, end, cell barcode and counts for each read for the sample in which the 'TST' protocol was used
Supplementary files format and content: scATACseq_Mouse_cortex_fragment_counts.tsv.gz: tab seperated flat text file containing regions as rows, cells as columns and fragment counts in each region for each cell as values.
Supplementary files format and content: Mouse_cortex_DGEM.tsv: tab seperated flat text file containing genes as rows, cells as columns and counts for each gene in each cell as values.

source_name: Cortex (P56)

extract_protocol:
µl of Protector RNase inhibitor (Sigma)). Nuclei concentration was assessed by the LUNA-FL Dual Fluorescence Cell Counter.
Single-nuclei libraries were generated using the 10x Chromium Single-Cell Instrument and NextGEM Single Cell Multiome ATAC + Gene Expression kit (10x Genomics) according to the manufacturer’s protocol. In brief, the single mouse brain nuclei were incubated for 60 min at 37°C with a transposase that fragments the DNA in open regions of the chromatin and adds adapter sequences to the ends of the DNA fragments. After generation of nanolitre-scale gel bead-in-emulsions (GEMs), GEMs were incubated in a C1000 Touch Thermal Cycler (Bio-Rad) under the following program: 37°C for 45 min, 25°C for 30 min and hold at 4°C. Incubation of the GEMs produced 10x barcoded DNA from the transposed DNA (for ATAC) and 10x barcoded, full-length cDNA from poly-adenylated mRNA (for GEX). Next quenching reagent (Multiome 10x kit) was used to  stop the reaction. After quenching, single-cell droplets were dissolved and the transposed DNA and full-length cDNA were isolated using Cleanup Mix containing Silane Dynabeads. To fill gaps and generate sufficient mass for library construction, the transposed DNA and cDNA were amplified via PCR: 72°C for 5 min; 98°C for 3 min; 7 cycles of 98°C for 20 s, 63°C for 30 s, 72°C for 1 min; 72°C for 1 min; and hold at 4°C. The pre-amplified product was used as input for both ATAC library construction and cDNA amplification for gene expression library construction. Illumina P7 sequence and a sample index were added to the single-strand DNA during ATAC library construction via PCR: 98°C for 45 s; 7-9 cycles of 98°C for 20 s, 67°C for 30 s, 72°C for 20 s; 72°C for 1 min; and hold at 4°C. The sequencing-ready ATAC library was cleaned up with SPRIselect beads (Beckman Coulter). Barcoded, full-length pre-amplified cDNA was further amplified via PCR: 98°C for 3 min; 6-9 cycles of 98°C for 15 s, 63°C for 20 s, 72°C for 1 min; 72°C for 1 min; and hold at 4°C. Subsequently, the amplified cDNA was fragmented, end- repaired, A-tailed and index adaptor ligated, with SPRIselect cleanup in between steps. The final gene expression library was amplified by PCR: 98°C for 45 s; 5-16 cycles of 98°C for 20 s, 54°C for 30 s, 72°C for 20 s. 72°C for 1 min; and hold at 4°C. The sequencing-ready GEX library was cleaned up with SPRIselect beads. Before sequencing, the fragment size of every library was analysed using the Bioanalyzer high-sensitivity chip. All 10x Multiome ATAC libraries were sequenced on NovaSeq6000 instruments (Illumina) with the following sequencing parameters: 50 bp read 1 – 8 bp index 1 (i7) – 16 bp index 2 (i5) - 49 bp read 2. All 10x Multiome GEX libraries were sequenced on NovaSeq6000 instruments with the following sequencing parameters: 28 bp read 1 – 10 bp index 1 (i7) – 10 bp index 2 (i5) – 75 bp read 2.
Single-cell Multiome (10X Genomics)

value: Cortex (P56)


title: 10x multiome (ATAC) on the mouse cortex using the 'TST' protocol


title: SUM159 pLV-KRAB + empty vector control, H3K9me3, abcam Ab8898, biol rep 2


title: mouse olfactory bulb, cKO, Input, rep 2

city: Houston

first: Debosmita

last: Sardar

address: 1 Baylor Plaza

institute: Baylor College of Medicine

data_processing:
Quality control was performed using fastQC (v0.11.7) and MultiQC (v1.11).
Reads were mapped to the mouse genome mm10 assembly using bowtie2
Using the HOMER software suite, bedgraph files and tag directories were made
findPeaks command in factor (for Sox2, Sox9) or histone (for H3-5HT) was used to filter ChIP peaks enriched over Input control
Annotation of enriched peaks was performed using annotatePeaks with mm10 assembly
Integrated Genome Browser compatible files were made using samtools, sort and index, deepTools bamCompare
Assembly: mm10
Supplementary files format and content: bw

extract_protocol:
Tissue was dissociated, crosslinked with 1.1% formaldehyde for 10 min, quenched and frozen. After thawing, cells were lysed, followed by nuclear lysis. Lysates were sonicated using a Diagenode Bioruptor.
ChIP-seq libraries were prepared using the TruSeq ChIP Library Preparation Kit (Illumina, IP-202-1012). 10 ng of DNA was used as starting material. Libraries ranging from 250-350 bp were extracted from agarose gel incisions and PCR amplified for 18 cycles. Libraries were purified using AMPure XP beads and quality assessed using a Standard Sensivity NGS Fragment Analysis Kit.


title: SUM159 pLV-KRAB + all 4-targeting gRNAs, H3K4me3, abcam Ab8580, biol rep 2


title: mouse olfactory bulb, cKO, ChIP-H35HT, rep 2

value: anti-H3Kme3Q5ser, EMD #ABE2580


title: Control 7, cartilage, 52 weeks

data_processing:
Fastq files for cartilage and synovium samples were piped into FastQC version 0.11.9 to create individual sample reports that were then compiled using MultiQC version 1.12. All cartilage samples were contained within a Phred score range of 31.80 to 39.36. All synovium samples were contained within a Phred score range of 25.05 to 38.84.
Using Salmon version 1.8.0, reads were quasi-mapped from untrimmed fastq files, and transcript quantification files were generated.
Differential gene expression analysis was performed in R version 4.2.1 using DESeq2 with RUVSeq adjustment on transcript quantification files produced by Salmon mapping.
Assembly: Sscrofa11.1
Supplementary files format and content: For each sample: Salmon transcript quantification file with transcript name, length, effective length, TPM, and number of reads

extract_protocol:
Cartilage specimens were homogenized in 2 ml tubes (MP Biomedical) containing 500 ml of frozen TRIzol (Life Technologies) using a sterile drill bit while tubes were submerged in liquid nitrogen. After one round of drilling, tubes received an additional 500 ml of liquid TRIzol, were flash frozen in liquid nitrogen, and again homogenized using the drill bit. Total RNA was extracted using phenol-chloroform and purified using PureLink RNA Mini Kit (Life Technologies).
Synovium specimens were immediately placed in 2 ml lysing matrix S tubes (MP Biomedicals, Santa Ana, CA) and homogenized in 1 ml TRIzol (Life Technologies, Carlsbad,CA) using a Fast Prep-24 Instrument (MP Biomedical). Samples were then flash frozen in liquid nitrogen, transferred to dry ice, and stored at -80 ̊C until RNA isolation. Total RNA was extracted using phenol-chloroform and purified using PureLink RNA Mini Kit (Life Technologies).
All cartilage and synovium RNA isolates were then library-prepped using KAPA mRNA HyperPrep with RiboErase (Roche) and subsequently pooled and sequenced together on a NovaSeq 6000 S2 Flow Cell with 100-bp paired-end reads (Biopolymers Facility, Harvard Medical School, Boston, MA).

value: Articular Cartilage

value: Control


title: SUM159 pLV-KRAB + all 4-targeting gRNAs, H3K4me3, abcam Ab8580, biol rep 1


title: CCB1243 (RoxS-t15-r1)

value: Bacterial cell


title: mouse olfactory bulb, cKO, ChIP-H35HT, rep 1


title: mouse olfactory bulb, cKO, Input, rep 1


title: 10x multiome (ATAC) on the mouse cortex using the 'TST_NP40_004' protocol


title: ACL reconstruction 7, cartilage, 52 weeks

value: ACL reconstruction


title: mouse olfactory bulb, control, ChIP-H35HT, rep 2

source_name: control

value: control


title: ACL reconstruction 6, cartilage, 52 weeks


title: mouse olfactory bulb, control, Input, rep 2


title: mouse olfactory bulb, control, ChIP-H35HT, rep 1


title: ACL reconstruction 5, cartilage, 52 weeks


title: B cells from IEI patients 1, 2, 3 and 4, ADT-derived cDNA and HTO-derived cDNA

description:
read1 file contains cell barcode and UMI; read2 file contains Antibody and hashtag Derived Tag reads
Antibody-derived oligonucleotide (ADT) and Hashtag-derived oligonucleotide (HTO)

library_source: other

data_processing:
Raw FASTQ files of the gene expression library were analysed using 10x Genomics Cell Ranger software v.6.1.1. For the quantification of antibody derived tags (ADT) and oligo hashtags, citeseq pipeline v.1.5.0 was used.
Generated count matrices were analyzed using Seurat v.4.1.0 (demultiplexing, quality control, normalization, clustering and differential gene expression)
Assembly: GRCh38
Supplementary files format and content: Cell Ranger output files (barcodes.tsv, features.tsv, matrix.mtx)

molecule: protein

source_name: Peripheral blood mononuclear cells

extract_protocol:
Frozen PBMCs were thawed, and B cell population was enriched using magnetic separation (Miltenyi 130-101-638). Samples were next labelled with oligonucleotide-tagged antibodies against CD11c, CD21, CD27 and CD85j (TotalSeq, BioLegend) and hashtagged with four different anti-human CD298/b2-microglobulin/ TotalSeq Hashtag antibodies. After labelled, cell counts were adjusted to 1,035 cells per microlitre before being loaded onto a Chromium Next GEM chip K (10X Genomics, 2000182).
Libraries' construction was performed according to Single cell 5' v2 protocol (CG000330 RevA, 10X Genomics). Briefly, B cells were resuspended in the master mix and loaded together with partitioning oil and gel beads into the chip to generate the gel bead-in-emulsion (GEM). The poly-A RNA from the cell lysate contained in every single GEM was retrotranscripted to cDNA, which contains an Ilumina R1 primer sequence, Unique Molecular Identifier (UMI) and the 10x Barcode. The pooled barcoded full-length cDNA from poly-adenylated mRNA and DNA from protein Feature barcode are amplified and separated by size selection fro generating  5' Gene expression libraries, and cell surface protein libraries, respectively. cDNA is  then cleaned up with Silane DynaBeads, amplified by PCR and the apropiated sized fragments were selected with SPRIselect reagent for subsequent library construction. During the library construction Ilumina R2 primer sequence, paired-end constructs with P5 and P7 sequences and a sample index were added. The library was quality controlled by Agilent 4150 TapeStation and quantified by RT-PCR using the KAPA library quantification kit for Illumina platforms (Roche, KK4824). Samples were sequenced on an Illumina NovaSeq with a sequencing depth of at least 50, 000 reads per cell.

value: Peripheral blood mononuclear cells

tag: cell population

value: B cells

value: IEI patients

tag: individuals

value: IEI patients 1, 2, 3 and 4

value: ADT and HTO

tag: adt

value: TotalSeq-C0154/anti CD27; TotalSeq-C0053/anti-CD11c; TotalSeq-C0181/anti-CD21; TotalSeq-C0896/anti-CD85j (ILT2)

tag: hto

value: IEI Patient 1 - Hashtag1 (TotalSeq-C0251/anti-human CD298/b2-microglobulin), IEI Patient 2 - Hashtag2 (TotalSeq-C0252/anti-human CD298/b2-microglobulin), IEI Patient 3 - Hashtag3 (TotalSeq-C0253/anti-human CD298/b2-microglobulin), IEI Patient 4 - Hashtag4 (TotalSeq-C0254/anti-human CD298/b2-microglobulin)


title: 10x multiome (ATAC) on the mouse cortex using the 'no permiabilization' protocol


title: Control 6, cartilage, 52 weeks

value: Yucatan minipig


title: 10x multiome (RNA) on the mouse cortex using the '10x complex' protocol


title: SUM159 pLV-KRAB + all 4-targeting gRNAs, H3K9me3, abcam Ab8898, biol rep 1

tag: cell line

tag: cell type

value: Triple-negative breast cancer

value: pLV-KRAB

value: All 4 gRNAs (vs ZEB1 promoter)


title: mouse olfactory bulb, control, Input, rep 1


title: ACL reconstruction 4, cartilage, 52 weeks


title: SUM159 pLV-KRAB + all 4-targeting gRNAs, H3K9me3, abcam Ab8898, biol rep 2


title: 10x multiome (ATAC) on the mouse cortex using the '10x complex' protocol

value: Cortex (P56)


title: 10x multiome (RNA) on the mouse cortex using the '10x complex UC' protocol


title: mouse olfactory bulb, odor, Input

source_name: odor treatment

value: odor treatment


title: 10x multiome (RNA) on the mouse cortex using the 'TST_NP40_004' protocol


title: ACL reconstruction 2, cartilage, 52 weeks

value: Articular Cartilage


title: mouse olfactory bulb, control, ChIP-Sox9

value: anti-Sox9, Abcam #ab5535


title: B cells from ICB patients 5, 6, 7 and 8, ADT-derived cDNA and HTO-derived cDNA

tag: disease state

value: ICB patients

value: ICB patients 5, 6, 7 and 8

tag: library type

value: ICB Patient 5 - Hashtag1 (TotalSeq-C0251/anti-human CD298/b2-microglobulin), ICB Patient 6 - Hashtag2 (TotalSeq-C0252/anti-human CD298/b2-microglobulin), ICB Patient 7 - Hashtag3 (TotalSeq-C0253/anti-human CD298/b2-microglobulin), ICB Patient 8 - Hashtag4 (TotalSeq-C0254/anti-human CD298/b2-microglobulin)


title: ACL reconstruction 3, cartilage, 52 weeks

value: ACL reconstruction


title: B cells from healthy controls 7 and 8, ADT-derived cDNA and HTO-derived cDNA

value: Peripheral blood mononuclear cells

value: B cells

value: healthy controls

value: healthy controls 7 and 8

value: healthy controls 7 - Hashtag3 (TotalSeq-C0253/anti-human CD298/b2-microglobulin), healthy controls 8 - Hashtag4 (TotalSeq-C0254/anti-human CD298/b2-microglobulin)


title: ACL reconstruction 1, cartilage, 52 weeks

value: Yucatan minipig


title: B cells from healthy controls 5 and 6, ADT-derived cDNA and HTO-derived cDNA

value: healthy controls 5 and 6

value: ADT and HTO

value: TotalSeq-C0154/anti CD27; TotalSeq-C0053/anti-CD11c; TotalSeq-C0181/anti-CD21; TotalSeq-C0896/anti-CD85j (ILT2)

value: healthy controls 5 - Hashtag1 (TotalSeq-C0251/anti-human CD298/b2-microglobulin), healthy controls 6 - Hashtag2 (TotalSeq-C0252/anti-human CD298/b2-microglobulin)


title: SUM159 pLV-KRAB + empty vector control, H3K9me3, abcam Ab8898, biol rep 1

value: Triple-negative breast cancer

tag: transduction (vector)

value: pLV-KRAB

value: No targeting gRNA (aka Empty Vector Control; EVC)


title: mouse olfactory bulb, control, Input

value: control


title: 10x multiome (RNA) on the mouse cortex using the 'no permiabilization' protocol

value: Cortex (P56)


title: B cells from healthy controls 3 and 4, ADT-derived cDNA and HTO-derived cDNA

value: healthy controls 3 and 4

value: healthy controls 3 - Hashtag3 (TotalSeq-C0253/anti-human CD298/b2-microglobulin), healthy controls 4 - Hashtag4 (TotalSeq-C0254/anti-human CD298/b2-microglobulin)


title: Control 5, cartilage, 52 weeks

value: Articular Cartilage

value: Control


title: Batch 2 5024

city: London

first: Florian

last: Klimm

address: Exhibition Rd, South Kensington

institute: Imperial College London

description: 10X Genomics

data_processing:
Alignment with STAR
Removing cells with less than 200 genes
Removing genes detected in less than 3 cells
Normalisation to 10,000 reads per cells
Log-transform and scaling
Assembly: Mus_musculus.GRCm38.102
Supplementary files format and content: h5ad

source_name: Whole embryo

growth_protocol: Breeding of the m.5024C>T and m.5019A>G heteroplasmic mouse lines and WT controls was performed according to the Animal (Scientific Procedures) Act 1986 under Home Office Project Licence P6C97520A. All experiments followed the ARRIVE guidelines and were approved by the University of Cambridge Animal Welfare Ethical Review Body (AWERB). Mice were kept in individually-ventilated cages at 20-24ºC, 45-65% humidity, with ad libitum access to food and water. Breeding females used for timed matings were aged between 8 and 12 weeks. To set up timed matings, stud males were first moved to an empty cage to acclimatise before introducing the female. Females were subsequently checked for vaginal plugs each morning, and noon on the day of a positive plug check was designated E0.5. At E8.5 following a positive vaginal plug check, pregnant females were culled by cervical dislocation, with death confirmed by exsanguination, and embryos taken for sample preparation.

extract_protocol:
E8.5 embryos were pooled and washed twice in chilled PBS before adding 100µl 1X Trypsin/EDTA and incubating at 37ºC for 10 minutes. Pools were then pipetted up and down gently 20 times using a P200 pipet to create a single-cell suspension and the trypsin was inactivated by addition of 900µl chilled L-15 medium + 2% FBS. Suspensions were then passed through a 50µm filter to remove any cell clumps/larger debris into 5ml round-bottomed polypropylene tubes and stained with viability dye. Live cells were sorted using a BD Melody flow sorter into a 1.5ml microcentrifuge tube containing L-15 medium + 2% FBS to a final volume of 47µl ready for single-cell sequencing
Library was performed according to the manufacter’s instructions (single cell 3’ v3 protocol, 10x Genomics).

value: Whole embryo


title: mouse brain, Gq-CNO, ChIP-Sox9

source_name: Gq-CNO

value: Gq-CNO

value: anti-Sox9, Abcam #ab5535


title: ACL transection alone 12, cartilage, 52 weeks

value: Yucatan minipig

value: ACL transection alone


title: Batch 2 WT

description: 10X Genomics

value: WT


title: B cells from healthy controls 1 and 2, ADT-derived cDNA and HTO-derived cDNA

value: Peripheral blood mononuclear cells

value: B cells

value: healthy controls

value: healthy controls 1 and 2

value: ADT and HTO

value: TotalSeq-C0154/anti CD27; TotalSeq-C0053/anti-CD11c; TotalSeq-C0181/anti-CD21; TotalSeq-C0896/anti-CD85j (ILT2)

value: healthy controls 1 - Hashtag1 (TotalSeq-C0251/anti-human CD298/b2-microglobulin), healthy controls 2 - Hashtag2 (TotalSeq-C0252/anti-human CD298/b2-microglobulin)


title: mouse olfactory bulb, odor, ChIP-Sox9

value: odor treatment


title: mouse brain, Gq-CNO, ChIP-Sox2

value: anti-Sox2, EMD #AB5603


title: Control 4, cartilage, 52 weeks

value: Articular Cartilage


title: B cells from ICB patients 1, 2, 3 and 4, ADT-derived cDNA and HTO-derived cDNA

value: ICB patients

value: ICB patients 1, 2, 3 and 4

value: ICB Patient 1 - Hashtag1 (TotalSeq-C0251/anti-human CD298/b2-microglobulin), ICB Patient 2 - Hashtag2 (TotalSeq-C0252/anti-human CD298/b2-microglobulin), ICB Patient 3 - Hashtag3 (TotalSeq-C0253/anti-human CD298/b2-microglobulin), ICB Patient 4 - Hashtag4 (TotalSeq-C0254/anti-human CD298/b2-microglobulin)


title: mouse brain, Gq-CNO, Input

value: Gq-CNO


title: Batch 1 5024

description: 10X Genomics

value: Whole embryo


title: B cells from IEI patients 1, 2, 3 and 4, mRNA-derived cDNA

description:
5' mRNA library: read1 file contains cell barcode and UMI; read2 file contains transcript
poly A RNA

value: IEI patients

value: IEI patients 1, 2, 3 and 4

value: m-RNA


title: ACL transection alone 11, cartilage, 52 weeks

value: Yucatan minipig

value: ACL transection alone


title: B cells from ICB patients 1, 2, 3 and 4, mRNA-derived cDNA

value: Peripheral blood mononuclear cells

value: B cells


title: mouse brain, control, ChIP-Sox9

value: control

value: anti-Sox9, Abcam #ab5535


title: ACL transection alone 10, cartilage, 52 weeks


title: mouse brain, control, ChIP-Sox2


title: ASF_ko

city: 上海

first: WENJU

last: QIAN

state: 上海

address: 徐汇区岳阳路

country: China

institute: 上海中科院

data_processing:
Illumina GA Pipeline v1.3 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence using , then mapped to mm10 whole genome using Bowtie2 v2.4.2.
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Mortazavi, 2008.
Genome_build: mm10

extract_protocol:
SRSF1 flox/flox and SRSF1 flox/flox Ins2-Cre mice pancreatic islet were collected.Then mRNA was harvested using Trizol reagent.
RNA libraries were prepared for sequencing using standard Lifetech protocol.

value: pancreatic islet

value: SRSF1 flox/flox Ins2-Cre


title: B cells from healthy controls 7 and 8, mRNA-derived cDNA

value: healthy controls

value: healthy controls 7 and 8


title: ASF_f/f

source_name: SRSF1 flox/flox mice pancreatic islet

value: SRSF1 flox/flox


title: mouse brain, control, Input


title: ACL transection alone 8, cartilage, 52 weeks

value: Articular Cartilage


title: Batch 2 5019

description: 10X Genomics


title: LocusB2_E5420_09S24

city: Berkeley

first: Sudha

last: Rajderkar

address: 1 Cyclotron Rd

institute: Lawrence Berkeley National Laboratory

description: Briefly, 2 million cells were cross-linked with 1% formaldehyde for 10min at RT and reaction was quenched using 125 mM of Glycine for 5 min at RT. Nuclei were isolated and directly applied for digestion using 4 cutter restriction enzyme MboI (NEB) at 37 °

data_processing:
base-calling using bcl2fastq
Contacts for Hi-C data were stored in the juicer Hi-C format (could be opened with Juicebox.js, Robinson et al, Cell Systems 6(2), 2018). For RNA-seq, reads were mapped to the mouse genome (mm10) using STAR align (V2.12).
Genome_build: mm10
Supplementary_files_format_and_content: Juicer hic format for Hi-C data and normalized read per million kilobases (RPKM) and expected_counts data for RNA-seq.

source_name: Embryonic Lung

extract_protocol:
For Hi-C, mouse liver samples were harvested upon euthanasia, flash frozen in liquid nitrogen and pulverized before 1% formaldehyde cross-linking for 15 mins. For RNA-seq, mouse embryonic tissues were harvested upon euthanasia and processed in a standardized manner using the Qiagen RNeasy Mini kit.
For Hi-C, thawed crosslinked tissued was dissociated with genteleMACs and processed downstream using standard protocols; chromtain was digested with Mbol.
Hi-C, RNA-seq

value: FVB

tag: Stage

value: Embryonic day 11.5


title: Control 3, cartilage, 52 weeks

value: Control


title: B cells from healthy controls 5 and 6, mRNA-derived cDNA

value: healthy controls 5 and 6


title: B cells from healthy controls 3 and 4, mRNA-derived cDNA

value: healthy controls 3 and 4

value: m-RNA


title: 10x multiome (ATAC) on the mouse cortex using the '10x complex UC' protocol

value: Cortex (P56)


title: mouse olfactory bulb tissue, Slc22a3-cKO, mCh astrocytes, rep 3

data_processing:
Quality control was performed using fastQC (v0.11.7) and MultiQC (v1.11).
Reads were mapped to the mouse genome mm10 assembly using STAR (v2.5.0a). Mapped reads were used to build count matrices using Bioconductor packages GenomicAlignments (v1.26.0) and GenomicFeatures (v1.42.2).
UCSC transcripts were downloaded from Illumina iGenomes in GTF file format.
DESeq2 (v1.30.1) was used for normalization and differential gene expression analysis.
Assembly: mm10
Supplementary files format and content: tab-delimited text files include RPM values

source_name: olfactory bulb

extract_protocol:
Total RNA was extracted using the RNeasy Micro Kit (Qiagen #74004)
cDNA synthesis and library construction with 8-bp single indices were done from 10 ng total RNA using Trio RNASeq System (NuGEN #0507-96).
A final library dilution of 1.3 pM was subjected to paired-end sequencing.

value: olfactory bulb

value: Gfap-Cre


title: mouse olfactory bulb tissue, Slc22a3-cKO, mCh astrocytes, rep 2


title: LocusB2_E5420_07S23

description: Briefly, 2 million cells were cross-linked with 1% formaldehyde for 10min at RT and reaction was quenched using 125 mM of Glycine for 5 min at RT. Nuclei were isolated and directly applied for digestion using 4 cutter restriction enzyme MboI (NEB) at 37 °C o/n. All libraries were constructed using standard illumina TruSeq LT library prep.


title: LocusB2_E5420_06S22


title: mouse olfactory bulb tissue, Slc22a3-cKO, mCh astrocytes, rep 1


title: ACL transection alone 7, cartilage, 52 weeks

value: Yucatan minipig

value: ACL transection alone


title: B cells from ICB patients 5, 6, 7 and 8, mRNA-derived cDNA

value: Peripheral blood mononuclear cells

value: B cells

value: ICB patients

value: ICB patients 5, 6, 7 and 8


title: B cells from healthy controls 1 and 2, mRNA-derived cDNA

value: healthy controls

value: healthy controls 1 and 2


title: LocusB2_E5420_05S21

value: FVB


title: mouse olfactory bulb tissue, control, mCh astrocytes, rep 3

value: Gfap-mCh


title: ACL transection alone 6, cartilage, 52 weeks

value: Articular Cartilage


title: Batch 1 WT

description: 10X Genomics

value: Whole embryo

value: WT


title: LocusB2_E5406_07S20

value: Embryonic day 11.5


title: mouse olfactory bulb tissue, control, mCh astrocytes, rep 2


title: 858_24h_3

city: Cardiff

first: Marcos

last: Quintela

state: --- Select One ---

address: 52 Maindy Rd, Hadyn Ellis Building

department: European Cancer Stem Cell Research Institute

institute: Cardiff University

data_processing:
FastQ files that contained high quality RNA sequencing reads were aligned to the 'GRCh38/hg38' genome build using STAR
Gene count tables were generated using the --quantMode GeneCounts argument in STAR
DESeq2 was used to identify significant differential expression between control and experimental samples
Assembly: hg38
Supplementary files format and content: Tab-delimited text file including per sample: Ensembl gene ID, total counts

source_name: OVCAR-3 cell line

growth_protocol: OVCAR-3 cells were grown in 12-well TC plates using RMPI 1640 medium (Gibco)

extract_protocol:
Following 4h and 24h of BET inhibition, total RNA samples were extracted using the Qiagen Rneasy mini kit (74106)
cDNA libraries were prepared at Novogene (Eukaryotic RNA-Seq, cDNA library)

treatment_protocol: OVCAR-3 cells were treated with DMSO, i-BET858 and i-BET151 (Stripped media, 1uM) for 4h and 24h prior to RNA extraction

tag: treatment length


title: 151_24h_3


title: Control 2, cartilage, 52 weeks

city: Boston

first: Martha

last: Murray

institute: Boston Children's Hospital

tag: breed

value: Control


title: mouse olfactory bulb tissue, control, mCh astrocytes, rep 1

value: olfactory bulb


title: 858_4h_3


title: DMSO_24h_3


title: LocusB2_E5406_06S19


title: LocusB2_E5406_05S18


title: ACL transection alone 9, cartilage, 52 weeks

tag: tissue


title: 151_4h_3


title: ACL transection alone 3, cartilage, 52 weeks


title: LocusB2_E5406_03S17

tag: genotype


title: mouse olfactory bulb tissue, Aldh1l1-GFP, GFP astrocytes, rep 3

value: untreated


title: mouse olfactory bulb tissue, Aldh1l1-GFP, GFP astrocytes, rep 2


title: mouse olfactory bulb tissue, Aldh1l1-GFP, GFP astrocytes, rep 1


title: ACL transection alone 2, cartilage, 52 weeks

value: Yucatan minipig


title: LocusB2_E5406_02S16

tag: strain


title: 858_24h_2

data_processing:
FastQ files that contained high quality RNA sequencing reads were aligned to the 'GRCh38/hg38' genome build using STAR
Gene count tables were generated using the --quantMode GeneCounts argument in STAR
DESeq2 was used to identify significant differential expression between control and experimental samples
Genome_build: hg38
Supplementary_files_format_and_content: Tab-delimited text file including per sample: Ensembl gene ID, total raw counts

tag: treatment


title: ACL transection alone 4, cartilage, 52 weeks

value: ACL transection alone


title: DMSO_4h_3


title: mouse olfactory bulb tissue, CNO-control, GFP astrocytes, rep 3

value: CNO-control


title: LocusB2_E5403_03S13


title: LocusB2_E5406_01S15


title: mouse olfactory bulb tissue, CNO-control, GFP astrocytes, rep 2


title: 858_24h_1


title: SUM159, wildtype, biol rep 3 (run 2)

data_processing:
RNA-seq data underwent pseudo-alignment and quantification with Salmon [10.1038/nmeth.4197] before import into R/Bioconductor using tximport [10.12688/f1000research.7563.2]
Assembly: GRCh38
Supplementary files format and content: Comma separated text files including length-scaled TPM values for each sample

growth_protocol: SUM159 cells were cultured in F12 Medium supplemented with 0.6% 1M Hepes, 5 µg/mL insulin, 1 µg/mL hydrocortisone, 1% Antibiotic-Antimycotic and 10% heat inactivated FBS; MDA-MB-231 cells were cultured in DMEM-Hi glucose-pyruvate + 10% heat inactivated FBS, 1% Antibiotic-Antimycotic.

extract_protocol:
Cells were washed twices before RNA was harvested using QIZsol Lysis reagent (QIAGEN). Approximately 1 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared by Australian Genome Research Facility, where libraries were preprared sequenced for 50bp single-end (SE) reads on the Illumina HiSeq 2500 system

treatment_protocol: Lentiviral particles were produced using HEK293T with co-transfection using third generation VSVG (Addgene plasmid #12259), GAG/POL (Addgene plasmid #12260) and pLV dCas9-KRAB +/-gRNA as previously described [doi:10.1039/c9sc01432b & 10.1016/j.omtn.2018.12.003]. Four days following transduction, 1.25 µg/mL and 0.75 µg/mL puromycin was used to select SUM159 and MDA-MB-231, respectively.

value: Triple negative breast cancer

value: NA (Wildtype)

tag: transduction (grna)

tag: sequencing run

value: run 2


title: ACL transection alone 1, cartilage, 52 weeks


title: mouse olfactory bulb tissue, CNO-control, GFP astrocytes, rep 1


title: ACL transection alone 5, cartilage, 52 weeks


title: 151_24h_2


title: LocusB2_E5403_10S14


title: Control 1, cartilage, 52 weeks


title: 151_24h_1


title: SUM159, wildtype, biol rep 2 (run 2)


title: SUM159, wildtype, biol rep 1 (run 2)


title: DMSO_24h_2


title: LocusB2_A60

source_name: Embryonic Heart

value: wildType


title: mouse olfactory bulb tissue, Gq-CNO, mCh neurons, rep 3

value: Gq-CNO


title: mouse olfactory bulb tissue, Gq-CNO, mCh neurons, rep 2


title: DMSO_24h_1


title: LocusB2_A59

value: FVB


title: MDA-MB-231 + pLV-KRAB + all 4 gRNAs, biol rep 3

value: pLV-KRAB

value: All 4 gRNAs (vs ZEB1 promoter)


title: MDA-MB-231 + pLV-KRAB + all 4 gRNAs, biol rep 2


title: 858_4h_2


title: mouse olfactory bulb tissue, Gq-CNO, mCh neurons, rep 1


title: mouse olfactory bulb tissue, Gq-Saline, mCh neurons, rep 3

value: Gq-Saline


title: MDA-MB-231 + pLV-KRAB + all 4 gRNAs, biol rep 1


title: LocusB2_A57

value: homozygous


title: LocusB2_A58

value: Embryonic day 11.5


title: 858_4h_1


title: 151_4h_2


title: mouse olfactory bulb tissue, Gq-Saline, mCh neurons, rep 2


title: LocusB2_A56


title: MDA-MB-231 + pLV-KRAB + gRNA4, biol rep 3

value: gRNA #4 (vs ZEB1 promoter)


title: 151_4h_1


title: LocusB2_A55


title: mouse hippocampus tissue, Gq-CNO, mCh neurons, rep 3

source_name: hippocampus

value: hippocampus


title: LocusB2_A54


title: DMSO_4h_2

value: Control


title: MDA-MB-231 + pLV-KRAB + gRNA4, biol rep 1


title: mouse olfactory bulb tissue, Gq-Saline, mCh neurons, rep 1

value: olfactory bulb


title: MDA-MB-231 + pLV-KRAB + gRNA4, biol rep 2


title: mouse hippocampus tissue, Gq-CNO, mCh neurons, rep 2


title: DMSO_4h_1


title: LocusB4_A44

source_name: Embryonic Gut


title: MDA-MB-231 + pLV-KRAB, biol rep 2

value: No targeting gRNA (aka Empty Vector Control; EVC)


title: LocusB4_A43


title: prostates, WT, 2r

city: Rochester

first: Hu

last: Li

address: 200 1st St SW

institute: Mayo Clinic

data_processing:
Fastq files of pair-end RNA-Seq reads were aligned with Tophat 2.0.14 to the reference genome UCSC mm10 using Bowtie2 2.2.6 with default parameters.
Reads that aligned to the mouse genome were then removed and the unaligned reads were mapped to the human genome.
Gene level counts were obtained using featureCounts 1.4.6 from the subRead package with gene models from corresponding UCSC annotation packages.
Assembly: mm10
Supplementary files format and content: raw counts as tab-delimited text files

source_name: Prostate

growth_protocol: Prostates of 2-month old mice on regular chow diet were isolated and snap frozen.

extract_protocol:
RNeasy Mini kit (#74104, Qiagen) was used to extract RNA according to manufacturer's instructions
300 ng of RNA were subjected to library preparation using TruSeq RNA Library Prep kit v2 (RS-122-2001, Illumina) according to manufacturer's instructions.

value: Prostate

value: Prostate homogenate

value: Pten +/+

tag: age

value: 2 months


title: prostates, WT, 3


title: mouse hippocampus tissue, Gq-Saline, mCh neurons, rep 3


title: MDA-MB-231 + pLV-KRAB, biol rep 1

value: Triple negative breast cancer

value: run 2


title: LocusB4_A42

value: FVB

value: wildType


title: mouse hippocampus tissue, Gq-Saline, mCh neurons, rep 2


title: prostates, WT, 1


title: MDA-MB-231, wildtype, biol rep 3

value: NA (Wildtype)


title: MDA-MB-231, wildtype, biol rep 2


title: mouse hippocampus tissue, Gq-Saline, mCh neurons rep 1

value: Gq-Saline


title: mouse cortex tissue, Gq-CNO, mCh neurons, rep 3

source_name: cortex

value: cortex

value: Gq-CNO


title: prostates, S380DD, 3

value: Pten S380D/S380D


title: LocusB4_A40

source_name: Embryonic Midbrain

value: Embryonic day 11.5


title: prostates, S380DD, 2


title: LocusB4_A39

value: homozygous


title: LocusB2_A53


title: mouse cortex tissue, Gq-CNO, mCh neurons, rep 2


title: MDA-MB-231 + pLV-KRAB, biol rep 3

value: pLV-KRAB


title: mouse cortex tissue, Gq-CNO, mCh neurons, rep 1


title: prostates, S380DD, 1


title: prostates, S380AA, 3

value: Pten S380A/S380A


title: SUM159 + pLV-KRAB + all 4 gRNAs, biol rep 2

value: All 4 gRNAs (vs ZEB1 promoter)

value: run 1


title: prostates, S380AA, 2

value: Prostate

value: Prostate homogenate


title: mouse hippocampus tissue, Gq-CNO, mCh neurons, rep 1

value: hippocampus


title: mouse cortex tissue, Gq-Saline, mCh neurons, rep 3


title: SUM159 + pLV-KRAB + all 4 gRNAs, biol rep 1

value: Triple negative breast cancer


title: LocusB4_A37

value: FVB


title: LocusB8_A36

source_name: Embryonic Neural tube

value: wildType


title: prostates, S380AA, 1

value: 2 months


title: SUM159 + pLV-KRAB + gRNA4, biol rep 3

value: gRNA #4 (vs ZEB1 promoter)


title: mouse cortex tissue, Gq-Saline, mCh neurons, rep 2

value: cortex

value: Gq-Saline


title: mouse cortex tissue, Gq-Saline, mCh neurons, rep 1


title: LocusB4_A41


title: LocusB8_A35


title: Liver

city: Shanghai

first: Lijian

last: Hui

address: yueyang road 320

department: SIBCB

institute: CEMCS, CAS

description: primary cell

data_processing:
Reads of RNA-seq samples were mapped to the mouse reference genome (mm10) using TopHat v.2.1.1
The genes expression level for each sample was calculated using Cufflinks v.2.2.1 as FPKM based on Refgene annotation from the UCSC genome browser.
We used htseq-count(ref.6) to count reads on genes. Differential expression analysis was performed using DESeq.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample.

source_name: Liver cells

growth_protocol: To induce ihep cells, 5x105 mouse tail fibroblast were seeded in dishes and overexpressed Foxa3, Gata4 and Hnf1a by lentivirus. Culture medium was replaced to blocks medium after 48hour.

extract_protocol:
RNA was extracted from iHep cells at different time points and liver with a Trizol (Invitrogen) according to the manufacturer’s instructions and quantified with a NanoDrop 2000 spectrophotometer (ThermoFisher) respectively.
Libraries were prepared with an Illumina TruSeq Stranded mRNA Library Preparation Kit

treatment_protocol: Cell were collected by cell scraper and washed by PBS once.

value: Liver cells

tag: overexpression

tag: time point


title: SUM159 + pLV-KRAB + gRNA4, biol rep 2

tag: cell line


title: iHep14d_rep2

source_name: mouse tail fibroblast overexpressed Foxa3, Gata4 and Hnf1a

tag: cell type

value: fibroblast undergoing iHep induction

value: Foxa3, Gata4 and Hnf1a


title: LocusB8_A34

value: Embryonic day 11.5


title: mouse olfactory bulb tissue, Gq-CNO, GFP astrocytes, rep 3

value: olfactory bulb

value: Gq-CNO


title: LocusB8_A33

value: homozygous


title: MDA-MB-231, wildtype, biol rep 1

value: NA (Wildtype)

value: run 2


title: SUM159 + pLV-KRAB + all 4 gRNAs, biol rep 3

value: pLV-KRAB

value: All 4 gRNAs (vs ZEB1 promoter)

value: run 1


title: LocusB4_A38

value: FVB

value: wildType


title: mouse olfactory bulb tissue, Gq-CNO, GFP astrocytes, rep 2


title: iHep14d_rep1


title: SUM159 + pLV-KRAB, biol rep 3

value: Triple negative breast cancer

value: No targeting gRNA (aka Empty Vector Control; EVC)


title: iHep6d_rep2


title: LocusB8_A32

source_name: Embryonic Forebrain


title: LocusB8_A31


title: mouse olfactory bulb tissue, Gq-Saline, GFP astrocytes, rep 3

value: Gq-Saline


title: iHep6d_rep1


title: SUM159 + pLV-KRAB, biol rep 1


title: mouse olfactory bulb tissue, Gq-Saline, GFP astrocytes, rep 2


title: SUM159, wildtype, biol rep 3


title: iHep4d_rep2


title: LocusB8_A29


title: mouse olfactory bulb tissue, Gq-Saline, GFP astrocytes, rep 1


title: SUM159, wildtype, biol rep 2


title: iHep4d_rep1


title: LocusB6_SR3_A28

source_name: Embryonic Face


title: SUM159, wildtype, biol rep 1


title: SUM159 + pLV-KRAB + gRNA4, biol rep 1

value: gRNA #4 (vs ZEB1 promoter)


title: mouse hippocampus tissue, Gq-CNO, GFP astrocytes, rep 2

value: hippocampus


title: LocusB6_SR3_A27


title: iHep2d_rep1

value: fibroblast undergoing iHep induction

value: Foxa3, Gata4 and Hnf1a


title: mouse hippocampus tissue, Gq-CNO, GFP astrocytes, rep 1


title: LocusB7_SR9_A26

value: Embryonic day 11.5


title: TTF

source_name: mouse tail fibroblast

value: fibroblast


title: mouse hippocampus tissue, Gq-Saline, GFP astrocytes, rep 3


title: LocusB7_SR9_A25


title: mouse olfactory bulb tissue, Gq-CNO, GFP astrocytes, rep 1

value: olfactory bulb

value: Gq-CNO


title: SUM159 + pLV-KRAB, biol rep 2


title: MERS-CoV KNIH002 small RNA 1

city: Seoul

first: HEE

last: CHO

address: 50 YONSEI-RO, SEODAEMUN-GU

institute: Yonsei University

description: Small RNA sequencing data

data_processing:
Reads were trimmed for adaptor sequence using Cutadapt (version 1.9.1).
Reads (≥16 nt) were aligned against MERS-CoV full genome (KT029139.1) and subgenome based on the full genome using bwa program (version 0.7.12).
Genome_build: KT029139
Supplementary_files_format_and_content: Tab-delimited text files for MERS-CoV KNIH002-derived small RNAs

source_name: Total small RNA from MERS-CoV infected Huh7 cells

growth_protocol: Huh7 cells were cultivated in Dulbecco's modified Eagle's medium supplemented with 10% fetal bovine serum, 2 mM L-glutamine, 100 U/ml of penicillin, 100 μg/ml streptomycin and 0.1 mM nonessential amino acids at 37°C in 5% CO2.

extract_protocol:
Total RNA was extracted from Huh7 cells using TRIzol according to the manufacturer's protocol.
RNA was prepared for illumina sequencing using the TrueSeq Small RNA Sample preparation kit according to manufacturer's protocol.

treatment_protocol: Huh7 cells were infected with MERS-CoV for 48 h.

value: Hepatocellular carcinoma cell line

tag: infection

value: MER-CoV KNIH002


title: Gata4_2d

data_processing:
CutAdapt v.1.16 was used to remove adaptor sequences from reads of rawdata.
Reads were mapped to the mouse reference genome (mm10) using bowtie v.1.1.1.
Peaks were called using macs v.1.3.7.1.
Quantile normalized to remove the bias across the samples by using haystack_bio v.0.5.5.
Genome_build: mm10
Supplementary_files_format_and_content: bigwig files were generated for visulization data in igv.

growth_protocol: To induce ihep cells, 5x10^5 mouse tail fibroblast were seeded in dishes and overexpressed Foxa3, Gata4 and Hnf1a by lentivirus. Culture medium was replaced to blocks medium after 48hour.

extract_protocol:
Sonicate the chromatin in nuclear extracts to fragments by ultrasonication (Covaris S220). Primary antibodies were used for immunoprecipitation in sonication supernatant by incubation at 4℃ overnight. Protein G Dynabeads (Life Technologies, 10004D) were used for pulling down antibody-chromatin complex followed by washing and eluting. Foxa3:5 micrograms for ChIP, from Santa Cruz, cat id sc-5361. Gata4:5 micrograms for ChIP, from Santa Cruz, cat id sc-1237. Hnf1a:5 micrograms for ChIP, from Santa Cruz, cat id sc-6547. CTCF:5 micrograms for ChIP, from Active Motif, cat id 61312. H3K27ac:5 micrograms for ChIP, from Abcam, cat id ab4729. H3K27me3:5 micrograms for ChIP, from CST, cat id 9733.
MinElute PCR purification kit (Qiagen) was used for ChIP fragments collection. NEBNext Ultra DNA Library Prep Kit was used for ChIP-seq library preparation.

tag: chip antibody


title: MERS-CoV KNIH002 small RNA 2

description: Small RNA sequencing data


title: scRNA-seq Control bone marrow Biol. Rep. 2

city: La Jolla

first: Isaac

middle: F.

last: López-Moyado

address: 9420 Athena Cir

department: Division of Signaling and Gene Expression

institute: La Jolla Institute for Immunology

description: 10x Genomics

data_processing:
Sample demultiplexing, barcode processing, alignment, filtering, UMI counting and aggregation of sequencing runs were performed using the Cell Ranger analysis pipeline (v.3.0.0).
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Bone marrow

extract_protocol: Tet1/2/3 f/f Cre-ERT2 Rosa26-LSL-YFP (or control Tet1/2/3 f/f Rosa26-LSL-YFP) mice were treated with tamoxifen for 5 consecutive days. Four weeks after final administration, bone marrow cells were prepared, counted and loaded onto the Chromium Controller (10X Genomics) for a target recovery of 10,000 single cells. Samples were processed per the manufacturer’s protocol and sequencig was conducted using a 75-bp kit with paired-end reads.

treatment_protocol: To delete floxed alleles using the Cre-ERT2 recombinase, tamoxifen (Sigma) was solubilized at 10 mg ml−1 in corn oil (Sigma) and delivered into mice by intraperitoneal injection of 2 mg tamoxifen per mouse every day for 5 consecutive days. The day of the last tamoxifen injection was designated Day 0.

value: Bone marrow

value: Tamoxifen intraperitoneal injection


title: LocusB8_A30

value: FVB


title: Foxa3_14d


title: mouse hippocampus tissue, Gq-Saline, GFP astrocytes, rep 2


title: mouse hippocampus tissue, Gq-Saline, GFP astrocytes, rep 1


title: LocusB5_SR13_A24

value: wildType


title: Foxa3_6d


title: scRNA-seq Control bone marrow Biol. Rep. 1

description: 10x Genomics


title: scRNA-seq Tet iTKO bone marrow Biol. Rep. 2

description: 10x Genomics

value: Tet1/2/3 f/f CreERT2


title: iHep2d_rep2


title: LocusB5_SR13_A22

value: homozygous


title: scRNA-seq Tet iTKO bone marrow Biol. Rep. 1

description: 10x Genomics


title: LocusB5_SR13_A21


title: mouse cortex tissue, Gq-CNO, GFP astrocytes, rep 2

value: cortex


title: LocusB5_SR13_A20