title: J32


title: J21

status: Public on Oct 02 2021

type: SRA

city: Zurich

first: Csaba

last: Földy

state: Zurich

address: Winterthurerstrasse 190

department: Brain Research Institute

country: Switzerland

institute: University of Zurich

description:
processed data file:
gene_counts.tsv
normalized_gene_counts.tsv

library_source: transcriptomic

data_processing:
Illumina RTA v1.12 was used for base calling, and Illumina bc12fastq v2.20 for demultiplexing and fastq file generation
Sequenced reads were pre-processed using Trimmomatic and Flexbar. Reads were aligned to GRCm38 genome using STAR aligner with parameters trimLeft=10, minTailQuality=15, minAverageQuality=20, and minReadLength=30.
Aligned reads were converted to gene counts using featureCounts. Outputs for different cells were merged into a single file using custom Python code
Ensembl names were converted to gene names using Ensembl's Mus_musculus.GRC38.86.gtf file (gene_counts.tsv)
Reads were normalized using scran, and normalized values are stored in normalized_gene_counts.tsv
Genome_build: GRCm38
Supplementary_files_format_and_content: tab delimited text files. gene_counts.tsv contains raw counts, with genes labeled by their gene names. normalized_gene_counts.tsv contains normalized (scran) counts of cells that passed quality control

molecule: total RNA

organism: Mus musculus

source_name: DG

extract_protocol:
single cell cytosol extraction via patch pipette
Nextera XT

tag: cell type

value: Dentate gyrus granule cell

tag: genotype/variation

value: DG

tag: quality control

value: Passed


title: J78

description:
processed data file:
gene_counts.tsv

value: Failed


title: J30

description:
processed data file:
gene_counts.tsv


title: J1_61


title: J11

description:
processed data file:
gene_counts.tsv


title: J10

description:
processed data file:
gene_counts.tsv


title: J84L

description:
processed data file:
gene_counts.tsv


title: J1


title: J48


title: 56


title: 61


title: 62


title: 60


title: 53


title: 54


title: IDS160

description:
processed data file:
gene_counts.tsv


title: 55

description:
processed data file:
gene_counts.tsv


title: 52


title: IDS157

description:
processed data file:
gene_counts.tsv


title: IDS148


title: IDS151


title: IDS155


title: IDS149

description:
processed data file:
gene_counts.tsv


title: IDS150

description:
processed data file:
gene_counts.tsv


title: IDS154


title: IDS156

description:
processed data file:
gene_counts.tsv


title: IDS147


title: IDS152


title: IDS153


title: IDS144


title: IDS146


title: IDS141


title: IDS140


title: IDS138

description:
processed data file:
gene_counts.tsv


title: IDS136


title: IDS159

description:
processed data file:
gene_counts.tsv


title: IDS139


title: IDS137


title: IDS135

description:
processed data file:
gene_counts.tsv


title: IDS142


title: IDS145


title: IDS143


title: IDS133


title: IDS130


title: IDS131


title: IDS132


title: IDS158


title: IDS128


title: IDS129


title: IDS123


title: IDS126

description:
processed data file:
gene_counts.tsv


title: IDS124


title: IDS122


title: IDS127


title: IDS121

description:
processed data file:
gene_counts.tsv


title: IDS125

description:
processed data file:
gene_counts.tsv


title: IDS120


title: IDS119


title: IDS114


title: IDS116


title: IDS113

description:
processed data file:
gene_counts.tsv


title: IDS117


title: IDS111


title: IDS118


title: IDS107


title: IDS106


title: IDS110


title: IDS105


title: IDS108


title: IDS112

description:
processed data file:
gene_counts.tsv


title: IDS101


title: IDSS90

description:
processed data file:
gene_counts.tsv


title: IDS102

description:
processed data file:
gene_counts.tsv


title: IDS115


title: IDS103

description:
processed data file:
gene_counts.tsv


title: IDSS79


title: IDSS72


title: IDSS67


title: IDSS40


title: IDSS43


title: IDSS57

description:
processed data file:
gene_counts.tsv


title: IDSS45

description:
processed data file:
gene_counts.tsv


title: IDSS62


title: IDSS25

description:
processed data file:
gene_counts.tsv


title: IDSS31


title: IDS95


title: IDS94


title: IDS93


title: IDS109


title: IDS92


title: IDS91


title: IDSS1


title: IDS87


title: IDS89


title: IDS88


title: IDS84


title: IDS83


title: IDS85


title: IDS82


title: IDS86


title: IDS80


title: IDS78


title: IDS81


title: IDS79


title: IDS104


title: IDS76


title: IDS74


title: IDS90

description:
processed data file:
gene_counts.tsv


title: IDS68


title: IDS67


title: IDS71


title: IDS70


title: IDS73


title: IDS64

description:
processed data file:
gene_counts.tsv


title: IDS65


title: IDS62


title: IDS57

description:
processed data file:
gene_counts.tsv


title: IDS59


title: IDS63


title: IDS56


title: IDS61


title: IDS51


title: IDS50


title: IDS75


title: IDS58


title: IDS69


title: IDS55

description:
processed data file:
gene_counts.tsv


title: IDS77


title: IDS54


title: IDS66


title: IDS53


title: IDS44


title: IDS52


title: IDS45

description:
processed data file:
gene_counts.tsv


title: IDS72


title: IDS38


title: IDS37


title: IDS49


title: IDS32


title: IDS48


title: IDS31


title: IDS46

description:
processed data file:
gene_counts.tsv


title: IDS35


title: IDS41


title: IDS60


title: IDS42


title: IDS47


title: IDS40


title: IDS24


title: IDS28


title: IDS39


title: IDS36


title: IDS34


title: IDS43


title: IDS22


title: IDS33


title: IDS18

description:
processed data file:
gene_counts.tsv


title: IDS29


title: IDS30


title: IDS27


title: IDS26


title: IDS15


title: IDS25

description:
processed data file:
gene_counts.tsv


title: IDS23


title: IDS12


title: IDS11


title: IDS10


title: IDS21


title: IDS8


title: IDS9


title: IDS5


title: IDS19


title: IDS20


title: IDS1


title: IDS17


title: 6VP_LNASPT6ctr_rep2 QHR4C-seq

city: Shanghai

first: Yuxiao

last: Zhou

address: Dongchuan Road NO.800

country: China

institute: Shanghai Jiaotong University

library_source: genomic

data_processing:
Library strategy: 4C-seq
Sequenced reads were trimmed for adaptor sequence, then aligned to the reference human genome (GRCh37/hg19) using the Bowtie program (version 1). Hisat and cufflinks softwares were used to handle data.
Genome_build: hg19, mm9
Supplementary_files_format_and_content: txt; bedgraph file; .hic file

molecule: genomic DNA

organism: Homo sapiens

source_name: HEC-1-B cells

growth_protocol: Human endometrial HEC-1-B cells (ATCC) were cultured in MEM medium (Hyclone), supplemented with 10% (v/v) FBS (Gibco), 2 mM glutamine (Gibco), 1 mM sodium pyruvate (Sigma), and 1× penicillin-streptomycin (Gibco).

extract_protocol:
QHR-4C used DNA to explore DNA interaction.
Libraries were prepared for sequencing using standard protocols.

tag: cell line

value: human endometrial adenocarcinoma

tag: Stage

value: tumor stage

tag: genotype

value: wild-type

tag: condition

value: control for SPT6 knockdown


title: 6VP_LNASPT6_rep2 QHR4C-seq

value: SPT6 knockdown


title: IDS16


title: IDS14


title: IDS13


title: 51VP_LNASPT6_rep2 QHR4C-seq


title: IDS6


title: IDS2


title: IDS3


title: IDS4


title: 6VP_LNASPT6_rep1 QHR4C-seq


title: 6VP_LNAeRNA_rep1 QHR4C-seq

value: eRNA knockdown


title: 6VP_LNAeRNA_rep2 QHR4C-seq


title: 6VP_LNASPT6ctr_rep1 QHR4C-seq


title: 6VP_LNAeRNActr_rep2 QHR4C-seq

value: control for eRNA knockdown


title: 12VP_LNAeRNA_rep2 QHR4C-seq


title: 12VP_LNAeRNActr_rep1 QHR4C-seq


title: 12VP_LNAeRNA_rep1 QHR4C-seq


title: 12VP_LNASPT6_rep2 QHR4C-seq


title: 6VP_LNAeRNActr_rep1 QHR4C-seq


title: 12VP_LNASPT6_rep1 QHR4C-seq


title: 51VP_LNAeRNActr_rep1 QHR4C-seq


title: 12VP_LNASPT6ctr_rep1 QHR4C-seq


title: 12VP_LNASPT6ctr_rep2 QHR4C-seq


title: 51VP_LNASPT6ctr_rep2 QHR4C-seq


title: 51VP_LNASPT6ctr_rep1 QHR4C-seq


title: 51VP_LNASPT6_rep1 QHR4C-seq


title: 51VP_LNAeRNA_rep1 QHR4C-seq


title: 51VP_LNAeRNA_rep2 QHR4C-seq


title: 12VP_OERNH_rep2 QHR4C-seq

value: RNase H1 overexpression


title: 51VP_LNAeRNActr_rep2 QHR4C-seq


title: 6VP_OERNH_rep1 QHR4C-seq


title: 12VP_OERNHctr_rep1 QHR4C-seq

value: control for RNase H1 overexpression


title: 51VP_OERNH_rep2 QHR4C-seq


title: 51VP_OERNHctr_rep2 QHR4C-seq


title: 6VP_on3g_rep2 QHR4C-seq

value: eRNA transcription activation CRISPRa


title: 6VP_onNC_rep2 QHR4C-seq

value: control for CRISPRa


title: 6VP_OERNHctr_rep2 QHR4C-seq


title: 6VP_OERNHctr_rep1 QHR4C-seq


title: 12VP_OERNH_rep1 QHR4C-seq


title: 6VP_OERNH_rep2 QHR4C-seq


title: 51VP_OERNHctr_rep1 QHR4C-seq


title: 12VP_LNAeRNActr_rep2 QHR4C-seq


title: 51VP_OERNH_rep1 QHR4C-seq


title: 51VP_onNC_rep1 QHR4C-seq


title: 6VP_OEdel_rep2 QHR4C-seq

value: del eRNA TSS

value: eRNA overexpression rescue eRNA TSS


title: 6VP_OEdel_rep1 QHR4C-seq


title: 12VP_OERNHctr_rep2 QHR4C-seq


title: 6VP_onNC_rep1 QHR4C-seq


title: 12VP_on3g_rep2 QHR4C-seq


title: 12VP_onNC_rep2 QHR4C-seq


title: 51VP_on3g_rep2 QHR4C-seq


title: 6VP_OENC_rep2 QHR4C-seq

value: control for eRNA overexpression


title: 51VP_on3g_rep1 QHR4C-seq


title: 12VP_OEdelctr_rep2 QHR4C-seq

value: control for eRNA overexpression rescue eRNA TSS


title: 12VP_OEdel_rep2 QHR4C-seq


title: 51VP_onNC_rep2 QHR4C-seq


title: 6VP_OEdelctr_rep2 QHR4C-seq


title: 12VP_OEdelctr_rep1 QHR4C-seq


title: 12VP_OENC_rep1 QHR4C-seq


title: 12VP_onNC_rep1 QHR4C-seq


title: 6VP_OEdelctr_rep1 QHR4C-seq


title: 12VP_OENC_rep2 QHR4C-seq


title: 6VP_OEeRNA_rep2 QHR4C-seq

value: eRNA overexpression


title: 6VP_OENC_rep1 QHR4C-seq


title: 6VP_on3g_rep1 QHR4C-seq


title: 6VP_OEeRNA_rep1 QHR4C-seq


title: 51VP_OEeRNA_rep1 QHR4C-seq


title: 12VP_on3g_rep1 QHR4C-seq


title: 51VP_OENC_rep2 QHR4C-seq


title: 12VP_OEeRNA_rep2 QHR4C-seq


title: 12VP_OEdel_rep1 QHR4C-seq


title: 51VP_OEdelctr_rep2 QHR4C-seq


title: HEC-1-B_rep4 total RNA-seq

data_processing:
Sequenced reads were trimmed for adaptor sequence, then aligned to the reference human genome (GRCh37/hg19) using the Bowtie program (version 1). Hisat and cufflinks softwares were used to handle data.
Genome_build: hg19, mm9
Supplementary_files_format_and_content: txt; bedgraph file; .hic file

extract_protocol:
Total RNA-seq used 1 ug total RNA to construct sequencing libraries.
Libraries were prepared for sequencing using standard protocols.


title: HEC-1-B_rep3 total RNA-seq


title: HEC-1-B_rep1 total RNA-seq


title: HEC-1-B_rep2 total RNA-seq


title: 12VP_OEeRNA_rep1 QHR4C-seq


title: H3K27ac_sg6_rep1 ChIP-seq

extract_protocol: Libraries were prepared for sequencing using standard protocols.

value: CRISPRi of elongation 1959 bp


title: H3K27ac_knc_rep2 ChIP-seq

value: human endometrial adenocarcinoma

value: control for CRISPRi of elongation


title: DRIP_LNA2eRNA_rep1 DRIP-seq

data_processing:
Library strategy: DRIP-seq
Sequenced reads were trimmed for adaptor sequence, then aligned to the reference human genome (GRCh37/hg19) using the Bowtie program (version 1). Hisat and cufflinks softwares were used to handle data.
Genome_build: hg19, mm9
Supplementary_files_format_and_content: txt; bedgraph file; .hic file

value: tumor stage

value: wild-type


title: DRIP_LNA2eRNA_rep3 DRIP-seq


title: DRIP_LNAeRNA1_rep3 DRIP-seq


title: 51VP_OEdel_rep2 QHR4C-seq


title: DRIP_LNAeRNA1_rep2 DRIP-seq


title: 51VP_OEeRNA_rep2 QHR4C-seq


title: 51VP_OEdelctr_rep1 QHR4C-seq


title: 51VP_OENC_rep1 QHR4C-seq


title: 51VP_OEdel_rep1 QHR4C-seq


title: H3K27ac_sg6_rep2 ChIP-seq


title: DRIP_LNA2eRNA_rep2 DRIP-seq


title: H3K27ac_sg5_rep2 ChIP-seq

value: CRISPRi of elongation 1158 bp


title: human_MeDIP_rep2 MeDIP-seq

extract_protocol:
MeDIP-seq: Genomic DNA was harvested and 1 ug of genomic DNA was used for the 5mC antibody immunoprecipitation.
Libraries were prepared for sequencing using standard protocols.


title: H3K27ac_sg5_rep1 ChIP-seq


title: human_MeDIP_rep1 MeDIP-seq


title: DRIP_WT_rep2 DRIP-seq


title: OEdelctr_rep3 RNA-seq

extract_protocol:
RNA was harvested using Trizol reagent. 1 ug of total RNA was used for the construction of sequencing libraries.
Libraries were prepared for sequencing using standard protocols.


title: DRIP_LNAeRNA1_rep1 DRIP-seq

value: eRNA knockdown


title: DRIP_WT_rep3 DRIP-seq

value: control for eRNA knockdown


title: OEdel_rep1 RNA-seq


title: OEdelctr_rep2 RNA-seq


title: OEeRNA_rep3 RNA-seq


title: OEeRNA_rep1 RNA-seq


title: OENC_rep3 RNA-seq


title: 6VP_K3g_1_rep1 QHR4C-seq

value: inhibit eRNA transcription initiation


title: 6VP_2E8_rep2 QHR4C-seq

value: deletion TSS by CRISPR


title: OENC_rep1 RNA-seq


title: DRIP_WT_rep1 DRIP-seq


title: 6VP_14G1_rep2 QHR4C-seq

value: insert pAS

value: interfere with transcription termination


title: 6VP_KNC_rep1 QHR4C-seq

value: control for CRISPRi


title: 6VP_A2__rep2 QHR4C-seq

value: control for deletion TSS by CRISPR


title: kii_rep3 RNA-seq

data_processing:
Sequenced reads were trimmed for adaptor sequence sequence, then aligned to the reference human genome (GRCh37/hg19) using the Bowtie program (version 1).Hisat and cuffilinks softwares were used to handle data.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample

growth_protocol: Human endometrial HEC-1-B cells (ATCC) were cultured in MEM medium (Hyclone), supplemented with 10% (v/v) FBS (Gibco), 2 mM glutamine (Gibco), 1 mM sodium pyruvate (Sigma), and 1× penicillin-streptomycin (Gibco). Human K562 cells (ATCC) were cultured in DMEM medium (Hyclone) supplemented with 10% (v/v) FBS and 1× penicillin-streptomycin. Cells were maintained at 37 °C in a humidified incubator containing 5% (v/v) of CO2, and were passaged every three days.

extract_protocol:
RNA was harvested using Trizol reagent. 1 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard protocols

tag: tissue

value: CRISPRi of initiation


title: 6VP_A2__rep1 QHR4C-seq


title: 6VP_K3g_2_rep2 QHR4C-seq


title: 6VP_14G1_rep1 QHR4C-seq


title: OEdel_rep2 RNA-seq

value: del eRNA TSS

value: eRNA overexpression rescue eRNA TSS


title: kii_rep2 RNA-seq


title: 6VP_K44_2_rep2 QHR4C-seq

value: inhibit eRNA transcription elongation


title: 6VP_2E8_rep1 QHR4C-seq

value: human endometrial adenocarcinoma


title: OEeRNA_rep2 RNA-seq

value: eRNA overexpression


title: 6VP_K44_1_rep1 QHR4C-seq

value: tumor stage


title: 6VP_KNC_rep2 QHR4C-seq

value: wild-type


title: OEdelctr_rep1 RNA-seq

value: control for eRNA overexpression rescue eRNA TSS


title: knc_rep2 RNA-seq

value: control for CRISPRi of initiation


title: knc_rep3 RNA-seq


title: knc_rep1 RNA-seq


title: sg6_rep3 RNA-seq

value: CRISPRi of elogation 1959 bp


title: OENC_rep2 RNA-seq

value: control for eRNA overexpression


title: sg6_rep2 RNA-seq


title: sg6_rep1 RNA-seq


title: sg5_rep3 RNA-seq

value: CRISPRi of elogation 1158 bp


title: KNC3_ RNA-seq

value: control for CRISPRi of elogation


title: RNHOE_rep2 RNA-seq

value: RNase H1 overexpression


title: RNHOE_rep1 RNA-seq


title: KNC2 _RNA-seq


title: RNHWT_rep2 RNA-seq

value: control for RNase H1 overexpression


title: RNHWT_rep1 RNA-seq


title: KNC1_ RNA-seq


title: kii_rep1 RNA-seq


title: LNAeRNA1_rep2 RNA-seq

value: eRNA knockdown


title: LNAeRNA2_rep1 RNA-seq


title: LNAeRNA1_rep3 RNA-seq


title: LNAeRNA2_rep3 RNA-seq


title: LNAeRNA2_rep2 RNA-seq


title: WTLNARNA_rep2 RNA-seq

value: control for eRNA knockdown


title: WTLNARNA_rep1 RNA-seq


title: 122E8_2_4C_rep2

description: del TSS

data_processing:
Library strategy: 4C-seq
Sequenced reads were trimmed for adaptor sequence and the bait sequence, then aligned to the reference human genome (GRCh37/hg19) using the Bowtie program (version 1). The reads per million (RPM) value was calculated using the r3Cseq program (version 1.20) in the R package (version 3.3.3).
Genome_build: hg19
Supplementary_files_format_and_content: bedgraph

extract_protocol:
After cross-linking with 2% formaldehyde, cells were lysed twice with cold lysis buffer, digested with DpnII, ligated with T4 DNA ligase.
4C libraries were generated by PCR.

tag: restriction enzyme

value: DpnII

value: del TSS


title: 1214G1_2_4C_rep2

description: insert Pas

value: insert Pas


title: LNAeRNA1_rep1 RNA-seq

value: human endometrial adenocarcinoma


title: 122E8_1_4C_rep1

description: del TSS


title: 12A2_1_4C_rep1

description: WT

value: WT


title: WTLNARNA_rep3 RNA-seq

value: tumor stage


title: sg5_rep2 RNA-seq

value: wild-type


title: 12K3g_2_4C_rep2


title: 12A2_2_4C_rep2

description: WT


title: 12K44_1_4C_rep1


title: sg5_rep1 RNA-seq


title: 12K44_2_4C_rep2


title: 12K3g_1_4C_rep1


title: 12KNC1_4C_rep1

description: WT


title: 512E8_1_4C_rep1

description: del TSS


title: 51A2_2_4C_rep2

description: WT


title: 12KNC2_4C_rep2

description: WT


title: 512E8_2_4C_rep2

description: del TSS


title: 51K44_2_4C_rep2


title: 51A2_1_4C_rep1

description: WT


title: 5114G1_1_4C_rep1

description: insert Pas


title: 51K3g_2_4C_rep2


title: CHIRPseq_odd_rep2

data_processing:
Library strategy: ChIRP-seq
Sequenced reads were trimmed for adaptor sequence sequence, then aligned to the reference human genome (GRCh37/hg19) using the Bowtie program (version 1).samtools and macs softwares were used to handle data.
Genome_build: hg19
Supplementary_files_format_and_content: bedgraph

source_name: human endometrial adenocarcinoma

extract_protocol:
ChIRP-seq:used eRNA 5'-biotin probes to bind eRNA transcripts-DNA-proteins complex and used streptavidin magnetic beads to capture complex,then purified the DNA for high-throughput sequencing.
ChIRP-seq: DNA libraries were prepared for sequencing using standard protocols
RNA-Seq:RNA was harvested using Trizol reagent. 1 ug of total RNA was used for the construction of sequencing libraries.ChIRP-seq:used eRNA 5'-biotin probes to bind eRNA transcripts-DNA-proteins complex and used streptavidin magnetic beads to capture complex,then purified the DNA for high-throughput sequencing.
RNA-Seq:RNA libraries were prepared for sequencing using standard protocols.ChIRP-seq: DNA libraries were prepared for sequencing using standard protocols

value: HEC-1-B cells

value: wild type


title: 51K3g_1_4C_rep1


title: 51K44_1_4C_rep1


title: 5114G1_2_4C_rep2

description: insert Pas


title: CHIRPseq_even_rep2


title: CHIRPseq_odd_rep1


title: 51KNC1_4C_rep1

description: WT


title: CHIRPseq_INPUT


title: CHIRPseq_NEAT1


title: RAD21_A2_rep2_ChIP-seq

description: lentivirus stable cell line

data_processing:
Sequenced reads were trimmed for adaptor sequence sequence, then aligned to the reference human genome (GRCh37/hg19) using the Bowtie program (version 1).samtools and macs softwares were used to handle data.
Genome_build: hg19
Supplementary_files_format_and_content: bedgraph

extract_protocol:
Lysates were clarified from sonicated nuclei and protein-DNA complexes were isolated with antibody.
DNA libraries were prepared for sequencing using standard protocols


title: 1214G1_1_4C_rep1

description: insert Pas


title: H3K27ac_knc_rep1 ChIP-seq

value: control for CRISPRi of elongation


title: RAD21_14G1_rep2_ChIP-seq

description: lentivirus stable cell line

value: eRNA polyadenylation sequence insertion


title: RAD21_14G1_rep1_ChIP-seq

description: lentivirus stable cell line


title: CTCF_14G1_rep1_ChIP-seq

description: lentivirus stable cell line


title: CTCF_14G1_rep2_ChIP-seq

description: lentivirus stable cell line


title: RAD21_A2_rep1_ChIP-seq

description: lentivirus stable cell line


title: CHIRPseq_even_rep1


title: 51KNC2_4C_rep2

description: WT


title: CTCF_A2_rep2_ChIP-seq

description: lentivirus stable cell line


title: CTCF_A2_rep1_ChIP-seq

description: lentivirus stable cell line


title: RAD21_on_NC_rep2_ChIP-seq

description: lentivirus stable cell line


title: CTCF_2E8_rep2_ChIP-seq

description: lentivirus stable cell line

value: eRNA TSS deletion


title: CTCF_2E8_rep1_ChIP-seq

description: lentivirus stable cell line


title: CTCF_on_NC_rep2_ChIP-seq

description: lentivirus stable cell line


title: CTCF_on_NC_rep1_ChIP-seq

description: lentivirus stable cell line


title: Pol2_on_NC_rep1_ChIP-seq

description: lentivirus stable cell line


title: H3K4me3_on_NC_rep1_ChIP-seq

description: lentivirus stable cell line


title: H3K27ac_on_NC_rep2_ChIP-seq

description: lentivirus stable cell line


title: H3K4me3_on_NC_rep2_ChIP-seq

description: lentivirus stable cell line


title: HEC-1-B_RAD21_K3g_rep2_ChIP-seq

description: lentivirus infection stable cell line

value: inhibit eRNA transcription initiation


title: Pol2_on_NC_rep2_ChIP-seq

description: lentivirus stable cell line


title: HEC-1-B_RAD21_K3g_rep1_ChIP-seq

description: lentivirus infection stable cell line


title: HEC-1-B_RAD21_K44_rep2_ChIP-seq

description: lentivirus infection stable cell line

value: inhibit eRNA transcription elongation


title: H3K27ac_on_NC_rep1_ChIP-seq

description: lentivirus stable cell line


title: HEC-1-B_RAD21_K44_rep1_ChIP-seq

description: lentivirus infection stable cell line


title: HEC-1-B_RAD21_KNC_rep1_ChIP-seq

description: lentivirus infection stable cell line

value: wide-type


title: HEC-1-B_CTCF_K3g_rep2_ChIP-seq

description: lentivirus infection stable cell line


title: HEC-1-B_RAD21_KNC_rep2_ChIP-seq

description: lentivirus infection stable cell line


title: HEC-1-B_CTCF_K44_rep1_ChIP-seq

description: lentivirus infection stable cell line


title: HEC-1-B_CTCF_KNC_rep2_ChIP-seq

description: lentivirus infection stable cell line


title: HEC-1-B_CTCF_K44_rep2_ChIP-seq

description: lentivirus infection stable cell line


title: HEC-1-B_CTCF_K3g_rep1_ChIP-seq

description: lentivirus infection stable cell line


title: HEC-1-B_H3K4me3_K3g_rep2_ChIP-seq

description: lentivirus infection stable cell line


title: HEC-1-B_CTCF_KNC_rep1_ChIP-seq

description: lentivirus infection stable cell line


title: HEC-1-B_H3K4me3_K44_rep2_ChIP-seq

description: lentivirus infection stable cell line


title: HEC-1-B_H3K4me3_K3g_rep1_ChIP-seq

description: lentivirus infection stable cell line


title: RAD21_on_NC_rep1_ChIP-seq

description: lentivirus stable cell line


title: HEC-1-B_H3K4me3_KNC_rep1_ChIP-seq

description: lentivirus infection stable cell line


title: HEC-1-B_Pol2_K3g_rep2_ChIP-seq

description: lentivirus infection stable cell line


title: HEC-1-B_H3K4me3_K44_rep1_ChIP-seq

description: lentivirus infection stable cell line


title: HEC-1-B_H3K4me3_KNC_rep2_ChIP-seq

description: lentivirus infection stable cell line


title: HEC-1-B_Pol2_K44_rep2_ChIP-seq

description: lentivirus infection stable cell line


title: HEC-1-B_Pol2_K3g_rep1_ChIP-seq

description: lentivirus infection stable cell line


title: HEC-1-B_Pol2_K44_rep1_ChIP-seq

description: lentivirus infection stable cell line


title: HEC-1-B_Pol2_KNC_rep1_ChIP-seq

description: lentivirus infection stable cell line


title: HEC-1-B_Pol2_KNC_rep2_ChIP-seq

description: lentivirus infection stable cell line


title: HEC-1-B_H3K27ac_K44_rep2_ChIP-seq

description: lentivirus infection stable cell line


title: HEC-1-B_H3K27ac_K44_rep1_ChIP-seq

description: lentivirus infection stable cell line


title: HEC-1-B_H3K27ac_K3g_rep1_ChIP-seq

description: lentivirus infection stable cell line


title: HEC-1-B_H3K27ac_K3g_rep2_ChIP-seq

description: lentivirus infection stable cell line


title: Pol2_14G1_rep2_ChIP-seq

description: CRISPR editing single-clone cell line

value: polyadenylation sequence insertion

tag: antibody


title: HEC-1-B_H3K27ac_KNC_rep1_ChIP-seq

description: lentivirus infection stable cell line


title: Pol2_2E8_rep2_ChIP-seq

description: CRISPR editing single-clone cell line


title: Pol2_14G1_rep1_ChIP-seq

description: CRISPR editing single-clone cell line


title: Pol2_A2_rep2_ChIP-seq

description: CRISPR editing single-clone cell line


title: Pol2_2E8_rep1_ChIP-seq

description: CRISPR editing single-clone cell line


title: H3K27ac_14G1_rep1_ChIP-seq

description: CRISPR editing single-clone cell line


title: Pol2_A2_rep1_ChIP-seq

description: CRISPR editing single-clone cell line


title: H3K27ac_14G1_rep2_ChIP-seq

description: CRISPR editing single-clone cell line


title: H3K27ac_2E8_rep2_ChIP-seq

description: CRISPR editing single-clone cell line


title: H3K27ac_A2_rep2_ChIP-seq

description: CRISPR editing single-clone cell line


title: H3K27ac_2E8_rep1_ChIP-seq

description: CRISPR editing single-clone cell line


title: H3K27ac_A2_rep1_ChIP-seq

description: CRISPR editing single-clone cell line


title: H3K4me3_14G1_rep2_ChIP-seq

description: CRISPR editing single-clone cell line


title: H3K4me3_2E8_rep2_ChIP-seq

description: CRISPR editing single-clone cell line


title: H3K4me3_14G1_rep1_ChIP-seq

description: CRISPR editing single-clone cell line


title: HEC-1-B_14G1_rep3 RNA-seq

tag: cell line background

value: CRISPR edittiing sinle-clone cell line


title: H3K4me3_2E8_rep1_ChIP-seq

description: CRISPR editing single-clone cell line


title: H3K4me3_A2_rep1_ChIP-seq

description: CRISPR editing single-clone cell line


title: HEC-1-B_14G1_rep2 RNA-seq


title: HEC-1-B_H3K27ac_KNC_rep2_ChIP-seq

description: lentivirus infection stable cell line


title: HEC-1-B_A2_rep5 RNA-seq


title: HEC-1-B_5E6 _rep1 RNA-seq

source_name: HEC-1-B_5E6 _RNA-seq


title: HEC-1-B_5E6 _rep2 RNA-seq


title: HEC-1-B_2E8 _rep1 RNA-seq

source_name: HEC-1-B_2E8 _RNA-seq


title: HEC-1-B_A2_rep3 RNA-seq


title: HEC-1-B_2E8 _rep2 RNA-seq


title: HEC-1-B_on_3g_rep3 RNA-seq

value: lentivirus infection stable cell line

value: eRNA transcription activation


title: healthy human airway epithelial cells, technical replicate 5 [17_3w]

city: Iowa City

first: Alejandro

middle: A.

last: Pezzulo

state: Iowa

address: 6316 Pappajohn Biomedical Discovery Building

department: Department of Internal Medicine

country: USA

institute: Universty of Iowa

data_processing:
Raw fastq files were aligned to human genome assembly GRCh38. Filtering, barcode counting, and UMI counting were performed with 10x CellRanger software. The five technical replicates were merged using CellRanger to create the processed file filtered_gene_bc_matrices_h5.h5.
Genome_build: GRCh38
Supplementary_files_format_and_content: HDF5 format file containing counts for each gene (row) and cell barcode (column)

molecule: polyA RNA

source_name: lung

extract_protocol:
Cultured cells were rinsed in PBS -/- and lifted in TrypLE for 45 min at 37C. Cells were centrifuged for 5 min at 200xrcf, supernatent was removed, and cells were resuspended in Phenol red-free DMEM:F12 with 0.04% non-acetylated BSA and counted.
10x Genomics Chromium Single Cell 3’ Reagent Kits v2 system

value: lung

value: healthy human airway epithelial cells


title: HEC-1-B_on_3g_rep2 RNA-seq

value: human endometrial adenocarcinoma


title: HEC-1-B_on_3g_rep1 RNA-seq


title: HEC-1-B_on_NC_rep2 RNA-seq


title: H3K4me3_A2_rep2_ChIP-seq

description: CRISPR editing single-clone cell line

value: tumor stage


title: healthy human airway epithelial cells, technical replicate 4 [17_7d]


title: HEC-1-B_on_NC_rep1 RNA-seq


title: HEC-1-B_K44_rep3 RNA-seq

description: lentivirus infection stable cell line


title: HEC-1-B_on_NC_rep3 RNA-seq


title: healthy human airway epithelial cells, technical replicate 2 [17_b]


title: healthy human airway epithelial cells, technical replicate 1 [13_b]


title: HEC-1-B_K44_rep1 RNA-seq

description: lentivirus infection stable cell line


title: HEC-1-B_14G1_rep1 RNA-seq


title: HEC-1-B_KNC_rep3 RNA-seq

description: lentivirus infection stable cell line

value: wild-type


title: HEC-1-B_A2_rep4 RNA-seq

value: HEC-1-B cells


title: HEC-1-B_KNC_rep2 RNA-seq

description: lentivirus infection stable cell line


title: HEC-1-B_K44_rep2 RNA-seq

description: lentivirus infection stable cell line


title: MOLM13_sgMEF2D_e5.1_rep2

city: Birmingham

first: Rui

last: Lu

state: AL

address: 1824 6th Ave S

institute: Univ of Alabama at Birmingham

data_processing:
The paired-end reads were mapped to the human genome (hg19) using STAR (v2.5.1b) with default parameters.
The read counts for genes with average FPKM > 1 in either control or knockout samples were used for DESeq2 (v3.11) to define differentially expressed genes (DEGs).
Genome_build: hg19
Supplementary_files_format_and_content: txt, raw read counts

source_name: acute myeloid leukemia

growth_protocol: Cells were cultured in RPMI with 10% FBS and penicillin/streptomycin.

extract_protocol:
Total RNA was isolated using TRI Reagent and Direct-zol RNA Miniprep Kits (Zymo Research, R2053).
RNA-seq libraries were generated using the NEBNext Ultra RNA Library Prep Kit for Illumina (New England Biolabs), following the manufacturer’s protocol. The quality and concertation of the libraries were examined by Bioanalyzer High Sensitivity DNA Chip (Agilent). The multiplexed RNA-Seq libraries were paired-end sequenced for 150 bp on the Illumina HiSeq 4000 platform.

treatment_protocol: Cells were lentivirally infected with indicated sgRNA for gene knockout

value: Cas9-expressing MOLM-13

tag: treatment

value: sgMEF2D e5.1 infection

tag: replicate

value: replicate 2


title: MOLM13_sgMEF2D_e2.1_rep2

value: sgMEF2D e2.1 infection


title: HEC-1-B_KNC_rep1 RNA-seq

description: lentivirus infection stable cell line


title: MOLM13_sgLuc_rep2

value: sgLuc infection


title: MOLM13_sgLuc_rep1

value: replicate 1


title: MV411_MEF2D_ChIP

data_processing:
All sequencing reads were mapped to the human genome (hg19) using the Bowtie2 (v2.2.3) and reads with a mapping score > 20 were selected for data analysis, after duplicated reads removed by SAMtools (v1.9).
MACS2 were used to ChIP-seq peaks using default parameters in paired-end mode.
Genome_build: hg19
Supplementary_files_format_and_content: txt, ChIP-seq MACS2 narrowpeak file

extract_protocol:
In brief, 20 million MOLM-13 or MV4-11 cells were cross-linked with formaldehyde (1%) for 10 minutes followed by quenching with 0.125 M glycine for 5 minutes at room temperature. After washing with cold PBS, cells were suspended in lysis buffer (50 mM HEPES pH 7.5, 150 mM NaCl, 1 mM EDTA, 0.5 mM EGTA, 1% TritonX-100, 0.1% SDS, 0.1% N-lauroylsarcosine, and protease inhibitor) and subjected to sonication to shear the chromatin DNA into sizes ranging from 200 to 500 bp. The fragmented chromatin was pre-cleared by centrifugation at 14,000 rpm for 15 min at 4°C. The supernatant was incubated with primary antibody and Protein A or G Dynabeads magnetic beads (Invitrogen) at 4°C overnight. After four times wash with high-salt buffer (20 mM Tris-HCl pH 8.0, 2 mM EDTA, 0.1% SDS, 500 mM NaCl, and 1% TritonX-100) and twice wash with TE buffer (10 mM Tris-HCl pH 8.0, 1 mM EDTA), chromatin was eluted from beads in elution buffer (50 mM Tris-HCl pH 8.0, 10 mM EDTA, 1% SDS). After reverse crosslinking, ChIP DNA was purifiied using DNA purification columns (Zymo Research) and subjected to downstream quantitative real-time PCR analysis (ChIP-qPCR) or library preparation for deep sequencing (ChIP-seq).
ChIP-seq library was prepared using NEBNext Library Prep Kit following the instructions and subjected to paired-end, 150-cycle sequencing on the Illumina HiSeq 4000 platform.

tag: chip antibody

value: MEF2D (Proteintech, 14353-1-AP)


title: healthy human airway epithelial cells, technical replicate 3 [17_2d]


title: ninaE G69D/+ repeat 2

city: New York

first: Hyung Don

last: Ryoo

state: NY

address: 550 First Avenue, MSB 497

department: Cell Biology

institute: NYU School of Medicine

data_processing:
We used the bcl2fastq2 Conversion software (v2.20) to convert per-cycle BCL base call files outputted by the sequencing instrument (RTA v3.4.4) into the fastq format in order to generate per-read per-sample fastq files.
For subsequent data processing steps, we used the Seq-N-Slide automated workflow developed by Igor Dolgalev (https://github.com/igordot/sns).
For read mapping, we used the alignment program STAR (v2.6.1d) to map reads of each sample to the Drosophila melanogaster reference genome dm6, and for quality control we used the application Fastq Screen (v0.13.0) to check for contaminating sequences.
We employed featureCounts (Subread package v1.6.3) to generate matrices of read counts for annotated genomic features.
For differential gene statistical comparisons between groups of samples contrasted by genotype, we used the DESeq2 package (R v3.6.1) in the R statistical programming environment.
Supplementary_files_format_and_content: Differential gene expression shown as xlsx file

organism: Drosophila melanogaster

source_name: R1-R6 photoreceptor

extract_protocol:
In brief, approximately 500 adult fly heads (from flies within 5 days of eclosion) per genotype were lysed in ice-cold nuclear isolation buffer (10 mM HEPES-KOH, pH 7.5; 2.5 mM MgCl2; 10 mM KCl) with a dounce homogenizer. The homogenate was filtered through a 40µm Flowmi cell strainer (WVR, cat. #BAH136800040), and the filtrate was incubated with anti-EGFP-coupled protein G Dynabeads (Invitrogen, cat. #10003D) for 1 hour at 4ºC. The beads were collected using a magnetic microcentrifuge tube holder (Sigma, cat. #Z740155). Following washes with wash buffer (PBS, pH 7.4; 2.5mM MgCl2), the beads were resuspended in a final volume of 150µL of wash buffer. Because the isolated nuclei remain intact until this stage, the ratio of the mRNAs within those nuclei should not be affected by any change in the levels of the Gal4 drivers. Then the post-isolation nuclei were suspended in 1mL of Trizol reagent (Life Technologies, cat. #15596018) for RNA extraction following standard procedures. Prior to RNA precipitation with isopropanol, 0.3M sodium acetate and glycogen were added to facilitate visualization of the RNA pellet. We then suspended the pellet in RNAse-free water and purified it using a Qiagen RNeasy MinElute cleanup kit (Qiagen, cat. #74204) following standard protocols.
For cDNA library preparation and ribodepletion, we utilized a custom Drosophila Nugen Ovation Trio low-input library preparation kit (Tecan Genomics), using approximately 20 ng total RNA per sample.

value: R1-R6 photoreceptor

value: ninaE G69D/+


title: ninaE G69D/+ repeat 3


title: MOLM13_MEF2D_ChIP


title: ninaE G69D/+ repeat 1


title: MOLM13_sgMEF2D_ATAC_rep2

data_processing:
All sequencing reads were mapped to the human genome (hg19) using the Bowtie2 (v2.2.3) and reads with a mapping score > 20 were selected for data analysis, after duplicated reads removed by SAMtools (v1.9).
MACS2 were used to ATAC-seq peaks using default parameters in paired-end mode.
Peaks from control and MEF2D knockout samples were merged and then used for counting reads in each sample to determine chromatin regions with differential accessibility using DESeq2.
Genome_build: hg19
Supplementary_files_format_and_content: txt, ATAC-seq peak files with the following columns: chromosome, start, stop, peak width in each replicate (bp), location, gene name

extract_protocol:
50,000 cells were used for each transposition reaction.
ATAC-seq was carried out utilizing the Epicentre Tn5 transposome and Illuminia kit according to standard manufacturer’s manuals.


title: MOLM13_sgMEF2D_e5.1_rep1


title: MOLM13_sgMEF2D_e2.1_rep1


title: MOLM13_sgLuc_ATAC_rep2


title: MOLM13_Input


title: MOLM13_sgLuc_ATAC_rep1


title: ninaE wild type repeat 3

value: ninaE wild type


title: MDBK Cas12/MER41.IL2RB-/- KO3 IFNG 4h rep1

city: Boulder

first: Edward

last: Chuong

state: CO

address: 3415 Colorado Ave, JSC Biotech Bldg

department: BioFrontiers/MCDB

institute: University of Colorado Boulder

data_processing:
Real-Time Analysis v3.4.4 was used for basecalling.
Adapters and low quality reads were trimmed using BBDuk v38.05 with arguments 'ktrim=f k=23 mink=11 hdist=1 maq=10 qtrim=r trimq=10 tpe tbo literal=AAAAAAAAAAAAAAAAAAAAAAA' and mapped to bosTau9 using hisat2 v2.1.0 with options '--rna-strandness RF --no-softclip'. Aligned fragments with an alignment score less than 10 were removed with samtools v1.10. Alignment files corresponding to technical replicates (designated as "s1", "s2", etc.) were merged, and all samples were mapped to genes in the complete refseq annotation using featureCounts v1.6.2 with options '-s 2 -t exon -g gene_id -0 -p'. For visualization aligned fragments were converted to stranded, CPM normalized bigwigs using deepTools bamCoverage v3.0.1.
Differentially expressed genes were called using DESeq2 v1.26.0 with designs '~ treatment` (wildtype) or '~ genotype + treatment + genotype:treatment' (MER41.IFNAR2-/- or MER41.IL2RB-/-). For the mutant differential expression analysis, normalized count data is derived from DESeq2 comparisons between KO IFNG vs WT IFNG. Genes with zero counts across all samples were removed.
Genome_build: bosTau9 (ARS-UCD1.2)
Supplementary_files_format_and_content: Tab-delimited text files with raw fragment counts for each gene
Supplementary_files_format_and_content: CPM normalized signal tracks in UCSC bigwig format
Supplementary_files_format_and_content: Tab-delimited text files including DESeq2 normalized counts

organism: Bos taurus

source_name: MDBK

growth_protocol: MDBK cells were routinely grown at 37C in 5% CO2 and O2 on coated plastic (VWR #10861-680, typically 1,000,000-2,000,000 cells in 10cm dishes) in MEM (Gibco #11095080) supplemented with 1X nonessential amino acids (Gibco #11140050), 1X penicillin-streptomycin (Gibco #15140122), and 10% fetal bovine serum (Gibco #10437010). BL3.1 cells were routinely grown at 37C in 5% CO2 and O2 on uncoated plastic (Greiner Bio-One #82050-856, typically 500,000-1,000,000 cells/mL in T75 flasks) in RPMI 1640 (Gibco #61770036) supplemented with 1X penicillin-streptomycin and 10% fetal bovine serum. Monocytes and leukocytes were derived from PBMC samples from two male “line 999” and are composed of the following breed makeup: 1/2 Angus, 1/4 Gelbvieh, 3/16 Charolais, 1/16 Hereford. Briefly, 15 mL of blood was combined with 15 mL 1X PBS (Gibco #14190144) and 15 mL Histopaque-1077 (Sigma-Aldrich #10771) and centrifuged for 45 minutes at 1,000 x g at room temperature. The monocyte layer was retained, washed in 50 mL of cold 1X PBS, and lysed in 1 mL Red Blood Cell Lysis Buffer (Roche #11814389001) for 5 minutes at 37°C and 5% CO2. The PBMCs were washed three times with 50 mL, 10 mL, and 10 mL cold 1X PBS, respectively, and resuspended in 45 mL of FBS-free RPMI 1640. Monocytes were isolated as described in (Chitko-McKown et al. 2003). Briefly, PBMCs were added to treated T75 flasks and incubated at 37°C and 5% CO2 overnight, and the non-adherent, predominantly leukocyte fraction was removed by washing with PBS. The remaining adherent population represents the monocyte fraction. Leukocytes were derived from the non-adherent fraction. Animals were housed at the U.S. Meat Animal Research Center (USMARC) feedlot in accordance with USDA animal care guidelines.

extract_protocol:
RNA from MDBK and BL3.1 was harvested using Zymo Quick-RNA Miniprep Plus Kit (Zymo #R1057). Monocyte and leukocyte lysates were prepared using Trizol (Invitrogen #11596026) reagent, and RNA was extracted using Zymo Direct-zol RNA Miniprep Plus kit (R2071). All lysates were frozen at -80°C prior to extraction, and all extracted RNA were stored at -80°C as single-use aliquots.
Libraries were generated with 200ng or 500ng RNA using KAPA mRNA HyperPrep Kit (KAPA #KK8581) according to the manufacturer's instructions. Briefly, single-indexed adapters (KAPA #KK8700) or unique dual-indexed adapters (KAPA #KK8727) were added to each sample at a final concentration of 78 nM. Excess adapter was removed using sequential 0.63X and 0.70X KAPA Pure Bead (KAPA #KK8002) cleanups. Purified, adapter-ligated samples were amplified for 10 (500ng input RNA) or 12 (200ng input RNA) cycles according to the manufacturer's instructions and purified using a 1.0X KAPA Pure Bead cleanup.

treatment_protocol: Cells were either untreated or stimulated with 100 ng/mL bovine IFNG (Kingfisher #RP0013B-005) for 2h or 4h. Monocyte and leukocyte samples were stimulated as PBMC samples, after which Trizol lysates were prepared from the adherent (monocyte) and non-adherent (lymphocyte) fractions.

tag: breed

value: not applicable

tag: age

tag: Sex

value: MDBK

value: enot applicablesCas12a/MER41.IL2RB-/-

value: IFNG

tag: timepoint


title: A2_rep2 RNA-seq

data_processing:
Sequenced reads were trimmed for adaptor sequence sequence, then aligned to the reference human genome (GRCh37/hg19) using the Bowtie program (version 1).Hisat and cuffilinks softwares were used to handle data.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample ...

value: human endometrial adenocarcinoma

value: tumor stage

value: wild type


title: MDBK Cas12/MER41.IL2RB-/- KO3 BSA rep1

tag: cell type

value: untreated


title: MOLM13_sgMEF2D_ATAC_rep1

value: Cas9-expressing MOLM-13


title: ninaE wild type repeat 1


title: ninaE wild type repeat 2


title: HEK293A-LATS1/2-DKO_Cd_REP3

city: IRVINE

first: Han

last: Han

state: CA

address: 3302A, Natural Sciences I

department: Developmental and Cell Biology

institute: University of California, Irvine

data_processing:
RTA 2.7.7 (RTA= real time analysis) software was used for basecalling.
Sequenced reads are aligned to hg38 genome using STAR with paramter
Genome_build: GRCh38.p13 (GCA_000001405.28), ensembl
Supplementary_files_format_and_content: text files with raw gene counts for every gene for each sample
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: HEK293A cell line

extract_protocol:
RNA was extracted using TriZol (cat#15596026)
Illumina TruSeq mRNA stranded

tag: aget

value: Cd


title: HEK293A-LATS1/2-DKO_Cd_REP2

tag: cell line


title: MDBK Cas12/MER41.IFNAR2-/- KO3 IFNG 4h rep2


title: A2_rep1 RNA-seq

value: HEC-1-B cells

tag: Stage


title: MDBK Cas12/MER41.IL2RB-/- KO1 BSA rep1

tag: genotype


title: MDBK Cas12/MER41.IL2RB-/- KO2 IFNG 4h rep1


title: HEK293A-LATS1/2-DKO_Zn_REP3

value: Zn


title: HEK293A-LATS1/2-DKO_Zn_REP1


title: MV411_Input


title: MDBK Cas12/MER41.IL2RB-/- KO2 BSA rep1


title: HEK293A-LATS1/2-DKO_Zn_REP2


title: HEK293A-LATS1/2-DKO_H2O_REP3


title: MDBK Cas12/MER41.IFNAR2-/- KO3 IFNG 4h rep1


title: MDBK Cas12/MER41.IFNAR2-/- KO3 BSA rep2


title: HEK293A-LATS1/2-DKO_H2O_REP2


title: HEK293A-LATS1/2-DKO_Cd_REP1


title: HEK293A_Cd_REP3

value: wildtype


title: MDBK Cas12/MER41.IFNAR2-/- KO3 BSA rep1


title: HEK293A-LATS1/2-DKO_H2O_REP1


title: MDBK Cas12/MER41.IFNAR2-/- KO2 IFNG 4h rep2


title: MDBK Cas12/MER41.IL2RB-/- KO1 IFNG 4h rep1


title: HEK293A_Cd_REP2


title: HEK293A_Cd_REP1


title: HEK293A_Zn_REP3


title: HEK293A_Zn_REP2


title: MDBK Cas12/MER41.IFNAR2-/- KO2 BSA rep2


title: MDBK Cas12/MER41.IFNAR2-/- KO2 IFNG 4h rep1


title: MDBK Cas12/MER41.IFNAR2-/- KO2 BSA rep1


title: MDBK Cas12/MER41.IFNAR2-/- KO1 IFNG 4h rep1


title: HEK293A_H2O_REP3


title: MDBK Cas12/MER41.IFNAR2-/- KO1 BSA rep1


title: HEK293A_H2O_REP2


title: MDBK Cas12/MER41.IFNAR2-/- KO1 BSA rep2


title: HEK293A_H2O_REP1


title: MDBK Cas12 IFNG 4h rep1

value: enot applicablesCas12a


title: MDBK Cas12 IFNG 4h rep2


title: S161

city: Aurora

first: Ellen

middle: L

last: Burnham

address: 13001 East 17th Place

department: Division of Pulmonary Sciences and Critical Care Medicine

institute: University of Colorado Anschutz Medical Campus

data_processing:
Default Illumina software was used for base-calling and generating .fastq files.
Using skewer v0.2.2, we removed Illumina universal library adaptors, trimmed the end of the read until bases had Phred Q-Score ≥ 10, and removed reads with length ≤31bp after trimming.
We used kallisto6 v0.46.0 for pseudo-alignment, with reference to the Ensembl v79 Homo sapiens genome assembly (pre-indexed by the kallisto developers).
Kallisto output was imported into R and summarized into gene-level counts using tximport v1.4.0.
17,602 genes with non-zero counts in at least 2/3rd of Batch 1 samples as well as 2/3rd of Batch 2 samples forward to subsequent analyses. Final count table for input into edgeR differential analysis is provided as supplementary file "count_table.txt".
Genome_build: Homo sapiens GRCh37 (Ensembl v79)

extract_protocol:
Bronchoscopy with bronchoalveolar lavage (BAL) was performed under conscious sedation (Bailey, et al., 2018; Fini, et al., 2017; Gaydos, et al., 2016). Briefly, the bronchoscope was wedged into a subsegment of either the right middle lobe or lingula, followed by instillation of 50-mL aliquots of sterile, room temperature 0.9% saline. Each 50-mL aliquot (up to four total) was immediately hand aspirated back into the syringe, then transferred to sterile 50-mL conical tubes, whereupon they were transported to the laboratory. The first aliquot of BAL was not used in these experiments. Second and subsequent BAL aliquots were combined, then centrifuged to separate cellular and acellular components. Cell counts were performed, and ≥ 95% BAL cell viability was determined for all subjects via trypan blue exclusion. Differentials were assessed after Diff-Quik staining by a single blinded observer. A proportion of BAL cells were snap frozen for RNA applications, while the remainder were used in ex vivo cell culture experiments.
RNA library creation and sequencing were performed at the Anschutz Medical Campus Genomics and Microarray Core in two batches: Batch 1 (TruSeq Stranded mRNA Library Prep Kit and Illumina HiSeq4000; Illumina Inc., San Diego, CA) and Batch 2 (Illumina TruSeq Stranded Total RNA kit, HiSeq2500) using manufacturer directions. Note that batch is provided as a variable in the sample metadata.

tag: group

value: T

value: Female

tag: bmi

tag: obese

value: no


title: leukocyte WT IFNG 2h rep3

description: cryptorchid male

source_name: Leukocyte

value: Type 999 (1/2 Angus, 1/4 Gelvieh, 3/16 Charolais, 1/16 Hereford)

value: 11 months

value: Male

value: Leukocyte


title: MDBK Cas12 ctrl BSA rep1

value: not applicable

value: MDBK


title: MDBK Cas12 ctrl BSA rep2


title: S145

value: yes


title: S150


title: leukocyte WT IFNG 2h rep2

description: cryptorchid male

value: IFNG


title: S128


title: S132


title: S142


title: leukocyte WT IFNG 2h rep1

description: cryptorchid male


title: leukocyte WT UT rep3

description: cryptorchid male

value: untreated


title: leukocyte WT UT rep2

description: cryptorchid male


title: S125


title: MDBK Cas12/MER41.IFNAR2-/- KO1 IFNG 4h rep2


title: HEK293A_Zn_REP1


title: S122


title: leukocyte WT UT rep1

description: cryptorchid male


title: S124


title: S120


title: monocyte WT IFNG 2h rep1

source_name: Monocyte

value: 8.5 months

value: Monocyte


title: monocyte WT IFNG 2h rep2


title: N148

value: C


title: N147


title: monocyte WT UT rep2

value: wildtype


title: N149


title: N145


title: BL3.1 WT IFNG 4h rep3


title: N143


title: N144


title: BL3.1 WT IFNG 4h rep2


title: BL3.1 WT IFNG 4h rep1


title: BL3.1 WT UT rep3


title: BL3.1 WT UT rep2


title: N125


title: N123


title: MJ125

value: M


title: MJ116


title: MJ117


title: MDBK WT IFNG 4h rep3


title: BL3.1 WT UT rep1


title: MDBK WT IFNG 4h rep1


title: MDBK WT IFNG 4h rep2


title: MJ112


title: MJ115


title: MDBK WT UT rep2


title: monocyte WT UT rep1


title: MJ109


title: MDBK WT UT rep3


title: MDBK IFNG 2h pSTAT1 rep2

data_processing:
Library strategy: CUT&RUN
Real-Time Analysis v3.4.4 was used for basecalling.
Adapters and low quality reads were trimmed using BBDuk v38.05 using options ‘ktrim=r k=34 mink=11 hdist=1 tpe tbo qtrim=r trimq=10’. Trimmed reads were aligned to the bosTau9 assembly using BWA-MEM v0.7.15, and only uniquely mapping reads with a minimum MAPQ of 10 were retained. Fragments aligning to the mitochondrial genome were removed, and alignments corresponding to technical replicates (designated as "s1", "s2") were merged. Peak calling was performed using complete and size subsetted alignment files with MACS2 v2.1.1 in a two-step process where separate sets of peaks were called with 1) single-end options ‘--format BAM --shift=-75 --extsize=150’ and 2) paired-end option ‘--format BAMPE’. For both modes only peaks with a p-value < 0.01 were retained, and all libraries were normalized against respective IgG control libraries. Independently, peaks were called from IgG control libraries using MACS2 v2.1.1 with paired-end option ‘--format BAMPE’ for visualizing background signal enrichment. Bigwig files were prepared from the MACS2 normalized bedgraph files using bedGraphToBigWig v4.
All merged peaks for a particular pulldown (across all replicates, untreated and IFNG-stimulated) were concatenated and merged, and aligned fragments were counted for each peak using bedtools v2.28.0. Differentially enriched peaks were called using DESeq2 v1.26.0 with design '~ treatment'. Genes with zero counts across all samples were removed.
Genome_build: bosTau9 (ARS-UCD1.2)
Supplementary_files_format_and_content: Normalized signal tracks corresponding to read coverage per 1 million fragments in UCSC bigwig format
Supplementary_files_format_and_content: Tab-delimited text files including unfiltered narrowPeaks called by MACS2 in UCSC BED format
Supplementary_files_format_and_content: Tab-delimited text files including DESeq2 normalized counts

growth_protocol: MDBK cells were routinely grown at 37C in 5% CO2 and O2 on coated plastic (VWR #10861-680, typically 1-2x10^6 cells in 10cm dishes) in MEM (Gibco #11095080) supplemented with 1X nonessential amino acids (Gibco #11140050), 1X penicillin-streptomycin (Gibco #15140122), and 10% fetal bovine serum (Gibco #10437010).

extract_protocol:
CUT&RUN pulldowns were generated using a protocol from Meers et al. 2019 (PMID: 31232687, https://dx.doi.org/10.17504/protocols.io.zcpf2vn). All buffers were prepared according to the “High Ca2+/Low Salt” section of the protocol using 0.04% digitonin. 500,000 viable cells were used for each pulldown. The following antibodies were used: rabbit anti-mouse IgG (1:100, Abcam #ab46540), rabbit anti-H3K27ac (1:100, Millipore #MABE647), rabbit anti-pRPB1-Ser5 (1:50, Cell Signalling #13523S), rabbit anti-STAT1 (1:100, Cohesion Biosciences #3322), rabbit anti-pSTAT1-Ser727 (1:100, Active Motif #39634). pA-MNase (gift from Steve Henikoff) was added to each sample following primary antibody incubation at a final concentration of 700 ng/mL. Chromatin digestion, release, and extraction was carried out according to Meers et al. 2019 (PMID: 31232687, https://dx.doi.org/10.17504/protocols.io.zcpf2vn). Pulldown success was determined by Qubit dsDNA High Sensitivity (Life Technologies #Q32851) and TapeStation 4200 HSD5000 (Agilent #50675588) before proceeding with library preparation.
Libraries were generated using a modified protocol for use with the KAPA HyperPrep Kit (Roche #KK8502). Briefly, the full volume of each pulldown (~30 uL) was diluted to 50 uL in nuclease-free water, and libraries were generated following the manufacturer’s protocol with the following modifications. Freshly diluted 0.200 uM single-index adapters were added to each library at a low concentration (9 nM) to minimize adapter dimer formation. Adapter-ligated libraries were treated with 0.2% SDS and 0.4 mg/mL Proteinase K for 1 h at 37°C and underwent a double-sided 0.8X/1.0X cleanup using KAPA Pure Beads (Roche #07983280001). Purified, adapter-ligated libraries were amplified using the following PCR cycling conditions: 45 s at 98°C, 15x(15 s at 98°C, 10 s at 60°C), 60 s at 72°C. Amplified libraries underwent a double-sided 0.8X/1.0X cleanup. The final libraries were quantified using Qubit dsDNA High Sensitivity and TapeStation 4200 HSD5000. Libraries were pooled and sequenced on an Illumina NovaSeq 6000 (University of Colorado Genomics Core) as 150bp paired-end reads.

treatment_protocol: Cells were either untreated or stimulated with 100 ng/mL bovine IFNG (Kingfisher #RP0013B-005) for 2h.

tag: antibody

value: Rabbit anti-pSTAT1-Ser727 (Active Motif #39634)


title: MDBK WT UT rep1


title: fzy-1;oma-1ts-gfp_input_repeat 2

city: Wuhan

first: Donglei

last: Zhang

address: 13 Hangkong Rd

department: Biochemistry and Molecular Biology

institute: Huazhong University of Science and Technology

data_processing:
CASAVA version 1.4 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence,then mapped to Caenorhabditis_elegans.wormbase.v1.0 whole genome using HISAT2 v2.0.5 with parameters -rna-strandness RF--dta-t-p 4
Fragments per Kilobase per Million Mapped Fragments(FPKM)were calculated using a protocol from Trapnell,C. et al, Nat Biotechnol,2010,then using HTSeq v0.6.0 with parameters -I gene_id-f bam -s reverse -a 10 -q to compare the number of Reads on each gene, and then the expression level of each gene was estimated.
Genome_build: Caenorhabditis_elegans.wormbase.v1.0
Supplementary_files_format_and_content: Matrix table with raw gene FPKM for every gene and related sample

organism: Caenorhabditis elegans

growth_protocol: Synchronized L1 animals were cultured at 25°C until they grew into early young adults, which were then collected and washed with M9 buffer (22 mM KH2PO4, 42 mM Na2HPO4, and 86 mM NaCl) several times. 100,000 adult worms were collected and frozen in liquid nitrogen.

extract_protocol:
Total RNA was extracted using the standard method with TRIzol reagent (Invitrogen).
RNA library was generated for high throughput sequencing using the VAHTS Universal V8 RNA-seq Library Prep Kit for Illumina (Vazyme #NR605-01).


title: fzy-1;oma-1ts-gfp_RIP_repeat 2


title: fzy-1;oma-1ts-gfp_RIP_repeat 1


title: MJ108


title: N142


title: fzy-1;oma-1ts-gfp_input_repeat 1


title: MJ107


title: oma-1ts-gfp_RIP_repeat 2


title: N122


title: MDBK UT pSTAT1 rep1


title: MDBK UT pSTAT1 rep2


title: MJ103


title: ATI_inj_4

city: Seoul

first: Yongsik

last: Cho

address: 1 Gwanak-ro, Gwanak-gu, Seoul 08826. School of Biological Sciences, SNU

country: South Korea

institute: Seoul National Universiy

data_processing:
Libraries were validated using the Agilent 2100 Bioanalyzer. RNA-seq was performed using the Illumina HiSeq 2500 sequencer at Macrogen, Inc. The reads were trimmed with Trimmomatic (v0.39) and aligned to the mouse reference genome (mm10) using STAR aligner (v2.7.6a). Gene counts were subsequently estimated using StringTie (v1.3.5). Differential expression analysis was conducted by using the edgeR R package (v3.12). Genes with transcripts per million (TPM) of >1 are plotted.
Genome_build: mm9
Supplementary_files_format_and_content: Matrix table with normalized counts for every gene and every sample

source_name: Mouse Achilles tendon

extract_protocol:
The Achilles tendon was separated from soleus muscle and were homogenized using a tissue homogenizer, and total RNA was extracted using TRI reagent and the manufacturer's protocol.
The sequencing library is prepared by random fragmentation of the DNA or cDNA sample, followed  by 5’ and 3’ adapter ligation. Alternatively, “tagmentation” combines the fragmentation and ligation  reactions into a single step that greatly increases the efficiency of the library preparation process.  Adapter-ligated fragments are then PCR amplified and gel purified.

treatment_protocol: The skin and synovial sheath on the right ankle were incised using a scalpel blade. The Achilles tendon was then separated from the soleus muscle. A 1.5-mm-diameter ear punch was placed on the lateral side of the Achilles tendon to fit only about half the diameter. The Achilles tendon was then transected with the punch, leaving a 0.75-mm semicircular defect on the lateral side.

tag: tissue

value: Achilles tendon

tag: strain

value: wild type


title: oma-1ts-gfp_input_repeat 2


title: ATI_inj_3


title: MDBK IFNG 2h pSTAT1 rep1

tag: treatment


title: oma-1ts-gfp_RIP_repeat 1


title: MDBK IFNG 2h STAT1 rep2

value: Rabbit anti-STAT1 (Cohesion Biosciences #3322)


title: MJ101

value: Female

value: no


title: ATI_sham_4


title: oma-1ts-gfp_input_repeat 1


title: ATI_inj_2


title: oma-1-gfp_RIP_repeat 1


title: oma-1-gfp_RIP_repeat 2


title: S153

value: T

value: Male


title: ATI_sham_3


title: ATI_inj_1


title: MDBK UT STAT1 rep2

value: MDBK


title: MDBK IFNG 2h STAT1 rep1


title: S162


title: MDBK UT STAT1 rep1


title: 8 d old ejaculatory bulb

city: Honolulu

first: Joanne

last: Yew

state: HI

address: 1993 East West Rd

department: PBRC

institute: Univ. of Hawaii at Manoa

data_processing:
base calling: Illumina HiSeq 2000 system
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then imported into TOPHAT (v2.0.5) for alignment.
Transcript assembly was performed using Bowtie (v.2.0.07)
Genome_build: Dmr6.05, r5.48
Supplementary_files_format_and_content: Bowtie output files including counts of mapped reads and records of gene and transcript identification.

source_name: ejaculatory bulb

growth_protocol: Flies were fed standard BDSC cornmeal media.

extract_protocol:
EBs were removed from ~200 CO2-anesthetized flies, flash frozen on dry ice, and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit v2 was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Flies were raised at 25 deg C, 12 H/ 12 H light/ dark cycle, 50% humidity.

value: 8 d

value: male


title: oma-1-gfp_inpt_repeat 2


title: MDBK IFNG 2h POL2RA rep2

value: Rabbit anti-pPOL2RA-Ser5 (Cell Signaling #13523S)

value: IFNG


title: oma-1-gfp_inpt_repeat 1


title: S160

value: yes


title: S151


title: fzy-1_oma-1_repeat 2

growth_protocol: Synchronized L1 animals were cultured at 25°C until they grew into early young adults, which were then collected and washed with M9 buffer (22 mM KH2PO4, 42 mM Na2HPO4, and 86 mM NaCl) several times. Early embryos were obtained by bleaching and washing with M9 buffer five times and ice water for the last time.

tag: development stage

value: early embryos


title: fzy-1_oma-1_repeat 3


title: S121


title: MDBK UT POL2RA rep2

value: untreated


title: S149


title: MDBK UT POL2RA rep1


title: fzy-1_oma-1_repeat 1


title: MJ123

value: M


title: MJ120


title: MJ118


title: ATI_sham_2


title: MDBK UT H3K27ac rep2

value: Rabbit anti-H3K27ac EMD (Millipore #MABE647)


title: MDBK IFNG 2h H3K27ac rep1


title: oma-1_repeat 2


title: ATI_sham_1

value: Achilles tendon


title: oma-1_repeat 3


title: MJ102


title: oma-1_repeat 1


title: MDBK IFNG 2h POL2RA rep1


title: MDBK IFNG 2h IgG rep2

description: Processed data available on GSM5605773

value: Rabbit anti-mouse IgG (Abcam #ab46540)


title: MJ114


title: MDBK UT H3K27ac rep1


title: MDBK IFNG 2h H3K27ac rep2


title: d23 PKCa-KR

type: RNA

city: Glasgow

first: Alison

last: Michie

address: 21 Shelley Road

department: Paul O'Gorman Leukaemia Research Centre

country: United Kingdom

institute: University of Glasgow

description: Affymetrix microarray gene chip analysis on PKCa-KR retrovirally transduced mouse B lineage cells that had been co-cultured for 23 days (late co-culture) to establish B cell transformation.

hyb_protocol: Following fragmentation, cRNA were hybridized for 16 hr at 45C on GeneChip™ Mouse Gene 1.0 ST Array in the GeneChip Hybridization Oven 640. Arrays were washed and stained in the Affymetrix Fluidics Station 400.

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

data_processing: The raw data were generated with GeneChip Operating Software (GCOS),with Affymetrix default analysis settings and RMA normalization and scaling.

label: biotin

source_name: PKCaKR Day23

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

growth_protocol: Hematopoietic stem and progenitor cells from fetal liver (d14 gestation) of wildtype mice were retrovrially-transduced with empty vector control (MIEV) or MIEV.PKCaKR plasmids. The transduced cells were cultured with OP9 ce;;s in the presence of cytokines IL7& Flt3L to promote B cell development. After day 7 of culture the cells were cultured in IL7 alone until day 17-23 when total RNA was extracted for microarray analysis.

extract_protocol: Qiagen RNeasy kit

value: B lineage cells

value: PKCa-KR


title: PKCaKR FL2 Day17

description: Affymetrix microarray gene chip analysis on PKCa-KR retrovirally transduced mouse B lineage cells that had been co-cultured for 17 days (late co-culture) to establish B cell transformation.


title: PKCaKR FL1 Day21

description: Affymetrix microarray gene chip analysis on PKCa-KR retrovirally transduced mouse B lineage cells that had been co-cultured for 21 days (late co-culture) to establish B cell transformation.


title: PKCaKR FL2 Day21


title: N2_repeat 2

value: wild type


title: MDBK IFNG 2h IgG rep1


title: MDBK UT IgG rep2

description: Processed data available on GSM5606771


title: PKCaKR FL1 Day17


title: N2_repeat 1


title: MIEV FL1 Day21

description: Affymetrix microarray gene chip analysis on MIEV retrovirally transduced mouse B lineage cells that had been co-cultured for 21 days (late co-culture) to establish B cell transformation.

value: MIEV-control


title: d23 MIEV

description: Affymetrix microarray gene chip analysis on MIEV retrovirally transduced mouse B lineage cells that had been co-cultured for 23 days (late co-culture) to establish B cell transformation.

source_name: MIEV Day23


title: HiChIP_SPT6_LNA_V5

data_processing:
Library strategy: HiChIP
Sequenced reads were trimmed for adaptor sequence, then aligned to the reference human genome (GRCh37/hg19) using the Bowtie program (version 1). Hisat and cufflinks softwares were used to handle data.
Genome_build: hg19, mm9
Supplementary_files_format_and_content: txt; bedgraph file; .hic file

extract_protocol:
HiChIP experiment used for analyzing chromatin interaction.
Libraries were prepared for sequencing using standard protocols.

value: human endometrial adenocarcinoma

value: tumor stage

value: RNase H1 D210N stable cell line

tag: condition

value: SPT6 knockdown


title: MIEV FL1 Day17

description: Affymetrix microarray gene chip analysis on MIEV retrovirally transduced mouse B lineage cells that had been co-cultured for 17 days (late co-culture) to establish B cell transformation.


title: mouse_MeDIP_rep2 MeDIP-seq

data_processing:
Sequenced reads were trimmed for adaptor sequence, then aligned to the reference human genome (GRCh37/hg19) using the Bowtie program (version 1). Hisat and cufflinks softwares were used to handle data.
Genome_build: hg19, mm9
Supplementary_files_format_and_content: txt; bedgraph file; .hic file

source_name: Mouse tissue

growth_protocol: Mouse were housed in SPF environment lab.

extract_protocol:
MeDIP-seq: Genomic DNA was harvested and 1 ug of genomic DNA was used for the 5mC antibody immunoprecipitation.
Libraries were prepared for sequencing using standard protocols.

value: cortex tissue

value: newborn

value: wild-type


title: ATAC-seq_MDBK IFNG 4h rep1

data_processing:
Real-Time Analysis v3.4.4 was used for basecalling.
Sequenced reads were trimmed for low-quality and adapter sequence using BBDuk v38.05 with arguments 'ktrim=r k=34 mink=11 hdist=1 tpe tbo qtrim=r trimq=10'. Trimmed reads were aligned to the bosTau9 assembly (chromosomal and mitochondrial scaffolds only) using Bowtie2 v2.2.9 with options '--end-to-end --very-sensitive -X 1000 --fr', and only uniquely mapping reads with a minimum MAPQ of 10 were retained. Fragments aligning to the mitochondrial genome were removed, and duplicates were removed using sambamba v0.6.9. ATAC-seq peak and normalized bedgraph files were prepared using MACS2 v.1.1 with options '--SPMR -B --keep-dup all --format BAMPE --call-summits' and the default FDR < 0.05 cutoff. Bigwig files were prepared from the MACS2 normalized bedgraph files using bedGraphToBigWig v4.
Genome_build: bosTau9 (ARS-UCD1.2)
Supplementary_files_format_and_content: Tab-delimited text files including narrowPeaks called by MACS2 in UCSC BED format
Supplementary_files_format_and_content: Normalized signal tracks corresponding to read coverage per 1 million fragments in UCSC bigwig format

growth_protocol: MDBK cells were routinely grown at 37C in 5% CO2 and O2 on coated plastic (VWR #10861-680, typically 1,000,000-2,000,000 cells in 10cm dishes) in MEM (Gibco #11095080) supplemented with 1X nonessential amino acids (Gibco #11140050), 1X penicillin-streptomycin (Gibco #15140122), and 10% fetal bovine serum (Gibco #10437010).

extract_protocol: 30 minutes before harvesting, cells were treated with 200 U/mL DNase I (Worthington Biochemical #LS002006) for 30 minutes. ATAC-seq libraries were prepared according to Corces et al. 2017 (PMID: 28846090) using 50,000 viable (>90%) MDBK cells with modifications to the preamplification and qPCR steps. Purified post-transposition samples were initially amplified by combining 20 uL transposed sample, 2.5 uL 25 uM i5 primer, 2.5 uL 25 uM i7 primer, and 25 uL 2X NEBNext Ultra II Q5 Master Mix (NEB #M0554S). PCR cycling conditions: 30 s at 98°C, 5x(10 s at 98°C, 30 s at 63°C, 45 s at 65°C). qPCR was performed as follows: 5 uL of preamplified sample was combined with 0.5 uL 25 uM i5 primer, 0.5 uL 25 uM i7 primer, 3.75 uL nuclease-free water (Invitrogen #10977023), 0.25 uL 25X SYBR Gold (Invitrogen #S11494), and 5 uL 2x NEBNext Ultra II Q5 Master Mix. qPCR cycling conditions: 30 s at 98°C, 20x(10 s at 98°C, 30 s at 63°C, 45 s at 65°C). Preamplified samples were amplified for another 7 cycles. Final libraries were cleaned using a 0.5X/1.3X double-sided bead cleanup using KAPA Pure Beads (Roche #07983280001) and quantified using Qubit dsDNA High Sensitivity (Life Technologies #Q32851) and TapeStation 4200 HSD5000 (Agilent #50675588. Libraries were pooled and sequenced on an Illumina NovaSeq 6000 (University of Colorado Genomics Core) as 150bp paired-end reads.

treatment_protocol: Cells were either untreated or stimulated with 100 ng/mL bovine IFNG (Kingfisher #RP0013B-005) for 4 hours.

value: MDBK

value: IFNG


title: 3-day-old hyphal culture, E_2

city: HANGZHOU

first: REHAB

middle: ABDELMONEM

last: MOHAMED

address: YUHANGTANG ROAD NO.,886

institute: ZHEJIANG UNIVERSITY

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm8 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Reads Per Kilobase of exon per Megabase of library size (FPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Data filtering steps.Prior to assembly, the low quality reads(1,reads containing sequencing adaptors; 2,reads containing sequencing primer;3, nucleotide with q quality score lower than 20 )were removed .software CutAdapter,parameters -o 5 -p 100
Read alignment software,software HISAT ,version 2.0 ,parameters -l fr-firststrand -mi 20 -mx 500000 -p 2 -b dta -q phred33-quals -x 9
perform expression level for mRNAs by calculating FPKM.stimate the expression levels of all transcripts.software StringTie ,version 1.3.0,parameters -b dta -q phred33-quals.
Supplementary_files_format_and_content: Cre1-specific transcriptome.xlsx (includes FPKM values for each Sample)

organism: Beauveria bassiana

source_name: Beauveria bassiana

extract_protocol:
Total RNA was extracted using Trizol reagent (Invitrogen, CA, USA) following the manufacturer's procedure. Total RNA quantity and purity were analyzed by Bioanalyzer 2100 and RNA 6000 Nano LabChip Kit (Agilent, CA, USA) with RIN number >7.0.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: ARSEF 2860

value: hyphal

tag: age

value: mutant


title: 3-day-old hyphal culture, WT_3


title: 3-day-old hyphal culture, E_1


title: HiChIP_WT_V5

source_name: HEC-1-B cells

value: control for HiChIP


title: mouse_MeDIP_rep1 MeDIP-seq


title: MIEV FL2 Day21

value: B lineage cells


title: Low breeding value for myoglobin content Individual 6

status: Public on Oct 01 2021

city: Zafra

first: María

middle: Muñoz

last: Muñoz

state: Badajoz

address: Centro I+D en Cerdo Ibérico, carretera Ex-101, km 4.7

country: Spain

institute: INIA

description:
Gene expression data from Longissimus dorsi tissue
Low_Mb_6

data_processing:
FastQC was used to evaluate the quality of the raw sequencing data
The sequences were trimmed to remove the sequencing adaptor and poly A and T tails with Trim Galore setting default values (stringency of 6bp) and paired-end reads where kept when both pairs were longer than 40 bp.
Hisat2 (Kim et al., 2019) was used to map the filtered reads against the pig reference genome (Sscrofa11.1).
HTseq-counts (Anders et al., 2015) was employed to obtain the raw counts for the genes and transcripts and to construct the read counts matrix
Genome_build: Sscrofa11.1
Supplementary_files_format_and_content: tab-delimited text files include counts for each gene or transcript per sample

organism: Sus scrofa

source_name: Longissimus dorsi, male

growth_protocol: Pigs fattened in a free-range system based on the ad libitum intake of acorns and grass.

extract_protocol:
RiboPure RNA isolation kit
Paired-end libraries were prepared using NEBNext® Ultra™ RNA Library Prep Kit -(Illumina, San Diego CA) for each sample. Multiplex sequencing of the libraries was carried out on a Novaseq 6000  sequence analyzer (Illumina, Inc) with four samples per lane, according to the manufacturer’s instruction at Novogene. Paired-end reads of 150 bp were generated.

treatment_protocol: Longissimus dorsii muscle were manteined at -80 ºC

tag: breed

value: Iberian

value: Low group myoglobin content

tag: myoglobin breeding value

tag: myoglobin content

value: Longissimus dorsi

tag: Sex

value: male


title: Low breeding value for myoglobin content Individual 3

description:
Gene expression data from Longissimus dorsi tissue
Low_Mb_3


title: 3-day-old hyphal culture, WT_2

value: wild type


title: High breeding value for myoglobin content Individual 6

description:
Gene expression data from Longissimus dorsi tissue
High_Mb_6

value: High group myoglobin content


title: HiChIP_eRNA_LNA_V5

tag: cell line

tag: cell type

value: human endometrial adenocarcinoma

value: tumor stage

value: RNase H1 D210N stable cell line

value: eRNA knockdown


title: N2_repeat 3

value: early embryos

tag: genotype


title: MDBK UT IgG rep1

value: MDBK

value: Rabbit anti-mouse IgG (Abcam #ab46540)

value: untreated

tag: timepoint


title: Mouse_rep3 total RNA-seq

extract_protocol:
Total RNA-seq used 1 ug total RNA to construct sequencing libraries.
Libraries were prepared for sequencing using standard protocols.

value: cortex tissue

tag: Stage

value: newborn

value: wild-type


title: 3-day-old hyphal culture, WT_1

value: ARSEF 2860

value: hyphal


title: High breeding value for myoglobin content Individual 4

description:
Gene expression data from Longissimus dorsi tissue
High_Mb_4

value: Iberian

tag: group

value: Longissimus dorsi


title: High breeding value for myoglobin content Individual 3

description:
Gene expression data from Longissimus dorsi tissue
High_Mb_3

value: male


title: ATAC-seq_MDBK IFNG 4h rep2

value: IFNG


title: MIEV FL2 Day17

value: B lineage cells

value: MIEV-control


title: Striatum/thalamus_subject8

city: Omaha

first: Eric

middle: S

last: Peeples

state: NE

address: 8200 Dodge Street

department: Pediatrics

institute: University of Nebraska Medical Center

description:
Obtained 30 min after injury
8S

data_processing:
miRNA-Seq results were aligned to mature mouse miRNA from miRBase using bowtie2 alignment
Differential expression analysis performed using EdgeR
Supplementary_files_format_and_content: miRNA-Seq in the remaining three (C is hypoxic-ischemic brain injury vs. controls in the cortex, B in the cerebellum, and S in striatum/thalamus)

source_name: Right striatum/thalamus

extract_protocol:
Each hemisphere was further dissected into three regions –  cortex, striatum/thalamus, and cerebellum – and then immediately frozen on dry ice and stored at -80°C until analysis. Regional brain tissue was then homogenized using a dounce homogenizer with Qiazol Lysis Reagent (Qiagen, Hilden, Germany) and the RNA extracted using the RNeasy Lipid Tissue Mini kit (Qiagen) per the manufacturer instructions.
For miRNA-Seq, libraries were prepared from 200 ng RNA per sample with the NEXTFLEX Small RNA Kit (PerkinElmer, Waltham, MA) per the manufacturer’s instructions. The libraries were then sequenced on the Illumina NextSeq 550 platform (San Diego, CA).

treatment_protocol: At postnatal day 9, pups of both sexes were randomized to HIBI or control. The HIBI groups were induced with 5% isoflurane and then were anesthetized with 2.5% isoflurane. Analgesia was provided by injection of 2 mg/kg bupivacaine at the incision site. A small vertical incision was made in the midline of the ventral neck and the neck was dissected in order to identify, isolate, and cauterize the right common carotid artery [11]. Surgeries took no longer than five minutes. The control group underwent the same anesthesia, analgesia, and dissection, but the neck was closed without vessel ligation. Pups were maintained at normothermia throughout surgery and recovery. Once the pups were fully recovered, they were returned to the dam and littermates for a two-hour recovery period. After recovery, groups were again separated, and the HIBI group underwent 30 minutes at 8% oxygen in a hypoxia chamber at normothermia while the sham control group spent the same 30 minutes separated from the dam but in a warm normoxic environment. At 30 minutes after hypoxia or normoxia, pups were euthanized.

tag: postnatal age

value: 9 days

tag: injury

value: Sham surgery without hypoxia


title: Striatum/thalamus_subject7

description:
Obtained 30 min after injury
7S

tag: strain

value: Right carotid ligation followed by 8percent oxygen for 30 min


title: Low breeding value for myoglobin content Individual 1

description:
Gene expression data from Longissimus dorsi tissue
Low_Mb_1

value: Low group myoglobin content

tag: tissue


title: Cerebellum_subject7

description:
Obtained 30 min after injury
7B

source_name: Right cerebellum


title: Mouse_rep2 total RNA-seq


title: Cortex_subject5

description:
Obtained 30 min after injury
5C

source_name: Right cortex


title: Striatum/thalamus_subject3

description:
Obtained 30 min after injury
3S


title: Cortex_subject3

description:
Obtained 30 min after injury
3C


title: 3-day-old hyphal culture, E_3

value: mutant


title: Cerebellum_subject3

description:
Obtained 30 min after injury
3B


title: Mouse_rep1 total RNA-seq


title: RS-B/RNAseq

city: Versailles

first: HAKIM

last: MIREAU

address: Route de Saint-Cyr

country: France

institute: INRAE

data_processing:
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence. After cytosolic, plastid and mitochondrial rRNA removal, reads comprised between 20-65 nucleotides were selected for mapping to the rapeseed mitochondrial genome using Bowtie 2 with default parameters but allowing 1 missmatch.
Genome_build: Brassica napus mitochondrial DNA (GenBank: AP006444.1) to which we manually added the orf138 gene.
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

organism: Brassica napus

source_name: Flower buds

extract_protocol:
Total RNAs were extracted from 1/10th of the lysates used for Ribo-Seq analysis (see GEO Submission (GSE178543)) and treated with the Ribo-Zero rRNA Removal Kit (Illumina). One hundred ng of the rRNA-depleted RNAs were used for library construction using the NEXTflex Rapid Directional qRNA-Seq Kit (Bioo Scientific) according the manufacturer’s instructions. Next generation sequencing was performed on a NextSeq 500 sequencer (single end, 75 nt).
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Pactol

value: Flower buds

tag: phenotype

value: Restored


title: RS-A/RNAseq


title: ATAC-seq_MDBK UT rep2

value: MDBK

tag: treatment

value: untreated


title: Cortex_subject2

description:
Obtained 30 min after injury
2C


title: ATAC-seq_MDBK UT rep1


title: Low breeding value for myoglobin content Individual 4

description:
Gene expression data from Longissimus dorsi tissue
Low_Mb_4


title: Low breeding value for myoglobin content Individual 2

description:
Gene expression data from Longissimus dorsi tissue
Low_Mb_2


title: CMS-A/RNAseq

value: Male sterile


title: Cerebellum_subject1

description:
Obtained 30 min after injury
1B


title: High breeding value for myoglobin content Individual 2

description:
Gene expression data from Longissimus dorsi tissue
High_Mb_2

value: Iberian

value: High group myoglobin content


title: Low breeding value for myoglobin content Individual 5

description:
Gene expression data from Longissimus dorsi tissue
Low_Mb_5

value: Longissimus dorsi

value: male


title: High breeding value for myoglobin content Individual 1

description:
Gene expression data from Longissimus dorsi tissue
High_Mb_1


title: High breeding value for myoglobin content Individual 5

description:
Gene expression data from Longissimus dorsi tissue
High_Mb_5


title: Cortex_subject8

description:
Obtained 30 min after injury
8C


title: Cerebellum_subject8

description:
Obtained 30 min after injury
8B


title: Cortex_subject7

description:
Obtained 30 min after injury
7C


title: Cortex_subject6

description:
Obtained 30 min after injury
6C


title: Cerebellum_subject6

description:
Obtained 30 min after injury
6B


title: Striatum/thalamus_subject5

description:
Obtained 30 min after injury
5S


title: Cerebellum_subject5

description:
Obtained 30 min after injury
5B


title: Cerebellum_subject4

description:
Obtained 30 min after injury
4B


title: Striatum/thalamus_subject4

description:
Obtained 30 min after injury
4S


title: CMS-B/RNAseq


title: Striatum/thalamus_subject2

description:
Obtained 30 min after injury
2S


title: Cortex_subject4

description:
Obtained 30 min after injury
4C


title: Striatum/thalamus_subject6

description:
Obtained 30 min after injury
6S


title: Cerebellum_subject2

description:
Obtained 30 min after injury
2B


title: Cortex_subject1

description:
Obtained 30 min after injury
1C


title: Striatum/thalamus_subject1

description:
Obtained 30 min after injury
1S


title: E14_rep2 Tn5 NakedDNA

city: Tianjin

first: Kuangyu

last: Yen

address: Nanjing Road

department: State Key Laboratory of Experimental Hematology

institute: Institute of Hematology and Blood Diseases Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College

data_processing:
All reads were trimmed via Trimmomatic version 0.33.0 using the NexteraPE adapter sequence
Trimmed reads were aligned to the mm10 or hg38 genome assembly using Bowtie2 version 2.2.7 with default parameters
Mapped reads were de-duplicated using Picard version 2.9.0 and filtered using samtools version 1.7 with the parameter "-F 780 -q 30"
Processed reads on the forward strand were shifted by +4bp and reads on the reverse strand were shifted by -5bp to get the centers of each Tn5 insertion event (insertion sites)
Genome_build: mm10 or hg38
Supplementary_files_format_and_content: bed files contain the single-base Tn5 insertion sites information. the 5th column indicate Tn5 insertion frequency, the 6th indicate the strand information

source_name: embryonic stem cell line

growth_protocol: E14 cells were maintained in 0.2% gelatin (Sigma)-coated plates 2i medium, which consisted of DMEM/F12 supplemented with Neurobasal medium, serum-free N2B27 medium supplemented with 10uM MEK inhibitor PD0325901 and 30uM GSK3 inhibitor CHIR99021 (both from Selleckchem), 2% KnockOutTM serum replacement (Gibco), 0.002% BSA (Gibco), 1mM MTG (Gibco), 1,000 U/ml LIF (Millipore), 0.1mM non-essential amino acid (NEAA) and 2 mM GlutaMAX Supplement (Gibco). Mouse HSPCs were cultured in IMDM (Gibco) supplemented with 15% FBS (Gibco), 10 ng/ml mIL-6, 10 ng/mL mIL-3, 50 ng/ml SCF, 20 ng/ml thrombopoietin (TPO, PeproTech) and 10 ng/ml Flt3 ligand (Flt3-L, PeproTech). The K562 cells were cultured in RPMI-1640 (Giboco) supplemented with 10% FBS.

extract_protocol:
DNA was purified with QIAamp DNA Mini Kit (QIAGEN) and 50ng DNA was used for the following procedure.
The DNA was added with a 50ul Transposition reaction mix (5 μL TTE Mix V50, 10 μL 5 X TTBL and use ddH2O from Vazyme TD501) and followed with incubation at 55C for 10 min. After tagmentation, VAHTS DNA Clean Beads were used to stop the reaction, and DNA was purified for final library construction (TruePrepTM DNA Library Prep Kit V2 for Illumina).

value: mouse embryonic stem cells (mESC)


title: E006_B992

city: Carrières sur Seine

first: Damien

last: VALOUR

state: Île-de-France

address: 34, rue Victor HUGO (Bât D)

department: PHASE

institute: INRA

description: Syntax of the sample names: SCNT_Gender_FoetusName_AI_Gender_FoetusName_slideName_DyeOfAIsample. Where the AI_Gender is either M or F and DyeOfAIsample (Control) is either Cy3 or Cy5.

hyb_protocol: Prior to hybridization, microarrays were prehybridized for 30 min at 50°C in a filtered solution of 1% BSA, 3.5X SSC, 0.1% SDS and rinsed twice at room temperature in ultrapure water for 5 min with orbital agitation. They were dried using compressed air. Each microarray was co-hybridized with two fluorescently labelled (Cy3 and Cy5) cDNA samples according to the experimental design (dye switch design). An evaluated amount of 500 ng of each labelled cDNA was fragmented for 30 min at 60°C in 1X fragmentation buffer (Agilent Technologies). Final volume of 200µL (adjusted with ultra-pure water). Hybridisation were performed on the ICE platform (previously, PICT Gem, Jouy en Josas, http://www4.jouy.inra.fr/gabi_eng/Our-resources/ICE-Integrated-Microgenomics-platform). In the experimental design of hybridization dye switch technique was used.  Fragmented labelled cDNA was hybridized for 17h at 60°C to the array. Afterwards arrays were washed and scanned. Images were processed and signals of expressed genes were extracted using the Genepix Pro 6.0.1.25 software. After hybridization, microarrays were washed at room temperature with orbital agitation successively twice for 5 min in a 2X SSC-0.1% SDS solution, once for 5 min in a 0.5X SSC-0.1% SDS solution and three times for 5 min in a 0.2X SSC solution. They were finally dried using compressed air.

scan_protocol: Scanner: Agilent G2505B Microarray Scanner System. Raw data set: Feature extraction with GenePix Pro 6.0.1.25 software. GenePix software was used to extract data at the CRB GADIE of Jouy-en-Josas (http://crb-gadie.inra.fr/)

data_processing: Intensity = Signal Median. Normalization = Signal Median were normalized using the Limma functions in R: log2, loess transformations, Median centring. Flags = -50, -100

source_name: E006 - Biological material: Foetus with no extra-embryonic tissues, no head, no tail - Experimental variables: i)Origin of the foetus: Somatic Cell Nuclear Transfer or Artificial Insemination ii)Gender: Female or Male iii)Foetus name

label_protocol: RNA samples were converted to cDNA and labeled using the protocol recommended by Invitrogen (SuperScript Indirect cDNA Labeling System), fluorescent dyes used in the experiment come from Amersham Biosciences (CyDye Post Labeling Reactive Dye Pack). Quality and quantity of labeled probes was controlled by migration of labeled cDNA samples on agarose gel and Nanodrop measurement. Frequencies of dye incorporation (FOI, rate per thousand labelled nucleotides) and cDNA concentrations were estimated for both dyes by measuring the absorbance at 260 nm, 550 nm and 650 nm on a Nanodrop spectrophotometer (Thermo Scientific). The following ratios were calculated: FOI per 1000 bases (Cy3) = 58.5 * Abs550/Abs260, FOI per 1000 bases (Cy5) = 35.1 * Abs650/Abs260.

extract_protocol: Total RNA was isolated from sample tissues (N=8) by using the standard protocol of RNA extraction with Trizol reagent and subjected to DNase I digestion to remove contaminating genomic DNA. The integrity of the total RNA was determined using the Agilent Bioanalyser 2100 (RIN: 8 to 10).

treatment_protocol: D30 foetuses were collected; the foetal tissues (whole body) were dissected out (no extra-embryonic tissue, no head, no tail) and immediately snap-frozen.

tag: annotation

value: Somatic Cell Nuclear Transfer (SCNT)

tag: gender

value: Female (F)

tag: foetus name

source_name: B992 - Biological material: Foetus with no extra-embryonic tissues, no head, no tail - Experimental variables: i)Origin of the foetus: Somatic Cell Nuclear Transfer or Artificial Insemination ii)Gender: Female or Male iii)Foetus name

value: Artificial Insemination (AI)

value: Male (M)


title: E14_rep1 Tn5 NakedDNA


title: E001_B949

source_name: E001 - Biological material: Foetus with no extra-embryonic tissues, no head, no tail - Experimental variables: i)Origin of the foetus: Somatic Cell Nuclear Transfer or Artificial Insemination ii)Gender: Female or Male iii)Foetus name

source_name: B949 - Biological material: Foetus with no extra-embryonic tissues, no head, no tail - Experimental variables: i)Origin of the foetus: Somatic Cell Nuclear Transfer or Artificial Insemination ii)Gender: Female or Male iii)Foetus name


title: B989B_B992

source_name: B989B - Biological material: Foetus with no extra-embryonic tissues, no head, no tail - Experimental variables: i)Origin of the foetus: Somatic Cell Nuclear Transfer or Artificial Insemination ii)Gender: Female or Male iii)Foetus name


title: E006_E018

source_name: E018 - Biological material: Foetus with no extra-embryonic tissues, no head, no tail - Experimental variables: i)Origin of the foetus: Somatic Cell Nuclear Transfer or Artificial Insemination ii)Gender: Female or Male iii)Foetus name


title: E001_B960

source_name: B960 - Biological material: Foetus with no extra-embryonic tissues, no head, no tail - Experimental variables: i)Origin of the foetus: Somatic Cell Nuclear Transfer or Artificial Insemination ii)Gender: Female or Male iii)Foetus name


title: B989B_B960


title: B989A_B949

source_name: B989A - Biological material: Foetus with no extra-embryonic tissues, no head, no tail - Experimental variables: i)Origin of the foetus: Somatic Cell Nuclear Transfer or Artificial Insemination ii)Gender: Female or Male iii)Foetus name


title: Xenograft SK-N-AS-TRAIL no dox 2

city: Amsterdam

first: Richard

last: Volckmann

state: Noord-Holland

address: van der Boechorststraat 6a

department: Laboratory of Experimental Oncology and Radiobiology

country: Netherlands

institute: msterdam UMC and University of Amsterdam

description:
Total RNA was isolated and analyzed on Affymetrix U133 Plus 2.0 to generate expression profile
nb2013

hyb_protocol: 10 µg of labeled cRNA was hybridized to Affymetrix Human genome U133 Plus 2.0 arrays according to manufacturer’s protocol (Affymetrix).

scan_protocol: Arrays were scanned with a GeneChip Scanner 3000 (Affymetrix) according to manufacturer’s protocol

data_processing: Expression data (cel files) were normalized with the MAS5.0 algorithm (target signal = 100) using GCOS software (Affymetrix)

source_name: Xenograft SK-N-AS-TRAIL no dox

label_protocol: RNA sample integrity was checked on an Agilent 2100 Bioanalyzer (Agilent Technologies). 4 µg of total RNA was used for cRNA synthesis and fragmented. Labeling was performed with One-Cycle cDNA synthesis Kit (Affymetrix) according to manufacturer’s protocol. Sample quality was checked on a Bioanalyzer prior and after fragmentation.

growth_protocol: SK-N-AS (1x1036) or SH-SY5Y (5x1036) cells were suspended in 200 μl of a 50% Matrigel solution in PBS and subcutaneously injected in NMRI-Foxn1nu/nu mice.

extract_protocol: Total RNA from frozen extracted tumors was isolated using Trizol (Invitrogen) and purified with RNeasy (Qiagen) according to manufacturer’s protocol

value: SK-N-AS-TRAIL

tag: xenograft

value: Neuroblastoma xenograft with mesenchymal phenotype


title: Xenograft SH-SY5Y control 3

description:
Total RNA was isolated and analyzed on Affymetrix U133 Plus 2.0 to generate expression profile
nb2207

source_name: Xenograft SH-SY5Y control

value: Neuroblastoma xenograft with adrenergic phenotype


title: Xenograft SH-SY5Y control 2

description:
Total RNA was isolated and analyzed on Affymetrix U133 Plus 2.0 to generate expression profile
nb2205


title: B989A_E018


title: Xenograft SH-SY5Y control 1

description:
Total RNA was isolated and analyzed on Affymetrix U133 Plus 2.0 to generate expression profile
nb2180


title: Xenograft SK-N-AS-TRAIL no dox 3

description:
Total RNA was isolated and analyzed on Affymetrix U133 Plus 2.0 to generate expression profile
nb2015


title: TNBC Breast Cancer Specimen 10

type: genomic

city: München

first: Philipp

last: Jurmeister

address: Thalkirchner Straße 36

department: Institute of Pathology

country: Germany

institute: Ludwig Maximilians University Hospital Munich

hyb_protocol: Bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium MethylationEPIC BeadChip using standard Illumina protocol

scan_protocol: Arrays were imaged using the Illumina iScan system with default settings

data_processing: Statistical analysis was performed using the minfi package running on RStudio version 1.1.463  based on the statistical language R version 3.5.1

label: Cy5 and Cy3

source_name: Breast biopsy

label_protocol: Standard Illumina protocol

extract_protocol: Semi-automated DNA extraction from FFPE samples was performed according the manufacturer’s instructions (Maxwell RSC FFPE Plus DNA Purification Kit, Custom, AX4920, Promega, Madison, USA).

value: Female

tag: subtype

value: TNBC

value: Negative


title: TNBC Breast Cancer Specimen 11


title: Xenograft SK-N-AS-TRAIL no dox 1

description:
Total RNA was isolated and analyzed on Affymetrix U133 Plus 2.0 to generate expression profile
nb1963

tag: cell line


title: TNBC Breast Cancer Specimen 13


title: nblw-adrn

description:
Total RNA was isolated and analyzed on Affymetrix U133 Plus 2.0 to generate expression profile
nb2321

source_name: nblw-adrn

growth_protocol: NBLW cells were cultured in RPMI 1640 (Invitrogen) containing 10% fetal calf serum.

extract_protocol: Total RNA was isolated using Trizol (Invitrogen) and purified with RNeasy (Qiagen) according to manufacturer’s protocol

value: Neuroblastoma cell line with adrenergic phenotype


title: nblw-mes_1

description:
Total RNA was isolated and analyzed on Affymetrix U133 Plus 2.0 to generate expression profile
nb2322

value: Neuroblastoma cell line with mesenchymal phenotype


title: TNBC Breast Cancer Specimen 8


title: Bel-7402 cells-PCDH

city: Hangzhou

first: Xiaomeng

last: Gao

address: 866 Yuhangtang Rd

institute: Zhejiang University

data_processing:
Using illumina Hiseq 2500 for sequencing and IIIumina Casava1.8 for base calling  to get Raw Reads in Fastq format and then filtering low-quality Reads through Seqtk to obtain Clean Reads
Genome mapping of the Clean Reads using Hisat2  (version: 2.0.4) spliced mapping to get BAM format files.
Ultilizing Stringtie (version: 1.3.0) to calculate the Fragments of genes and normalized through TMM (trimmed mean of M values), and then FPKM value was obtained with Perl Script
EdgeR was used to analyze the differential gens and FDR (False Discovery Rate) determined the range of p-value
Genome_build: hg38
Supplementary_files_format_and_content: Abundance measurements of genes were gathered in one file with xls.

source_name: Human hepatocellular carcinoma

growth_protocol: Human hepatocellular carcinoma cell line Bel-7402 was purchased from the Shanghai Cell Bank of Chinese Academy of Sciences, and was cultured in RPMI-1640. All cells were cultured at 37°C with 5% CO2 atmosphere, and all mediums were supplemented with 10% heat-inactivated fetal bovine serum (Gibco, Thermo Fisher Scientific) as well as 100 IU/mL penicillin and 100 ug/mL streptomycin.

extract_protocol:
Bel-7402 cells stably overexpressing pCDH, pCDH-WSB1 and pCDH-ΔSOCS by lentivirus transfection were harvested and washed for 3 times with pre-cold PBS. Total RNA of the cells was extracted by TRIzol reagent and sent to Bohao Biotechnology (Shanghai, China) for RNA expression profiling.
Standard IIIumina protocols

treatment_protocol: Bel-7402 cells were transduced with lentivirus companied by polybrene (6 mg/ml) at the MOI of 5-10 to obtain stable cell strains.

value: Lentivirus infection

tag: genotype/variation

value: stably overexpressing pCDH


title: Bel-7402 cells-PCDH-WSB1

value: stably overexpressing pCDH-WSB1


title: nblw-motherline

description:
Total RNA was isolated and analyzed on Affymetrix U133 Plus 2.0 to generate expression profile
nb2320

source_name: nblw-motherline

value: Neuroblastoma cell line with heterogeneous phenotype


title: WCM155 RGD rep3

city: New York

first: Olivier

last: Elemento

address: 1305 York Avenue

institute: WEILL MEDICAL COLLEGE OF CORNELL UNIV

data_processing:
Illumina Casava1.7 software used for basecalling.
All reads were independently aligned with STAR_2.4.0f141 for sequence alignment against the human genome sequence build hg19, downloaded via the UCSC genome browser [http://hgdownload.soe.ucsc.edu/goldenPath/hg19/bigZips/], and SAMTOOLS v0.1.1942 for sorting and indexing reads. Cufflinks (2.0.2)43 was used to estimate the expression values (FPKMS), and GENCODE v1944 GTF file for annotation. The gene counts were obtained using htseq-count.
Genome_build: hg19
Supplementary_files_format_and_content: Tab-delimited text files include FPKM values for each Sample

source_name: WCM155 prostate cancer organoid

extract_protocol:
RNA was extracted from frozen material for RNA-sequencing (RNA-seq) using the Promega Maxwell 16 MDx instrument, (Maxwell 16 LEV simplyRNA Tissue Kit (cat. # AS1280))
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: RNA-sequencing and data processing of synthetic organoids was performed according to the protocol described earlier by our group. Briefly, RNA was extracted from frozen material for RNA-sequencing (RNA-seq) using the Promega Maxwell 16 MDx instrument, (Maxwell 16 LEV simplyRNA Tissue Kit (cat. # AS1280)). Specimens were prepared for RNA sequencing using TruSeq RNA Library Preparation Kit v2. RNA integrity was verified using the Agilent Bioanalyzer 2100 (Agilent Technologies). cDNA was synthesized from total RNA using Superscript III (Invitrogen). Sequencing was then performed on HiSeq 2000, or HiSeq 2500.

tag: donor

value: Neuroendocrine prostate cancer (NEPC)

value: RGD


title: TNBC Breast Cancer Specimen 12


title: WCM155 RGD rep2


title: Bel-7402 cells-PCDH-ΔSOCS

value: stably overexpressing pCDH-{delta}SOCS


title: WCM155 RGD rep1


title: WCM155 REDV rep3

value: REDV


title: WCM155 REDV rep2


title: WCM155 MATRIGEL rep3

value: MATRIGEL


title: WCM155 MATRIGEL rep2


title: TNBC Breast Cancer Specimen 4


title: WCM155 REDV rep1


title: TNBC Breast Cancer Specimen 7


title: WCM155 MATRIGEL rep1


title: WCM155 GFOGER rep3

value: GFOGER


title: LowHR Breast Cancer Specimen 22

value: LowHR

value: Positive


title: TNBC Breast Cancer Specimen 5

value: Female


title: TNBC Breast Cancer Specimen 9

value: TNBC


title: LowHR Breast Cancer Specimen 21

value: Negative


title: LowHR Breast Cancer Specimen 18


title: LowHR Breast Cancer Specimen 23


title: TNBC Breast Cancer Specimen 2


title: WCM155 GFOGER rep2


title: LowHR Breast Cancer Specimen 20


title: WCM155 GFOGER rep1


title: PRP-2

first: Dengfeng

last: Ruan

state: China

address: 88 Jie Fang Road

department: Department of Orthopedic Surgery

institute: The Second Affiliated Hospital, Zhejiang University School of Medicine

data_processing:
The RNA sequencing reads were aligned to reference genome Oryctolagus_cuniculus.OryCun2.0.98 using STAR (2.7.2a)
per gene counts were calculated using featureCounts (v1.6.5)
Genome_build: Oryctolagus_cuniculus.OryCun2.0.98
Supplementary_files_format_and_content: tab-delimited text files include count values for each Sample

organism: Oryctolagus cuniculus

source_name: tendon stem/progenitor cells (TSPCs)

extract_protocol:
After isolation of total RNA by total RNA TRIzol® Reagent (Invitrogen; Carlsbad, California, USA), mRNA was purified by magnetic beads, digested into short fragments, and then reverse transcribed into double-stranded cDNAs.
A sequencing library was constructed with Illumina TruseqTM RNA sample prep Kit (Illumina; San Diego, California, USA) and sequenced on an Illumina Hiseq platform.

treatment_protocol: We assigned the TSPCs into two experimental groups: TSPCs cultured in medium with or without 10% (v/v) PRP.

tag: cell type

value: tendon stem/progenitor cells (TSPCs)

tag: breed

value: New Zealand White rabbits

value: TSPCs cultured in medium with 10% (v/v) PRP


title: LowHR Breast Cancer Specimen 19


title: TNBC Breast Cancer Specimen 6


title: TNBC Breast Cancer Specimen 3


title: WCM1358 RGD rep2

source_name: WCM1358 prostate cancer organoid

value: Castration resistant prostate cancer (CRPC)


title: TNBC Breast Cancer Specimen 1


title: noPRP-2

value: TSPCs cultured in medium without PRP


title: LowHR Breast Cancer Specimen 17


title: WCM1358 RGD rep1


title: WCM1358 RGD rep3


title: PRP-1


title: noPRP-1


title: WCM1358 REDV rep2


title: set4 deletion mutant Rep 3

city: Baltimore

first: Erin

middle: M

last: Green

state: MD

address: 1000 Hilltop Cir, Bs 325

department: Biological Sciences

institute: UMBC

data_processing:
Data quality visualized using FastQC
Adaptor removal and read trimming performed with Trimmomatic in paired-end mode (Headcrop:10 used to trim first 10 bases)
Read mapping performed with BWA-MEM through Galaxy
Transcript assembly performed with Stringtie through Galaxy
Log fold-change values calculated using DeSeq2
Genome_build: sacCer3
Supplementary_files_format_and_content: excel file with log fold change values calculated from DeSeq2 (mut/wt)

organism: Saccharomyces cerevisiae

source_name: whole cell lysate

growth_protocol: YPD medium, 30 degrees C, mid log phase growth

extract_protocol:
total RNA isolation from yeast with rRNA depletion using Illumina ribo zero kit
standard Illumina library preparation using stranded TruSeq library preparation kit

tag: genotype


title: LowHR Breast Cancer Specimen 15


title: set4 deletion mutant Rep 2


title: LowHR Breast Cancer Specimen 16


title: set4 deletion mutant Rep 1