title: ChIP-seq analysis of ZNF358 genomic target locations in HEK293, THC0404TANM_ZNF358_ChIP1


title: ChIP-seq analysis of ZNF207 genomic target locations in HEK293, THC0402TAND_ZNF207_ChIP1

status: Public on Nov 11 2024

type: SRA

city: Toronto

first: Arttu

last: Jolma

state: Ontario

address: 160 College Street, Room 1350

department: Donnelly Centre

country: Canada

institute: University of Toronto

library_source: genomic

data_processing:
Constant flank derived bases were removed with Cutadapt (using the adapters AGATCGGAAGAGCACACGTCTGAACTCCAGTCA and AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT).
Reads were mapped into human genome build hg38 with bowtie2 (options: --very-sensitive, --no-unal). The mapped trimmed reads were filtered using samtools (options: -q 30, -F 1548, version 1.20)
Peak calling was performed with MACS2 using sample-specific backgrounds [made by merging pull-down experiments; PMID: 27852650].
Assembly: hg38
Supplementary files format and content: Bigwig files are based on Bowtie2 mapping followed by MACS3 peak calling.
Supplementary files format and content: Narrowpeak files have been derived following the custom Peak calling was performed with MACS2 using sample-specific backgrounds [made by merging pull-down experiments; PMID: 27852650].

molecule: genomic DNA

organism: Homo sapiens

growth_protocol: HEK293 cells were grown and maintained in high glucose DMEM supplemented with 10% FBS. TF cell lines were established via transfection and selection of transfected cells in 200ug/ml of hygromycin in growth media.

extract_protocol:
20 million cells were cross-linked with 1% formaldehyde and palletted in cold PBS. Cell pallettes were lysed in a 3 step lysis procedure and chromatin was sonicated at the last step. Sonicated chromatin ws immunoprecipitated using anti-eGFP IgG (Rabbit polycclonal, abcam290) coated magnetic beads. For "input" control samples, 10ul of pre-IP sample were collected. After de-cross linking and DNA purification, both ChIP and Input samples were eluted in 60ul of elution buffer.
NEBNext® Ultra™ II DNA Library Prep Kit for Illumina® kit and protocol

treatment_protocol: Established TF cell lines were treated with 1ug/ml of doxycycline 24 hours prior to cross linking. The TF expressions were confirmed using fluorescent microscopy and observation of GFP.

tag: cell line

tag: hngc symbol_of_the_analyzed_protein

tag: sample type

value: ChIP

value: Not approved


title: ChIP-seq analysis of NCOA2 genomic target locations in HEK293, THC0401TANM_NCOA2_ChIP2


title: ChIP-seq analysis of ZNF207 genomic target locations in HEK293, THC0402TANM_ZNF207_ChIP1


title: ChIP-seq analysis of NCOA2 genomic target locations in HEK293, THC0401TAND_NCOA2_ChIP2


title: ChIP-seq analysis of GATAD2B genomic target locations in HEK293, THC0398TAND_GATAD2B_ChIP1


title: ChIP-seq analysis of ZHX2 genomic target locations in HEK293, THC0399TANM_ZHX2_ChIP1

value: No expert curation due to insufficient peak numbers


title: ChIP-seq analysis of ZNF347 genomic target locations in HEK293, THC0396TANM_ZNF347_ChIP1

value: Approved


title: ChIP-seq analysis of ZHX2 genomic target locations in HEK293, THC0399TAND_ZHX2_ChIP1


title: ChIP-seq analysis of ZNF497 genomic target locations in HEK293, THC0397TAND_ZNF497_ChIP1


title: ChIP-seq analysis of ZNF20 genomic target locations in HEK293, THC0395TANM_ZNF20_ChIP1


title: ChIP-seq analysis of ZNF497 genomic target locations in HEK293, THC0397TANM_ZNF497_ChIP1


title: Pre-IP control THC0394TANM_ZBTB5_INPUT1

value: Input


title: ChIP-seq analysis of ZNF20 genomic target locations in HEK293, THC0395TAND_ZNF20_ChIP1


title: ChIP-seq analysis of NCOA1 genomic target locations in HEK293, THC0393TANM_NCOA1_ChIP1


title: Pre-IP control THC0394TAND_ZBTB5_INPUT1


title: ChIP-seq analysis of TPRX1 genomic target locations in HEK293, THC0391TANM_TPRX1_ChIP1


title: ChIP-seq analysis of NCOA1 genomic target locations in HEK293, THC0393TAND_NCOA1_ChIP1


title: ChIP-seq analysis of FLYWCH1 genomic target locations in HEK293, THC0390TAND_FLYWCH1_ChIP1


title: ChIP-seq analysis of ZNF326 genomic target locations in HEK293, THC0388TAND_ZNF326_ChIP1


title: ChIP-seq analysis of ZNF160 genomic target locations in HEK293, THC0387TANM_ZNF160_ChIP1


title: Pre-IP control THC0386TAND_PRDM13_INPUT1


title: ChIP-seq analysis of FLYWCH1 genomic target locations in HEK293, THC0390TANM_FLYWCH1_ChIP1


title: ChIP-seq analysis of GATAD2B genomic target locations in HEK293, THC0398TANM_GATAD2B_ChIP1


title: ChIP-seq analysis of TPRX1 genomic target locations in HEK293, THC0391TAND_TPRX1_ChIP1


title: ChIP-seq analysis of NANOGNB genomic target locations in HEK293, THC0383TAND_NANOGNB_ChIP1

value: NANOGNB


title: ChIP-seq analysis of DMRTB1 genomic target locations in HEK293, THC0382TAND_DMRTB1_ChIP1


title: ChIP-seq analysis of ZNF48 genomic target locations in HEK293, THC0381TANM_ZNF48_ChIP1


title: ChIP-seq analysis of ZNF280D genomic target locations in HEK293, THC0380TANM_ZNF280D_ChIP1


title: ChIP-seq analysis of ZNF280D genomic target locations in HEK293, THC0380TAND_ZNF280D_ChIP1


title: ChIP-seq analysis of ZNF48 genomic target locations in HEK293, THC0381TAND_ZNF48_ChIP1


title: ChIP-seq analysis of ZNF326 genomic target locations in HEK293, THC0388TANM_ZNF326_ChIP1


title: ChIP-seq analysis of ZNF160 genomic target locations in HEK293, THC0387TAND_ZNF160_ChIP1


title: ChIP-seq analysis of ZNF493 genomic target locations in HEK293, THC0389TAND_ZNF493_ChIP1


title: Pre-IP control THC0386TANM_PRDM13_INPUT1


title: ChIP-seq analysis of ZNF493 genomic target locations in HEK293, THC0389TANM_ZNF493_ChIP1


title: ChIP-seq analysis of NCOA1 genomic target locations in HEK293, THC0385TAND_NCOA1_ChIP2


title: ChIP-seq analysis of ZNF347 genomic target locations in HEK293, THC0396TAND_ZNF347_ChIP1


title: ChIP-seq analysis of NANOGNB genomic target locations in HEK293, THC0383TANM_NANOGNB_ChIP1


title: ChIP-seq analysis of PRDM8 genomic target locations in HEK293, THC0377TAND_PRDM8_ChIP1


title: ChIP-seq analysis of ZNF14 genomic target locations in HEK293, THC0378TANM_ZNF14_ChIP1


title: ChIP-seq analysis of TET2 genomic target locations in HEK293, THC0376TANM_TET2_ChIP2


title: ChIP-seq analysis of NCOA1 genomic target locations in HEK293, THC0385TANM_NCOA1_ChIP2


title: ChIP-seq analysis of DMRTB1 genomic target locations in HEK293, THC0382TANM_DMRTB1_ChIP1


title: ChIP-seq analysis of ZNF142 genomic target locations in HEK293, THC0379TANM_ZNF142_ChIP1


title: ChIP-seq analysis of GTF2IRD2B genomic target locations in HEK293, THC0375TAND_GTF2IRD2B_ChIP2


title: ChIP-seq analysis of ZNF609 genomic target locations in HEK293, THC0374TANM_ZNF609_ChIP2


title: ChIP-seq analysis of ZNF230 genomic target locations in HEK293, THC0373TANM_ZNF230_ChIP2


title: ChIP-seq analysis of ZNF142 genomic target locations in HEK293, THC0379TAND_ZNF142_ChIP1


title: ChIP-seq analysis of ZNF14 genomic target locations in HEK293, THC0378TAND_ZNF14_ChIP1


title: ChIP-seq analysis of PRDM8 genomic target locations in HEK293, THC0377TANM_PRDM8_ChIP1


title: ChIP-seq analysis of ZNF385B genomic target locations in HEK293, THC0372TAND_ZNF385B_ChIP2


title: ChIP-seq analysis of TET2 genomic target locations in HEK293, THC0376TAND_TET2_ChIP2


title: ChIP-seq analysis of GTF2IRD2B genomic target locations in HEK293, THC0375TANM_GTF2IRD2B_ChIP2


title: ChIP-seq analysis of ZNF609 genomic target locations in HEK293, THC0374TAND_ZNF609_ChIP2


title: ChIP-seq analysis of ZNF230 genomic target locations in HEK293, THC0373TAND_ZNF230_ChIP2


title: ChIP-seq analysis of ZNF385B genomic target locations in HEK293, THC0372TANM_ZNF385B_ChIP2


title: ChIP-seq analysis of ZFPM1 genomic target locations in HEK293, THC0371TANM_ZFPM1_ChIP2


title: ChIP-seq analysis of ZFPM1 genomic target locations in HEK293, THC0371TAND_ZFPM1_ChIP2


title: ChIP-seq analysis of PRDM5 genomic target locations in HEK293, THC0369TANM_PRDM5_ChIP1


title: ChIP-seq analysis of ZNF107 genomic target locations in HEK293, THC0370TAND_ZNF107_ChIP1


title: ChIP-seq analysis of TCF20 genomic target locations in HEK293, THC0368TANM_TCF20_ChIP2


title: ChIP-seq analysis of GTF2IRD2 genomic target locations in HEK293, THC0367TANM_GTF2IRD2_ChIP2


title: ChIP-seq analysis of TCF20 genomic target locations in HEK293, THC0368TAND_TCF20_ChIP2


title: ChIP-seq analysis of GTF2IRD2 genomic target locations in HEK293, THC0367TAND_GTF2IRD2_ChIP2


title: ChIP-seq analysis of ZNF516 genomic target locations in HEK293, THC0366TANM_ZNF516_ChIP2


title: ChIP-seq analysis of ZNF516 genomic target locations in HEK293, THC0366TAND_ZNF516_ChIP2


title: ChIP-seq analysis of ZNF229 genomic target locations in HEK293, THC0365TAND_ZNF229_ChIP2


title: ChIP-seq analysis of ZNF362 genomic target locations in HEK293, THC0364TANM_ZNF362_ChIP2


title: ChIP-seq analysis of ZNF229 genomic target locations in HEK293, THC0365TANM_ZNF229_ChIP2


title: ChIP-seq analysis of ZFAT genomic target locations in HEK293, THC0363TANM_ZFAT_ChIP2

value: ZFAT


title: ChIP-seq analysis of ZNF362 genomic target locations in HEK293, THC0364TAND_ZNF362_ChIP2


title: ChIP-seq analysis of CPXCR1 genomic target locations in HEK293, THC0361TAND_CPXCR1_ChIP1


title: ChIP-seq analysis of ZMAT4 genomic target locations in HEK293, THC0362TAND_ZMAT4_ChIP1


title: ChIP-seq analysis of ZNF107 genomic target locations in HEK293, THC0370TANM_ZNF107_ChIP1


title: ChIP-seq analysis of SON genomic target locations in HEK293, THC0360TANM_SON_ChIP2

value: SON


title: ChIP-seq analysis of SON genomic target locations in HEK293, THC0360TAND_SON_ChIP2


title: ChIP-seq analysis of PRDM5 genomic target locations in HEK293, THC0369TAND_PRDM5_ChIP1


title: ChIP-seq analysis of GRHL3 genomic target locations in HEK293, THC0359TANM_GRHL3_ChIP2


title: ChIP-seq analysis of ZNF510 genomic target locations in HEK293, THC0358TANM_ZNF510_ChIP2


title: ChIP-seq analysis of ZNF510 genomic target locations in HEK293, THC0358TAND_ZNF510_ChIP2


title: ChIP-seq analysis of CPXCR1 genomic target locations in HEK293, THC0361TANM_CPXCR1_ChIP1


title: ChIP-seq analysis of GRHL3 genomic target locations in HEK293, THC0359TAND_GRHL3_ChIP2


title: ChIP-seq analysis of ZNF226 genomic target locations in HEK293, THC0357TAND_ZNF226_ChIP2


title: ChIP-seq analysis of ZNF226 genomic target locations in HEK293, THC0357TANM_ZNF226_ChIP2


title: ChIP-seq analysis of ZNF385A genomic target locations in HEK293, THC0356TANM_ZNF385A_ChIP2


title: ChIP-seq analysis of ZNF385A genomic target locations in HEK293, THC0356TAND_ZNF385A_ChIP2


title: ChIP-seq analysis of ZMAT1 genomic target locations in HEK293, THC0354TAND_ZMAT1_ChIP1


title: ChIP-seq analysis of CASZ1 genomic target locations in HEK293, THC0353TAND_CASZ1_ChIP1


title: ChIP-seq analysis of SLC2A4RG genomic target locations in HEK293, THC0355TAND_SLC2A4RG_ChIP2


title: ChIP-seq analysis of SLC2A4RG genomic target locations in HEK293, THC0355TANM_SLC2A4RG_ChIP2


title: ChIP-seq analysis of CASZ1 genomic target locations in HEK293, THC0353TANM_CASZ1_ChIP1


title: ChIP-seq analysis of ZFAT genomic target locations in HEK293, THC0363TAND_ZFAT_ChIP2


title: ChIP-seq analysis of ZHX3 genomic target locations in HEK293, THC0352TAND_ZHX3_ChIP2


title: ChIP-seq analysis of ZHX3 genomic target locations in HEK293, THC0352TANM_ZHX3_ChIP2


title: ChIP-seq analysis of ZGLP1 genomic target locations in HEK293, THC0351TANM_ZGLP1_ChIP2


title: ChIP-seq analysis of ZGLP1 genomic target locations in HEK293, THC0351TAND_ZGLP1_ChIP2


title: ChIP-seq analysis of ZNF507 genomic target locations in HEK293, THC0350TAND_ZNF507_ChIP2


title: ChIP-seq analysis of ZNF207 genomic target locations in HEK293, THC0349TANM_ZNF207_ChIP2


title: ChIP-seq analysis of ZNF358 genomic target locations in HEK293, THC0348TAND_ZNF358_ChIP2


title: ChIP-seq analysis of ZNF358 genomic target locations in HEK293, THC0348TANM_ZNF358_ChIP2


title: ChIP-seq analysis of ZMAT1 genomic target locations in HEK293, THC0354TANM_ZMAT1_ChIP1


title: ChIP-seq analysis of ZFPM2 genomic target locations in HEK293, THC0346TANM_ZFPM2_ChIP1


title: ChIP-seq analysis of ZFPM2 genomic target locations in HEK293, THC0346TAND_ZFPM2_ChIP1


title: ChIP-seq analysis of SALL3 genomic target locations in HEK293, THC0347TANM_SALL3_ChIP2


title: ChIP-seq analysis of ZHX2 genomic target locations in HEK293, THC0344TANM_ZHX2_ChIP2


title: ChIP-seq analysis of SOHLH1 genomic target locations in HEK293, THC0345TANM_SOHLH1_ChIP1


title: ChIP-seq analysis of ZHX2 genomic target locations in HEK293, THC0344TAND_ZHX2_ChIP2


title: ChIP-seq analysis of ZNF497 genomic target locations in HEK293, THC0342TANM_ZNF497_ChIP2


title: ChIP-seq analysis of ZNF507 genomic target locations in HEK293, THC0350TANM_ZNF507_ChIP2


title: ChIP-seq analysis of GATAD2B genomic target locations in HEK293, THC0343TANM_GATAD2B_ChIP2


title: ChIP-seq analysis of SOHLH1 genomic target locations in HEK293, THC0345TAND_SOHLH1_ChIP1


title: ChIP-seq analysis of ZNF497 genomic target locations in HEK293, THC0342TAND_ZNF497_ChIP2


title: ChIP-seq analysis of ZNF347 genomic target locations in HEK293, THC0340TAND_ZNF347_ChIP2


title: ChIP-seq analysis of ZNF347 genomic target locations in HEK293, THC0340TANM_ZNF347_ChIP2


title: ChIP-seq analysis of RLF genomic target locations in HEK293, THC0339TANM_RLF_ChIP2

value: RLF


title: ChIP-seq analysis of RLF genomic target locations in HEK293, THC0339TAND_RLF_ChIP2


title: ChIP-seq analysis of ZFPM1 genomic target locations in HEK293, THC0338TANM_ZFPM1_ChIP1


title: ChIP-seq analysis of ZNF20 genomic target locations in HEK293, THC0341TAND_ZNF20_ChIP2


title: ChIP-seq analysis of NCOA1 genomic target locations in HEK293, THC0337TANM_NCOA1_ChIP1


title: ChIP-seq analysis of ZNF207 genomic target locations in HEK293, THC0349TAND_ZNF207_ChIP2


title: ChIP-seq analysis of NCOA1 genomic target locations in HEK293, THC0337TAND_NCOA1_ChIP1


title: ChIP-seq analysis of TPRX1 genomic target locations in HEK293, THC0336TANM_TPRX1_ChIP2


title: ChIP-seq analysis of TPRX1 genomic target locations in HEK293, THC0336TAND_TPRX1_ChIP2


title: ChIP-seq analysis of SALL3 genomic target locations in HEK293, THC0347TAND_SALL3_ChIP2


title: ChIP-seq analysis of ZNF493 genomic target locations in HEK293, THC0334TANM_ZNF493_ChIP2


title: ChIP-seq analysis of GATAD2B genomic target locations in HEK293, THC0343TAND_GATAD2B_ChIP2


title: ChIP-seq analysis of FLYWCH1 genomic target locations in HEK293, THC0335TAND_FLYWCH1_ChIP2


title: ChIP-seq analysis of ZNF160 genomic target locations in HEK293, THC0333TANM_ZNF160_ChIP2


title: ChIP-seq analysis of FLYWCH1 genomic target locations in HEK293, THC0335TANM_FLYWCH1_ChIP2


title: ChIP-seq analysis of ZNF493 genomic target locations in HEK293, THC0334TAND_ZNF493_ChIP2


title: ChIP-seq analysis of RBSN genomic target locations in HEK293, THC0331TANM_RBSN_ChIP2

value: RBSN


title: ChIP-seq analysis of ZNF326 genomic target locations in HEK293, THC0332TANM_ZNF326_ChIP2


title: ChIP-seq analysis of ZFAT genomic target locations in HEK293, THC0330TANM_ZFAT_ChIP1


title: ChIP-seq analysis of ZFAT genomic target locations in HEK293, THC0330TAND_ZFAT_ChIP1


title: ChIP-seq analysis of ZNF160 genomic target locations in HEK293, THC0333TAND_ZNF160_ChIP2


title: ChIP-seq analysis of RBSN genomic target locations in HEK293, THC0331TAND_RBSN_ChIP2


title: ChIP-seq analysis of ARID2 genomic target locations in HEK293, THC0329TANM_ARID2_ChIP1


title: ChIP-seq analysis of ZNF20 genomic target locations in HEK293, THC0341TANM_ZNF20_ChIP2


title: ChIP-seq analysis of ZNF326 genomic target locations in HEK293, THC0332TAND_ZNF326_ChIP2


title: ChIP-seq analysis of DMRTB1 genomic target locations in HEK293, THC0327TANM_DMRTB1_ChIP2


title: ChIP-seq analysis of ZNF48 genomic target locations in HEK293, THC0326TANM_ZNF48_ChIP2


title: ChIP-seq analysis of ARID2 genomic target locations in HEK293, THC0329TAND_ARID2_ChIP1


title: ChIP-seq analysis of NANOGNB genomic target locations in HEK293, THC0328TANM_NANOGNB_ChIP2


title: ChIP-seq analysis of NANOGNB genomic target locations in HEK293, THC0328TAND_NANOGNB_ChIP2


title: ChIP-seq analysis of DMRTB1 genomic target locations in HEK293, THC0327TAND_DMRTB1_ChIP2


title: ChIP-seq analysis of ZFPM1 genomic target locations in HEK293, THC0338TAND_ZFPM1_ChIP1


title: ChIP-seq analysis of ZNF48 genomic target locations in HEK293, THC0326TAND_ZNF48_ChIP2


title: ChIP-seq analysis of PRMT3 genomic target locations in HEK293, THC0323TANM_PRMT3_ChIP2


title: ChIP-seq analysis of PRMT3 genomic target locations in HEK293, THC0323TAND_PRMT3_ChIP2


title: ChIP-seq analysis of ZNF142 genomic target locations in HEK293, THC0325TAND_ZNF142_ChIP2


title: ChIP-seq analysis of SLC2A4RG genomic target locations in HEK293, THC0322TANM_SLC2A4RG_ChIP1


title: ChIP-seq analysis of SLC2A4RG genomic target locations in HEK293, THC0322TAND_SLC2A4RG_ChIP1


title: ChIP-seq analysis of ZNF280D genomic target locations in HEK293, THC0324TAND_ZNF280D_ChIP2


title: ChIP-seq analysis of MKX genomic target locations in HEK293, THC0320TANM_MKX_ChIP2

value: MKX


title: ChIP-seq analysis of MKX genomic target locations in HEK293, THC0320TAND_MKX_ChIP2


title: ChIP-seq analysis of KDM2A genomic target locations in HEK293, THC0319TANM_KDM2A_ChIP2


title: ChIP-seq analysis of ZNF474 genomic target locations in HEK293, THC0318TAND_ZNF474_ChIP2


title: ChIP-seq analysis of KDM2A genomic target locations in HEK293, THC0319TAND_KDM2A_ChIP2


title: ChIP-seq analysis of ZNF14 genomic target locations in HEK293, THC0317TANM_ZNF14_ChIP2


title: ChIP-seq analysis of ZNF14 genomic target locations in HEK293, THC0317TAND_ZNF14_ChIP2


title: ChIP-seq analysis of ZNF474 genomic target locations in HEK293, THC0318TANM_ZNF474_ChIP2


title: ChIP-seq analysis of ZNF280B genomic target locations in HEK293, THC0316TANM_ZNF280B_ChIP2


title: ChIP-seq analysis of PRDM8 genomic target locations in HEK293, THC0315TANM_PRDM8_ChIP2


title: ChIP-seq analysis of ZNF280B genomic target locations in HEK293, THC0316TAND_ZNF280B_ChIP2


title: ChIP-seq analysis of ZNF280D genomic target locations in HEK293, THC0324TANM_ZNF280D_ChIP2


title: ChIP-seq analysis of CTCF genomic target locations in HEK293, THC0313TAND_CTCF_ChIP2

value: CTCF


title: ChIP-seq analysis of CTCF genomic target locations in HEK293, THC0313TANM_CTCF_ChIP2


title: ChIP-seq analysis of ZNF471 genomic target locations in HEK293, THC0310TANM_ZNF471_ChIP2


title: ChIP-seq analysis of MBNL2 genomic target locations in HEK293, THC0311TAND_MBNL2_ChIP2


title: ChIP-seq analysis of LEUTX genomic target locations in HEK293, THC0312TAND_LEUTX_ChIP2

value: LEUTX


title: ChIP-seq analysis of SALL3 genomic target locations in HEK293, THC0314TANM_SALL3_ChIP1


title: ChIP-seq analysis of MBNL2 genomic target locations in HEK293, THC0311TANM_MBNL2_ChIP2


title: ChIP-seq analysis of ZNF471 genomic target locations in HEK293, THC0310TAND_ZNF471_ChIP2


title: ChIP-seq analysis of ZNF107 genomic target locations in HEK293, THC0309TANM_ZNF107_ChIP2


title: ChIP-seq analysis of ZNF107 genomic target locations in HEK293, THC0309TAND_ZNF107_ChIP2


title: ChIP-seq analysis of ZNF275 genomic target locations in HEK293, THC0308TANM_ZNF275_ChIP2


title: ChIP-seq analysis of ZNF275 genomic target locations in HEK293, THC0308TAND_ZNF275_ChIP2


title: ChIP-seq analysis of PRDM5 genomic target locations in HEK293, THC0307TANM_PRDM5_ChIP2


title: ChIP-seq analysis of PRDM5 genomic target locations in HEK293, THC0307TAND_PRDM5_ChIP2


title: ChIP-seq analysis of PRDM8 genomic target locations in HEK293, THC0315TAND_PRDM8_ChIP2


title: ChIP-seq analysis of SALL3 genomic target locations in HEK293, THC0314TAND_SALL3_ChIP1


title: ChIP-seq analysis of RLF genomic target locations in HEK293, THC0306TAND_RLF_ChIP1


title: ChIP-seq analysis of YY1 genomic target locations in HEK293, THC0305TANM_YY1_ChIP2


title: ChIP-seq analysis of LEUTX genomic target locations in HEK293, THC0312TANM_LEUTX_ChIP2


title: ChIP-seq analysis of ADNP genomic target locations in HEK293, THC0304TAND_ADNP_ChIP2

value: ADNP


title: ChIP-seq analysis of YY1 genomic target locations in HEK293, THC0305TAND_YY1_ChIP2


title: ChIP-seq analysis of ZMAT4 genomic target locations in HEK293, THC0301TANM_ZMAT4_ChIP2


title: ChIP-seq analysis of ADNP genomic target locations in HEK293, THC0304TANM_ADNP_ChIP2


title: ChIP-seq analysis of RLF genomic target locations in HEK293, THC0306TANM_RLF_ChIP1


title: ChIP-seq analysis of ZNF470 genomic target locations in HEK293, THC0302TAND_ZNF470_ChIP2


title: ChIP-seq analysis of ZXDC genomic target locations in HEK293, THC0303TANM_ZXDC_ChIP2

value: ZXDC


title: ChIP-seq analysis of ZMAT4 genomic target locations in HEK293, THC0301TAND_ZMAT4_ChIP2


title: ChIP-seq analysis of RBSN genomic target locations in HEK293, THC0298TAND_RBSN_ChIP1


title: ChIP-seq analysis of CPXCR1 genomic target locations in HEK293, THC0299TAND_CPXCR1_ChIP2


title: ChIP-seq analysis of CPXCR1 genomic target locations in HEK293, THC0299TANM_CPXCR1_ChIP2


title: ChIP-seq analysis of TSC22D1 genomic target locations in HEK293, THC0297TANM_TSC22D1_ChIP2


title: ChIP-seq analysis of ZNF251 genomic target locations in HEK293, THC0300TANM_ZNF251_ChIP2


title: ChIP-seq analysis of HMGN3 genomic target locations in HEK293, THC0296TANM_HMGN3_ChIP2


title: ChIP-seq analysis of TSC22D1 genomic target locations in HEK293, THC0297TAND_TSC22D1_ChIP2


title: ChIP-seq analysis of HMGN3 genomic target locations in HEK293, THC0296TAND_HMGN3_ChIP2


title: ChIP-seq analysis of ZNF470 genomic target locations in HEK293, THC0302TANM_ZNF470_ChIP2


title: ChIP-seq analysis of ZXDA genomic target locations in HEK293, THC0295TAND_ZXDA_ChIP2

value: ZXDA


title: ChIP-seq analysis of ZXDA genomic target locations in HEK293, THC0295TANM_ZXDA_ChIP2


title: ChIP-seq analysis of ZXDC genomic target locations in HEK293, THC0303TAND_ZXDC_ChIP2


title: ChIP-seq analysis of ZMAT1 genomic target locations in HEK293, THC0293TANM_ZMAT1_ChIP2


title: ChIP-seq analysis of ZNF395 genomic target locations in HEK293, THC0294TANM_ZNF395_ChIP2


title: ChIP-seq analysis of ZNF395 genomic target locations in HEK293, THC0294TAND_ZNF395_ChIP2


title: ChIP-seq analysis of ZNF234 genomic target locations in HEK293, THC0292TAND_ZNF234_ChIP2


title: ChIP-seq analysis of CASZ1 genomic target locations in HEK293, THC0291TAND_CASZ1_ChIP2


title: ChIP-seq analysis of CASZ1 genomic target locations in HEK293, THC0291TANM_CASZ1_ChIP2


title: ChIP-seq analysis of ZNF251 genomic target locations in HEK293, THC0300TAND_ZNF251_ChIP2


title: ChIP-seq analysis of ZNF234 genomic target locations in HEK293, THC0292TANM_ZNF234_ChIP2


title: ChIP-seq analysis of PRMT3 genomic target locations in HEK293, THC0290TAND_PRMT3_ChIP1


title: ChIP-seq analysis of ZMAT4 genomic target locations in HEK293, THC0362TANM_ZMAT4_ChIP1


title: ChIP-seq analysis of TMF1 genomic target locations in HEK293, THC0289TAND_TMF1_ChIP2


title: ChIP-seq analysis of ZMAT1 genomic target locations in HEK293, THC0293TAND_ZMAT1_ChIP2


title: ChIP-seq analysis of PRMT3 genomic target locations in HEK293, THC0290TANM_PRMT3_ChIP1


title: ChIP-seq analysis of HMG20A genomic target locations in HEK293, THC0288TANM_HMG20A_ChIP2


title: ChIP-seq analysis of HMG20A genomic target locations in HEK293, THC0288TAND_HMG20A_ChIP2


title: Mouse_SI_TGFbKO_MERFISH

type: RNA

city: Seattle

first: Maximilian

last: Heeg

state: WA

address: 615 Westlake Ave N

country: USA

institute: Allen Institute for Immunology

description:
WT: top left
KO: bottom right

hyb_protocol: not applicable

scan_protocol: Xenium analyzer and MERSCOPE were used to image target RNA positions and cell boundaries. Proprietary software was used to decode and return RNA positions as outputs from each machine, along with raw images of cell nucleus and boundary stainings.

data_processing:
Cell nuclei were segmented using Cellpose 2.0 (Pachitariu et al. 2022). Cell boundaries were predicted using the nuclear staining and transcript positions using Baysor (Petukhov et al. 2021). Experiments were integrated using scVI (Lopez et al 2018). Celltypes were assigned manually, and the processed object is stored as an Anndata object in h5ad format containing both metadata and raw gene expression counts (Wolf et al 2018).
Raw detected RNA counts per cell

molecule: total RNA

organism: Mus musculus

source_name: FFPE block

label_protocol: not applicable

extract_protocol: 5 um-thick microtome sections of Formalin-Fixed Paraffin-Embedded tissues.

tag: strain

tag: tissue

value: Small Intestine

tag: treatment

value: infection with LCMV

tag: timepoint

value: day 8 after infection


title: ChIP-seq analysis of RBSN genomic target locations in HEK293, THC0298TANM_RBSN_ChIP1

value: ChIP

value: Not approved


title: ChIP-seq analysis of ZUP1 genomic target locations in HEK293, THC0287TANM_ZUP1_ChIP2

value: No expert curation due to insufficient peak numbers


title: Young_collagenase

city: Boston

first: Kseniia

last: Petrova

state: MA

address: 200 Longwood

department: System's biology

institute: HMS

library_source: transcriptomic single cell

data_processing:
inDrops standard pipeline
Assembly: Daphnia Magna DM3 genome assembly BioProject ID: PRJNA624896; Fields et al
Supplementary files format and content: .mtx contains counts in csc format; genes.tsv files contain list of genes, corresponding to columns in the mtx file; barcodes.tsv file contains sample information for each cell corresponding to rows of .mtx file

molecule: polyA RNA

organism: Daphnia magna

source_name: whole body

extract_protocol:
dissociation with collagenase (4 mg / ml) treatment
according to the inDrops protocol ()

treatment_protocol: standard Daphnia lab protocol

value: whole body


title: ChIP-seq analysis of TMF1 genomic target locations in HEK293, THC0289TANM_TMF1_ChIP2


title: ChIP-seq analysis of ZUP1 genomic target locations in HEK293, THC0287TAND_ZUP1_ChIP2


title: Articular chondrocytes, bleomycin, rep 4

city: Seoul

first: Jin-Hong

last: Kim

address: 1 Gwanak-ro, Gwanak-gu

country: South Korea

institute: Seoul National University

library_source: transcriptomic

data_processing:
Reads were trimmed with Trimmomatic and aligned to the reference genome Mus musculus (GRCm38) using STAR aligner. The relative abundance of each transcript was quantified in read count using --quantMode GeneCounts option of STAR aligner.
Assembly: mm38
Supplementary files format and content: tab file includes FPKM values for each sample.

source_name: articular chondrocytes

growth_protocol: Mouse articular chondrocytes were maintained in DMEM supplemented with 10% FBS, 100 U/mL penicillin, and 100 μg/mL streptomycin in a humidified 37 °C, 5% CO2, and 3% O2 atmosphere.

extract_protocol:
Total RNA was extracted using the TRI reagent (Molecular Research Center, Inc.).
One microgram of total RNA was converted into cDNA libraries using the TruSeq Stranded mRNA Library Prep kit (Illumina) in accordance with the TruSeq Standard mRNA Reference Guide, # 1000000040498 v00. Final cDNA libraries were analyzed for size distribution, quantified on Agilent Technologies 2100 Bioanalyzer using a DNA 1000 chip, and normalized to 2 nM for sequencing. RNA sequencing libraries were constructed by Macrogen.

treatment_protocol: Prior to bleomycin treatment, mouse primary chondrocytes were treated with hyaluronidase type I-S (4 U/mL) for 4 h under serum-free condition, two days after seeding. Cells were treated with 50 μg/mL of bleomycin in serum-supplemented medium for 24 h. Then, cells were washed twice with PBS and incubated in fresh medium for five days. For doxorubicin treatment, mouse primary chondrocytes were treated with 50 nM of doxorubicin in serum-supplemented medium for five days. Fresh medium was supplemented every 48 h. One ng/mL of interleukin-1 beta or or an equal volume of PBS in serum-supplemented medium for 24 h.

tag: cell type

value: articular chondrocytes

value: bleomycin


title: ChIP-seq analysis of ZNF385C genomic target locations in HEK293, THC0286TANM_ZNF385C_ChIP2


title: Articular chondrocytes, vehicle control, rep 4

value: vehicle


title: Articular chondrocytes, il1b, rep 3

value: interleukin-1 beta


title: ChIP-seq analysis of ZFPM2 genomic target locations in HEK293, THC0285TANM_ZFPM2_ChIP2


title: ChIP-seq analysis of ZNF385C genomic target locations in HEK293, THC0286TAND_ZNF385C_ChIP2


title: Articular chondrocytes, doxorubicin, rep 3

value: doxorubicin


title: Articular chondrocytes, bleomycin, rep 3


title: ChIP-seq analysis of ZNF233 genomic target locations in HEK293, THC0284TAND_ZNF233_ChIP2


title: Articular chondrocytes, doxorubicin, rep 2


title: Articular chondrocytes, il1b, rep 2


title: ChIP-seq analysis of NCOA1 genomic target locations in HEK293, THC0283TANM_NCOA1_ChIP2


title: ChIP-seq analysis of NCOA1 genomic target locations in HEK293, THC0283TAND_NCOA1_ChIP2


title: ChIP-seq analysis of ZNF233 genomic target locations in HEK293, THC0284TANM_ZNF233_ChIP2


title: Articular chondrocytes, vehicle control, rep 3


title: Articular chondrocytes, vehicle control, rep 2


title: Articular chondrocytes, doxorubicin, rep 4


title: Articular chondrocytes, il1b, rep 1


title: Articular chondrocytes, bleomycin, rep 2


title: Articular chondrocytes, doxorubicin, rep 1


title: ChIP-seq analysis of TIGD3 genomic target locations in HEK293, THC0282TANR_TIGD3_ChIP2

value: Approved


title: ChIP-seq analysis of ZBED5 genomic target locations in HEK293, THC0278TANR_ZBED5_ChIP2


title: Articular chondrocytes, vehicle control, rep 1


title: Articular chondrocytes, bleomycin, rep 1


title: Articular chondrocytes, il1b, rep 4


title: ChIP-seq analysis of ZFPM2 genomic target locations in HEK293, THC0285TAND_ZFPM2_ChIP2


title: ChIP-seq analysis of ARID2 genomic target locations in HEK293, THC0275TANN_ARID2_ChIP2


title: ChIP-seq analysis of ZNF609 genomic target locations in HEK293, THC0274TANN_ZNF609_ChIP1


title: ChIP-seq analysis of SP110 genomic target locations in HEK293, THC0273TANN_SP110_ChIP2


title: C57BL/6, nicotine, rep 3

city: Haikou

first: Feifan

last: Zhou

address: 58 Renmin Avenue

country: China

institute: Hainan University

data_processing:
Reads obtained from the sequencing machines includes raw reads containing adapters or low quality bases which will affect the following assembly and analysis. Thus, to get high  quality clean reads, reads were further filtered by fastp (version 0.18.0).
Short reads alignment tool Bowtie2  (version 2.2.8) was used for mapping reads to ribosome RNA (rRNA) database. The rRNA mapped reads then will be removed. The remaining clean   reads were further used in assembly and gene abundance calculation.
An index of the reference genome was built, and paired-end clean reads were mapped to the    reference genome using HISAT2. 2.4  with “-rna-strandness RF” and other parameters set as a default.
The mapped reads of each sample were assembled by using StringTie v1.3.1 in a reference-based approach. For each transcription region, a FPKM (fragment per kilobase of transcript per million mapped reads) value was calculated to quantify its expression abundance and variations, using RSEM software.
Given FPKM(A) to be the expression of gene A, C to be number of fragments mapped to gene A, N to be total number of fragments that mapped to reference genes, and L to be number of bases on gene A. The FPKM method is able to eliminate the influence of different gene lengths and sequencing data amount on the calculation of gene expression. Therefore,    the calculated gene expression can be directly used for comparing the difference of gene expression among samples.
Assembly: mm10
Supplementary files format and content: textfile includes raw counts for each sample
Supplementary files format and content: text files include FPKM values for each sample

source_name: nucleus accumbens

extract_protocol:
Total RNA was extracted using Trizol reagent (Invitrogen,15596018)
The cell lysis or the extracted total RNA was mixed with 1ul of 10uM Oligo-dT primer and 1ul of 10uM dNTP reagent and then incubated at 72℃ for 3min. The reverse transcription reaction was performed in 1X Super Script II first-strand buffer system with 200U of Super Script II reverse transcriptase，0.1ul  of TSO （100uM），20U RNAse Inhibitor，0.75ul of DTT（100mM），3ul of Betaine（5M）and 0.09ul of MgCl2（1M）. The full length cDNA was synthesized at 42℃ for 90min and then with 10 cycles of 50℃ for 2min and 42℃ for 2min. Finally, the product was incubated at 70℃ for 15min to inactive the enzyme activation. After amplified the synthesized cDNA with 10 to15 cycles of PCR amplification, the product was purified and used for library construction. After analyzed by Agilent Bioanalyzer and quantified by real time PCR, the library was sequenced with Illumina Novaseq platform.

value: nucleus accumbens


title: C57BL/6, nicotine, rep 4


title: C57BL/6, nicotine, rep 2


title: ChIP-seq analysis of SNAPC2 genomic target locations in HEK293, THC0271TANN_SNAPC2_ChIP2


title: C57BL/6, nicotine, rep 1


title: ChIP-seq analysis of ZNF428 genomic target locations in HEK293, THC0280TANR_ZNF428_ChIP2


title: C57BL/6, caffeine, rep 3


title: ChIP-seq analysis of THAP2 genomic target locations in HEK293, THC0259TANN_THAP2_ChIP2


title: C57BL/6, caffeine, rep 4


title: C57BL/6, caffeine, rep 2


title: C57BL/6, caffeine, rep 1


title: ChIP-seq analysis of SCML4 genomic target locations in HEK293, THC0258TANN_SCML4_ChIP2


title: ChIP-seq analysis of ZNF428 genomic target locations in HEK293, THC0279TANR_ZNF428_ChIP1


title: Pre-IP control THC0254TANN_ZNF503_INPUT1

value: Input


title: ChIP-seq analysis of CAMTA1 genomic target locations in HEK293, THC0257TANN_CAMTA1_ChIP2


title: ChIP-seq analysis of CPXCR1 genomic target locations in HEK293, THC0276TANN_CPXCR1_ChIP1


title: ChIP-seq analysis of THAP2 genomic target locations in HEK293, THC0251TANN_THAP2_ChIP1


title: C57BL/6, arecoline, rep 2


title: C57BL/6, arecoline, rep 1


title: ChIP-seq analysis of CAMTA1 genomic target locations in HEK293, THC0249TANN_CAMTA1_ChIP1


title: ChIP-seq analysis of SCML4 genomic target locations in HEK293, THC0250TANN_SCML4_ChIP1


title: C57BL/6, saline, rep 4


title: ChIP-seq analysis of FBXL19 genomic target locations in HEK293, THC0248TANN_FBXL19_ChIP2


title: C57BL/6, saline, rep 3


title: C57BL/6, saline, rep 2


title: C57BL/6, arecoline, rep 3


title: ChIP-seq analysis of YY1 genomic target locations in HEK293, THC0261TANN_YY1_ChIP2


title: ChIP-seq analysis of CHAMP1 genomic target locations in HEK293, THC0246TANN_CHAMP1_ChIP2


title: Lung CDDO biol rep 5

city: Heidelberg

first: Nikolas

last: Gunkel

state: *Not Applicable

address: Im Neuenheimer Feld 280

department: Research Group Cancer Drug Development

country: Germany

institute: German Cancer Research Center (DKFZ)

data_processing:
For the analysis of the known reference transcriptome assembly, RNA sequencing data were processed automatically via the One Touch Pipeline (OTP) (Resinger et al. 2017).
The BAM files were produced with the following configuration(s): RNA PAIRED bulk
Alignment program: STAR Version 2.5.3a --twopassMode Basic --twopass1readsN -1 --genomeLoad NoSharedMemory --outSAMtype BAM Unsorted SortedByCoordinate --limitBAMsortRAM 100000000000 --outBAMsortingThreadN=1 --outSAMstrandField intronMotif --outSAMunmapped Within KeepPairs --outFilterMultimapNmax 1 --outFilterMismatchNmax 5 --outFilterMismatchNoverLmax 0.3 --chimSegmentMin 15 --chimScoreMin 1 --chimScoreJunctionNonGTAG 0 --chimJunctionOverhangMin 15  --chimSegmentReadGapMax 3 --alignSJstitchMismatchNmax 5 -1 5 5 --alignIntronMax 1100000 --alignMatesGapMax 1100000 --alignSJDBoverhangMin 3 --alignIntronMin 20
Merging/duplication marking program: Sambamba Version 0.6.5
SAMtools program: Version 1.6
Pipeline: RNAseqWorkflow:1.3.0
Assembly: Reference genome: 1KGRef_PhiX (H. sapiens) and GRCm38mm10_PhiX (M.musculus)
Supplementary files format and content: read counts FPKM TPM .tsv

source_name: lung

growth_protocol: NCI-H526 cells were maintained in RPMI supplemented with 10 % fetal bovine serum (FBS), 100 U/mL penicillin and 100 µg/mL streptomycin at 37 °C in a 5 % CO2 atmosphere.

extract_protocol:
Total RNA was extracted from mouse tissues and tumors using the Nucleospin RNA kit (Macherey-Nagel).
RNA was submitted to the NGS Core Facility of the German Cancer Research Center where the high-throughput sequencing including library preparation and data quality control was performed. Sequencing libraries were prepared using TruSeq Stranded mRNA Library Prep Kit (Illumina) and IDT Unique Dual Indexes for Illumina (Integrated DNA Technologies) and sequenced using NovaSeq 6000 sequencing system (paired-end mode, read length 100 bp, S4 flow cell; Illumina), yielding on average 52 million reads per sample (32–76 million).

treatment_protocol:
To generate a subcutaneous SCLC-tumor model, H526 cells were resuspended in a 1:1 (vol/vol) mix of ice-cold growth factor-reduced Matrigel (Corning) and PBS. Overall, 100 µl of this cell suspension containing 2 million H526 cells was injected subcutaneously into the flank of anesthetized mice.
4 weeks later, tumor bearing animals were randomly distributed to experimental groups and injected daily for 4 consecutive days with 3 mg/kg CDDO-me or vehicle i.p.
Harvested tissues were stored in RNAlater at -80 °C before further processing.

value: lung

value: NSG

tag: Sex

value: female

value: CDDO-me


title: C57BL/6, arecoline, rep 4


title: ChIP-seq analysis of CXXC4 genomic target locations in HEK293, THC0243TANN_CXXC4_ChIP2


title: Lung CDDO biol rep 4


title: ChIP-seq analysis of YY1 genomic target locations in HEK293, THC0253TANN_YY1_ChIP1


title: ChIP-seq analysis of ATMIN genomic target locations in HEK293, THC0244TANN_ATMIN_ChIP2

value: ATMIN


title: ChIP-seq analysis of NCOA1 genomic target locations in HEK293, THC0242TANN_NCOA1_ChIP2

value: ChIP


title: Lung CDDO biol rep 3


title: Lung vehicle biol rep 5


title: ChIP-seq analysis of AKNA genomic target locations in HEK293, THC0241TANN_AKNA_ChIP2

value: AKNA


title: ChIP-seq analysis of FBXL19 genomic target locations in HEK293, THC0240TANN_FBXL19_ChIP1


title: ChIP-seq analysis of ZNF142 genomic target locations in HEK293, THC0325TANM_ZNF142_ChIP2


title: Lung vehicle biol rep 4


title: Lung CDDO biol rep 1


title: Lung vehicle biol rep 3


title: ChIP-seq analysis of JRK genomic target locations in HEK293, THC0239TANN_JRK_ChIP1

value: JRK


title: Lung vehicle biol rep 2


title: ChIP-seq analysis of ZBED4 genomic target locations in HEK293, THC0245TANN_ZBED4_ChIP2

value: Not approved


title: ChIP-seq analysis of CHAMP1 genomic target locations in HEK293, THC0238TANN_CHAMP1_ChIP1

value: No expert curation due to insufficient peak numbers


title: ChIP-seq analysis of ATMIN genomic target locations in HEK293, THC0236TANN_ATMIN_ChIP1


title: Lung vehicle biol rep 1


title: C57BL/6, saline, rep 1


title: ChIP-seq analysis of ZBED4 genomic target locations in HEK293, THC0237TANN_ZBED4_ChIP1


title: Liver CDDO biol rep 5

source_name: liver

value: liver


title: ChIP-seq analysis of AKNA genomic target locations in HEK293, THC0233TANN_AKNA_ChIP1


title: ChIP-seq analysis of CXXC4 genomic target locations in HEK293, THC0235TANN_CXXC4_ChIP1


title: Lung CDDO biol rep 2


title: ChIP-seq analysis of NCOA1 genomic target locations in HEK293, THC0234TANN_NCOA1_ChIP1


title: Liver CDDO biol rep 4


title: Liver CDDO biol rep 2


title: ChIP-seq analysis of CAMTA2 genomic target locations in HEK293, THC0232TANN_CAMTA2_ChIP2


title: Liver CDDO biol rep 3


title: Liver vehicle biol rep 5

value: vehicle


title: ChIP-seq analysis of KIN genomic target locations in HEK293, THC0229TANN_KIN_ChIP2

value: KIN


title: Liver vehicle biol rep 4


title: Liver vehicle biol rep 3


title: Liver vehicle biol rep 1


title: Liver vehicle biol rep 2


title: ChIP-seq analysis of ZBED5 genomic target locations in HEK293, THC0227TANN_ZBED5_ChIP2


title: Kidney CDDO biol rep 5

source_name: kidney

value: kidney


title: ChIP-seq analysis of JRK genomic target locations in HEK293, THC0247TANN_JRK_ChIP2

value: Approved


title: ChIP-seq analysis of KDM5B genomic target locations in HEK293, THC0226TANN_KDM5B_ChIP2


title: ChIP-seq analysis of POGK genomic target locations in HEK293, THC0225TANN_POGK_ChIP2

value: POGK


title: ChIP-seq analysis of PRDM13 genomic target locations in HEK293, THC0223TANN_PRDM13_ChIP1


title: Kidney CDDO biol rep 3


title: ChIP-seq analysis of PRDM10 genomic target locations in HEK293, THC0222TANN_PRDM10_ChIP1


title: Kidney CDDO biol rep 2


title: ChIP-seq analysis of CAMTA2 genomic target locations in HEK293, THC0224TANN_CAMTA2_ChIP1


title: ChIP-seq analysis of AHCTF1 genomic target locations in HEK293, THC0220TANN_AHCTF1_ChIP1


title: ChIP-seq analysis of KIN genomic target locations in HEK293, THC0221TANN_KIN_ChIP1


title: Kidney vehicle biol rep 4


title: ChIP-seq analysis of PRDM13 genomic target locations in HEK293, THC0231TANN_PRDM13_ChIP2


title: ChIP-seq analysis of ZBED5 genomic target locations in HEK293, THC0219TANN_ZBED5_ChIP1


title: ChIP-seq analysis of PRDM10 genomic target locations in HEK293, THC0230TANN_PRDM10_ChIP2


title: Kidney vehicle biol rep 5


title: ChIP-seq analysis of POGK genomic target locations in HEK293, THC0217TANN_POGK_ChIP1


title: ChIP-seq analysis of KDM5B genomic target locations in HEK293, THC0218TANN_KDM5B_ChIP1


title: Kidney vehicle biol rep 1


title: ChIP-seq analysis of ZNF827 genomic target locations in HEK293, THC0216TANN_ZNF827_ChIP2


title: Kidney vehicle biol rep 2


title: Kidney vehicle biol rep 3


title: ChIP-seq analysis of AHCTF1 genomic target locations in HEK293, THC0228TANN_AHCTF1_ChIP2


title: Kidney CDDO biol rep 4


title: ChIP-seq analysis of ZNF750 genomic target locations in HEK293, THC0215TANN_ZNF750_ChIP2


title: Heart CDDO biol rep 2

source_name: heart

value: heart


title: Heart CDDO biol rep 3


title: ChIP-seq analysis of ZNF446 genomic target locations in HEK293, THC0213TANN_ZNF446_ChIP2


title: Heart CDDO biol rep 4


title: ChIP-seq analysis of ZNF503 genomic target locations in HEK293, THC0211TANN_ZNF503_ChIP2


title: ChIP-seq analysis of ZNF507 genomic target locations in HEK293, THC0212TANN_ZNF507_ChIP2


title: Heart CDDO biol rep 1


title: Heart CDDO biol rep 5


title: ChIP-seq analysis of ZNF606 genomic target locations in HEK293, THC0214TANN_ZNF606_ChIP2


title: ChIP-seq analysis of ZNF500 genomic target locations in HEK293, THC0210TANN_ZNF500_ChIP2


title: Heart vehicle biol rep 4


title: Heart vehicle biol rep 5


title: Heart vehicle biol rep 3


title: Heart vehicle biol rep 2


title: ChIP-seq analysis of ZNF750 genomic target locations in HEK293, THC0207TANN_ZNF750_ChIP1


title: Liver CDDO biol rep 1


title: ChIP-seq analysis of ZNF827 genomic target locations in HEK293, THC0208TANN_ZNF827_ChIP1


title: ChIP-seq analysis of ZNF606 genomic target locations in HEK293, THC0206TANN_ZNF606_ChIP1


title: Spleen, immune cells, GEX, Inlet3

city: Chapel Hill

first: Ageliki

middle: Tsagaratou

last: Tsagaratou

state: NC

address: 8001-B Burnett-Womack Bldg.

department: Department of Genetics

institute: University of North Carolina at Chapel Hill

description: GEX (3' mRNA) library

data_processing:
Fastq files from each 10x Genomics library were pooled together and processed with the cellranger multi pipeline using Cell Ranger version 7.1.0
Assembly: mm10

source_name: Spleen

growth_protocol: Not applicable

extract_protocol:
Spleens were harvested from male, 8 week-old CD45.1 recipients of CD45.2 Tet2/3 DKO T cells after 2 days (3 replicates) and 10 days (3 replicates) post transfer. Splenocytes were dissociated and 2 million cells were stained with fixable viability dye (dilution 1:1000), anti-CD45.2 PE (clone: 104, RRID: AB_313445, Biolegend) and anti CD45.1-BV421 (clone: A20, RRID: AB_10896421, Biolegend). To allow multiplexing of cells, splenocytes from each condition were stained with TotalSeq antibodies (Biolegend) and were incubated for 30 minutes on ice
Cells were washed 3 times to allow removal of excess antibodies. After sorting, CD45.1+ cells were provided to the UNC Advanced Analytical core for library preparation. Cells were counted and viability was assessed using a Luna-FX7 automated cell counter (Logos biosystems).  Briefly, cell viability was assessed and 5.000 per biological replicate and per condition were pooled yielding a total of 30,000 cells (15,000 for day 2 and 15.000 for day 10 post transfer). 10.000 cells were loaded in 10x Genomics Chromium Single Cell 3’ inlets (three inlets in total were used). Single-cell gel beads in emulsion (GEM) were generated.

value: Spleen

value: Immune cells

tag: genotype

value: wild type

value: mixed sample (10 days after transfer of Tet2/3 DKO T cells; 2 days after transfer of Tet2/3 DKO T cells)


title: Heart vehicle biol rep 1

value: NSG

value: female


title: Spleen, immune cells, GEX, Inlet2

description: GEX (3' mRNA) library


title: ChIP-seq analysis of ZNF446 genomic target locations in HEK293, THC0205TANN_ZNF446_ChIP1

value: ChIP


title: ChIP-seq analysis of ZNF503 genomic target locations in HEK293, THC0203TANN_ZNF503_ChIP1


title: Spleen, immune cells, GEX, Inlet1

description: GEX (3' mRNA) library


title: Spleen, immune cells, CSP, Inlet3

description: CSP (Cell Surface Protein) library

library_source: other

molecule: protein


title: ChIP-seq analysis of CTCF genomic target locations in HEK293, THC0201TANN_CTCF_ChIP1

value: CTCF


title: Spleen, immune cells, CSP, Inlet1

description: CSP (Cell Surface Protein) library


title: ChIP-seq analysis of DZIP1 genomic target locations in HEK293, THC0200TANN_DZIP1_ChIP2


title: ChIP-seq analysis of BHLHA9 genomic target locations in HEK293, THC0198TANN_BHLHA9_ChIP2


title: Hepa 1-6 cell, Sms-OE-2, rep 3

city: Guangzhou

first: Yining

last: Sun

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

institute: Nanfang hospital, Southern medical university

data_processing:
High quality of clean reads were filtered by Cutadapt (version:cutadapt-1.9). Sequence quality was verified using FastQC (0.11.9)
Reads were aligned to mouse reference genome using HISAT2 (version:hisat2-2.2.1) package
The mapped reads of each sample were assembled using StringTie (version:stringtie-2.1.6).
Transcriptomes from all samples were merged to reconstruct a comprehensive transcriptome using gffcompare software (version:gffcompare-0.9.8). StringTie and ballgown (http://www.bioconductor.org/packages/release/bioc/html/ballgown.html) were used to estimate the expression levels of all transcripts and perform expression abundance for mRNAs by calculating FPKM value
Genes differential expression analysis was performed by DESeq2 software between two different groups
Assembly: GCA_001632555.1
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

source_name: tumor

growth_protocol: Hepa 1-6 cells were orthotopically injected into the right lobe of mice liver. 14 days after, tumors were harvested and tissue tumor RNA was harvested.

extract_protocol:
RNA was harvested using AG RNAex Pro Reagent (Accurate Biology). 2ug of total RNA was used for the construction of sequencing libraries.
RNA library for RNA-seq were prepared using Dynabeads Oligo (dT) (Thermo Fisher, CA, USA), divalent cations (Magnesium RNA Fragmentation Module (NEB, cat.e6150, USA), SuperScript™II Reverse Transcriptase (Invitrogen, cat. 1896649, USA), E. coli DNA polymerase I (NEB, cat.m0209, USA) and RNase H (NEB, cat.m0297, USA), dUTP Solution (Thermo Fisher, cat. R0133, CA, USA) and UDG enzyme (NEB, cat.m0280, MA, US) following the manufacturer's protocols.

treatment_protocol: No additional treatment

value: tumor

value: Hepa 1-6

value: Hepatocarcinoma cell

value: Sms overexpression


title: Spleen, immune cells, CSP, Inlet2

description: CSP (Cell Surface Protein) library


title: Hepa 1-6 cell, Sms-OE-2, rep 2


title: Hepa 1-6 cell, Sms-OE-1, rep 3


title: Hepa 1-6 cell, Sms-OE-1, rep 2


title: ChIP-seq analysis of TIGD7 genomic target locations in HEK293, THC0194TANN_TIGD7_ChIP2

value: Not approved


title: Hepa 1-6 cell, Sms-OE-1, rep 1


title: ChIP-seq analysis of SETBP1 genomic target locations in HEK293, THC0196TANN_SETBP1_ChIP2


title: Hepa 1-6 cell, Control, rep 3

value: WT


title: ChIP-seq analysis of SP140 genomic target locations in HEK293, THC0193TANN_SP140_ChIP2

value: Approved


title: Hepa 1-6 cell, Control, rep 2


title: ChIP-seq analysis of ZNF507 genomic target locations in HEK293, THC0204TANN_ZNF507_ChIP1


title: ChIP-seq analysis of DZIP1 genomic target locations in HEK293, THC0192TANN_DZIP1_ChIP1


title: Kidney CDDO biol rep 1

value: kidney

value: CDDO-me


title: ChIP-seq analysis of AC092835 genomic target locations in HEK293, THC0191TANN_AC092835_ChIP1


title: ChIP-seq analysis of ZNF500 genomic target locations in HEK293, THC0202TANN_ZNF500_ChIP1


title: ChIP-seq analysis of BHLHA9 genomic target locations in HEK293, THC0190TANN_BHLHA9_ChIP1


title: F4/80, Sms-OE, rep 3

description: Sample 6

growth_protocol: Hepa 1-6 cells were orthotopically injected into the right lobe of mice liver. 14 days after, tumors were harvested, and F4/80 cells were isolated and RNA of F4/80 cells was harvested.

value: macrophage

value: Sms-OE


title: ChIP-seq analysis of CTCF genomic target locations in HEK293, THC0209TANN_CTCF_ChIP2


title: ChIP-seq analysis of ZFTA genomic target locations in HEK293, THC0189TANN_ZFTA_ChIP1

value: ZFTA


title: F4/80, Sms-OE, rep 2

description: Sample 5


title: ChIP-seq analysis of ZFTA genomic target locations in HEK293, THC0197TANN_ZFTA_ChIP2


title: Hepa 1-6 cell, Sms-OE-2, rep 1


title: ChIP-seq analysis of AC092835 genomic target locations in HEK293, THC0199TANN_AC092835_ChIP2


title: ChIP-seq analysis of SETBP1 genomic target locations in HEK293, THC0188TANN_SETBP1_ChIP1

value: No expert curation due to insufficient peak numbers


title: ChIP-seq analysis of TIGD7 genomic target locations in HEK293, THC0186TANN_TIGD7_ChIP1


title: ChIP-seq analysis of ELF3 genomic target locations in HEK293, THC0187TANN_ELF3_ChIP1


title: F4/80, Control, rep 2

description: Sample 2

value: WT Control


title: ChIP-seq analysis of ELF3 genomic target locations in HEK293, THC0195TANN_ELF3_ChIP2


title: ChIP-seq analysis of GLYR1 genomic target locations in HEK293, THC0184TANN_GLYR1_ChIP1


title: ChIP-seq analysis of ZSCAN25 genomic target locations in HEK293, THC0183TANN_ZSCAN25_ChIP1


title: Articular chondrocytes, vehicle, rep 3

extract_protocol:
Total RNA was extracted using the TRI reagent (Molecular Research Center, Inc.).
One microgram of total RNA was converted into cDNA libraries using the TruSeq Stranded mRNA Sample Prep kit (Illumina) in accordance with the TruSeq Standard mRNA Sample Preparation Guide, Part #15031047 Rev. E. Final cDNA libraries were analyzed for size distribution, quantified on Agilent Technologies 2100 Bioanalyzer using a DNA 1000 chip, and normalized to 2 nM for sequencing. RNA sequencing libraries were constructed by Macrogen.

treatment_protocol: Two days after seeding, mouse primary chondrocytes were treated with hyaluronidase type I-S (4 U/mL) for 4 h under serum-free condition prior to bleomycin treatment. Cells were treated with 50 μg/mL of bleomycin or an equal volume of PBS in serum-supplemented medium for 24 h. Then, cells were washed twice with PBS and incubated in fresh medium containing DMSO or 20 μM of ST045849 for five days. Fresh medium was supplemented every 48 h.

value: articular chondrocytes

value: vehicle plus DMSO


title: Articular chondrocytes, bleomycin plus ST045849, rep 3

value: bleomycin plus ST045849


title: Articular chondrocytes, bleomycin plus DMSO, rep 3

value: bleomycin plus DMSO


title: F4/80, Control, rep 1

description: Sample 1

value: tumor


title: Articular chondrocytes, bleomycin plus ST045849, rep 2


title: ChIP-seq analysis of SGSM2 genomic target locations in HEK293, THC0180TANN_SGSM2_ChIP2

value: ChIP


title: ChIP-seq analysis of NACC2 genomic target locations in HEK293, THC0179TANN_NACC2_ChIP1


title: Hepa 1-6 cell, Control, rep 1

value: Hepa 1-6

value: Hepatocarcinoma cell


title: Articular chondrocytes, vehicle, rep 2


title: ChIP-seq analysis of TRAFD1 genomic target locations in HEK293, THC0178TANN_TRAFD1_ChIP1


title: Articular chondrocytes, bleomycin plus DMSO, rep 2


title: ChIP-seq analysis of YY1 genomic target locations in HEK293, THC0177TANN_YY1_ChIP2


title: ChIP-seq analysis of SAFB2 genomic target locations in HEK293, THC0176TANN_SAFB2_ChIP2

value: Not approved


title: F4/80, Control, rep 3

description: Sample 3


title: F4/80, Sms-OE, rep 1

description: Sample 4


title: Articular chondrocytes, bleomycin plus DMSO, rep 1


title: Articular chondrocytes, vehicle, rep 1


title: ChIP-seq analysis of ZSCAN2 genomic target locations in HEK293, THC0174TANN_ZSCAN2_ChIP2

value: Approved


title: Articular chondrocytes, bleomycin plus ST045849, rep 1


title: Chipseq_CD8_Input_2

city: Dallas

first: Chen

last: Yao

state: Texas

address: 5901 FOREST PARK RD, NS6 218

institute: UT Southwestern Medical Center

description: Chipmentation

data_processing:
ScRNA-Seq: Fastq files of gene expression were aligned to mm10 using cellranger count (Cell Ranger v6.0.0), which perform filtering, barcode counting, and UMI counting at the same time.
ATAC-Seq: Raw sequencing data were processed with CASAVA 1.8.2 to generate FastQ files. ATAC-seq reads were mapped to the mouse genome (build mm10) with Bowtie 1.1.1. Peaks were identified using MACS (v 1.4.3; default p-value threshold of 1E-5) .
Multiome: Cell versus gene matrix of UMI counts for gene expression assay and cell versus fragment matrix for ATAC assay were generated from fastq files aligned to mm10 using cellranger-arc (v 2.0.0).
ChIP-Seq: Raw sequencing data were processed with CASAVA 1.8.2 to generate FastQ files. ChIP-seq reads were mapped to the mouse genome (build mm10) with Bowtie 1.1.1. Peaks were identified using MACS (v 1.4.3; default p-value threshold of 1E-5) .
Assembly: mm10
Supplementary files format and content: ScRNA-Seq: matrix H5 files
Supplementary files format and content: ATAC-Seq: BigWig files
Supplementary files format and content: ScATAC-Seq:atac_fragments.tsv.gz
Supplementary files format and content: ChIP-Seq: BigWig files

extract_protocol:
P14 cells isolated from spleen were sorted for scRNA-Seq, mutiome or ATAC-Seq anallysis. Sorted CD8 T cells were used for ChIP-Seq experiment.
We used Chromium Next GEM Single Cell 5' Kit (10x Genomics) to generate scRNA-Seq libraries according to the manufacturer’s protocol. ATAC-Seq libraries were generated using a FASTATAC protocol (Corces, M. R. et al. Nat. Genet. 48, 1193–1203 (2016)). We used Chromium Next GEM Single Cell Multiome ATAC + Gene Expression Reagent Kits (10x Genomics) to generate scRNA-Seq-multiome and scATAC-Seq-multiome libraries according to the manufacturer’s protocol. ChIP-Seq was performed according to the published chipmentation protocol (Schmidl, C., Rendeiro, A. F., Sheffield, N. C., & Bock, C. (2015).http://doi.org/10.1038/nmeth.3542).

value: Spleen

value: ex vivo


title: ChIP-seq analysis of ZSCAN25 genomic target locations in HEK293, THC0175TANN_ZSCAN25_ChIP2


title: Chipseq_CD8_NRF2_2

description: Chipmentation


title: ChIP-seq analysis of SMYD3 genomic target locations in HEK293, THC0173TANN_SMYD3_ChIP1


title: Chipseq_CD8_Input_1

description: Chipmentation


title: ChIP-seq analysis of SP140 genomic target locations in HEK293, THC0185TANN_SP140_ChIP1


title: ChIP-seq analysis of NACC2 genomic target locations in HEK293, THC0171TANN_NACC2_ChIP2


title: ChIP-seq analysis of THAP11 genomic target locations in HEK293, THC0172TANN_THAP11_ChIP2


title: Chipseq_CD8_NRF2_1

description: Chipmentation


title: ChIP-seq analysis of TBPL1 genomic target locations in HEK293, THC0170TANN_TBPL1_ChIP1


title: ChIP-seq analysis of ZBTB8A genomic target locations in HEK293, THC0181TANN_ZBTB8A_ChIP1


title: scRNAseq_Multiome_P14_Cl13_D7_Spleen_CA_NRF2

description: 10x Genomics

value: CD8 P14


title: ChIP-seq analysis of AC008770 genomic target locations in HEK293, THC0167TANN_AC008770_CHIP2

value: CHIP


title: ChIP-seq analysis of ZBED3 genomic target locations in HEK293, THC0168TANN_ZBED3_ChIP1


title: scATACseq_Multiome_P14_Cl13_D7_Spleen_CA_NRF2

description: 10x Genomics


title: ChIP-seq analysis of ANKZF1 genomic target locations in HEK293, THC0165TANN_ANKZF1_ChIP1


title: ChIP-seq analysis of PEG3 genomic target locations in HEK293, THC0164TANN_PEG3_ChIP1


title: ChIP-seq analysis of ARHGAP35 genomic target locations in HEK293, THC0166TANN_ARHGAP35_ChIP1


title: ATAC_P14_Cl13_D7_TerminallyExhaused_KeaP1KO_1

description: FASTATAC


title: ATAC_P14_Cl13_D7_TerminallyExhaused_KeaP1KO_3

description: FASTATAC


title: scRNAseq_Multiome_P14_Cl13_D7_Spleen_pMig_Control

description: 10x Genomics

value: WT


title: ChIP-seq analysis of AKAP8 genomic target locations in HEK293, THC0163TANN_AKAP8_CHIP1

value: No expert curation due to insufficient peak numbers


title: ATAC_P14_Cl13_D7_TerminallyExhaused_Control_2

description: FASTATAC


title: ATAC_P14_Cl13_D7_TerminallyExhaused_Control_1

description: FASTATAC

data_processing:
ScRNA-Seq: Fastq files of gene expression were aligned to mm10 using cellranger count (Cell Ranger v6.0.0), which perform filtering, barcode counting, and UMI counting at the same time.
ATAC-Seq: Raw sequencing data were processed with CASAVA 1.8.2 to generate FastQ files. ATAC-seq reads were mapped to the mouse genome (build mm10) with Bowtie 1.1.1. Peaks were identified using MACS (v 1.4.3; default p-value threshold of 1E-5) .
Assembly: mm10
Supplementary files format and content: ScRNA-Seq: matrix H5 files
Supplementary files format and content: ATAC-Seq: BigWig files


title: ChIP-seq analysis of PHF21A genomic target locations in HEK293, THC0162TANN_PHF21A_ChIP1


title: ATAC_P14_Cl13_D7_TerminallyExhaused_Control_3

description: FASTATAC


title: ChIP-seq analysis of TERB1 genomic target locations in HEK293, THC0160TANN_TERB1_ChIP1


title: scRNAseq_P14_Cl13_D7_NRF2OE

description: 10x Genomics


title: ChIP-seq analysis of AKAP8L genomic target locations in HEK293, THC0161TANN_AKAP8L_ChIP2


title: scRNAseq_P14_Cl13_D7_pMig_Control

description: 10x Genomics


title: scRNAseq_P14_Cl13_D7_Keap1KO

description: 10x Genomics


title: ChIP-seq analysis of ZBTB40 genomic target locations in HEK293, THC0159TANN_ZBTB40_ChIP1


title: scRNAseq_P14_Cl13_D7_Control

description: 10x Genomics


title: ChIP-seq analysis of RFX8 genomic target locations in HEK293, THC0157TANN_RFX8_CHIP1


title: ChIP-seq analysis of ZBTB41 genomic target locations in HEK293, THC0155TANN_ZBTB41_ChIP2


title: ChIP-seq analysis of THAP11 genomic target locations in HEK293, THC0156TANN_THAP11_ChIP1


title: ChIP-seq analysis of ZBTB46 genomic target locations in HEK293, THC0158TANN_ZBTB46_ChIP1


title: ATAC_P14_Cl13_D7_TerminallyExhaused_KeaP1KO_2

description: FASTATAC


title: ChIP-seq analysis of SAFB2 genomic target locations in HEK293, THC0154TANN_SAFB2_ChIP1


title: HCT116wt_DMSO_3days_SON_CutTag_rep2

city: Cambridge

first: Brian

last: Liau

address: 12 Oxford St.

department: Department of Chemistry and Chemical Biology

institute: Harvard University

data_processing:
Reads were aligned to hg38 using Burrow-Wheeler Aligner (BWA-mem, v  0.7.15)
Sam files were converted to bam files and sorted using Samtools view and sort (v 1.5)
Identical equence reads were collapsed to avoid PCR duplicates using Picard Tools MarkDuplicates(v 2.18.5) with Java (v 1.8.0) with parameters VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true
Bedgraph files averaging replicates were constructed from deduplicated bam files using Deeptools (v 3.4.3) bamCompare with -normalizeUsing RPKM --operation mean --scaleFactorsMethod None -of bedgraph --binSize 20000
Assembly: hg38
Supplementary files format and content: RPKM normalized 20kb bedgraph files are provided for each Cut&Tag condition with replicates averaged.

growth_protocol: K562 cells were grown in RPMI-1640 supplemented with 10% FBS, 100 U/mL penicillin and 100 μg/mL streptomycin. HCT116 cells were grown in McCoy's 5A medium supplemented with 10% FBS, 100 U/mL penicillin and 100 μg/mL streptomycin.

extract_protocol:
Cells were harvested and nuclei were isolated and lightly fixed with 0.1% formaldehyde for 2 minutes. Nuclei were bound to Concavalin A beads and anti-SON antibody was added at 4C overnight. Following addition of secondary antibody and subsequent washes, pA-Tn5 was added.
Chromatin was tagmented with PA-Tn5 and DNA was extracted and amplified by PCR.
Cut&Tag

treatment_protocol: Cells were treated at 10uM DNMT1i or 0.1% DMSO for 3 days.

value: colorectal carcinoma


title: HCT116wt_DMSO_3days_SON_CutTag_rep1


title: scATACseq_Multiome_P14_Cl13_D7_Spleen_pMig_Control

description: 10x Genomics


title: HCT116wt_DNMT1i_3days_SON_CutTag_rep2


title: ChIP-seq analysis of ZSCAN4 genomic target locations in HEK293, THC0153TANN_ZSCAN4_ChIP2


title: HCT116wt_DNMT1i_3days_SON_CutTag_rep1


title: ChIP-seq analysis of DNTTIP1 genomic target locations in HEK293, THC0152TANN_DNTTIP1_ChIP1


title: ChIP-seq analysis of TBPL1 genomic target locations in HEK293, THC0150TANN_TBPL1_ChIP2


title: K562wt_DMSO_3days_SON_CutTag_rep2

value: chronic myeloid leukemia


title: ChIP-seq analysis of ZBTB40 genomic target locations in HEK293, THC0149TANN_ZBTB40_ChIP2


title: ChIP-seq analysis of ZBTB8A genomic target locations in HEK293, THC0147TANN_ZBTB8A_ChIP2


title: ChIP-seq analysis of GLYR1 genomic target locations in HEK293, THC0148TANN_GLYR1_ChIP1


title: K562wt_DMSO_3days_SON_CutTag_rep1


title: ChIP-seq analysis of TIGD3 genomic target locations in HEK293, THC0146TANN_TIGD3_ChIP2


title: ChIP-seq analysis of ZSCAN25 genomic target locations in HEK293, THC0145TANN_ZSCAN25_ChIP1


title: ChIP-seq analysis of ARHGAP35 genomic target locations in HEK293, THC0142TANN_ARHGAP35_ChIP2


title: skin_19024

city: Beijing

first: Rui-Ting

last: Li

state: Beijing

address: No.20 Dongda Street, Fengtai District

department: State Key Laboratory of Pathogen and Biosecurity

institute: Beijing Institute of Microbiology and Epidemiology

data_processing:
After sequencing, perl script was used to filter the original data (Raw Data) to clean reads by removing contaminated reads for adapters and low-quality reads.
Clean reads were aligned to the monkey genome (ensembl_112_macaca_fascicularis) using Hisat2. The number of reads mapped to each gene in each sample was counted by HTSeq and FPKM was then calculated  to estimate the expression level of genes in each sample.
Assembly: ensembl_112_macaca_fascicularis
Supplementary files format and content: tab-delimited excel files include FPKM values for each sample …

organism: Macaca fascicularis

source_name: skin

extract_protocol:
Total RNA from spleen/skin  were extracted using TRIzol (Invitrogen, Carlsbad, CA, USA)  and DNase I (NEB, USA) treated, respectively.
Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® (#E7530L, NEB, USA) following the manufacturer’s recommendations

value: skin

value: sham


title: skin_20150


title: skin_19120


title: skin_19036

value: AR-MPXV


title: ChIP-seq analysis of ZBTB8B genomic target locations in HEK293, THC0141TANN_ZBTB8B_ChIP2


title: skin_19016


title: ChIP-seq analysis of ZBED3 genomic target locations in HEK293, THC0140TANN_ZBED3_ChIP2


title: skin_19030


title: ChIP-seq analysis of PHF21A genomic target locations in HEK293, THC0144TANN_PHF21A_ChIP2


title: ChIP-seq analysis of AC008770 genomic target locations in HEK293, THC0139TANN_AC008770_CHIP1


title: skin_19164


title: ChIP-seq analysis of ZSCAN18 genomic target locations in HEK293, THC0138TANN_ZSCAN18_ChIP1


title: ChIP-seq analysis of THYN1 genomic target locations in HEK293, THC0151TANN_THYN1_ChIP1


title: spleen_19120

source_name: spleen

value: spleen


title: spleen_19024


title: ChIP-seq analysis of TIGD5 genomic target locations in HEK293, THC0137TANN_TIGD5_ChIP1

value: ChIP


title: ChIP-seq analysis of ZBTB46 genomic target locations in HEK293, THC0136TANN_ZBTB46_ChIP2


title: K562wt_DNMT1i_3days_SON_CutTag_rep2


title: spleen_19036


title: ChIP-seq analysis of TRAFD1 genomic target locations in HEK293, THC0135TANN_TRAFD1_ChIP2


title: K562wt_DNMT1i_3days_SON_CutTag_rep1


title: spleen_19030


title: ChIP-seq analysis of ZBTB8A genomic target locations in HEK293, THC0134TANN_ZBTB8A_ChIP1


title: Middle-Aged (12-month-old female)

first: Pin-Ji

last: Lei

state: Massachusetts

address: 100 Blossom Street

department: Department of Radiation Oncology

institute: Massachusetts General Hospital

description: Single-cell RNA sequencing

data_processing:
Cellranger (Version 3.0.2, https://support.10xgenomics.com/single-cell-gene-expression/software/overview/welcome) was used to pre-process the fastq-format raw data. Cellranger aggr was used to combine data from different runs.
Seurat was employed for graph-based single-cell clustering. To ensure the selection of high-quality single-cell transcriptomic profiles, cells that had less than 100 genes or more than 10,000 featured RNAs detected or more than 25% mitochondrial genes, were excluded. Genes expressed in less than 3 cells were also removed.
Cell cycle regression was performed based on the Seurat cell cycle scoring and regression method.
Assembly: mm10
Supplementary files format and content: The processed data files are TSV format, including the single-cell RNA sequencing barcodes, gene annotation, and expression matrix.

source_name: Middle-Aged (12-month-old female)

growth_protocol: C57BL/6 mice were housed at the COX-7 and CNY-9 animal facilities at Massachusetts General Hospital. Both male and female mice of ages 6 weeks, 12 months, and 18 months were utilized for this study. The 18-month-old mice were provided by the National Institute on Aging/National Institutes of Health. All animal procedures were subjected to review and approval by the Institutional Animal Care and Use Committees (IACUC) at Massachusetts General Hospital.

extract_protocol:
The collected lymphatic vessels were transferred into 1.5 mL Eppendorf tubes containing 1 mL of digestion buffer [10 mL Dulbecco's Modified Eagle Medium (DMEM) with 20 mg Collagenase I, 5 mg Elastase, 8 mg Dispase, and 1 mg DNaseI]. The vessels were incubated in a 37 oC swirling water bath for approximately 40 minutes, with the digestion content being resuspended every 5 minutes. After digestion, the samples were filtered through a 70 μM nylon mesh and quenched by adding Fetal Bovine Serum (FBS) to a final concentration of 10%. The samples were then centrifuged at 300 rcf for 5 minutes at 4 oC. The pelleted cells were resuspended in 1 mL of ACK lysis buffer and kept at room temperature for 2 minutes to remove the red blood cells. The ACK lysis reaction was quenched by adding 9 mL of FACS buffer (2% FBS + 1X DPBS). The resulting 10 mL sample was centrifuged at 300 rcf for 5 minutes at 4 oC. The pelleted cells were resuspended in 150-200 μL of FACS buffer and filtered through a 35 μM nylon cell strainer. Cell viability was confirmed by Trypan Blue (Gibco) staining through manual counting as well as TC20 automated cell counting (Bio-Rad). Only samples with > 74% live cells were processed with 10X Genomics Single Cell 3’ Reagent Kit-based Gel Bead-In-Emulsions (GEM) reactions, followed by Illumina sequencing.
10x genomics Chromium Single Cell 3' Reagent (v2 Chemistry) was used for library preparation.
10x genomics single-cell mRNA sequencing.

treatment_protocol: Mice were anesthetized with ketamine (100 mg/kg) and xylazine (10 mg/kg) via intraperitoneal injection. The fur was removed using a depilatory cream (Nair Hair Removal Lotion) and the surgical site was disinfected. An incision was made in the abdominal midline from the lower part of the mouse's body to the chest, and the skin was opened to expose the collecting lymphatic vessels that connect the inguinal lymph node and axillary lymph node. To enhance the visibility of the lymphatic vessels, 4 μL of Evans Blue (0.1% diluted in PBS) was injected into the inguinal lymph node. The collecting lymphatic vessels were isolated under a stereo microscope, and fat and connective tissues were removed. The isolated lymphatic vessels were immediately transferred to a Petri dish containing fresh Hanks' Balanced Salt Solution (HBSS) and kept on ice until digestion. Throughout the dissection, mice were kept under anesthesia to minimize pain and discomfort.

value: Collecting lymphatic vessel in dermis

tag: library sequencing

value: NextSeq2000 High Output PE26/98


title: spleen_19016


title: Aged (18-month-old male)

description: Single-cell RNA sequencing

source_name: Aged (18-month-old male)


title: Middle-Aged (12-month-old male)

description: Single-cell RNA sequencing

source_name: Middle-Aged (12-month-old male)


title: ChIP-seq analysis of SGSM2 genomic target locations in HEK293, THC0133TANN_SGSM2_ChIP1


title: Young (6-week-old female)

description: Single-cell RNA sequencing

source_name: Young (6-week-old female)


title: Young (6-week-old male)

description: Single-cell RNA sequencing

source_name: Young (6-week-old male)


title: ChIP-seq analysis of SGSM2 genomic target locations in HEK293, THC0132TANN_SGSM2_ChIP2

value: Not approved


title: spleen_20150


title: ChIP-seq analysis of NACC2 genomic target locations in HEK293, THC0131TANN_NACC2_ChIP1

value: Approved


title: Fetal brain, ZIKV MR766, pooled sample

city: Singapore

first: Ashley

last: St John

address: 8 College Rd

country: Singapore

institute: Duke-NUS

data_processing:
The demultiplexing, barcode processing, gene counting and aggregation were made using Cell Ranger Software v6.1.1
Assembly: mm10
Supplementary files format and content: h5 files, tab-separated values files and matrix files

source_name: Brain cells

extract_protocol:
Freshly prepared single cell suspension from E16.5 fetal brains were processed usuing the Chromium Next GEM Single Cell 3' Kit v3.1 (10x Genomics, PN-1000269) and the Chromium Next GEM Chip G Single Cell Kit (10x Genomics, PN-1000127) to generate the Gems with the 10x Genomics Chromium Controller.
The library was built using the 3' Feature Barcode Kit (10x Genomics, PN-1000262), the Dual Index Kit NN Set A (10x Genomics, PN-1000243), and the Dual Index Kit TT Set A (10x Genomics, PN-1000215).

treatment_protocol: Upon succesful mating, fetuses from pregnant dams were injected via the intracranial route in utero at E13.5 with either saline, ZIKV H/PF/2013 or ZIKV MR766 and the fetal brains were individually collected at E16.5 and processed to single cell syspensions.

value: Brain cells

value: ZIKV infectpom


title: spleen_19164


title: Fetal brain, ZIKV H/PF/2013, pooled sample


title: Negative control siRNA 2

city: Pittsburgh

first: Shu-Ting

last: Cho

state: PA

address: 450 Technology Drive

department: Computational and Systems Biology

institute: University of Pittsburgh

hyb_protocol: Affymetrix microarray

scan_protocol: Affymetrix microarray

data_processing: RMA

label: biotin

source_name: Pulmonary artery endothelial cell isolated from lungs

label_protocol: Affymetrix microarray

growth_protocol: primary human pulmonary arterial endothelial cells (hPAECs) were inculated at 37C.

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

treatment_protocol: ADAR1 siRNAs, NOCT siRNAs, or non-specific siRNAs were tranfected into hPAECs for 48 hours

value: Lung endothelial cells

value: wildtype


title: ADAR1 and NOCT knockdown 2


title: Negative control siRNA 3


title: ADAR1 and NOCT knockdown 1


title: ADAR1 and NOCT knockdown 3


title: Negative control siRNA 1


title: ChIP-seq analysis of TRAFD1 genomic target locations in HEK293, THC0130TANN_TRAFD1_ChIP1


title: Fetal brain, uninfected, pooled sample

value: Saline


title: ADAR1 knockdown 3


title: Aged (18-month-old female)

description: Single-cell RNA sequencing

source_name: Aged (18-month-old female)


title: ADAR1 knockdown 2


title: ADAR1 knockdown 1


title: Pre-IP control THC0069TSNN_ZNF367_INPUT1

value: Input

value: No expert curation due to insufficient peak numbers


title: CG646B

type: genomic

city: Vancouver

first: Michael

middle: S.

last: Kobor

state: BC

address: 950 West 28th Avenue

department: Medical Genetics

institute: Centre for Molecular Medicine and Therapeutics / University of British Columbia

hyb_protocol: Bisulfite converted DNAs were hybridized to beadchips provided the Illumina Infinium MethylationHM450K BeadChip Kit

data_processing:
Signal intensity is measured with the Illumina HiScan system to generate beta values, a measure of the degree of methylation at a locus
Normalized Beta values

source_name: Blood

label_protocol: Sample barcoding and staining were carried out by following the instructions of Illumina provided in the Infinium MethylationHM450K BeadChip Kit

growth_protocol: Monocytes, defined as CD14+, were separated using immune-magnetic capturing methods (Miltenyi AutoMACS)

extract_protocol: DNA was isolated from the purified monocytes using a column-based method and assessed for quality using NanoDrop, bisulfite converted using EZ-96 DNA Methylation kits (Zymo Research, Irvine, CA)

value: Blood

value: Monocytes


title: CG647A

scan_protocol: Signal intensity is measured with the Illumina HiScan system to generate beta values, a measure of the degree of methylation at a locus


title: CG647B


title: Pre-IP control THC0064TSNN_PHF20_INPUT1


title: ChIP-seq analysis of ZNF215 genomic target locations in HEK293, THC0119TANN_ZNF215_ChIP1


title: CG646A


title: ChIP-seq analysis of PHF20 genomic target locations in HEK293, THC0036TSNN_PHF20_ChIP2


title: ChIP-seq analysis of PHF20 genomic target locations in HEK293, THC0035TSNN_PHF20_ChIP1


title: CG645B


title: ChIP-seq analysis of ZNF367 genomic target locations in HEK293, THC0046TSNN_ZNF367_ChIP2


title: ChIP-seq analysis of BATF2 genomic target locations in HEK293, THC0117TANN_BATF2_CHIP2

value: CHIP


title: CG645A


title: ChIP-seq analysis of RFX5 genomic target locations in HEK293, THC0121TANN_RFX5_CHIP2


title: S_2107_023547

first: Petter

last: Bjornstad

state: Washington

address: 750 Republican St

department: Division of Metabolism, Endocrinology and Nutrition

institute: University of Washington

description: 10x Genomics

data_processing:
Sample demultiplexing, barcode processing, and gene expression quantifications were performed with the cellranger v6 (10x Genomics) pipeline.
SoupX was employed, as noted per sample in the supplemental materials for this manuscript, using default parameters.
Integration was conducted with RunHarmony, embedded within Seurat v4.0.0.
Assembly: hg38, v. GRCh38-2020-A
Supplementary files format and content: Tab-separated values files
Supplementary files format and content: Matrix files

source_name: Kidney cortex

extract_protocol:
Cortical human kidney biopsies that had been stored in Cryostor were subjected to a cellular RNA extraction protocol from the Kidney Precision Medicine Project.
Library construction was performed according to the manufacturer's instructions (single cell 3' v3 protocol, 10x Genomics)

treatment_protocol: Where indicated, patients were prescribed and had been administered an SGLT2 inhibitor, averaging 6 months treatment prior to kidney biopsy

value: Kidney cortex

value: Kidney and immune cells

tag: disease

value: Type 1 Diabetes


title: ChIP-seq analysis of TIGD4 genomic target locations in HEK293, THC0113TANN_TIGD4_ChIP1

data_processing:
Constant flank derived bases were removed with Cutadapt (using the adapters AGATCGGAAGAGCACACGTCTGAACTCCAGTCA and AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT).
Reads were mapped into human genome build hg38 with bowtie2 (options: --very-sensitive, --no-unal). The mapped trimmed reads were filtered using samtools (options: -q 30, -F 1548, version 1.20)
Peak calling was performed with MACS2 using sample-specific backgrounds [made by merging pull-down experiments; PMID: 27852650].
Assembly: hg38
Supplementary files format and content: Bigwig files are based on Bowtie2 mapping followed by MACS3 peak calling.
Supplementary files format and content: Narrowpeak files have been derived following the custom Peak calling was performed with MACS2 using sample-specific backgrounds [made by merging pull-down experiments; PMID: 27852650].

extract_protocol:
20 million cells were cross-linked with 1% formaldehyde and palletted in cold PBS. Cell pallettes were lysed in a 3 step lysis procedure and chromatin was sonicated at the last step. Sonicated chromatin ws immunoprecipitated using anti-eGFP IgG (Rabbit polycclonal, abcam290) coated magnetic beads. For "input" control samples, 10ul of pre-IP sample were collected. After de-cross linking and DNA purification, both ChIP and Input samples were eluted in 60ul of elution buffer.
NEBNext® Ultra™ II DNA Library Prep Kit for Illumina® kit and protocol

value: ChIP


title: ChIP-seq analysis of ADNP2 genomic target locations in HEK293, THC0120TANN_ADNP2_CHIP2


title: ChIP-seq analysis of ZBED9 genomic target locations in HEK293, THC0116TANN_ZBED9_ChIP2


title: S_2107_023610

description: 10x Genomics


title: S_2107_023592

description: 10x Genomics


title: CG644B


title: ChIP-seq analysis of ZBTB47 genomic target locations in HEK293, THC0114TANN_ZBTB47_ChIP2


title: S_2107_023556

description: 10x Genomics

value: Lean Control


title: S_2107_023520

description: 10x Genomics


title: S_2107_023538

description: 10x Genomics


title: ChIP-seq analysis of ZSCAN4 genomic target locations in HEK293, THC0112TANN_ZSCAN4_ChIP1

value: Not approved


title: CG644A


title: CG643B


title: S_2103_004154

description: 10x Genomics


title: S_2103_004163

description: 10x Genomics


title: ChIP-seq analysis of BATF2 genomic target locations in HEK293, THC0118TANN_BATF2_CHIP1

value: Approved


title: S_2103_004181

description: 10x Genomics


title: ChIP-seq analysis of ZNF318 genomic target locations in HEK293, THC0111TANN_ZNF318_ChIP2


title: S_2107_023619

description: 10x Genomics


title: S_2103_004145

description: 10x Genomics


title: ChIP-seq analysis of ZNF367 genomic target locations in HEK293, THC0045TSNN_ZNF367_ChIP1


title: S_2103_004127

description: 10x Genomics


title: CG642B


title: S_2103_004118

description: 10x Genomics


title: ChIP-seq analysis of TIGD5 genomic target locations in HEK293, THC0110TANN_TIGD5_ChIP2


title: S_2103_004109

description: 10x Genomics


title: ChIP-seq analysis of ANKZF1 genomic target locations in HEK293, THC0109TANN_ANKZF1_CHIP2


title: CG642A


title: S_2103_004100

description: 10x Genomics


title: CG641A


title: CG640B


title: S_2103_004091

description: 10x Genomics


title: S_2103_004064

description: 10x Genomics


title: ChIP-seq analysis of AKAP8 genomic target locations in HEK293, THC0108TANN_AKAP8_CHIP1


title: S_2103_004046

description: 10x Genomics


title: CG640A


title: ChIP-seq analysis of SMYD3 genomic target locations in HEK293, THC0106TANN_SMYD3_ChIP1


title: S_2103_004037

description: 10x Genomics


title: CG643A


title: S_2103_004028

description: 10x Genomics


title: S_2103_004019

description: 10x Genomics


title: CG639A


title: S_2007_004216

description: 10x Genomics


title: S_2007_004028

description: 10x Genomics


title: S_2007_004263

description: 10x Genomics


title: ChIP-seq analysis of TIGD3 genomic target locations in HEK293, THC0104TANN_TIGD3_ChIP1


title: CG638B


title: S_2007_003840

description: 10x Genomics


title: ChIP-seq analysis of AKAP8 genomic target locations in HEK293, THC0103TANN_AKAP8_CHIP2


title: S_2103_004073

description: 10x Genomics


title: S_2007_003934

description: 10x Genomics


title: ChIP-seq analysis of ZSCAN12 genomic target locations in HEK293, THC0107TANN_ZSCAN12_ChIP1


title: S_2007_003793

description: 10x Genomics


title: CG638A


title: S_2007_003138

description: 10x Genomics


title: CG637B


title: S_2007_003091

description: 10x Genomics


title: CG637A


title: S_2007_002950

description: 10x Genomics


title: ChIP-seq analysis of ZBED2 genomic target locations in HEK293, THC0099TANN_ZBED2_ChIP1


title: S_2007_002997

description: 10x Genomics


title: S_2007_003044

description: 10x Genomics


title: CG639B


title: ChIP-seq analysis of RFX8 genomic target locations in HEK293, THC0100TANN_RFX8_CHIP2


title: S_2007_002809

description: 10x Genomics


title: S_2006_004078

description: 10x Genomics


title: ChIP-seq analysis of ZSCAN18 genomic target locations in HEK293, THC0105TANN_ZSCAN18_ChIP2


title: CG636B


title: ChIP-seq analysis of ZNF318 genomic target locations in HEK293, THC0102TANN_ZNF318_ChIP1


title: CG636A


title: S_1907_005225

description: 10x Genomics


title: S_1907_004896

description: 10x Genomics


title: S_1907_004802

description: 10x Genomics


title: ChIP-seq analysis of THYN1 genomic target locations in HEK293, THC0092TANN_THYN1_ChIP2


title: ChIP-seq analysis of SP140L genomic target locations in HEK293, THC0090TANN_SP140L_ChIP2


title: CG635B


title: ACCEPT_sample_99

first: Jen Jen

last: Yeh

state: North Carolina

address: 450 West drive

institute: The University of North Carolina at Chapel Hill

data_processing:
BCL files were converted to FASTQ files using bcl2fastq2 conversion software 2.20.0
Individual lane files were combined into one FASTQ file for each sample
Salmon (v1.5.2 with options gcBias and seqBias) was used to derive read count, gene-length and total read count normalized counts (TPM)
Assembly: GENCODE Release 38 (GrCh38.p13)
Supplementary files format and content: comma-separated file containing Bulk RNAseq gene expression normalized TPM for all samples

source_name: Primary  PDAC

extract_protocol:
Total RNA was extracted from cassettes using the AllPrep DNA/RNA FFPE Kit (Qiagen, 80234). RNA was quantified using the Qubit RNA HS Assay Kit (Invitrogen, Q32852) and quality assessed with the 4150 TapeStation System (Agilent) and RNA ScreenTape Analysis Kit (Agilent, 5067-5576).
For samples below dv200 30%, a 1.1X or a 1.1X and successive 1.0X bead cleanups was completed using RNAClean XP Beads (Beckman Coulter, A63987) cDNA libraries were prepped with the KAPA Stranded RNA-Seq Kit with RiboErase (HMR) (Roche, KR1151) if total RNA was >25ng and >24% dv200. If dv200 was below 50%, the low input KAPA Prep protocol was used. 17 cycles were used for the final PCR cycle. The remaining samples were prepped using AmpliSeq for Illumina Transcriptome Human Gene Expression Panel (Illumina, 20019170, 20019102).16 cycles were used to amplify target regions in the cDNA

value: Primary  PDAC

value: Gemcitabine/Afatinib


title: ChIP-seq analysis of ZBED2 genomic target locations in HEK293, THC0101TANN_ZBED2_ChIP2

first: Arttu

last: Jolma

address: 160 College Street, Room 1350

institute: University of Toronto


title: S_1907_004614

description: 10x Genomics


title: ChIP-seq analysis of DNTTIP1 genomic target locations in HEK293, THC0087TANN_DNTTIP1_ChIP2


title: S_1907_004567

description: 10x Genomics


title: ACCEPT_sample_97

value: Gemcitabine


title: CG635A


title: ChIP-seq analysis of GLYR1 genomic target locations in HEK293, THC0088TANN_GLYR1_ChIP2


title: CG634B


title: ACCEPT_sample_95


title: ChIP-seq analysis of PEG3 genomic target locations in HEK293, THC0086TANN_PEG3_ChIP2


title: CG634A


title: ACCEPT_sample_92


title: CG633B


title: ACCEPT_sample_91


title: ChIP-seq analysis of RFX5 genomic target locations in HEK293, THC0085TANN_RFX5_ChIP1


title: ChIP-seq analysis of TERB1 genomic target locations in HEK293, THC0084TANN_TERB1_ChIP2


title: ACCEPT_sample_89


title: ACCEPT_sample_90


title: CG633A


title: ACCEPT_sample_87


title: ChIP-seq analysis of ZBED5 genomic target locations in HEK293, THC0083TANN_ZBED5_ChIP1


title: ACCEPT_sample_84


title: ACCEPT_sample_81


title: ACCEPT_sample_8


title: ACCEPT_sample_78


title: ACCEPT_sample_80


title: ACCEPT_sample_93


title: ACCEPT_sample_96


title: CG632B


title: ACCEPT_sample_73


title: ChIP-seq analysis of ZBED5 genomic target locations in HEK293, THC0081TANN_ZBED5_ChIP2


title: CG631A


title: CG630A


title: ChIP-seq analysis of YY1 genomic target locations in HEK293, THC0080TANN_YY1_ChIP1


title: ACCEPT_sample_74


title: ChIP-seq analysis of ZNF428 genomic target locations in HEK293, THC0082TANN_ZNF428_ChIP2


title: CG632A


title: ACCEPT_sample_72


title: ChIP-seq analysis of ZBTB41 genomic target locations in HEK293, THC0079TANN_ZBTB41_ChIP1


title: ACCEPT_sample_71


title: CG631B


title: CG629A


title: ChIP-seq analysis of ZNF215 genomic target locations in HEK293, THC0078TANN_ZNF215_ChIP2


title: ACCEPT_sample_64


title: CG629B


title: ACCEPT_sample_69


title: ACCEPT_sample_67


title: ACCEPT_sample_85


title: ChIP-seq analysis of ZSCAN12 genomic target locations in HEK293, THC0076TANN_ZSCAN12_ChIP2


title: ChIP-seq analysis of ZSCAN2 genomic target locations in HEK293, THC0077TANN_ZSCAN2_ChIP1


title: ACCEPT_sample_63


title: CG628B


title: ACCEPT_sample_58


title: ChIP-seq analysis of ZNF428 genomic target locations in HEK293, THC0075TANN_ZNF428_ChIP1


title: CG628A


title: ChIP-seq analysis of ZBTB47 genomic target locations in HEK293, THC0074TANN_ZBTB47_ChIP1


title: ACCEPT_sample_62


title: ACCEPT_sample_55


title: ACCEPT_sample_56


title: ACCEPT_sample_53


title: ACCEPT_sample_52


title: ChIP-seq analysis of ZBED9 genomic target locations in HEK293, THC0073TANN_ZBED9_ChIP1


title: RASH_sample_240

value: Gemcitabine/Erlotinib + No_further


title: RASH_sample_244

value: Gemcitabine/Erlotinib


title: CG627B


title: CG627A


title: CG626B


title: ChIP-seq analysis of TIGD4 genomic target locations in HEK293, THC0071TANN_TIGD4_ChIP2


title: ACCEPT_sample_24


title: RASH_sample_232


title: CG626A


title: RASH_sample_230


title: ChIP-seq analysis of ADNP2 genomic target locations in HEK293, THC0070TANN_ADNP2_ChIP1


title: RASH_sample_229

value: Gemcitabine/Erlotinib + FOLFIRINOX


title: RASH_sample_234


title: CG625B


title: ACCEPT_sample_23


title: ChIP-seq analysis of SP140L genomic target locations in HEK293, THC0072TANN_SP140L_ChIP1


title: Tumor CDDO biol rep 5

source_name: xenograft

value: xenograft

value: small cell lung cancer

value: CDDO-me


title: RASH_sample_223


title: CG625A

value: Blood

value: Monocytes


title: RASH_sample_220


title: ACCEPT_sample_22


title: CG624A


title: Tumor CDDO biol rep 3


title: RASH_sample_216


title: CG623B


title: RASH_sample_211


title: Tumor CDDO biol rep 2


title: RASH_sample_199


title: CG623A


title: CG622B


title: Tumor CDDO biol rep 1


title: RASH_sample_167


title: RASH_sample_160


title: CG622A


title: ACCEPT_sample_16


title: RASH_sample_162


title: RASH_sample_143


title: Tumor vehicle biol rep 4

value: vehicle


title: CG621B


title: Tumor CDDO biol rep 4


title: Tumor vehicle biol rep 5


title: CG620B


title: Tumor vehicle biol rep 2


title: RASH_sample_158


title: RASH_sample_116


title: CG620A


title: ACCEPT_sample_108


title: ACCEPT_sample_13


title: RASH_sample_218


title: ACCEPT_sample_102


title: Tumor vehicle biol rep 1


title: CG619B


title: Liver cancer stem cells, Upper Chamber, 2

first: changgui

last: zhong

state: Guangdong

address: Guangzhou University Town, Panyu District, Guangzhou

institute: South China University of Technology

data_processing:
we used Fastp (version 0.23.1) to perform basic statistics on the quality of the raw reads.
Discard a paired reads if either one read contains adapter contamination
Discard a paired reads if more than 10% of bases are uncertain in either one read
Discard a paired reads if the proportion of low quality (Phred quality <5) bases is over 50% in either one read.
Assembly: HG38
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample

source_name: Liver

extract_protocol:
RNA was harvested using HiScript III RT SuperMix for qPCR(+gDNA wiper) (Vazyme). 1.3 ug of total RNA was used for the construction of sequencing libraries.
Sequencing libraries were generated using NEBNext Ultra RNA Library Prep Kit for Illumina (NEB, USA, Catalog #: E7530L) following manufacturer’s recommendations

value: Liver

value: Liver cancer stem cells

value: Upper Chamber


title: donor_3387_subcutaneous adipose tissue

city: Palo Alto

first: Lattice

last: Data Coordination

state: CA

address: 3165 Porter Drive

department: Genetics

institute: Stanford University

data_processing:
Per sample, reads were transformed into a raw counts matrix with 10x Genomics CellRanger software1 6.0.1
raw_matrix_normalized:False; raw_matrix_value_scale:linear; raw_matrix_feature_keys:gene symbol; raw_matrix_background_barcodes_included:False
Assembly: raw_matrix_assembly:GRCh38; raw_matrix_genome_annotation:GENCODE 32
Supplementary files format and content: raw_matrix_file_format:hdf5; raw_matrix_value_units:UMI

source_name: subcutaneous adipose tissue

extract_protocol:
Adipose tissue biopsies with at least 1g  were obtained from adult patients without severe morbid states or obesity complications who had signed in advance a written informed consent before undergoing elective abdominal surgeries. Five patients donated subcutaneous adipose tissue and visceral adipose tissue samples (paired). Tissues were immediately delivered from the operating room to the lab, where they were snap frozen in liquid nitrogen and stored at −80°C.
13,000-16,500 nuclei/sample were  loaded onto 10X Chromium Controller (10X GENOMICS, CA, USA) according to the manufacturer’s protocol (Chromium Next GEM Chip C. Chromium Next GEM Single Cell 3’ Kits v3.1).

value: subcutaneous adipose tissue

tag: raw matrix_cellranger_assay_chemistry

tag: assay

value: female

tag: ethnicity

value: Arab

tag: age

value: 34.3 years

value: TRUE

tag: donor id


title: CG619A


title: RASH_sample_130

value: Primary  PDAC


title: RASH_sample_147

value: Gemcitabine/Erlotinib


title: CG621A


title: Tumor vehicle biol rep 3

tag: cell line


title: CG618A


title: CG617B


title: donor_3384_visceral fat

source_name: visceral fat

value: visceral fat

value: male

value: Jewish Israeli

value: 33.7 years


title: Liver cancer stem cells, Upper Chamber, 1


title: donor_3387_visceral fat


title: donor_3357_visceral fat

value: 29.3 years


title: donor_3382_visceral fat

value: 41.8 years


title: Liver cancer stem cells, Upper Chamber, 3


title: CG617A

value: Blood

value: Monocytes


title: CG616B


title: Liver cancer stem cells, Lower Chamber, 1

value: Liver

value: Liver cancer stem cells

value: Lower Chamber


title: Liver cancer stem cells, Lower Chamber, 2


title: CG616A


title: donor_3350_visceral fat

value: female

value: 28.6 years


title: Liver cancer stem cells, siFASN_3

value: FASN knockdown


title: Liver cancer stem cells, siFASN_2


title: TMA2, cap76, PtID19, virusnegative, response1, treatmentpre, LocalDisease1, Metastasis1, Survival0

city: Stanford

first: Magdalena

last: Matusiak

state: California

address: 300 Pasteur Dr

department: Pathology

data_processing:
Base calls from the NextSeq were de-multiplexed and converted to FASTQ format with bcl2fastq (NextSeq system suite software, Illumina v2.20.0.422). The five-base unique molecular identifier (UMI) sequence and the G-overhang were extracted from FASTQ data, and A-tails were removed with umi_homopolymer.py (github.com/jwfoley/3SEQtools). Reads were aligned and further processed to remove duplicates using STAR v2.7.3a (github.com/alexdobin/STAR)
Assembly: hg38
Supplementary files format and content: .csv format; provides raw counts for each sequencing library

source_name: Merkel cell carcinoma

extract_protocol: Sequencing libraries were prepared according to the Smart-3Seq protocol for LCM HS caps, as previously described with slight modifications (see Foley et al. doi: 10.1101/gr.234807.118)

value: Merkel cell carcinoma

value: tissue

value: tumor

value: negative

value: ICB

tag: cpi orr

tag: local disease

tag: progress to_metastatic_disease

tag: pat id

tag: baseline fu_biopsy

value: pre


title: TMA2, cap71, PtID72, virusnegative, responseNA, treatmentpre, LocalDisease0, Metastasis1, Survival0

tag: tissue

tag: treatment


title: TMA2, cap70, PtID22, virusnegative, response0, treatmentFU, LocalDisease1, Metastasis1, Survival0

tag: cell type

value: FU


title: TMA2, cap74, PtID68, virusnegative, responseNA, treatmentpre, LocalDisease0, Metastasis1, Survival1

tag: genotype


title: TMA2, cap75, PtID54, viruspositive, response1, treatmentFU, LocalDisease0, Metastasis1, Survival0

value: positive


title: TMA2, cap73, PtID69, virusnegative, responseNA, treatmentpre, LocalDisease0, Metastasis0, Survival1


title: TMA2, cap68, PtID17, virusnegative, response1, treatmentpre, LocalDisease0, Metastasis1, Survival0


title: TMA2, cap77, PtID79, virusnegative, response1, treatmentFU, LocalDisease1, Metastasis1, Survival0


title: CG615B


title: Liver cancer stem cells, Lower Chamber, 3


title: CG615A


title: TMA2, cap67, PtID79, virusnegative, response1, treatmentpre, LocalDisease1, Metastasis1, Survival0


title: TMA2, cap66, PtID33, viruspositive, response1, treatmentpre, LocalDisease0, Metastasis1, Survival0


title: TMA2, cap65, PtID25, viruspositive, response0, treatmentFU, LocalDisease1, Metastasis1, Survival0


title: Liver cancer stem cells, siControl_2

value: WT


title: TMA2, cap64, PtID40, viruspositive, response0, treatmentpost, LocalDisease0, Metastasis1, Survival0

value: post


title: Liver cancer stem cells, siControl_3


title: CG614B

value: Blood

value: Monocytes


title: TMA2, cap62, PtID6, viruspositive, response0, treatmentpost, LocalDisease1, Metastasis0, Survival0


title: Liver cancer stem cells, siFASN_1

value: Liver

value: Liver cancer stem cells


title: Liver cancer stem cells, siControl_1


title: CG613B


title: TMA2, cap63, PtID3, virusnegative, response0, treatmentpost, LocalDisease0, Metastasis1, Survival1


title: bulk naïve CD8+ T cells, ME patient 982

city: Ithaca

first: David

middle: S

last: Iu

state: NY

address: 427 Biotechnology Building

department: Molecular Biology and Genetics

institute: Cornell University

data_processing:
fastq files were trimmed to remove low quality and adaptor sequences as described (Martin, 2011). Trimmed reads were then aligned to hg38 using bowtie2 (v2.4.5; Langmead et al., 2019). Mitochondrial reads and blacklisted regions (Amemiya et al., 2019) were removed, and PICARD (v2.26.1) and samtools (v1.18; Danecek et al., 2021) were used to sort and remove duplicate reads.
Peaks were called using MACS3 (v3.0.0b1; Zhang et al., 2008; callpeak –f BAMPE –g hg –B –q 0.01). Consensus peaks from all cell types and biological conditions were then merged by muMerge (v1.1.0; Rubin et al., 2021) to create a unified set of chromatin accessible regions (ChARs). featureCounts under subread (v2.0.3; Liao et al., 2014) was used to calculate raw read counts per ChAR.
Assembly: hg38
Supplementary files format and content: comma-delimited file with consensus chromatin accessible regions and their raw counts per sample

source_name: naive CD8+ T cell

extract_protocol:
CD3+ cells were enriched using the CD3+ MicroBeads (Miltenyi Biotech Cat#130-097-043) from PBMCs. After enrichment, cells were incubated with Aqua dead cell stain kit (Thermo) with Human TruStain FcX™ Fc Receptor Blocking Solution (Biolegend) for 10 minutes at room temperature. Fluorescently labeled antibodies (CD4-FITC Cat#357406, CD8a-BV785 Cat#301406, CD45RA-BV650 Cat#304136, CCR7-APC-Cy7 Cat#353212, and CD56-PE-Cy7 Cat#362510 all from BioLegend) were subsequently added to the cells and incubated on ice for 30 minutes. 1 mL of FACS buffer (heat inactivated FBS, 0.5M EDTA pH8.0 1x PBS) was added to the cells, mixed well and centrifuged at 300 rcf for 5 minutes at 4 °C. The supernatant was removed and the cells were washed once more. The final cell pellet was resuspended in 100µl of FACS buffer and kept on ice in the dark. Flow sorting was performed on a FACSARia Fusion at the Cornell BRC Flow Cytometry Facility. Live and CD56 negative cells were selected for CD4 and CD8 expressions. Naïve cells were sorted as CD45RA+CCR7+. Memory cells were sorted as CD45RA-CCR7+/-. Nuclei were prepared from 12,000-50,000 sorted CD8 T cells using a modified Omni-ATAC-seq protocol. Briefly, cells were pelleted at 500 xg for 5 minutes at 4°C, supernatant removed, and cells were permeablized in cold lysis/permeabilization buffer with 0.1% NP40, 0.1% Tween-20, and 0.01% digitonin for 3 minutes. Cells were washed three times with fresh 1 x RSB-T (10mM Tris pH 7-8, 10mM NaCl, 3 mM MgCl2, and 0.1% Tween-20). Cells were pelleted and supernatant removed. 1x PBS + 10% DMSO  is used to slow freeze the cell pellet and placed in a Mr. Frosty for slow freezing at -80°C for processing.
Nuclei were prepared from 12,000-50,000 CD8+ T cells sorted as described above, using a modified Omni-ATAC-seq protocol (Corces et al., 2017). Briefly, cells were pelleted at 500 xg for 5 minutes at 4C, supernatant removed, and cells were permeablized in 50 ul cold lysis/permeabilization buffer with 0.1% NP40, 0.1% Tween-20, and 0.01% digitonin for 3 minutes on ice. Lysis was quenched by adding 1mL ice-cold RSB-T (10mM Tris pH 7-8, 10mM NaCl, 3 mM MgCl2, and 0.1% Tween-20). Nuclei were pelleted at 500 xg for 10 minutes at 4C and supernatant was replaced with 50 ul 1x PBS + 10% DMSO for slow freezing and storage at -80C. For tagmentation, nuclei were thawed and washed twice with 1x RSB+T before resuspending in 25 ul Tagmentation buffer (1x Cutsmart buffer (NEB), 10% DMF, 0.1% Tween-20, 0.01% digitonin, and 0.1uM Tn5). Nuclei were tagmented for 30 minutes at 37C with 500 rpm shaking on an Eppendorf Thermomixer. Following tagmentation, DNA was purified using a Zymo clean and concentrate-5 column and PCR performed using Nextera primers containing unique dual indices and 2X NEBNext High Fidelity master mix for 11-13 cycles (depending on starting input; 72C for 5min, 98C 30sec, cycles of 98C 10 sec, 63C 30 sec, 72C 1min). PCR products were purified using SparQ beads (Quanta Bio) and resuspended in 0.1X TE. Libraries were checked on a Fragment Analyzer (Agilent) and size selected using a Pippin HT (Sage Sciences).  Libraries were shallow sequenced on a MiSeq at Cornell BRC Genomics to check the balance of the pooled libraries. The pool was adjusted and sent for sequencing on two NovaSeq6000 (Illumina) S4 lanes at URMC to a depth of 50M reads per library.

value: naive CD8+ T cell

tag: phenotype

value: ME patient