title: 17A_M_2544


title: 17A_M_2545

status: Public on Jul 02 2023

type: SRA

city: La Jolla

first: Joseph

middle: R

last: Ecker

state: CA

address: 10010 North Torrey Pines Road

department: Genomic Analysis Laboratory

country: USA

institute: HHMI-Salk-Institute

library_source: genomic

data_processing:
Reads trimed with Cutadapt for adapters and low quality bases (Phred score >= 20)
The resulting files are mapped to in-silico bisulfite converted mm10 reference genome using Bismark.
The raw BAM file will be filtered using samtools to filter reads by MAPQ > 10 and use Picard to remove PCR duplicates
Tab-delimited files (ALLC files) describing the quantity of unmethylated and methylated cytosine base calls will be generated with in-house developing package using the filtered BAM files
Assembly: mm10
Supplementary files format and content: tab-delimited files (ALLC files) describing the quantity of unmethylated and methylated cytosine base calls. Columns are: 1. Chromosome, 2. Position, 3. Strand, 4. Cytosin Context, 5. methylated base call, 6. total mapped base call, 7. not used, place holder column
Library strategy: snmC-seq3

molecule: genomic DNA

organism: Mus musculus

source_name: C57BL/6J Male P56 Mouse Brain

growth_protocol: All mice are C57BL/6J Male, brain dissected in P56

extract_protocol:
the brain of P56 male C57BL/6J mouse will be removed and cut into 600 microns thick coronal sections using a tissue matrix. Then each region will be microdissected from the coronal tissue sections based on identified landmarks and brain atlas coordinates, as defined in Allen brain atlas CCF3 (Avaliable at: http://atlas.brain-map.org). For each dissection region, the tissue from several littermate mice will be combined together into to separate replicate groups. The number of animals in a replicate depends on the size of the tissue. Nuclei preparation will be stained with the fluorescently labeled anti-NeuN body and nucleic acid stain Hoechst 33342.
Library prepared following protocol discribed in Luo, Chongyuan, Angeline Rivkin, Jingtian Zhou, Justin P. Sandoval, Laurie Kurihara, Jacinta Lucero, Rosa Castanon, et al. 2018. “Robust Single-Cell DNA Methylome Profiling with snmC-seq2.” Nature Communications 9 (1): 3824.

tag: brain region

tag: age

tag: strain


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title: 17A_M_1099


title: 17A_M_1101


title: 17A_M_1103


title: 17A_M_1098


title: 17A_M_1096


title: 17A_M_1102


title: 17A_M_1113


title: 17A_M_1100


title: 17A_M_1097


title: 17A_M_1109


title: 17A_M_1094


title: 17A_M_1093


title: 17A_M_1095


title: 17A_M_1092


title: 17A_M_1091


title: 17A_M_1088


title: 17A_M_1090


title: 17A_M_1089


title: 17A_M_1087


title: 17A_M_1082


title: 17A_M_1085


title: 17A_M_1081


title: 17A_M_1079


title: 17A_M_1084


title: 17A_M_1080


title: 17A_M_1078


title: 17A_M_1104


title: 17A_M_1083


title: 17A_M_1075


title: 17A_M_1074


title: 17A_M_1072


title: 17A_M_1077


title: 17A_M_1073


title: 17A_M_1071


title: 17A_M_1069


title: 17A_M_1070


title: 17A_M_1067


title: 17A_M_1064


title: 17A_M_1059


title: 17A_M_1060


title: 17A_M_1063


title: 17A_M_1057


title: 17A_M_1055


title: 17A_M_1058


title: 17A_M_1056


title: 17A_M_1076


title: 17A_M_1054


title: 17A_M_1052


title: 17A_M_1053


title: 17A_M_1048


title: 17A_M_1047


title: 17A_M_1050


title: 17A_M_1049


title: 17A_M_1051


title: 17A_M_1045


title: 17A_M_1068


title: 17A_M_1042


title: 17A_M_1043


title: 17A_M_1061


title: 17A_M_1046


title: 17A_M_1041


title: 17A_M_1044


title: 17A_M_1040


title: 17A_M_1062


title: 17A_M_1036


title: 17A_M_1039


title: 17A_M_1037


title: 17A_M_1034


title: 17A_M_1035


title: 17A_M_1032


title: 17A_M_1031


title: 17A_M_1030


title: 17A_M_1029


title: 17A_M_1028


title: 17A_M_1027


title: 17A_M_1026


title: 17A_M_1025


title: 17A_M_1020


title: 17A_M_1024


title: 17A_M_1038


title: 17A_M_1019


title: 17A_M_1021


title: 17A_M_1023


title: 17A_M_1018


title: 17A_M_1033


title: 17A_M_1017


title: 17A_M_825


title: 17A_M_821


title: 17A_M_824


title: 17A_M_820


title: 17A_M_822


title: 17A_M_1016


title: 17A_M_818


title: 17A_M_816


title: 17A_M_814


title: 17A_M_817


title: 17A_M_815


title: 17A_M_819


title: 17A_M_808


title: 17A_M_809


title: 17A_M_823


title: 17A_M_826


title: 17A_M_805


title: 17A_M_804


title: 17A_M_801


title: 17A_M_803


title: 17A_M_802


title: 17A_M_799


title: 17A_M_800


title: 17A_M_798


title: 17A_M_811


title: 17A_M_796


title: 17A_M_795


title: 17A_M_794


title: 17A_M_789


title: 17A_M_792


title: 17A_M_797


title: 17A_M_810


title: 17A_M_785


title: 17A_M_784


title: 17A_M_807


title: 17A_M_787


title: 17A_M_783


title: 17A_M_786


title: 17A_M_806


title: 17A_M_788


title: 17A_M_780


title: 17A_M_779


title: 17A_M_778


title: 17A_M_782


title: 17A_M_775


title: 17A_M_776


title: 17A_M_790


title: 17A_M_773


title: 17A_M_770


title: 17A_M_769


title: 17A_M_774


title: 17A_M_768


title: 17A_M_767


title: 17A_M_764


title: 17A_M_772


title: 17A_M_763


title: 17A_M_793


title: 17A_M_781


title: 17A_M_761


title: 17A_M_756


title: 17A_M_758


title: 17A_M_759


title: 17A_M_757


title: 17A_M_760


title: 17A_M_777


title: 17A_M_765


title: 17A_M_754


title: 17A_M_753


title: 17A_M_751


title: 17A_M_750


title: 17A_M_752


title: 17A_M_749


title: 17A_M_766


title: 17A_M_771


title: 17A_M_747


title: 17A_M_745


title: 17A_M_762


title: 17A_M_742


title: 17A_M_740


title: 17A_M_746


title: 17A_M_743


title: 17A_M_755


title: 17A_M_744


title: 17A_M_738


title: 17A_M_741


title: 17A_M_736


title: 17A_M_735


title: 17A_M_737


title: 17A_M_734


title: 17A_M_739


title: 17A_M_733


title: 17A_M_732


title: 17A_M_729


title: 17A_M_730


title: 17A_M_731


title: 17A_M_727


title: 17A_M_726


title: 17A_M_724


title: 17A_M_723


title: 17A_M_722


title: 17A_M_720


title: 17A_M_725


title: 17A_M_728


title: 17A_M_721


title: 17A_M_719


title: 17A_M_718


title: 17A_M_717


title: 17A_M_714


title: 17A_M_716


title: 17A_M_713


title: 17A_M_715


title: 17A_M_711


title: 17A_M_712


title: 17A_M_706


title: 17A_M_710


title: 17A_M_708


title: 17A_M_707


title: 17A_M_703


title: 17A_M_705


title: 17A_M_704


title: 17A_M_698


title: 17A_M_694


title: 17A_M_700


title: 17A_M_701


title: 17A_M_691


title: 17A_M_690


title: 17A_M_695


title: 17A_M_692


title: 17A_M_693


title: 17A_M_689


title: 17A_M_702


title: 17A_M_688


title: 17A_M_683


title: 17A_M_685


title: 17A_M_684


title: 17A_M_699


title: 17A_M_679


title: 17A_M_681


title: 17A_M_696


title: 17A_M_680


title: 17A_M_677


title: 17A_M_697


title: 17A_M_709


title: 17A_M_676


title: 17A_M_678


title: 17A_M_682


title: 17A_M_675


title: 17A_M_687


title: 17A_M_686


title: 17A_M_673


title: 17A_M_672


title: 17A_M_669


title: 17A_M_671


title: 17A_M_670


title: 17A_M_674


title: 17A_M_666


title: 17A_M_663


title: 17A_M_668


title: 17A_M_665


title: 17A_M_664


title: 17A_M_662


title: 17A_M_660


title: 17A_M_661


title: 17A_M_659


title: 17A_M_658


title: 17A_M_657


title: 17A_M_656


title: 17A_M_651


title: 17A_M_652


title: 17A_M_654


title: 17A_M_644


title: 17A_M_646


title: 17A_M_649


title: 17A_M_647


title: 17A_M_648


title: 17A_M_645


title: 17A_M_643


title: 17A_M_667


title: 17A_M_641


title: 17A_M_642


title: 17A_M_637


title: 17A_M_636


title: 17A_M_571


title: 17A_M_570


title: 17A_M_640


title: 17A_M_639


title: 17A_M_566


title: 17A_M_569


title: 17A_M_567


title: 17A_M_568


title: 17A_M_565


title: 17A_M_655


title: 17A_M_650


title: 17A_M_653


title: 17A_M_563


title: 17A_M_564


title: 17A_M_557


title: 17A_M_559


title: 17A_M_555


title: 17A_M_560


title: 17A_M_562


title: 17A_M_556


title: 17A_M_554


title: 17A_M_561


title: 17A_M_558


title: 17A_M_552


title: 17A_M_550


title: 17A_M_551


title: 17A_M_545


title: 17A_M_549


title: 17A_M_547


title: 17A_M_548


title: 17A_M_542


title: 17A_M_546


title: 17A_M_543


title: 17A_M_540


title: 17A_M_544


title: 17A_M_537


title: 17A_M_535


title: 17A_M_541


title: 17A_M_534


title: 17A_M_539


title: 17A_M_538


title: 17A_M_533


title: 17A_M_536


title: 17A_M_532


title: 17A_M_529


title: 17A_M_528


title: 17A_M_530


title: 17A_M_527


title: 17A_M_526


title: 17A_M_553


title: 17A_M_525


title: 17A_M_531


title: 17A_M_524


title: 17A_M_523


title: 17A_M_522


title: 17A_M_519


title: 17A_M_521


title: 17A_M_520


title: 17A_M_516


title: 17A_M_517


title: 17A_M_515


title: 17A_M_514


title: 17A_M_509


title: 17A_M_317


title: 17A_M_510


title: 17A_M_313


title: 17A_M_511


title: 17A_M_508


title: 17A_M_512


title: 17A_M_311


title: 17A_M_316


title: 17A_M_315


title: 17A_M_312


title: 17A_M_314


title: 17A_M_307


title: 17A_M_308


title: 17A_M_305


title: 17A_M_306


title: 17A_M_518


title: 17A_M_300


title: 17A_M_301


title: 17A_M_299


title: 17A_M_298


title: 17A_M_297


title: 17A_M_296


title: 17A_M_292


title: 17A_M_310


title: 17A_M_293


title: 17A_M_309


title: 17A_M_291


title: 17A_M_290


title: 17A_M_289


title: 17A_M_304


title: 17A_M_283


title: 17A_M_286


title: 17A_M_303


title: 17A_M_287


title: 17A_M_282


title: 17A_M_284


title: 17A_M_281


title: 17A_M_280


title: 17A_M_285


title: 17A_M_277


title: 17A_M_276


title: 17A_M_275


title: 17A_M_295


title: 17A_M_278


title: 17A_M_274


title: 17A_M_273


title: 17A_M_270


title: 17A_M_269


title: 17A_M_268


title: 17A_M_267


title: 17A_M_279


title: 17A_M_261


title: 17A_M_260


title: 17A_M_265


title: 17A_M_266


title: 17A_M_262


title: 17A_M_256


title: 17A_M_257


title: 17A_M_259


title: 17A_M_258


title: 17A_M_255


title: 17A_M_254


title: 17A_M_253


title: 17A_M_272


title: 17A_M_252


title: 17A_M_250


title: 17A_M_251


title: 17A_M_249


title: 17A_M_638


title: 17A_M_271


title: 17A_M_263


title: 17A_M_264


title: 17A_M_247


title: 17A_M_246


title: 17A_M_245


title: 17A_M_243


title: 17A_M_244


title: 17A_M_241


title: 17A_M_242


title: 17A_M_240


title: 17A_M_239


title: 17A_M_237


title: 17A_M_235


title: 17A_M_238


title: 17A_M_248


title: 17A_M_288


title: 17A_M_236


title: 17A_M_233


title: 17A_M_230


title: 17A_M_232


title: 17A_M_228


title: 17A_M_225


title: 17A_M_227


title: 17A_M_229


title: 17A_M_231


title: 17A_M_223


title: 17A_M_224


title: 17A_M_221


title: 17A_M_222


title: 17A_M_220


title: 17A_M_218


title: 17A_M_217


title: 17A_M_212


title: 17A_M_234


title: 17A_M_214


title: 17A_M_211


title: 17A_M_213


title: 17A_M_226


title: 17A_M_206


title: 17A_M_207


title: 17A_M_208


title: 17A_M_209


title: 17A_M_205


title: 17A_M_203


title: 17A_M_202


title: 17A_M_201


title: 17A_M_200


title: 17A_M_199


title: 17A_M_219


title: WT-5 +Serum RNA-SEQ

city: Nanjing

first: Xiaoxu

last: Liu

state: Jiangsu

address: 2 Sipailou

department: Institute of Life Sciences

country: China

institute: Southeast University

library_source: transcriptomic

data_processing:
The clean reads were subjected to TopHat and Cufflinks pipeline based on Human genome (UCSC genome, GRCh37/hg19) . The Cuffdiff program within Cufflinks was used to test statistically significant differences of genes expressions between control and AFF1 KO as well as wildtype and AFF4 KO cells.
Assembly: hg19

molecule: total RNA

organism: Homo sapiens

growth_protocol: DMEM (HyClone) supplemented with 10% FBS (Ex-Cell Bio) and 1% Penicillin-Streptomycin (HyClone), at 37°C with 5% CO2 in a humidified incubator and routinely passaged 2-3 times a week.

extract_protocol:
Total RNA was extracted by using the RNeasy kit (Qiagen) according to the instructions of the manufacturer. RNA was treated with DNase I (NEB) and re-purified on the column.
To generate RNA-seq library, total RNA was polyadenylated, fragmented and reversed. Then reversed cDNA was ligated to adapters for sequencing (Illumina).

treatment_protocol: For serum induction, the complete medium of 60%-70% confluent HCT116 cells was replaced with fresh medium without FBS after washed by PBS for three times. The starved cells were incubated for 40 hours. The incomplete medium was changed with pre-heated complete medium and the cells were incubated for 30 minutes

tag: cell line

tag: cell type

value: human colon cancer cells

tag: treatment

value: Serum induction

tag: genotype

value: WT


title: 17A_M_198


title: AFF4 KO-6 +Serum RNA-SEQ

value: AFF4 KO


title: WT-6 +Serum RNA-SEQ


title: AFF1 KO-4 +Serum RNA-SEQ

value: AFF1 KO


title: 17A_M_215


title: 17A_M_216


title: 17A_M_210


title: 17A_M_197


title: WT-4 +Serum RNA-SEQ


title: AFF1 KO-3 +Serum RNA-SEQ


title: 17A_M_196


title: 17A_M_194


title: 17A_M_204


title: 17A_M_192


title: 17A_M_193


title: AFF4 MT-2 +Serum RNA-SEQ

data_processing:
The clean reads were subjected to TopHat and Cufflinks pipeline based on Human genome (UCSC genome, GRCh37/hg19) . The Cuffdiff program within Cufflinks was used to test statistically significant differences of genes expressions between control and AFF4 mutant cells.
Assembly: hg19
Supplementary files format and content: bw

treatment_protocol: For serum induction, the complete medium of 60%-70% confluent HCT116 cells was replaced with fresh medium without FBS after washed by PBS for three times. The starved cells were incubated for 40 hours. The incomplete medium was changed with pre-heated complete medium and the cells were incubated for 30 minutes before fixation for ChIP-seq.

value: Human colon cancer cells

value: AFF4 MT


title: AFF4 MT-1 +Serum RNA-SEQ


title: WT-2 +Serum RNA-SEQ


title: 17A_M_191


title: 17A_M_190


title: AFF4 KO-5 +Serum RNA-SEQ


title: 17A_M_189


title: 17A_M_188


title: 17A_M_186


title: 17A_M_187


title: a-input

city: Chongqing

first: Yu

last: Shi

state: Chongqing

address: 10 Changjiang Branch Road

department: Cardiology

institute: Military Medical University

data_processing:
The resulting raw image data file is recognized by CASAVA base.
Since chip-Seq interrupt fragments are usually small, and the percentage of unique sequences in the total number of sequences is the focus of attention,BWA (Burrows Wheeler Aligner) can be used to more accurately compare reads to reference genomes (Li, H. and R. Durbin, 2009).
The main purpose of data filtering is to remove low quality data and ensure the quality of clean data.We cut off the sequencing joints and low-quality fragments of the sequencing data in the way of trim. If the length of the remaining reads after trimming is long enough, they can still be used for the subsequent analysis, so as to efficiently utilize the sequencing data. The subsequent analysis is based on clean data.
MACS2 software (Yong Zhang,Tao Liu et al., 2008) (threshold qvalue<=0.05) was used to complete peak calling, and statistics were conducted on the number, width and distribution of peaks to screen out peak related genes, etc.
Assembly: rn6
Supplementary files format and content: peak text files

organism: Rattus norvegicus

source_name: neonatal primary cardiomyocytes-IgG

growth_protocol: Neonata primary rat cardiomyocytes were routinely cultured on precoated plates in DMEM medium supplemented with 10% FBS.

extract_protocol:
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody.
Cells were fixed with formaldehyde and DNA was crosslinked to proteins;Cells were lysed, chromatin was separated, and chromatin was randomly cleaved by ultrasound or enzyme treatment.Then the specific recognition reaction of antigen and antibody is used to precipitate the DNA fragment bound to the target protein.DNA fragments were released and extracted by cross-linking.Library construction (including terminal repair, addition of A, addition of connector, length screening, PCR amplification) and high-throughput sequencing.For chip-SEq, there is usually enough broken chromatin left to be used directly for subsequent DNA extraction as a control, called Input.Mock immunoprecipitation can also be simulated using homotype antibodies, pre-immunization sera, or antibodies of the same species origin. The resulting DNA can be extracted as a control, known as Mock.Usually, before building the library, if some target sequences are known, the effect of ChIP can be verified by qPCR, etc.After the library was constructed, quality inspection was carried out. After passing the quality inspection, subsequent machine sequencing was carried out.

treatment_protocol: The cardiomyocytes were treated with α-KG  (5mM) or control (PBS) for 24 hours.

tag: tissue

value: heart

value: neonatal primary cardiomyocytes

value: Sprague Dawley

value: alpha KG

tag: chip-antibody

value: IgG


title: α-KG-1


title: c-input

value: PBS control


title: α-KG-2


title: ctrl-2


title: 17A_M_195


title: 17A_M_184


title: 17A_M_185


title: ctrl-1


title: 17A_M_183


title: 17A_M_513


title: WT-3 +Serum RNA-SEQ


title: 17A_M_182


title: HMVEC CD36KD 2

city: St Louis

first: Nada

last: Abumrad

address: 660 S. Euclid

institute: Washington University

data_processing:
Basecalling with Illumina RTA 1.9
Demultiplexing with Illumina bcl2fastq2
Fastq files were combined and aligned with STAR 2.5.1a
Gene counts quantitated with Subread:featureCount 1.4.6-p5 with CPM and RPKM transformations added with custom Rscripting.
Assembly: Ensembl GRCh38.76
Supplementary files format and content: Gene counts with CPM and RPKM in tab-delimitted text format

source_name: HMVEC-d Ad

growth_protocol: HMVEC-d Ad were grown and maintained in EGM2-MV media (Lonza).

extract_protocol:
RNA was extracted from treated cells using Trizol (Life Technologies) followed by sample cleanup using Rneasy mini kit (Qiagen)
Takara Clontech SMARTer

treatment_protocol: Cells were transfected with either Control (GFP) or or CD36 siRNA (4392420, assay ID: s2646, ThermoFisher Scientific) using Lipofectamine RNAiMAX.  Cells were harvested 72 hours post-transfection.

value: HMVEC-d Ad

value: dermal microvascular endothelial

value: CD36 knockdown

value: transfected with CD36 siRNA

tag: timepoint

value: 72 hrs post transfection


title: 17A_M_181


title: HMVEC CD36KD 1


title: HMVEC Control 2

value: Control knockdown

value: transfected with Control (GFP) siRNA


title: HMVEC CD36KD 3


title: 17A_M_180


title: 17A_M_179


title: HMVEC Control 3


title: HMVEC Control 1


title: WT-1 +Serum RNA-SEQ

value: Serum induction

value: WT


title: CC1680.202.Wk4

city: New York

first: Ariela

last: Buxbaum Grice

state: New York

address: 1 Gustave Levy Pl

department: Psychiatry

institute: Mount Sinai School of Medicine

data_processing:
Raw reads were aligned to hg38 with STAR
RNA quality control was performed using RSeQC and Picard
Expression outliers  were removed if seen in WGCNA or differential expression (limma) analyses
Assembly: hg38
Supplementary files format and content: tab-delimited text file with raw counts for each sample

source_name: Blood

extract_protocol:
RNA extraction was performed with the PAXgene Blood RNA Kit (Qiagen), according to manufacturer protocol
Libraries were prepared using the TruSeq Stranded kit (Illumina), according to manufacturer protocol

value: Blood

value: ADNP

tag: rin

tag: mutation class

value: Class I

tag: Sex

value: M


title: 17A_M_177


title: 17A_M_176


title: CC1680.202.Wk2


title: CC1668.201.Wk2


title: CC1668.201.Wk4


title: CC1680.202.Post

value: Post-Infusion


title: 17A_M_173


title: 17A_M_175


title: 17A_M_174


title: CC1668.201.Pre

value: Baseline


title: 17A_M_171


title: CC1668.201.Post

description:
Removed: Swap Suspected
CC1409-203-Post


title: CC1628.201.Wk4

description:
Removed: Swap Suspected
CC1360-201-Post


title: 17A_M_170


title: CC1628.201.D1


title: CC1628.201.Wk2


title: 17A_M_166


title: 17A_M_169


title: CC1566.203.Wk4

value: Class II


title: CC1628.201.Wk1


title: CC1628.201.Pre


title: 17A_M_164


title: 17A_M_167


title: 17A_M_178


title: 17A_M_168


title: CC1566.203.Wk1


title: CC1566.203.Wk2


title: 17A_M_163


title: CC1566.203.Post


title: 17A_M_162


title: 17A_M_172


title: CC1420.204.Wk4

value: F


title: 17A_M_159


title: 17A_M_161


title: 17A_M_158


title: 17A_M_160


title: CC1628.201.Post


title: CC1420.204.Wk2


title: CC1566.203.Pre


title: CC1566.203.D1


title: CC1420.204.Wk1


title: ATAC T47D_Clone28_24hour_rep2

city: Charlottesville

first: Thomas

middle: G

last: Scott

state: VA

address: 1340 Jefferson Park Ave, Pinn Hall 6225

department: Biochemistry and Molecular Genetics

institute: University of Virginia

library_source: other

data_processing:
Adapter trimming: cutadapt v1.8.1
UMI trimming and reverse complementing: seqtk v1.3
FASTQ deduplication: https://github.com/guertinlab/fqdedup v1.0.0
FASTQ pairing: fastq_pair v1.0
Alignment: bowtie2 v2.4.4
File manipulation: samtools v1.9
File manipulation: https://github.com/guertinlab/seqOutBias v1.3.1
All details and code: https://guertinlab.github.io/TRPS1_ER/Vignette.html
Assembly: hg38
Supplementary files format and content: bigWig counts files
Supplementary files format and content: Peak counts file

molecule: other

growth_protocol: T47D cells (RRID:CVCL_0553) (ATCC) were cultured in RPMI 1640 medium (Gibco) supplemented with 10% fetal bovine serum (Gemini) and 10ug/ml insulin from bovine pancreas (Sigma, made as a 1000x solution in 1% aqueous glacial acetic acid).

extract_protocol:
At the time of harvest, cells were moved to ice and scraped in 1mL ice cold PBS, and 100μL (∼5 x 10^4 cells) were transferred to 1.5 mL tubes. Cells were centrifuged at 500 x g for 5 minutes at 4°C, and the pellets were resuspended in 50 μL cold lysis buffer (10mM Tris-HCl, 10mM NaCl, 3mM MgCl2, 0.1% NP-40, 0.1% Tween-20, 0.01% Digitonin, adjusted to pH 7.4) and incubated on ice for 3 minutes. Samples were washed with 1 mL cold wash buffer (10mM Tris-HCl, 10mM NaCl, 3mM MgCl2, 0.1% Tween-20). Cells were centrifuged at 500 x g for 10 minutes at 4°C, and pellets were resuspended in the transposition reaction mix (25 μL 2X TD buffer (Illumina), 2.5 μL TDE1 Tn5 transposase (Illumina), 16.5 μL PBS, 0.5 μL 1% Digitonin, 0.5 μL 10% Tween-20, 5 μL nuclease-free water) and incubated in a thermomixer at 37°C and 100rpm for 30 minutes.
DNA was extracted with the DNA Clean and Concentrator-5 Kit (Zymo Research). Sequencing adapters were attached to the transposed DNA fragments using NEBNext Ultra II Q5 PCR mix (New England Biolabs), and libraries were amplified with 8 cycles of PCR. PEG-mediated size fractionation (Lis 1980) was performed on the libraries by mixing SPRIs-elect beads (Beckman) with each sample at a 0.5:1 ratio, then placing the reaction vessels on a magnetic stand. The right side selected sample was transferred to a new reaction vessel, and more beads were added for a final ratio of 1.8:1. The final size-selected sample was eluted into nuclease-free water. This size selection protocol was repeated to further remove large fragments.

treatment_protocol: ATAC-seq libraries were prepared as previously described (Grandi et al. 2022), with modifications. 4 replicates were performed from cells treated and collected at different times in the same day. 4*105 cells per sample were plated in each well of a 6-well plate 2 days before harvest. Cells were treated with DMSO or 50nM dTAG-13 and 50nM dTAGV-1 in DMSO at various time points and collected simultaneously.

value: 50nM dTAG-13 + 50nM dTAG-V-1 for 24 hours


title: 17A_M_156


title: ATAC T47D_Clone28_24hour_rep3


title: CC1420.204.D1


title: CC1420.204.Post


title: ATAC T47D_Clone28_4hour_rep3

value: 50nM dTAG-13 + 50nM dTAG-V-1 for 4 hours


title: 17A_M_155


title: ATAC T47D_Clone28_4hour_rep4


title: ATAC T47D_Clone28_24hour_rep4


title: 17A_M_294


title: ATAC T47D_Clone28_24hour_rep1


title: CC1420.204.Pre


title: 17A_M_154


title: ATAC T47D_Clone28_4hour_rep1


title: ATAC T47D_Clone28_4hour_rep2


title: 17A_M_153


title: CC1409.203.Wk4


title: ATAC T47D_Clone28_2hour_rep4

value: 50nM dTAG-13 + 50nM dTAG-V-1 for 2 hours


title: CC1409.203.Wk2


title: 17A_M_157


title: 17A_M_152


title: ATAC T47D_Clone28_2hour_rep2


title: ATAC T47D_Clone28_2hour_rep1


title: 17A_M_165


title: 17A_M_151


title: ATAC T47D_Clone28_1hour_rep4

value: 50nM dTAG-13 + 50nM dTAG-V-1 for 1 hour


title: ATAC T47D_Clone28_2hour_rep3


title: CC1409.203.Wk1


title: ATAC T47D_Clone28_1hour_rep2


title: ATAC T47D_Clone28_0.5hour_rep4

value: 50nM dTAG-13 + 50nM dTAG-V-1 for 30 minutes


title: 17A_M_150


title: ATAC T47D_Clone28_1hour_rep1


title: 17A_M_149


title: 17A_M_148


title: ATAC T47D_Clone28_0.5hour_rep3


title: CC1409.203.Pre


title: ATAC T47D_Clone28_0.5hour_rep2


title: CC1409.203.Post


title: ATAC T47D_Clone28_0.5hour_rep1


title: CC1368.202.Wk4


title: 17A_M_147


title: 17A_M_146


title: ATAC T47D_Clone28_0hour_rep4

value: 0.1% v/v DMSO for 24 hours


title: ATAC T47D_Clone28_0hour_rep3


title: CC1368.202.Wk2


title: ATAC T47D_Clone28_0hour_rep2


title: 17A_M_145


title: ATAC T47D_Clone28_0hour_rep1


title: 17A_M_144


title: T47D_Clone28_YAP_dTAG_rep4

data_processing:
Adapter trimming: cutadapt v3.4
FASTQ pairing: fastq_pair v1.0
Alignment: bowtie2 v2.2.9
File manipulation: samtools v1.12
File manipulation: bedtools/2.29.2
File manipulation: deeptools/3.5.1
All details and code: https://guertinlab.github.io/TRPS1_ER/Vignette.html
Assembly: hg38
Supplementary files format and content: bigWig counts files
Supplementary files format and content: Peak counts file

extract_protocol:
At the time of harvest, cells were fixed with 1% formaldehyde (Sigma) for 10 minutes at 37°C and quenched with 125mM Glycine (Fisher) for 10 minutes at 37°C. Plates were moved to ice, and cells were washed and scraped into ice cold PBS containing Complete EDTA-free Protease Inhibitor Cocktail (Roche). Cells were pelleted in aliquots of 3.6*107 cells, snap frozen in liquid nitrogen, and stored at -80°C. Pellets were thawed, and cells were lysed in 1mL Cell Lysis Buffer (85mM KCl, 0.5%NP40, 5mM PIPES pH 8.0), with protease inhibitor cocktail added fresh, for 10 minutes with rotation at 4°C. Nuclei were pelleted at 3300g at 4°C for 5 minutes and resuspended in 500μL ChIP lysis buffer (0.5% SDS, 10mM EDTA, 50mM Tris-HCl pH 8.1), with protease inhibitor cocktail added fresh, for 10 minutes with rotation at 4°C. Lysates were moved to 15ml polystyrene conical tubes (Falcon) and sonicated in a Biorupter UCD-200 (Diagenode) on high for 30 seconds on and 30 seconds off for 4 sets of 5 cycles. Before each set, ice in the water bath was replaced, and samples were gently vortexed to mix. Sonicated lysates were then move to 1.5ml tubes and clarified by centrifugation at 14,000rpm for 15 min in 4°C. 500μL of the supernatant was diluted into 6.5mL Dilution Buffer (0.01% SDS, 1.1% Triton X-100, 1.2mM EDTA, 167mM NaCl, 16.6mM Tris-HCl pH 8.0), with protease inhibitor cocktail added fresh ( 1*106 cells in 200μL). 1ml ( 5*106 cells) was aliquoted into each of 3 tubes with antibody (1.25 μg anti-HA, Cell Signaling #3724S, 2.5μg anti-ER, Millipore #06-935, or 2.5μg IgG control, Cell Signaling #2729S), and incubated with end-over-end rotation at 4°C overnight. 50μL Protein A/G Magnetic Beads (Pierce) per sample were washed with bead washing buffer (PBS with 0.1% BSA and 2mM EDTA) and then incubated with samples for 2 hours with rotation at 4°C. The samples were washed once each with low salt immune complex buffer (0.1% SDS, 1% Triton x-100, 2mM EDTA, 150mM NaCl, 20mM Tris HCl pH8.0), high salt immune complex buffer (0.1% SDS, 1% Triton x-100, 2mM EDTA, 500mM NaCl, 20mM Tris Hcl pH 8.0), LiCl immune complex buffer (0.25M LiCl, 1% NP-40, 1% deoxycholate, 1mM EDTA, 10mM Tris-HCl pH8.0), and 1xTE (10mM Tris-HCl, 1mM EDTA pH8.0). Immune complexes were eluted in elution solution, (1% SDS, 0.1M sodium bicarbonate) in a thermomixer for 30 min at 65°C at 1,200rpm. Crosslinks were reversed and proteins were digested with the addition of 200mM NaCl and 2ul Proteinase K in a thermocycler at 65°C for 16 hours.
DNA was purified with a Qiaquick PCR cleanup (Qiagen), and libraries were prepared with a NEBNext Ultra II Library Prep Kit (New England Biolabs).

treatment_protocol: 2.4*107 cells per sample were plated across 3 15cm dishes 2 days before harvest. Cells were treated with DMSO or 50nM dTAG-13 and 50nM dTAGV-1 in DMSO for 30 minutes and collected simultaneously.

tag: chip antibody

value: YAP


title: CC1368.202.D1


title: CC1368.202.Wk1


title: T47D_Clone28_YAP_dTAG_rep3


title: T47D_Clone28_YAP_dTAG_rep1


title: T47D_Clone28_YAP_dTAG_rep2


title: ATAC T47D_Clone28_1hour_rep3


title: 17A_M_143


title: 17A_M_142


title: CC1409.203.D1


title: T47D_Clone28_YAP_DMSO_rep4


title: CC1368.202.Post


title: T47D_Clone28_YAP_DMSO_rep3


title: T47D_Clone28_YAP_DMSO_rep2


title: T47D_Clone28_YAP_DMSO_rep1


title: CC1360.201.Wk4


title: T47D_Clone28_PR_dTAG_rep3

value: PR


title: T47D_Clone28_PR_dTAG_rep4


title: CC1368.202.Pre


title: T47D_Clone28_PR_dTAG_rep2


title: CC1360.201.Wk2


title: CC1360.201.Wk1


title: 17A_M_140


title: 17A_M_138


title: T47D_Clone28_PR_dTAG_rep1


title: T47D_Clone28_PR_DMSO_rep4


title: T47D_Clone28_PR_DMSO_rep3


title: 17A_M_137


title: T47D_Clone28_PR_DMSO_rep1


title: CC1360.201.D1


title: T47D_Clone28_PR_DMSO_rep2


title: T47D_Clone28_CTCFHA_dTAG_rep4

value: CTCF + HA


title: CC1360.201.Post

value: Blood


title: T47D_Clone28_CTCFHA_dTAG_rep3


title: 17A_M_136


title: CC1329.202.Wk4

value: ADNP


title: 17A_M_141


title: T47D_Clone28_CTCFHA_dTAG_rep1


title: T47D_Clone28_CTCFHA_dTAG_rep2


title: 17A_M_135


title: CC1329.202.Wk2

value: Class I


title: 17A_M_134


title: spindrop mES HEK293T species mixing nuclei

city: Cambridge

first: Florian

last: Hollfelder

address: 80 tennis court road

country: United Kingdom

institute: University of Cambridge

description: spindrop

library_source: transcriptomic single cell

data_processing:
FastQC quality control
Pheniqs for demultiplexing
zUMIs to generate gene expression matrices using mouse and human references with Ensembl v99 annotations
Seurat v3 for data integration and analysis
Assembly: GRCm38 genome (Ensembl 99) and GRCh38 genome (Ensembl 99)
Supplementary files format and content: UMI quantified reads mapping to intronic and exonic regions. Downsampled to 20,000 reads per cell when indicated in the file header.

organism:
Homo sapiens
Mus musculus

source_name: kidney, Embryo

extract_protocol:
HEK293T cultured in DMEM supplemented with 10% FBS, mESC cells cultured in 2i/LIF. HEK293T were dissociated with Trypsin-EDTA for 5 minutes at 37C , mESCs were dissociated with Accutase. Mouse brain dissections were dissociated with  with TrypLE Express for 15 minutes at 37C. For nuclei preparations the Nuclei EZ prep kit. For the paraformaldehyde (PFA) treatment, 4% PFA was used. Live celsl were stained with Calcein-AM, PFA-fixed cells and nuclei were stained with Vybrant green.
Bead barcoding: indrop v3 protocol, encapsulation: spinDrop protocol, downstream library preparation: inDrop v3 protocol
inDrop v3 protocol

value: kidney, Embryo

value: HEK293T, mESC

value: cultured cells

value: WT/WT

value: HEK293T cultured in DMEM supplemented with 10% FBS, mESC cells cultured in 2i/LIF. HEK293T were dissociated with Trypsin-EDTA for 5 minutes at 37C , mESCs were dissociated with Accutase. Nuclei were recovered using the Nuclei EZ Prep kit and pooled at equal concentrations and stained with Vybrant Green before being processed using spinDrop.


title: 17A_M_139


title: CC1329.202.Wk1

value: F


title: T47D_Clone28_CTCFHA_DMSO_rep2


title: spindrop mES HEK293T species mixing

description: spindrop

value: HEK293T cultured in DMEM supplemented with 10% FBS, mESC cells cultured in 2i/LIF. HEK293T were dissociated with Trypsin-EDTA for 5 minutes at 37C , mESCs were dissociated with Accutase. Cells were pooled at equal concentrations and stained with Calcein-AM before being processed using spinDrop.


title: T47D_Clone28_CTCFHA_DMSO_rep1


title: 17A_M_133


title: CC1329.202.D1


title: CC1329.202.Post

description:
Removed: Gene expression Outlier
CC1668-201-Pre

value: Post-Infusion


title: NKT-3

city: Hangzhou

first: Wang

last: Qian

state: Zhejiang

address: 2318 Yuhangtang Road

institute: Hangzhou Normal University

data_processing:
Illumina Casava 1.8 software used for basecalling
Raw data (raw reads) of fastp format were firstly processed through in-house perl scripts..In this step, clean data (clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data. At the same time, Q20, Q30 and GC content the clean data were calculated. All the downstream analyses were based on the clean data with high quality.
Reference genome and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built using Hisat2 v2.0.5 and paired-end clean reads were aligned to the reference genome using Hisat2 v2.0.5.
featureCounts v1.5.0-p3 was used to count the reads numbers mapped to each gene.
Differential expression analysis of two conditions/groups (two biological replicates per condition) was performed using the DESeq2 R package (1.20.0).
Assembly: GRCh38.107
Supplementary files format and content: tab-delimited text files include FPKM values and gene count for each Sample

extract_protocol:
Total RNA was isolated using TRIzol (Invitrogen) according to the manufacturer’s instructions.
RNA libraries for RNA-seq were prepared using NEBNext® Ultra™ RNA Library Prep Kit for Illumina® following manufacturer's protocols.

value: 200 uM NKT for 24 h


title: NKT-2


title: 17A_M_131


title: T47D_Clone28_CTCF_dTAG_rep4

value: CTCF

value: 50nM dTAG-13 + 50nM dTAG-V-1 for 30 minutes


title: CC1329.202.Pre

value: Baseline


title: NKT-1


title: T47D_Clone28_CTCF_dTAG_rep3


title: CC1327.202.Wk4

value: M


title: T47D_Clone28_CTCFHA_DMSO_rep3

value: CTCF + HA

value: 0.1% v/v DMSO for 24 hours


title: CTL-3

value: Without special treatment


title: CC1327.202.Wk2

value: Blood

value: ADNP

value: Class I


title: T47D_Clone28_CTCFHA_DMSO_rep4


title: T47D_Clone28_CTCF_dTAG_rep1


title: T47D_Clone28_CTCF_dTAG_rep2


title: CTL-2


title: 17A_M_128


title: CTL-1


title: 17A_M_127


title: 17A_M_129


title: CC1327.202.D1


title: CC1327.202.Wk1


title: CC1327.202.Post


title: 17A_M_132


title: T47D_Clone28_CTCF_DMSO_rep3


title: T47D_Clone28_CTCF_DMSO_rep4


title: aWAT_PenX-Scr_rep4

city: Neuherberg

first: Maria

last: Rohm

address: Ingolstädter Landstraße 1

department: Institute for Diabetes and Cancer

country: Germany

institute: Helmholtz Munich

data_processing:
Raw data (raw reads) of FASTQ format were firstly processed through fastp. In this step, clean data (clean reads) were obtained by removing reads containing adapter and poly-N sequences and reads with low quality from raw data.
Reference genome and gene model annotation files were downloaded from genome website browser (NCBI/UCSC/Ensembl) directly. Paired-end clean reads were mapped to the reference genome using HISAT2 software.
Featurecounts was used to count the read numbers mapped of each gene, including known and novel genes.
Differential expression analysis between two groups (four biological replicates per condition) was performed using DESeq2 R package. The resulting P values were adjusted using the Benjamini and Hochberg’s approach for controlling the False Discovery Rate (FDR).
Assembly: mm10
Supplementary files format and content: tab-delimited file includes raw counts for each samples

source_name: abdominal white adipose tissue

growth_protocol: Male BALB/c mice obtained from the Charles River Laboratories were maintained in a climate-controlled environment (22-24 °C, ~50% humidity) with specific pathogen-free conditions under 12-h dark-light cycles (6 a.m. - 6 p.m.) in the animal facility of the Helmholtz Munich. Mice were fed ad libitum with regular rodent chow.

extract_protocol:
Total RNA was extracted using Qiazol lysis reagent and the RNeasy Mini kit. A total amount of 1 µg RNA per sample was used as input material for the RNA sample preparations.
Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina (NEB, USA) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample.

treatment_protocol: Mice were injected with 0.5*106 C26 colon carcinoma cells in PBS subcutaneously into the right flank. Tumor growth and body weight were measured daily for up to 16 d post tumor cell injection. Pen-X-ACIP or Pen-X-Scr were dissolved in sterile 5% DMSO, PBS and injected intraperitoneally at a dosage of 10mg/kg in 50 µl volume twice daily at 6 a.m. and 6 p.m., starting 7 days after tumor cell injection. Mice were killed at 9-11 a.m. by cervical dislocation 16 d after tumor cell injection.

value: abdominal white adipose tissue

value: wildtype

value: BALB/c

value: male

tag: disease

value: C26 tumor bearing

value: PenX-Scr


title: CC1327.202.Pre


title: 17A_M_130


title: aWAT_PenX-Scr_rep3


title: 17A_M_126


title: T47D_Clone28_IgG_dTAG_rep4

value: IgG


title: Retinoblastoma cell line-WERI-Rb-1

city: Shanghai

first: Ludi

last: Yang

state: Shanghai

address: ZhiZaoju road，833，Shanghai, China

institute: Ninth People’s Hospital, Shanghai JiaoTong University School of Medicine

data_processing:
Raw reads in fastq format were processed to remove contaminating adapter sequences using Trimmomatics
Quality distribution plot and base content distribution were generated by FASTQC
eccDNA-seq reads were aligned to the hg38 genome using bwa.
The circular DNA was detected by the Circle-Map
Assembly: hg38
Supplementary files format and content: bed
Library strategy: Circle-Seq

source_name: Retinoblastoma cell line-WERI-Rb-1

growth_protocol: Retinoblastoma cells were cultured in a T25 or T75 with 1640

extract_protocol:
Genomic DNA was extracted from cells using Qiagen kits
Libraries for next-generation sequencing were prepared using the NEBNext Ultra DNA Library Kit for Illumina according to the manufacturer’s protocol (New England Biolabs)

value: Retinoblastoma cell line-WERI-Rb-1


title: Retinoblastoma cell line-Y79

source_name: Retinoblastoma cell line-Y79

value: Retinoblastoma cell line-Y79


title: SIRT,rep2

city: ShangHai

first: Jialun

last: Li

address: NO. 500 Dongchuan Road, Minhang distinct

institute: WuHu Hospital, East China Normal University

data_processing:
RNA-seq reads were aligned to the human genome (assembly hg38) using Hisat2 v.2.2.1 with default parameters
Samtools was used to additionally remove nonuniquely mapped reads, as well as reads with a sequencing quality score q < 20
FeatureCounts v.2.0 was used to generate a matrix of mapped fragments per RefSeq annotated gene, with annotations from Gencodev26
Read counts have been normalized across samples with the median-of-ratios method proposed by Anders and Huber, to make these counts comparable between samples
BigWig files were generated using deeptools bamCoverage58 with --bs 60 and –normalize Using RPKM options.
Assembly: hg38
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample

source_name: HeLa

growth_protocol: HeLa cells were cultured in Dulbecco’s modified Eagle’s medium (DMEM) (Gibco) supplemented with 10% FBS, 100 U/ml penicillin, and 100 mg/ml streptomycin in 5% CO2 at 37 °C.

extract_protocol:
Total RNA for RNA-seq analysis was extracted from cells using RNAiso Plus Reagent (Takara) according to the manufacturer’s instructions. The RNA was dissolve in DEPC-treated H2O.
The RNA-seq library was prepared using NEBNext Ultra RNA Library Prep Kit for Illumina® according to the instruction manual.

treatment_protocol: HeLa cells were treated with 1 μM TSA or DMSO for 12 h. CRISPR-Cas9-V2 sgRNA plasmids for HDAC1/2/3, SIRT7 or vector were transfected into HeLa with LipoFiter (Hanbio) according to the manufacturer’s instructions, 48 h after infection, puromycin was added at a final concentration of 1 μg/μl to select for transfected cells. After selection with puromycin for 72 h, the cells were collected for RNA extraction and RNA-seq analysis.

value: HeLa


title: SIRT,rep1


title: aWAT_PenX-Scr_rep2


title: SIRT,rep3


title: Retinoblastoma tissue-3

source_name: Retinoblastoma tissue-3

value: Retinoblastoma tissue-3


title: T47D_Clone28_IgG_dTAG_rep2

value: 50nM dTAG-13 + 50nM dTAG-V-1 for 30 minutes


title: HDAC,rep3


title: T47D_Clone28_IgG_dTAG_rep3


title: HDAC,rep2


title: aWAT_PenX-ACIP_rep4

value: PenX-ACIP


title: aWAT_PenX-Scr_rep1


title: aWAT_PenX-ACIP_rep3


title: T47D_Clone28_IgG_dTAG_rep1


title: T47D_Clone28_CTCF_DMSO_rep2

value: CTCF

value: 0.1% v/v DMSO for 24 hours


title: vec,rep3


title: Retinoblastoma tissue-2

source_name: Retinoblastoma tissue-2

value: Retinoblastoma tissue-2


title: Retinoblastoma tissue-1

source_name: Retinoblastoma tissue-1

value: Retinoblastoma tissue-1


title: T47D_Clone28_IgG_DMSO_rep4


title: aWAT_PenX-ACIP_rep2

value: abdominal white adipose tissue


title: Retinoblastoma cell-shSUZ12-3

data_processing:
Raw reads in fastq format were processed to remove contaminating adapter sequences using Trimmomatics
Quality distribution plot and base content distribution were generated by FASTQC
RNAseq reads were aligned to the hg38 genome using STAR.
Read counts for individual gene of each sample were produced with HTSeq-count
Assembly: hg38
Supplementary files format and content: txt(gene expression of all sample)

extract_protocol:
RNA was extracted using Trizol following the manufacturer's protocol.
Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample.

value: retinoblastoma


title: Retinoblastoma cell-shSUZ12-2


title: aWAT_PenX-ACIP_rep1

value: wildtype

value: BALB/c


title: T47D_Clone28_IgG_DMSO_rep2


title: TSA,rep3

value: TSA


title: T47D_Clone28_IgG_DMSO_rep1


title: Retinoblastoma cell-shSUZ12-1


title: HDAC,rep1


title: Retinoblastoma cell-shNC3

value: shNC


title: 400-JX-2 H3K4me2_EBwt2

city: Ann Arbor

first: Fengbiao

last: Mao

state: Michigan

address: 1301 Catherine St

department: Department of Pathology

institute: University of Michigan

data_processing:
library strategy: Cut&Run
Cleaned sequencing reads by Cut&Run were mapped to the mm10 genome of mouse by using Bowtie2 (v2-2.2.4) with parameters “-q --phred33  --end-to-end --very-sensitive --no-mixed --no-discordant --phred33 -I 10 -X 700”. Then, we removed duplicated reads using SAMtools (v1.5). Fragments of sizes ≤ 120 bp for PRDM16 Cut&Run were selected for downstream analysis while fragments of sizes > 120 bp for H3K4 methylation Cut&Run were selected for downstream analysis.
Filtered BAM files of mapping results were merged for the same sample using SAMtools and converted to BED format by using BEDTools. Peaks regions were called for each sample by using MACS2 from BAM files of Cut&Run with parameters  -f BAMPE -g mm -B -q 0.01 --extsize 147 --keep-dup auto”. The ucsc-tool “bedGraphToBigWig” was used to convert the bedgraph files generated by MACS2 to bigwig files. Ratio values of treat_pileup versus control_lambda for visualization in IGV were generated by bigwigCompare in deepTools2 from bigwig files generated by ucsc-tool “bedGraphToBigWig”.
We mapped the paired-end reads to both mouse and fly genomes and normalized mouse profiles using the number of fly reads. Differential peaks between groups were called by MACS2 subcommand “bdgdiff”.
Homer v4.10 was employed to perform gene annotation of peaks and differential peaks. Heatmap of signals of PRDM16 and H3K4 methylation were plotted by deepTools. Violin plots of PRDM16 and H3K4 methylation were performed by R package ggpubr.
Genome_build: mm10
Supplementary_files_format_and_content: peaks in text format

growth_protocol: EB were cultured in Knock-out DMEM supplemented with 10%  FBS ,1% NEAA, 1% L-Glutamine and 0.01mM 2-mercaptoethanol.ES cells are cultured with 5%FBS, 15%KSR in KNOCK-OUT DMEM with LIF in Matrigel plate.（0.01mM 2-mercaptoethanol, 0.1mM NEAA, 50U/ML PS, 1/100 100X L-Glutamine added)

extract_protocol:
Cut & Run experiments were performed using 2X106 cells for PRDM16,H3K4me1 or H3K4me2 antibodies, according to Cut & Run protocols.
Libraries were prepared with the Illumina TruSeq protocol according to the manufacturer’s protocol.

tag: strain background

value: wild type

value: EB differentiation day 6th from ES

tag: antibody

value: H3K4me2 (millipore, 07-030)


title: Retinoblastoma cell-shNC2


title: TSA,rep2

value: HeLa


title: T47D_Clone28_HA_dTAG_rep4

value: HA


title: TSA,rep1


title: 329-BZ-22 H3K4me2_EBko2

value: Prdm16 KO


title: 329-BZ-21 H3K4me2_EBko1


title: 329-BZ-19 H3K4me1_EBko2

value: H3K4me1 (abcam ab8895)


title: 329-BZ-20 H3K4me2_EBwt1


title: DMSO,rep3

value: DMSO


title: T47D_Clone28_HA_dTAG_rep2

value: 50nM dTAG-13 + 50nM dTAG-V-1 for 30 minutes


title: vec,rep2


title: T47D_Clone28_IgG_DMSO_rep3

value: IgG

value: 0.1% v/v DMSO for 24 hours


title: Retinoblastoma cell-shNC1


title: Sample_R25_05_p50_3

city: Suzhou

first: Wanshi

address: 苏州大学

institute: 苏州大学

data_processing:
Illumina bcf2fastq v2.20 software used for basecalling.
fastp version 0.20.1 software was first used for adpter removing, then low-quality  bases and N-bases or low-quality reads were filtered out.Then sequencing reads were mapped to the Rat genome （Hg38.p13) using HISAT2 version 2.2.1.0 with parameters --rna-strandness rf --fr
Counts and Fragments Per Kilobase of exon model per Million mapped fragments(FPKM) of each gene was calculated using htseq-count version 0.11.2
Assembly: Hg38.p13
Supplementary files format and content: Matrix table with raw counts for every gene and every sample.

extract_protocol:
Total RNA from heart samples was extracted using the mirVana™ miRNA Isolation Kit (Ambion, AM1561) following the manufacturer’s protocol.
The libraries were constructed using TruSeq Stranded Total RNA with Ribo-Zero Gold according to the manufacturer’s instructions.

value: human bronchial epithelial cells

value: multiple exposures (ME) group

value: 0.02 Gy once every three days for 25 exposures,50th passage


title: DMSO,rep2


title: T47D_Clone28_HA_dTAG_rep1


title: 329-BZ-18 H3K4me1_EBko1


title: vec,rep1


title: Sample_R25_05_p50_2


title: 329-BZ-17 H3K4me1_EBwt2


title: Sample_R25_05_p50_1


title: Sample_R25_05_p30_3

value: 0.02 Gy once every three days for 25 exposures,30th passage


title: T47D_Clone28_HA_DMSO_rep3


title: T47D_Clone28_HA_dTAG_rep3


title: T47D_Clone28_CTCF_DMSO_rep1

value: CTCF


title: T47D_Clone28_HA_DMSO_rep2


title: 329-BZ-16 H3K4me1_EBwt1


title: T47D_Clone28_HA_DMSO_rep4


title: Sample_R25_05_p30_2


title: Sample_R25_05_p30_1


title: 329-BZ-13 PRDM16_EBwt2


title: T47D_Clone28_HA_DMSO_rep1


title: T47D_Clone28_ER_dTAG_rep3

value: ER


title: Sample_R25_05_p10_3

value: 0.02 Gy once every three days for 25 exposures,10th passage


title: Sample_R25_05_p10_2


title: 329-BZ-15 PRDM16_EBko2

value: EB differentiation day 6th from ES


title: DMSO,rep1


title: T47D_Clone28_ER_dTAG_rep4


title: Sample_R25_05_p10_1


title: T47D_Clone28_ER_dTAG_rep1


title: 329-BZ-11 PRDM16_ESko2

value: ES CELLS


title: 621-JX-6 PRDM16_ESko1


title: T47D_Clone28_ER_dTAG_rep2


title: Sample_R1_05_p50_3

value: single exposures (SE) group

value: single dose of 0.5 Gy for one time,50th passage


title: T47D_Clone28_ER_DMSO_rep4


title: 621-JX-5 PRDM16_ESwt2

value: wild type


title: Sample_R1_05_p50_2


title: 329-BZ-8 PRDM16_ESwt1


title: 329-BZ-14 PRDM16_EBko1

value: Prdm16 KO


title: T47D_Clone28_ER_DMSO_rep2


title: Sample_R1_05_p50_1


title: Sample_R1_05_p30_2

value: single dose of 0.5 Gy for one time,30th passage


title: 329-BZ-12 PRDM16_EBwt1


title: Sample_R1_05_p30_3


title: 329-BZ-7 H3K4me1_ESko2

value: H3K4me1 (abcam ab8895)


title: T47D_Clone28_24hour_rep4

data_processing:
Adapter trimming: cutadapt v1.8.1
UMI trimming and reverse complementing: seqtk v1.3
FASTQ deduplication: https://github.com/guertinlab/fqdedup v1.0.0
FASTQ pairing: fastq_pair v1.0
Alignment: bowtie2 v2.4.4
File manipulation: samtools v1.9
File manipulation: https://github.com/guertinlab/seqOutBias v1.3.1
All details and code: https://guertinlab.github.io/TRPS1_ER/Vignette.html
Assembly: hg38
Supplementary files format and content: Stranded bigWig counts files
Supplementary files format and content: Gene counts files

extract_protocol:
Cell permeabilization was performed as previously described (Mahat et al. 2016), with modifications. At the time of harvest, cells were scraped in 10mL ice cold PBS and washed in 5mL buffer W (10mM Tris-HCl pH 7.5, 10mM KCl, 150mM sucrose, 5mM MgCl2, 0.5mM CaCl2, 0.5mM DTT, 0.004U/mL SUPERaseIN RNase inhibitor (Invitrogen), Complete protease inhibitors (Roche)). Cells were permeabilized by incubating with buffer P (10 mM Tris-HCl pH 7.5, KCl 10 mM, 250 mM sucrose , 5 mM MgCl2, 1 mM EGTA, 0.05% Tween-20, 0.1% NP40, 0.5 mM DTT, 0.004 units/mL SUPERaseIN RNase inhibitor (Invitrogen), Complete protease inhibitors (Roche)) for 3 minutes on ice. Cells were washed with 10 mL buffer W before being transferred into 1.5mL tubes using wide bore pipette tips. Finally, cells were resuspended in 50μL buffer F (50mM Tris-HCl pH 8, 5mM MgCl2, 0.1mM EDTA, 50% Glycerol, 0.5 mM DTT). Cells were snap frozen in liquid nitrogen and stored at -80°C.
PRO-seq libraries were prepared as previously described (Judd et al. 2020), with modifications. RNA extraction after the run-on reaction was performed with 500μL Trizol LS (Thermo Fisher) followed by 130μL chloroform (Sigma). The equivalent of 1μL of 50μM for each adapter was used. A random eight base unique molecular identifier (UMI) was included at the 5′ end of the adapter ligated to the 3′ end of the nascent RNA. 37°C incubations were performed with rotation with 1.5mL tubes placed in 50mL conical tubes in a hybridization oven. For the reverse transcription reac- tion, RP1 was used at 100μM and dNTP mix was used at 10mM each. Libraries were amplified by PCR for a total of 8 cycles in 100μL reactions with Phusion polymerase (New England Biolabs). No PAGE purification was performed to ensure that our libraries were not biased against short nascent RNA insertions.

treatment_protocol: 4 replicates were performed from cells treated and collected at different times in the same day. 8*106 cells per sample were plated in 15cm dishes 2 days before harvest. Cells were treated with DMSO or 50nM dTAG-13 and 50nM dTAGV-1 in DMSO at various time points and collected simultaneously.

value: 50nM dTAG-13 + 50nM dTAG-V-1 for 24 hours


title: T47D_Clone28_24hour_rep3


title: 329-BZ-4 H3K4me1_ESwt1


title: T47D_Clone28_ER_DMSO_rep1

value: 0.1% v/v DMSO for 24 hours


title: 329-BZ-3 H3K4me2_ESko1

value: H3K4me2 (millipore, 07-030)


title: Sample_Ctrl_3

value: human bronchial epithelial cells

value: Ctrl

value: 50th passage


title: 329-BZ-5 H3K4me1_ESwt2


title: T47D_Clone28_4hour_rep2

value: 50nM dTAG-13 + 50nM dTAG-V-1 for 4 hours


title: Sample_R1_05_p10_2

value: single dose of 0.5 Gy for one time,10th passage


title: Sample_Ctrl_2


title: 400-JX-1 H3K4me2_ESko2


title: Sample_R1_05_p10_1


title: T47D_Clone28_ER_DMSO_rep3

value: ER


title: 329-BZ-6 H3K4me1_ESko1


title: T47D_Clone28_4hour_rep3


title: 329-BZ-1 H3K4me2_ESwt1


title: 329-BZ-2 H3K4me2_ESwt2


title: Sample_Ctrl_1


title: Sample_R1_05_p10_3


title: HCT116_AFF4 KO-CSTF2+Serum

data_processing:
Clean reads were aligned to the Human genome (UCSC genome, GRCh37/hg19) using Bowtie2 (v2.2.5) with default mode . Peak calling was performed with MACS2.
For peaks, associated control samples were used to determine statistical enrichment at a p < 1e-8 and FDR < 0.05. For Pol II peaks, the enrichments were determined at p < 1e-8 and FDR < 0.05.
The ChIP-seq enrichment is displayed as reads per million (RPM). Gene annotations and transcript start site information were from Human genome (UCSC genome, GRCh37/hg19) by R package ChIPseeker.
Assembly: hg19

extract_protocol:
For ChIP-seq,cells were crosslinked with 1% formaldehyde for 10 min and quenched with glycine for 5 min at the room temperature. Fixed cells were sonicated and immunoprecipitated with the mixture of beads and antibody overnight at 4 ℃. ChIP-DNA was purified using PCR purification kit (Qiagen) and performed for qPCR using iTaq™ Universal SYBR® Green Supermix (Bio-Rad) on CFX96 (Bio-Rad).
The ChIP-seq libraries were prepared with VAHTS Universal DNA Library Prep Kit for Illumina V3

value: human colon cancer cells

value: Serum induction

value: abclonal


title: Sample_R1_05_p30_1

value: single exposures (SE) group


title: HCT116_AFF4 MT-CSTF2+Serum


title: muscle_2

city: Ningbo

first: Zhaoshou

last: Ran

address: Fenghua Road 818, Jiangbei Districta

department: Institute of Marine Science

institute: Ningbo University

data_processing:
The library preparations were sequenced on an Illumina Hiseq 4000 platform in Novogene Bioinformatics Technology Co., Ltd (Beijing, China).
Raw data of fastq format were firstly processed through inhouse perl scripts.
Transcriptome assembly was accomplished by using Trinity with min_kmer_cov set to 2 by default and all other parameters set default.
Gene function was annotated based on the following seven databases: Nr (non-redundant protein sequences), Nt (non-redundant nucleotide sequences), Swiss Prot, KOG (eukaryotic Orthology Groups; BLASTx, version v2.2.26, E-value = 1 × 10-5), Pfam (Protein family; HMMER 3.0 Package, hmmscan, E-value = 0.01), KO (KEGG Ortholog; KEGG Automatic Annotation Server, E-value = 1 × 10-10) and GO (Gene Ontology; Blast2GO v2.5, E-value = 1 × 10-6). Thereafter, the homology of deduced proteins with other organisms, gene categorizing, functional phylogenetic classification and biological pathways were further analyzed based on NR, GO, KOG and KEGG, respectively.
To estimate the expression level of each gene, the transcriptome obtained from Trinity was used as the reference sequence (REF), the clean reads from each sample were mapped to REF by using RSEM software (bowtie2, default parameters). The count of mapped reads of each gene was further estimated using expected number of fragments per kilobase of transcript per millions base pairs sequenced (FPKM). The analyses of DEGs between tissues were performed using the DESeq R package (1.10.1).
Supplementary files format and content: FPKM values for each sample

organism: Sinonovacula constricta

source_name: foot muscle

extract_protocol:
RNA was isolated using the TRIzol reagent (Invitrogen, USA). The resulting RNA was further treated with RNase-free DNase I (Invitrogen, USA) to remove any contaminating genomic DNA.
Approximately 1.5 μg RNA per sample was used as input material for the RNA sample preparations. The sequence libraries were generated using NEB Next® Ultra™ RNA Library Prep Kit for Illumina® (NEB) following the manufacturer's recommendations.

value: foot muscle


title: T47D_Clone28_2hour_rep1

value: 50nM dTAG-13 + 50nM dTAG-V-1 for 2 hours


title: muscle_1


title: mantle_2

source_name: mantle

value: mantle


title: T47D_Clone28_24hour_rep2


title: T47D_Clone28_2hour_rep3


title: T47D_Clone28_2hour_rep2


title: T47D_Clone28_4hour_rep4