title: K562, WT, E50_dCas9-KRAB, sgRNA_Control

description: Library name: Sample 1

data_processing:
The raw sequencing data were processed using nf-core/rnaseq v3.14.0 of the nf-core collection of workflows (Ewels et al., 2020), utilising reproducible software environments from the Bioconda (Grüning et al., 2018) project.
The pipeline was executed with Nextflow v23.10.1 (Di Tommaso et al., 2017)
Sequencing reads were aligned to the hg38 reference genome (Gencode primary assembly GRCh38) and GENCODE comprehensive gene annotation (V44) using STAR (2.7.10a).
Post-alignment, gene-level quantification was performed using Salmon (1.10.1).
Gene counts were normalized using the median ratio method in DESeq2 (v1.42.1)
Assembly: Gencode primary assembly GRCh38
Supplementary files format and content: tab delimited text file includes raw counts for each sample
Supplementary files format and content: bigwigs from nf-core/rnaseq pipeline

growth_protocol: K562 cells were cultured in RPMI 1640 (Gibco) supplemented with 10% FBS (Sigma) and 1% pen–strep (Gibco) and refreshed every 2-3 days. Cells were grown at a maximal density of 5x10^5 cells/ml.

extract_protocol:
RNA was isolated using conventional TRIzol extraction and isopropanol precipitation. 1ug purified RNA per sample was used as input for NEBNext Poly(A) mRNA Magnetic Isolation Module (NEB, cat. no E7490) to enrich for polyA mRNA. Sequencing libraries were then produced using NEBNext Ultra II Directional RNA Library Prep Kit (NEB, cat. no. E7645).
Sequencing libraries were pooled and paired-end sequenced (2 × 100 bp) on an Illumina Nextseq 2000 platform.

treatment_protocol: K562 cells expressing dCas9-KRAB were transduced with lentivirus containing an sgRNA-BFP against a target factor or control. Transductions were performed by incubating cells overnight with 50% medium and 50% lentivirus-containing supernatant. The next day, cells were refreshed. From day 2 to 6, cells were selected using 1 ug/ml Puromycin (Sigma, Cat#P9620) and refreshed daily. At sample harvest, one million cells were sorted BFP-high to contain an sgRNA.


title: K562,EC100-GFP;RAD21-AID,DMSO,rep2,MS4A3

status: Public on Feb 19 2025

type: SRA

city: Utrecht

first: Peter

last: Krijger

address: Uppsalalaan 8

country: Netherlands

institute: Hubrecht Institute

description: Library name: sample17

library_source: genomic

data_processing:
4C-seq reads were mapped to the hg38 reference genome and processed using pipe4C (https://github.com/deLaatLab/pipe4C).
Normalized 4C coverage was calculated using R (rproject.org). Counts at non-blind fragments were adjusted to 1 million intra-chromosomal mapped reads after exclusion of the two highest-count fragments.
Count data was smoothed using a running mean with a window size of 21 fragments using the R package caTools v1.18.2.
Assembly: hg38
Supplementary files format and content: wig, bed
Library strategy: 4C-seq

molecule: genomic DNA

organism: Homo sapiens

growth_protocol: EC100-GFP RAD21-AID and EC100-GFP LDB1-FKBP  K562 cells were cultured in RPMI 1640 (Gibco) supplemented with 10% FBS (Sigma) and 1% pen–strep (Gibco). Cells were grown at a maximal density of 5x10^5 cells/ml. Experiments were performed maximum 1 week after FACS sorting cells GFP positive for 2 consecutive weeks with gating based on non-GFP expressing K562 cells.

extract_protocol:
4C templates preparation was performed as described in PMID: 31351925. In short, 5-10M cells were crosslinked with 2% formaldehyde for 10 minutes and quenched with 0.125M final concentration glycine on ice. Pellets were resuspended in lysis buffer (50 mM Tris-HCl pH 7.5, 0.5% NP-40, 1% TritonX-100, 150 mM NaCl, 5 mM EDTA) for 20 minutes on ice. Then, SDS (0.3% final concentration) was added, followed by TritonX-100 (2.5% final concentration), and chromatin was digested in situ using 100U Csp6I (ThermoFisher Cat#ER0211). DNA was then ligated using T4 ligase (Roche Cat#10799009001), decrosslinked by overnight ProtK treatment (Roche Cat#3115801001), and purified using isopropanol precipitation. Samples were then digested using 50U NlaIII (NEB Cat#R0125), ligated at a concentration of 5ng template/ul, and final 4C templates were purified with P-Beads (Macherey Nagel Cat#744100.34). 4C PCRs were performed in a two-step manner using the Expand Long Template PCR system (Roche Cat#11759060001).
Indexed Illumina sequencing adapters were introduced to ligation fragments of interest with a two-step PCR strategy using ELT PCR System (Roche, cat. no. 11681842001).

treatment_protocol: To deplete RAD21, cells were treated with 1μM 5-Ph-IAA (MedChemExpress, Cat#HY-134653) for 2 hours.To deplete LDB1, dTAG-7 (TOCRIS, Cat#6912) was added to the medium in a final concentration of 500nM for 4 hours.

tag: cell line

tag: genotype

tag: treatment

value: DMSO

tag: replicate

tag: viewpoint


title: K562,EC100-GFP;RAD21-AID,DMSO,rep1,LMO2

description: Library name: sample13


title: K562,EC100-GFP;RAD21-AID,DMSO,rep1,MS4A3

description: Library name: sample14


title: K562,EC100-GFP;RAD21-AID,DMSO,rep1,MYC

description: Library name: sample15

value: MYC


title: S2 cells, H4K20me1 ChIP with Abcam ab9051 antibody, replicate 1

city: Boston

first: Stephen

last: Gisselbrecht

state: MA

address: 77 Avenue Louis Pasteur, Rm 468

department: Division of Genetics, Department of Medicine

country: USA

institute: Brigham and Women's Hospital

description: Library name: H4K20me1-Abcam9051-R1

data_processing:
bcl2fastq is used for base calling.
Trim galore (v. 0.6.6) was used to remove adaptor sequences and bases with sequencing quality below 30.
Reads were then mapped to dm3 using bowtie2 (v. 2.5.1) with the settings “--sensitive-local --no-discordant --no-mixed”. PCR duplicates were called using Picard MarkDuplicates. Libraries were filtered for alignments above mapq 30.
Peak calling was performed using MACS2 (v. 2.1.1.20160309) with the corresponding input reads as control and the settings “--broad -g dm -f BAMPE”.
Following ENCODE guidelines, we used the irreproducible discovery rate (IDR) framework to identify peaks that are consistent between the two replicate samples that used the same antibody. For calling peaks found to be reproducible by IDR analysis, a more relaxed threshold of “-p 1e3” was used to call peaks in each library before running IDR (v. 2.0.2).
Assembly: dm3
Supplementary files format and content: broadPeak (except for input samples)
Supplementary files format and content: bedfiles of consistent peaks between replicates called by IDR (except for input samples)

organism: Drosophila melanogaster

extract_protocol:
Cells were fixed for 10 minutes in 1% formaldehyde, quenched, and frozen. Chromatin was sonicated with a Bioruptor Plus (Diagenode) at high power for 30 seconds on and 30 seconds off. Sixty cycles was chosen to fragment DNA with a peak of fragments ~200 - 600 bp.
100 µg chromatin as measured from the decrosslinked sample was aliquoted to each ChIP reaction. Eluted DNA was decrosslinked and purified using Monarch PCR and DNA Cleanup Kit (New England Biolab T1030S). DNA was quantified using Qubit HS dsDNA and High Sensitivity D5000 DNA ScreenTape assays (Agilent). Sequencing libraries were generated using NEBNext Ultra II (E7645S) with NEBNext multiplex oligos for Illumina (E7335S). The number of PCR cycles was selected according to manufacturer’s recommendations for the mass of DNA in each library. Input, H4K20me1 libraries using Abcam 9051 antibodies, and H3K27me3 libraries were amplified with 3 cycles of PCR, while H4K20me1 libraries using the Active Motif or Thermo antibodies required 6 cycles of PCR. QC of sequencing libraries was performed using Qubit High Sensitivity dsDNA assays for DNA concentration and High Sensitivity D1000 and D5000 DNA ScreenTape assays (Agilent)  for fragment length distributions. Libraries generated using the Active Motif or Thermo H4K20me1 antibodies were size-selected them with SPRISelect beads (Beckman Coulter B23317) prior to sequencing, using a right-side size selection with 0.4x bead ratio to remove large fragments.

tag: chip antibody

value: Abcam ab9051

tag: batch


title: DLN_ kidney-3

city: kunming

first: Zhendong

last: Gao

state: -- Please Select --

address: No. 452 Fengyuan Road, Panlong District

country: China

institute: Yunnan Agricultural University

description: Library name: DLN_S3

library_source: transcriptomic

data_processing:
TransDecoder v2.0.1 software package
Assembly: corrected-pacbio-reads
Supplementary files format and content: Processed_data.txt

molecule: polyA RNA

organism: Bos frontalis

source_name: kidney

extract_protocol:
RNA was extracted from each tissue using TRIzol reagent (Invitrogen) according to the manufacturer’s protocol
The library preparation and sequencing were performed at Wuhan Frasergen Gene Biotechnology Co., Ltd (Wuhan, China) using the PacBio Sequel II platform with a total of 6 SMRT cells

tag: tissue

value: kidney

tag: cell type

value: Histiocyte

value: PolyA


title: S2 cells, H3K27me3 ChIP, replicate 1

description: Library name: H3K27me3-R1

value: Epicypher 13-0055


title: K562, WT, E50_dCas9-KRAB, sgRNA_SMC1A

description: Library name: Sample 2

molecule: total RNA


title: DLN_ kidney-2

description: Library name: DLN_S2


title: K562,EC100-GFP;LDB1-FKBP,dTAG,rep1,MYC

description: Library name: sample9

value: dTAG


title: K562,EC100-GFP;LDB1-FKBP,dTAG,rep2,MYC

description: Library name: sample12


title: K562,EC100-GFP;LDB1-FKBP,dTAG,rep2,LMO2

description: Library name: sample10


title: K562,EC100-GFP;LDB1-FKBP,dTAG,rep2,MS4A3

description: Library name: sample11


title: DLN_heart-2

description: Library name: DLN_X2

source_name: heart

value: heart


title: DLN_spleen-2

description: Library name: DLN_P2

source_name: spleen

value: spleen


title: DLN_rectum-1

description: Library name: DLN_ZC1

source_name: rectum

value: rectum


title: DLN_ liver-2

description: Library name: DLN_G2

source_name: liver

value: liver


title: K562,EC100-GFP;LDB1-FKBP,dTAG,rep1,LMO2

description: Library name: sample7


title: K562,EC100-GFP;LDB1-FKBP,dTAG,rep1,MS4A3

description: Library name: sample8


title: DLN_lung-2

description: Library name: DLN_F2

source_name: lung

value: lung


title: DLN_abomasum-1

description: Library name: DLN_ZW1

source_name: abomasum

value: abomasum


title: K562,EC100-GFP;RAD21-AID,DMSO,rep2,LMO2

description: Library name: sample16


title: DLN_abomasum-3

description: Library name: DLN_ZW3


title: DLN_ileum-3

description: Library name: DLN_HC3

source_name: ileum

value: ileum


title: K562,EC100-GFP;LDB1-FKBP,DMSO,rep2,MYC

description: Library name: sample6


title: DLN_rumen-1

description: Library name: DLN_LW1

source_name: rumen

value: rumen


title: DLN_ileum-1

description: Library name: DLN_HC1


title: K562,EC100-GFP;LDB1-FKBP,DMSO,rep2,LMO2

description: Library name: sample4


title: DLN_heart-1

description: Library name: DLN_X1


title: DLN_ duodenum-2

description: Library name: DLN_SEC2

source_name: duodenum

value: duodenum


title: DLN_ liver-1

description: Library name: DLN_G1


title: DLN_ duodenum-3

description: Library name: DLN_SEC3


title: DLN_ kidney-1

description: Library name: DLN_S1


title: K562,EC100-GFP;LDB1-FKBP,DMSO,rep1,MYC

description: Library name: sample3

value: DMSO


title: K562,EC100-GFP;LDB1-FKBP,DMSO,rep1,MS4A3

description: Library name: sample2


title: DLN_rectum-2

description: Library name: DLN_ZC2


title: K562,EC100-GFP;LDB1-FKBP,DMSO,rep1,LMO2

description: Library name: sample1


title: DLN_abomasum-2

description: Library name: DLN_ZW2


title: DLN_spleen-1

description: Library name: DLN_P1


title: DLN_lung-3

description: Library name: DLN_F3


title: CC84

type: RNA

city: Milan

first: Loris

last: De Cecco

address: via Venezian 1

country: Italy

institute: IRCSS Istituto Nazionale Tumori

hyb_protocol: Illumina WG-DASL hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were processed and normalised using quantile normalisation with BeadStudio software

label: biotin

source_name: Formalin-fixed, paraffin-embedded (FFPE) primary tumor

label_protocol: Illumina WG-DASL protocol

extract_protocol: RNA was extracted with miRNeasy  kit (Qiagen) in accordance with the manufacture's protocol.

value: HPV-positive squamous oropharyngeal carcinoma (OPC)

tag: age

tag: Sex

value: M

tag: site

value: OPC

value: not available


title: DLN_ileum-2

description: Library name: DLN_HC2

value: Histiocyte

value: PolyA


title: K562,EC100-GFP;LDB1-FKBP,DMSO,rep2,MS4A3

description: Library name: sample5


title: DLN_lung-1

description: Library name: DLN_F1


title: K562,EC100; LDB1-FKBP,2,DMSO

library_source: other

data_processing:
Raw reads were aligned to the hg38 reference genome using BWA (v0.7.17-r1188) and filtered with a minimum mapping quality (MQ) of 15 using Samtools (v1.18).
Bigwig files were created with deeptools (v3.5.4) with the following parameters: --ignoreForNormalization chrM, --binSize 10, --minMappingQuality ${MQ}, --normalizeUsing RPGC, and --effectiveGenomeSize 2913022398.
Read counts were generated with featureCounts (v2.0.6) using GENCODE V44 as the annotation reference.
Read counts were filtered for minimal 5 counts in the DMSO samples and normalized using DeSeq2 (1.38.3 ) with DMSO as reference.
Assembly: hg38
Supplementary files format and content: counts (tsv) and DESeq2 normalized counts (tsv)
Library strategy: Bru-Seq

molecule: other

extract_protocol:
After indicated treatment of cells, nascent RNA was labeled by addition of BrU (5-Bromouridine, Sigma-Aldrich, #850187) to K562 cell culture medium in 2mM final concentration for 6 minutes. Cells were then immediately put on ice, centrifuged for 4 minutes at 200G at 4 degrees and resuspended in TRIzol (Invitrogen). RNA was isolated using conventional TRIzol extraction and isopropanol precipitation, and final pellet was resuspended in DEPC.
50ug of total RNA was used for BrU pulldown, following a protocol adapted from Roberts 2015. In short, per sample 6ug of Anti-BrdU antibody (BD Pharmingen, #555627) was incubated with 30ul of Protein G Dynabeads (ThermoFisher) for 10 minutes at room temperature, and washed in PBS-T. Beads were then blocked with 0.05 ug/ul BSA in PBS-T for 30 minutes and washed with PBS-TR (PBS-T supplemented with RNAseOUT (ThermoFisher)). RNA was diluted in PBS-TR and heated at 65 degrees for 5 minutes, after which it was added to antibody-coated beads at room temperature for 1 hour in 300ul total volume. Beads were then washed three times in PBS-TR, and BrU-labeled enriched RNA was extracted using TRIzol. Pellets were resuspended in 5ul DEPC, which was used as input for NEBNext Ultra II Directional RNA Library Prep Kit (NEB, cat. no. E7645).

treatment_protocol: To perform acute RAD21 depletion, cells were incubated with 1μM 5-Ph-IAA (MedChemExpress, Cat#HY-134653). Depletion was confirmed using flow cytometry (for RAD21-mCherry) and western blot for endogenous RAD21 protein. To deplete MED23 and LDB1, dTAG-7 (TOCRIS, Cat#6912) was added to the medium in a final concentration of 500nM.

value: EC100; LDB1-FKBP


title: CC83

value: F

value: II


title: DC06

value: I


title: DJ98

value: III


title: K562,EC100; LDB1-FKBP,1,dTAG-7


title: DLN_rumen-2

description: Library name: DLN_LW2


title: DLN_ liver-3

description: Library name: DLN_G3

value: liver


title: K562,EC100; LDB1-FKBP,1,DMSO


title: DC12


title: DLN_ duodenum-1

description: Library name: DLN_SEC1


title: K562,EC100; LDB1-FKBP,2,dTAG-7


title: DLN_heart-3

description: Library name: DLN_X3

value: heart


title: DLN_rumen-3

description: Library name: DLN_LW3


title: K562,EC100; MED23-FKBP,2,dTAG-7

value: EC100; MED23-FKBP


title: K562,EC100; MED23-FKBP,2,DMSO


title: CC41


title: DC11


title: Escherichia coli Nissle 1917, Tagatose condition, TEX treated

city: Seoul

first: Sung Ho

last: Yoon

address: 120 Neungdong-ro, Gwangjin-gu

department: Department of Bioscience and Biotechnology

country: South Korea

institute: Konkuk University

description: Terminator exonuclease (TEX) treated sample

data_processing:
The quality of the raw RNA sequencing data was assessed with FastQC (v0.12.1), followed by trimming using Trimmomatic (v0.39).
The trimmed data were aligned to the complete genome sequences of the reference strain using READemption (v2.0.4).
Transcriptional start sites (TSS) were predicted using the modular command-line tool  ANNOgesic (v1.1.14) ('tss_ps' subcommand) with keeping all parameters at their default settings excepth ‘height’ (7, Default: 0.3), and ‘enrichment_factor’ (0.3, Default: 2.0).
Assembly: GCF_021559835.1
Supplementary files format and content: The wiggle files contain raw counts for each sample, separated by forward and reverse strands.

organism: Escherichia coli Nissle 1917

source_name: micro-organism strain

extract_protocol:
The bacterial cultures were immediately mixed with two volumes of RNAprotect Bacteria Reagent (Qiagen) and incubated for 5 minutes at room temperature (RT). Following centrifugation at 10,000 g for 5 minutes at RT, the supernatant was discarded, and the cell pellets were stored at –80 °C if not processed immediately. Bacterial cells were lysed with 10 mg/ml lysozyme in TE buffer (pH 8.0) for 5 minutes at 25 °C. Total RNA was extracted using the mirVana miRNA Isolation Kit (Ambion) according to the manufacturer's instructions. Residual DNA in the total RNA sample was digested with Turbo DNase (Applied Biosystems) for 30 minutes at 37 °C and removed using the filter cartridges provided with the mirVana kit. Purified RNA was stored at –80 °C. The quantity and purity of the purified RNA were assessed using a bioanalyzer (Agilent Technologies).
High-quality RNA samples (RNA integrity number [RIN] > 8.0) were used for dRNA-seq library preparation. The dRNA-seq libraries were prepared as follows: half of the RNA was treated with terminator exonuclease (TEX, Epicentre), while equal amounts of untreated RNA were prepared as controls. For cDNA synthesis, RNA fragments were poly(A)-tailed using E. coli Poly(A) polymerase (NEB), and 5’ triphosphate (5’PPP) structures were converted to 5’ monophosphate (5’P) structures using RNA 5’ Polyphosphatase (Epicentre). RNA sequencing adapters with barcodes were then ligated to the 5’-monophosphate ends of the fragments using T4 RNA ligase (NEB). Adapter-ligated RNAs were purified and size-filtered twice using 1.2× Agencourt AMPure XP beads (Beckman Coulter Genomics). First-strand cDNA was synthesized using an oligo(dT)-adapter primer and M-MLV reverse transcriptase (Invitrogen). The synthesized cDNA was purified using 0.8× Agencourt AMPure XP beads twice. cDNA amplification was carried out via PCR using Phusion High-Fidelity DNA Polymerase (NEB). The final amplified cDNA was purified using 0.8× Agencourt AMPure XP beads. Sequencing was performed on an Illumina NextSeq 500 system (Illumina) in 75 bp single-end mode.

value: WT


title: DC15


title: K562,EC100; MED23-FKBP,1,dTAG-7


title: DLN_spleen-3

description: Library name: DLN_P3

value: spleen


title: MIA Male Weaned A9 [A9_P_M_W]

city: Urbana

first: Sandra

last: Rodriguez Zas

state: IL

address: 1207 W. Gregory Dr.

institute: University of Illinois

description:
MIA Male Weaned A9
RodriguezZas_Pig_D22__Hypothalamus_pig_GEO_counts.csv

data_processing:
Quality-scores line in fastq files processed with Casava1.8 use an ASCII offset of 33
Sequences were trimmed for adaptor seuqences and masked for low-complexity and low-quality
150 nt paired-end reads were assembled into transcript isoforms and mapped to the pig genome (assembly 11.1) using Kallisto v0.43 (Bray et al., 2016)
Assembly: Sus scrofa genome (version 11.1)
Supplementary files format and content: cvs format,  transcripts per million (TPM) values for each sample, one column per sample

organism: Sus scrofa

source_name: Hypothalamus

extract_protocol:
RNA was extracted from all samples using standards protocols. TRIzol reagent (Life Technologies, Grand Island, New York) was used to isolate total RNA and the QIAGEN RNeasy kit (Qiagen, Valencia, California) was use for purification
The RNAseq libraries were prepared with Illumina's 'TruSeq Stranded mRNAseq Sample Prep kit' (Illumina). Read 1 aligns to the antisense strand and read 2 aligns to the sense strand. The libraries were quantitated by qPCR and sequenced on 4 lanes first and 5 lanes later for 101 cycles from one end of the fragments on a HiSeq 4000 with a HiSeq 4000 sequencing kit version 1. Fastq files were generated and demultiplexed with with the bcl2fastq v2.17.1.14 Conversion Software (Illumina).

value: Hypothalamus

tag: sampleID

value: 22 day old

tag: mia

value: MIA

value: Male

value: Weaned


title: MIA Male Weaned A8 [A8_P_M_W]

description:
MIA Male Weaned A8
RodriguezZas_Pig_D22__Hypothalamus_pig_GEO_counts.csv


title: CC48

value: HPV-positive squamous oropharyngeal carcinoma (OPC)

value: OPC


title: MIA Male Weaned A7 [A7_P_M_W]

description:
MIA Male Weaned A7
RodriguezZas_Pig_D22__Hypothalamus_pig_GEO_counts.csv


title: K562,EC100; MED23-FKBP,1,DMSO

value: DMSO


title: MIA Male Weaned A6 [A6_P_M_W]

description:
MIA Male Weaned A6
RodriguezZas_Pig_D22__Hypothalamus_pig_GEO_counts.csv


title: DK01

value: M


title: K562,EC100; RAD21-AID,2,IAA

value: EC100; RAD21-AID

value: IAA


title: MIA Male Weaned A5 [A5_P_M_W]

description:
MIA Male Weaned A5
RodriguezZas_Pig_D22__Hypothalamus_pig_GEO_counts.csv


title: MIA Male Weaned A4 [A4_P_M_W]

description:
MIA Male Weaned A4
RodriguezZas_Pig_D22__Hypothalamus_pig_GEO_counts.csv


title: MIA Male Weaned A3 [A3_P_M_W]

description:
MIA Male Weaned A3
RodriguezZas_Pig_D22__Hypothalamus_pig_GEO_counts.csv


title: MIA Male Weaned A10 [A10_P_M_W]

description:
MIA Male Weaned A10
RodriguezZas_Pig_D22__Hypothalamus_pig_GEO_counts.csv


title: Escherichia coli Nissle 1917, Tagatose condition, TEX untreated

description: Terminator exonuclease (TEX) non-treated sample


title: K562,EC100; RAD21-AID,2,DMSO


title: MIA Male Weaned A2 [A2_P_M_W]

description:
MIA Male Weaned A2
RodriguezZas_Pig_D22__Hypothalamus_pig_GEO_counts.csv


title: K562,EC100; RAD21-AID,1,IAA


title: MIA Male Weaned A1 [A1_P_M_W]

description:
MIA Male Weaned A1
RodriguezZas_Pig_D22__Hypothalamus_pig_GEO_counts.csv


title: MIA Male Nursed A8 [A8_P_M_N]

description:
MIA Male Nursed A8
RodriguezZas_Pig_D22__Hypothalamus_pig_GEO_counts.csv

value: Nursed


title: MIA Male Nursed A6 [A6_P_M_N]

description:
MIA Male Nursed A6
RodriguezZas_Pig_D22__Hypothalamus_pig_GEO_counts.csv


title: DJ97

value: not available


title: 5d, seq batch 2, rep4

city: Bellaterra

first: Jose Luis

last: Riechmann

state: Barcelona

address: Campus UAB - Edifici CRAG

country: Spain

institute: Center for Research in Agricultural Genomics

data_processing:
“FastQC” and “TrimGalore!” software was used for raw Illumina reads quality control analysis and  trimming  of  reads  containing  adaptor-   or  vector-derived  sequences, respectively
rRNA was detected and removed using “SortMeRNA 2.1b” software
Cleaned reads together with the transcriptome of Arabidopsis thaliana (as of 31 January 2019), including ncRNA, were used to quantify gene expression at transcript level using the software “Salmon v0.12.0”
Raw counts aggregated by gene were obtained using tximport and the result was used as input to DESeq2 (software versions as of 31 January 2019). Then, genes adding up to less than 10 counts across all 48 samples were removed
Assembly: Arabidopsis_thaliana.TAIR10.cdna.all.fa and Arabidopsis_thaliana.TAIR10.ncrna.fa files from EnsemblPlants, as of 31 January 2019
Supplementary files format and content: Tab-delimited matrix table with unnormalized gene counts for every gene and all 48 samples, after removing genes with less than 10 counts across all samples

organism: Arabidopsis thaliana

source_name: Inflorescences

growth_protocol: pAP1:AP1-GR ap1 cal plants were grown on a soil:vermiculite:perlite mixture at 21ºC under long day conditions (16h light, 8h darkness), after a 4-days period of stratification at 4ºC in darkness.

extract_protocol:
RNA was harvested using trizol and separated from the protein fraction with chloroform. RNA was precipitated from the organic phase using isopropanol, resuspended in LiCl and finally washed with ethanol and resuspended in DEPC-treated water
PolyA-mRNA

treatment_protocol: For induction, inflorescences were treated with a DEX-induction solution (2µM DEX, 0.01% (v/v) ethanol, and 0.01% Silwet L-77). Using plastic pipettes, the solution was directly applied onto the inflorescences so that the cauliflower-like structures were completely drenched. First induction was performed 8h after lights on, and daily inductions, at 4h after lights on.

value: Inflorescences

value: Col-0 (pAP1:AP1-GR ap1cal mutant)

tag: time point

value: 5 days after induction

tag: biological replicate

tag: sequencing batch


title: K562,EC100,GFP_low

data_processing:
Reads containing sgRNA sequences were trimmed and mapped to the sgRNA sequences in the custom library.
Mageck MLE (Wang, Wang et al. 2019) was run using 624 negative control (non-targeting) sgRNAs present in the library for normalization.
A cell line transduced with the library not sorted for GFP was set as baseline. Per TSS, a beta score was calculated per gate. The effect on each reporter was calculated by subtracting the beta scores of the GFP-high from the GFP-low population. These scores were normalized by dividing by the log2FC of the HBG reporter TSS sgRNA in the specific clone
Assembly: CRISPRi_LaatCustom_library.tsv
Supplementary files format and content: raw counts (tsv) and normalized results (tsv)
Library strategy: CRISPR screen

growth_protocol: dCas9-KRAB was randomly integrated into E0, E50, E100, EC100 reporter cell lines via lentiviral transduction of a modified version of pHR-SFFV-dCas9-BFP-KRAB (Addgene plasmid #46911). dCas9-BFP-KRAB cells were bulk sorted for BFP integration and continuously cultured on blasticidin (0.7 ug/ml, Sigma, Cat#15205).

extract_protocol:
DNA was isolated using phenol chloroform extraction, followed by isopropanol precipitation.
guideRNA sequences were amplified using Q5 PCR (NEB, Cat#M0491L) with primers containing overhangs for Illumina sequencing.

treatment_protocol: For library CRISPRi screening, dCas9-BFP-KRAB, HBG-GFP reporter cells were transduced with sgRNA library virus at low MOI overnight with 8 ug/ml polybrene (Merck), and the next day refreshed in medium containing blasticidin. One day later, cells were selected using 1 ug/ml Puromycin (Sigma, Cat#P9620) and refreshed daily. After 5 days of selection, cells were sorted on a Becton Dickinson SORP FACSAria FUSION Flow Cytometer. Live cells were gated for sgRNA-BFP with a threshold based on untransduced cells containing dCas9-KRAB-BFP of the corresponding reporter. From this population, cells were sorted for the highest and lowest 10% GFP level for that specific reporter line.

tag: cell line

tag: sort gate


title: K562,EC100; RAD21-AID,1,DMSO

tag: genotype

tag: treatment


title: MIA Male Nursed A7 [A7_P_M_N]

description:
MIA Male Nursed A7
RodriguezZas_Pig_D22__Hypothalamus_pig_GEO_counts.csv


title: DC16

value: I


title: DC10

value: F


title: DC14

value: III


title: 4d, seq batch 2, rep4

value: 4 days after induction


title: DLN_rectum-3

description: Library name: DLN_ZC3

value: rectum

value: Histiocyte

value: PolyA


title: DC13

value: HPV-positive squamous oropharyngeal carcinoma (OPC)

value: OPC


title: DK00


title: MIA Male Nursed A5 [A5_P_M_N]

description:
MIA Male Nursed A5
RodriguezZas_Pig_D22__Hypothalamus_pig_GEO_counts.csv

value: Hypothalamus

value: 22 day old

value: MIA

value: Male


title: MIA Male Nursed A3 [A3_P_M_N]

description:
MIA Male Nursed A3
RodriguezZas_Pig_D22__Hypothalamus_pig_GEO_counts.csv

value: Nursed


title: K562,EC100,GFP_high


title: 3d, seq batch 2, rep4

value: Inflorescences

value: 3 days after induction


title: MIA Male Nursed A4 [A4_P_M_N]

description:
MIA Male Nursed A4
RodriguezZas_Pig_D22__Hypothalamus_pig_GEO_counts.csv


title: MIA Male Nursed A2 [A2_P_M_N]

description:
MIA Male Nursed A2
RodriguezZas_Pig_D22__Hypothalamus_pig_GEO_counts.csv


title: MIA Male Nursed A1 [A1_P_M_N]

description:
MIA Male Nursed A1
RodriguezZas_Pig_D22__Hypothalamus_pig_GEO_counts.csv


title: 2d, seq batch 2, rep4

value: Col-0 (pAP1:AP1-GR ap1cal mutant)

value: 2 days after induction


title: K562,E50,GFP_high


title: MIA Female Weaned A8 [A8_P_F_W]

description:
MIA Female Weaned A8
RodriguezZas_Pig_D22__Hypothalamus_pig_GEO_counts.csv

value: Female

value: Weaned


title: MIA Female Weaned A7 [A7_P_F_W]

description:
MIA Female Weaned A7
RodriguezZas_Pig_D22__Hypothalamus_pig_GEO_counts.csv


title: CC38

value: M

value: III


title: 1d, seq batch 2, rep4

value: 1 day after induction


title: MIA Female Weaned A6 [A6_P_F_W]

description:
MIA Female Weaned A6
RodriguezZas_Pig_D22__Hypothalamus_pig_GEO_counts.csv


title: MIA Female Weaned A5 [A5_P_F_W]

description:
MIA Female Weaned A5
RodriguezZas_Pig_D22__Hypothalamus_pig_GEO_counts.csv


title: 5d, seq batch 2, rep3

value: 5 days after induction


title: MIA Female Weaned A3 [A3_P_F_W]

description:
MIA Female Weaned A3
RodriguezZas_Pig_D22__Hypothalamus_pig_GEO_counts.csv


title: MIA Female Weaned A4 [A4_P_F_W]

description:
MIA Female Weaned A4
RodriguezZas_Pig_D22__Hypothalamus_pig_GEO_counts.csv


title: MIA Female Weaned A2 [A2_P_F_W]

description:
MIA Female Weaned A2
RodriguezZas_Pig_D22__Hypothalamus_pig_GEO_counts.csv


title: 4d, seq batch 2, rep3

value: 4 days after induction


title: MIA Female Weaned A1 [A1_P_F_W]

description:
MIA Female Weaned A1
RodriguezZas_Pig_D22__Hypothalamus_pig_GEO_counts.csv


title: 0d, seq batch 2, rep4

value: 0 days after induction


title: K562,E0,Unsorted

value: Unsorted


title: K562,E0,GFP_low


title: K562,E50,GFP_low


title: MIA Female Nursed A6 [A6_P_F_N]

description:
MIA Female Nursed A6
RodriguezZas_Pig_D22__Hypothalamus_pig_GEO_counts.csv

value: Hypothalamus

value: 22 day old


title: 3d, seq batch 2, rep3


title: MIA Female Nursed A7 [A7_P_F_N]

description:
MIA Female Nursed A7
RodriguezZas_Pig_D22__Hypothalamus_pig_GEO_counts.csv

value: MIA


title: MIA Female Nursed A5 [A5_P_F_N]

description:
MIA Female Nursed A5
RodriguezZas_Pig_D22__Hypothalamus_pig_GEO_counts.csv

value: Nursed


title: 2d, seq batch 2, rep3

value: Inflorescences


title: MIA Female Nursed A4 [A4_P_F_N]

description:
MIA Female Nursed A4
RodriguezZas_Pig_D22__Hypothalamus_pig_GEO_counts.csv


title: MIA Female Nursed A3 [A3_P_F_N]

description:
MIA Female Nursed A3
RodriguezZas_Pig_D22__Hypothalamus_pig_GEO_counts.csv


title: K562,E0,GFP_high


title: K562,EC100-GFP;RAD21-AID,IAA,rep2,GFP

data_processing:
4C-seq reads were mapped to the hg19 reference genome modified with integrated reporter sequences (PMID: 35710842) and processed using pipe4C (https://github.com/deLaatLab/pipe4C).
Normalized 4C coverage was calculated using R (rproject.org). Counts at non-blind fragments were adjusted to 1 million intra-chromosomal mapped reads after exclusion of the two highest-count fragments.
Count data was smoothed using a running mean with a window size of 21 fragments using the R package caTools v1.18.2.
Assembly: hg19 with integrated reporter sequences (PMID: 35710842)
Supplementary files format and content: wig, bed
Library strategy: 4C-seq

growth_protocol: EC100-GFP RAD21-AID K562 cells were cultured in RPMI 1640 (Gibco) supplemented with 10% FBS (Sigma) and 1% pen–strep (Gibco). Cells were grown at a maximal density of 5x10^5 cells/ml. Experiments were performed maximum 1 week after FACS sorting cells GFP positive for 2 consecutive weeks with gating based on non-GFP expressing K562 cells.

treatment_protocol: To deplete RAD21, cells were treated with 1μM 5-Ph-IAA (MedChemExpress, Cat#HY-134653) for 2 hours.

value: IAA

tag: replicate

tag: viewpoint

value: GFP


title: 1d, seq batch 2, rep3

value: Col-0 (pAP1:AP1-GR ap1cal mutant)


title: MIA Female Nursed A1 [A1_P_F_N]

description:
MIA Female Nursed A1
RodriguezZas_Pig_D22__Hypothalamus_pig_GEO_counts.csv

value: Female


title: MIA Female Nursed A2 [A2_P_F_N]

description:
MIA Female Nursed A2
RodriguezZas_Pig_D22__Hypothalamus_pig_GEO_counts.csv


title: K562,EC100-GFP;RAD21-AID,IAA,rep1,GFP


title: Control Male Weaned A9 [A9_C_M_W]

description:
Control Male Weaned A9
RodriguezZas_Pig_D22__Hypothalamus_pig_GEO_counts.csv

value: Control

value: Male

value: Weaned


title: 0d, seq batch 2, rep3


title: K562,E100,GFP_low


title: Control Male Weaned A8 [A8_C_M_W]

description:
Control Male Weaned A8
RodriguezZas_Pig_D22__Hypothalamus_pig_GEO_counts.csv


title: Control Male Weaned A7 [A7_C_M_W]

description:
Control Male Weaned A7
RodriguezZas_Pig_D22__Hypothalamus_pig_GEO_counts.csv


title: 5d, seq batch 2, rep2


title: K562-CRISPRi-sgMED23


title: 4d, seq batch 2, rep2


title: Control Male Weaned A3 [A3_C_M_W]

description:
Control Male Weaned A3
RodriguezZas_Pig_D22__Hypothalamus_pig_GEO_counts.csv


title: Control Male Weaned A5 [A5_C_M_W]

description:
Control Male Weaned A5
RodriguezZas_Pig_D22__Hypothalamus_pig_GEO_counts.csv


title: Control Male Weaned A4 [A4_C_M_W]

description:
Control Male Weaned A4
RodriguezZas_Pig_D22__Hypothalamus_pig_GEO_counts.csv


title: Control Male Weaned A6 [A6_C_M_W]

description:
Control Male Weaned A6
RodriguezZas_Pig_D22__Hypothalamus_pig_GEO_counts.csv


title: Control Male Weaned A2 [A2_C_M_W]

description:
Control Male Weaned A2
RodriguezZas_Pig_D22__Hypothalamus_pig_GEO_counts.csv


title: S1097

city: Nanchang

first: Xueyang

last: Li

address: yongwai street

institute: the first affliated hospital of nanchang university

description: Library name: S1097

data_processing:
CLC Genomics Workbench v 11.0.1
Sequence reads were trimmed for adaptor sequence/low-quality sequence using CLC genomic benchwork (parameter- Quality limit: 0.05)
Trimmed sequence reads were mapped to GrCM38/mm10 using CLC genomic benchwork (parameters- mismath cost: 2 insertion cost: 3 deletion cost: 3 length fraction: 0.8 similarity fraction: 0.8)
Read count extraction and normalization were performed using CLC genomic benchwork
Assembly: mm10
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample esv files include FPKM values for each Sample

organism: Mus musculus

source_name: small intestine

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen). 1.3 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using SMARTER mRNA-Seq Library Prep Kit following manufacturer's protocols.

value: small intestine

value: hM3Dq/ Villin-Cre

value: injected with 200 μg/kg of CNO


title: S1093

description: Library name: S1093


title: 3d, seq batch 2, rep2

value: 3 days after induction


title: S1094

description: Library name: S1094


title: 2d, seq batch 2, rep2

value: 2 days after induction


title: 1d, seq batch 2, rep2

value: 1 day after induction


title: Control Male Weaned A1 [A1_C_M_W]

description:
Control Male Weaned A1
RodriguezZas_Pig_D22__Hypothalamus_pig_GEO_counts.csv

value: Hypothalamus

value: 22 day old


title: K562-CRISPRi-sgMED16


title: S1092

description: Library name: S1092


title: 0d, seq batch 2, rep2

value: 0 days after induction


title: K562-CRISPRi-sgCCNC


title: Control Male Nursed A9 [A9_C_M_N]

description:
Control Male Nursed A9
RodriguezZas_Pig_D22__Hypothalamus_pig_GEO_counts.csv

value: Nursed


title: S1090

description: Library name: S1090


title: Control Male Nursed A8 [A8_C_M_N]

description:
Control Male Nursed A8
RodriguezZas_Pig_D22__Hypothalamus_pig_GEO_counts.csv


title: 5d, seq batch 2, rep1

value: Inflorescences

value: 5 days after induction


title: K562,EC100-GFP;RAD21-AID,DMSO,rep2,GFP

value: DMSO

value: GFP


title: K562,EC100-GFP;RAD21-AID,DMSO,rep1,GFP


title: S1087

description: Library name: S1087


title: 4d, seq batch 2, rep1

value: Col-0 (pAP1:AP1-GR ap1cal mutant)

value: 4 days after induction


title: 3d, seq batch 2, rep1


title: S1084

description: Library name: S1084

value: Wild type


title: K562,E100,GFP_high


title: Control Male Nursed A6 [A6_C_M_N]

description:
Control Male Nursed A6
RodriguezZas_Pig_D22__Hypothalamus_pig_GEO_counts.csv

value: Control

value: Male


title: S1082

description: Library name: S1082

value: small intestine

value: injected with 200 μg/kg of CNO


title: HCT116_LIG4_KO_AID_RAD21_yH2AX_ChIP_seq_4OHT_Figure2c_replicate 2

city: Bethesda

first: Christophe

middle: E

last: Redon

state: MD

address: 37 Convent Drive

institute: NIH

data_processing:
BAM files were filtered using alignmentSieve to remove reads shorter than 40bp
For peak calling the MACS2 algorithm was used.
Nascent strand reads were called by comparison to genomic DNA.
Peaks were filtered to accept the top 40% by q-value based on the raw output
Assembly: hg19
Supplementary files format and content: Bed file format showing: AsiSI TADs and random TADs AsiSI cut sites in U2OS NS-seq peaks AsiSI cut sites in LIG4-/- AID RAD21 AsiSI-HCT116 replication timing in U2OS
Supplementary files format and content: BigWig file format of BrdU-seq NS-seq and ChIP-seq

source_name: Colon

growth_protocol: AsiSI-U2OS cells were grown in DMEM medium 10% FBS. AID RAD21 HCT116 and AID RAD21 AsiSI HCT116 are grown in McCoy's 5A medium with 10% FBS

extract_protocol:
DNA from cell cultures was isolated size fractionated and subject to exunuclease digestion as described in Aladjem et al. Science 281 1005 1998. and Wang et al. Molecular and Cellular Biology 24:3373-86 2004. For ChipSeq DNA molecules were enriched using antibodies against proteins of interest. For BrdU seq extraction was performed using a protocol modified from Marchal et al. 2018
Samples were eluted and then purified by Monarch PCR & DNA Cleanup Kit (NEBT1030S). 100 ng of samples were used to generate the library. The kits used for the library were NEBNext Ultra II DNA Library Prep Kit for Illumina (NEB E7805S) and NEBNext Multiplex Oligos for Il-lumina (Index Primers Set 1 and Set 2) (NEB E7335S and E7500S).

treatment_protocol: 4OHT was added at a concentration of 300 nM for 4h to induce DNA DSBs. Where relevant WEE1i was added at a concentration of 10 uM for 1h.

value: Colon

value: colorectal carcinoma

value: HCT116 LIG4 KO


title: 2d, seq batch 2, rep1

value: 2 days after induction


title: HCT116_LIG4_KO_AID_RAD21_yH2AX_ChIP_seq_control_Figure2c_replicate 1

value: No treatment


title: HCT116_LIG4_KO_AID_RAD21_yH2AX_ChIP_seq_control_Figure2c_replicate 2


title: K562-CRISPRi-sgMED12


title: S1067

description: Library name: S1067


title: S1065

description: Library name: S1065


title: Control Male Nursed A4 [A4_C_M_N]

description:
Control Male Nursed A4
RodriguezZas_Pig_D22__Hypothalamus_pig_GEO_counts.csv

value: Hypothalamus

value: 22 day old

value: Nursed


title: HCT116_LIG4_KO_AID_RAD21_Input_yH2AX_ChIP_seq_Figure2c_replicate 2


title: Control Male Nursed A5 [A5_C_M_N]

description:
Control Male Nursed A5
RodriguezZas_Pig_D22__Hypothalamus_pig_GEO_counts.csv


title: 1d, seq batch 2, rep1

value: Inflorescences

value: 1 day after induction


title: HCT116_LIG4_KO_AID_RAD21_Input_yH2AX_ChIP_seq_Figure2c_replicate 1


title: K562-CRISPRi-sgControl


title: 0d, seq batch 2, rep1

value: Col-0 (pAP1:AP1-GR ap1cal mutant)

value: 0 days after induction


title: HCT116_LIG4_KO_AID_RAD21_yH2AX_ChIP_seq_4OHT_Figure2c_replicate 1


title: 5d, seq batch 1, rep4

value: 5 days after induction


title: Control Male Nursed A2 [A2_C_M_N]

description:
Control Male Nursed A2
RodriguezZas_Pig_D22__Hypothalamus_pig_GEO_counts.csv

value: Control


title: S1062

description: Library name: S1062

value: Wild type


title: HCT116_LIG4_KO_AID_RAD21_Input_BrdU_seq_Figure2c_EDF5g_replicate 2


title: Control Male Nursed A7 [A7_C_M_N]

description:
Control Male Nursed A7
RodriguezZas_Pig_D22__Hypothalamus_pig_GEO_counts.csv

value: Male


title: 4d, seq batch 1, rep4

value: 4 days after induction


title: Control Male Nursed A10 [A10_C_M_N]

description:
Control Male Nursed A10
RodriguezZas_Pig_D22__Hypothalamus_pig_GEO_counts.csv


title: HIV-1 BAL+cART_3

city: Chicago

first: Ramon

last: Lorenzo-Redondo

address: 303 E Superior St.

institute: Northwestern University

description:
Library name: CO-iM +HIV1 BAL +cART 25
Eukaryotic Strand-specific Transcriptome Resequencing
MGL_25

data_processing:
Sequencing data was demultiplexed and trimmed using Trimmomatic v0.36 to remove adapters and low-quality reads.
Trimmed reads were aligned to the Homo sapiens reference genome GRCh38 and transcripts quantified using the Hisat2-StringTie pipeline58
Assembly: GRCh38

source_name: Cerebral organoid

growth_protocol: Cerebral organoids were generated from iPSC-Ru line by mixing iPSC with HPCs to form CO-iMs or without mixing with HPCs to form COs. Stemdiff cerebral organoid kit was used throughout with MCSF (50ng/ml) and IL-3 (20ng/ml).

extract_protocol:
Organoids were stored in RNAlater (500 ml/organoid) at -20°C until processing. RNA extraction was performed using the RNeasy mini kit (Qiagen).
stranded library preparation,150 bp paired-end sequencing and ≥30million reads

treatment_protocol: Around 65 day old CO-iMs were infected with HIV-1 at p24=10ng/ml for 3 days, organoids were washed and replaced with fresh maturation media and 2 days later processed for extraction of total RNA. Some Co-iMs were left as un-infected and some were infected and treated with anti-retrovirals (dolutegravir at 3.9 mg/ml and nevirapine  at 10mM) that were added 24 h prior to infection, at the time of infection, and after day 3 wash.

value: Cerebral organoid

value: iPSC-Ru

value: human induced pluripotent stem cells

value: WT

value: HIV-1 BAL+cART


title: HCT116_LIG4_KO_AID_RAD21_Input_BrdU_seq_Figure2c_EDF5g_replicate 1

value: Colon

value: colorectal carcinoma

value: HCT116 LIG4 KO

value: No treatment


title: 3d, seq batch 1, rep4

value: Inflorescences

value: 3 days after induction


title: HIV-1 BAL+cART_2

description:
Library name: CO-iM +HIV1 BAL +cART 24
Eukaryotic Strand-specific Transcriptome Resequencing
MGL_24


title: Control Male Nursed A3 [A3_C_M_N]

description:
Control Male Nursed A3
RodriguezZas_Pig_D22__Hypothalamus_pig_GEO_counts.csv

value: Hypothalamus

value: 22 day old

value: Nursed


title: 2d, seq batch 1, rep4

value: Col-0 (pAP1:AP1-GR ap1cal mutant)

value: 2 days after induction


title: Control Female Weaned A9 [A9_C_F_W]

description:
Control Female Weaned A9
RodriguezZas_Pig_D22__Hypothalamus_pig_GEO_counts.csv

value: Control

value: Female

value: Weaned


title: HIV-1 BAL+cART_1

description:
Library name: CO-iM +HIV1 BAL +cART 15
Eukaryotic Strand-specific Transcriptome Resequencing
MGL_21

value: Cerebral organoid

value: iPSC-Ru

value: human induced pluripotent stem cells


title: HCT116_LIG4_KO_AID_RAD21_BrdU_seq_IAA_Figure2c_EDF5g_replicate 2

value: Colon

value: IAA-treated


title: Control Male Nursed A1 [A1_C_M_N]

description:
Control Male Nursed A1
RodriguezZas_Pig_D22__Hypothalamus_pig_GEO_counts.csv

value: Male


title: S1064

description: Library name: S1064

value: small intestine

value: Wild type

value: injected with 200 μg/kg of CNO


title: Control Female Weaned A8 [A8_C_F_W]

description:
Control Female Weaned A8
RodriguezZas_Pig_D22__Hypothalamus_pig_GEO_counts.csv

value: Hypothalamus


title: 1d, seq batch 1, rep4

value: Inflorescences

value: 1 day after induction


title: HCT116_LIG4_KO_AID_RAD21_BrdU_seq_IAA_Figure2c_EDF5g_replicate 1

value: colorectal carcinoma

value: HCT116 LIG4 KO


title: 0d, seq batch 1, rep4

value: Col-0 (pAP1:AP1-GR ap1cal mutant)

value: 0 days after induction


title: 5d, seq batch 1, rep3

value: 5 days after induction


title: HCT116_LIG4_KO_AID_RAD21_BrdU_seq_IAA_4OHT_Figure2c_EDF5g_replicate 2

value: 4OHT and IAA-treated


title: Control Female Weaned A6 [A6_C_F_W]

description:
Control Female Weaned A6
RodriguezZas_Pig_D22__Hypothalamus_pig_GEO_counts.csv

value: 22 day old

value: Control

value: Female

value: Weaned


title: HIV-1 BAL_2

description:
Library name: CO-iM + HIV1 BAL 19
Eukaryotic Strand-specific Transcriptome Resequencing
MGL_15

value: Cerebral organoid

value: iPSC-Ru

value: human induced pluripotent stem cells

value: WT

value: HIV-1 BAL


title: HIV-1 BAL_1

description:
Library name: CO-iM + HIV1 BAL 12
Eukaryotic Strand-specific Transcriptome Resequencing
MGL_12


title: HCT116_LIG4_KO_AID_RAD21_BrdU_seq_control_Figure2c_EDF5g_replicate 2

value: Colon

value: No treatment


title: 4d, seq batch 1, rep3

value: Inflorescences

value: 4 days after induction


title: HCT116_LIG4_KO_AID_RAD21_BrdU_seq_control_Figure2c_EDF5g_replicate 1

value: colorectal carcinoma

value: HCT116 LIG4 KO


title: Control Female Weaned A5 [A5_C_F_W]

description:
Control Female Weaned A5
RodriguezZas_Pig_D22__Hypothalamus_pig_GEO_counts.csv

value: Hypothalamus


title: 3d, seq batch 1, rep3

value: Col-0 (pAP1:AP1-GR ap1cal mutant)

value: 3 days after induction


title: Uninfected_6

description:
Library name: CO-iM 6
Eukaryotic Strand-specific Transcriptome Resequencing
MGL_6

value: Uninfected


title: HCT116_LIG4_KO_AID_RAD21_BrdU_seq_4OHT_Figure2c_EDF5g_replicate 2


title: HIV-1 BAL_3

description:
Library name: CO-iM + HIV1 BAL 21
Eukaryotic Strand-specific Transcriptome Resequencing
MGL_19


title: Control Female Weaned A7 [A7_C_F_W]

description:
Control Female Weaned A7
RodriguezZas_Pig_D22__Hypothalamus_pig_GEO_counts.csv

value: 22 day old

value: Control

value: Female


title: Control Female Weaned A3 [A3_C_F_W]

description:
Control Female Weaned A3
RodriguezZas_Pig_D22__Hypothalamus_pig_GEO_counts.csv

value: Weaned


title: Uninfected_5

description:
Library name: CO-iM 5
Eukaryotic Strand-specific Transcriptome Resequencing
MGL_5

value: Cerebral organoid

value: iPSC-Ru

value: human induced pluripotent stem cells


title: Uninfected_4

description:
Library name: CO-iM 4
Eukaryotic Strand-specific Transcriptome Resequencing
MGL_4

value: WT


title: HCT116_LIG4_KO_AID_RAD21_BrdU_seq_4OHT_Figure2c_EDF5g_replicate 1

value: Colon


title: 2d, seq batch 1, rep3

value: Inflorescences

value: 2 days after induction


title: AsiSI_U2OS_WEE1i_yH2AX_ChIP_seq_EDF9gh_replicate 2

source_name: Bone

value: Bone

value: Osteosarcoma

value: Wild-type AsiSI_U2OS


title: 1d, seq batch 1, rep3

value: Col-0 (pAP1:AP1-GR ap1cal mutant)

value: 1 day after induction


title: HCT116_LIG4_KO_AID_RAD21_BrdU_seq_IAA_4OHT_Figure2c_EDF5g_replicate 1

value: colorectal carcinoma

value: HCT116 LIG4 KO

value: 4OHT and IAA-treated


title: Uninfected_3

description:
Library name: CO 10
Eukaryotic Strand-specific Transcriptome Resequencing
CO_10

value: Uninfected


title: 0d, seq batch 1, rep3

value: 0 days after induction


title: Control Female Weaned A10 [A10_C_F_W]

description:
Control Female Weaned A10
RodriguezZas_Pig_D22__Hypothalamus_pig_GEO_counts.csv

value: Hypothalamus

value: 22 day old

value: Control

value: Female

value: Weaned


title: Uninfected_2

description:
Library name: CO 9
Eukaryotic Strand-specific Transcriptome Resequencing
CO_9

value: Cerebral organoid

value: iPSC-Ru

value: human induced pluripotent stem cells

value: WT


title: CC44

value: HPV-positive squamous oropharyngeal carcinoma (OPC)

value: M

value: OPC

value: not available


title: 5d, seq batch 1, rep2

value: Inflorescences

value: Col-0 (pAP1:AP1-GR ap1cal mutant)

value: 5 days after induction


title: Uninfected_1

description:
Library name: CO 8
Eukaryotic Strand-specific Transcriptome Resequencing
CO_8

value: Uninfected


title: AsiSI_U2OS_WEE1i_yH2AX_ChIP_seq_EDF9gh_replicate 1

value: Bone

value: Osteosarcoma

value: Wild-type AsiSI_U2OS


title: 4d, seq batch 1, rep2

value: 4 days after induction


title: Control Female Weaned A1 [A1_C_F_W]

description:
Control Female Weaned A1
RodriguezZas_Pig_D22__Hypothalamus_pig_GEO_counts.csv

value: Hypothalamus

value: 22 day old

value: Control

value: Female

value: Weaned


title: AsiSI_U2OS_WEE1i_TIPIN_ChIP_seq_Figure4d_replicate 2


title: AsiSI_U2OS_WEE1i_TIPIN_ChIP_seq_Figure4d_replicate 1


title: 3d, seq batch 1, rep2

value: 3 days after induction


title: hiPSC-CM 5

first: Paul

middle: W.

last: Burridge

address: 320 East Superior Street

description: hiPSC-CM 5

data_processing:
Reads were mapped to the GRCh38 reference human genome using Subread software.
Gene expression levels were estimated using featureCounts function in the Subread software.
Gene expression data was log2 normalized.
Assembly: GRCh38
Supplementary files format and content: Microsoft Excel Workbook includes log 2 normalized gene counts for each sample.

source_name: Control hiPSC-CM 5

extract_protocol:
RNA was extracted using 300 µL of TRIzol Reagent. RNA was then purified using the Direct-zol RNA MicroPrep kit, including on-column Dnase digestion to remove genomic DNA.
RNA libraries for RNA-seq were prepared using DNBSEQ Eukaryotic strand-specific mRNA library protocol.

value: Control hiPSC-CM 5

value: hiPSC-CM


title: Control Female Weaned A4 [A4_C_F_W]

description:
Control Female Weaned A4
RodriguezZas_Pig_D22__Hypothalamus_pig_GEO_counts.csv


title: hiPSC-CM 4

description: hiPSC-CM 4

source_name: Control hiPSC-CM 4

value: Control hiPSC-CM 4


title: Control Female Weaned A2 [A2_C_F_W]

description:
Control Female Weaned A2
RodriguezZas_Pig_D22__Hypothalamus_pig_GEO_counts.csv


title: hiPSC-CM 3

description: hiPSC-CM 3

source_name: Control hiPSC-CM 3

value: Control hiPSC-CM 3


title: 2d, seq batch 1, rep2

value: Inflorescences

value: Col-0 (pAP1:AP1-GR ap1cal mutant)

value: 2 days after induction


title: AsiSI_U2OS_WEE1i_TIMELESS_ChIP_seq_Figure4d_replicate 1

value: Bone


title: 1d, seq batch 1, rep2

value: 1 day after induction


title: AsiSI_U2OS_WEE1i_BrdU_seq_Figure4a_EDF9f_replicate 1

value: Osteosarcoma

value: Wild-type AsiSI_U2OS


title: hiPSC-CM 2

description: hiPSC-CM 2

source_name: Control hiPSC-CM 2

value: Control hiPSC-CM 2


title: hiPSC-CM 1

description: hiPSC-CM 1

source_name: Control hiPSC-CM 1

value: Control hiPSC-CM 1


title: Control Female Weaned A11 [A11_C_F_W]

description:
Control Female Weaned A11
RodriguezZas_Pig_D22__Hypothalamus_pig_GEO_counts.csv

value: Hypothalamus

value: 22 day old

value: Control


title: Control Female Nursed A6 [A6_C_F_N]

description:
Control Female Nursed A6
RodriguezZas_Pig_D22__Hypothalamus_pig_GEO_counts.csv

value: Female

value: Nursed


title: Control Female Nursed A8 [A8_C_F_N]

description:
Control Female Nursed A8
RodriguezZas_Pig_D22__Hypothalamus_pig_GEO_counts.csv


title: 0d, seq batch 1, rep2

value: 0 days after induction


title: 5d, seq batch 1, rep1

value: 5 days after induction


title: AsiSI_U2OS_WEE1i_4OHT_BrdU_seq_Figure4a_EDF9f_replicate 2


title: Control Female Nursed A5 [A5_C_F_N]

description:
Control Female Nursed A5
RodriguezZas_Pig_D22__Hypothalamus_pig_GEO_counts.csv


title: hiPSC-EC 2

description: hiPSC-EC 2

source_name: Control hiPSC-EC 2

value: Control hiPSC-EC 2

value: hiPSC-EC


title: 3d, seq batch 1, rep1

value: Inflorescences

value: Col-0 (pAP1:AP1-GR ap1cal mutant)

value: 3 days after induction


title: 4d, seq batch 1, rep1

value: 4 days after induction


title: Control Female Nursed A4 [A4_C_F_N]

description:
Control Female Nursed A4
RodriguezZas_Pig_D22__Hypothalamus_pig_GEO_counts.csv


title: AsiSI_U2OS_siTP53BP1_BrdU_seq_EDF7d_replicate 2

value: Bone

value: Osteosarcoma

value: siRNA-treated


title: AsiSI_U2OS_WEE1i_4OHT_BrdU_seq_Figure4a_EDF9f_replicate 1

value: Wild-type AsiSI_U2OS


title: 2d, seq batch 1, rep1

value: 2 days after induction


title: Control Female Nursed A9 [A9_C_F_N]

description:
Control Female Nursed A9
RodriguezZas_Pig_D22__Hypothalamus_pig_GEO_counts.csv

value: Hypothalamus

value: 22 day old


title: AsiSI_U2OS_WEE1i_TIMELESS_ChIP_seq_Figure4d_replicate 2


title: hiPSC-EC 1

description: hiPSC-EC 1

source_name: Control hiPSC-EC 1

value: Control hiPSC-EC 1


title: Control Female Nursed A3 [A3_C_F_N]

description:
Control Female Nursed A3
RodriguezZas_Pig_D22__Hypothalamus_pig_GEO_counts.csv

value: Control

value: Female

value: Nursed


title: AsiSI_U2OS_WEE1i_BrdU_seq_Figure4a_EDF9f_replicate 2


title: Control Female Nursed A7 [A7_C_F_N]

description:
Control Female Nursed A7
RodriguezZas_Pig_D22__Hypothalamus_pig_GEO_counts.csv


title: AsiSI_U2OS_siTP53BP1_BrdU_seq_EDF7d_replicate 1


title: hiPSC-MEC 3

description: hiPSC-MEC 3

value: hiPSC-MEC


title: Control Female Nursed A2 [A2_C_F_N]

description:
Control Female Nursed A2
RodriguezZas_Pig_D22__Hypothalamus_pig_GEO_counts.csv


title: Control Female Nursed A10 [A10_C_F_N]

description:
Control Female Nursed A10
RodriguezZas_Pig_D22__Hypothalamus_pig_GEO_counts.csv


title: 1d, seq batch 1, rep1

value: 1 day after induction


title: hiPSC-EC 3

description: hiPSC-EC 3

source_name: Control hiPSC-EC 3

value: Control hiPSC-EC 3

value: hiPSC-EC


title: hiPSC-MEC 2

description: hiPSC-MEC 2


title: Control Female Nursed A1 [A1_C_F_N]

description:
Control Female Nursed A1
RodriguezZas_Pig_D22__Hypothalamus_pig_GEO_counts.csv


title: hiPSC-MEC 1

description: hiPSC-MEC 1


title: AsiSI_U2OS_siTP53BP1_4OHT_BrdU_seq_EDF7d_replicate 2


title: AsiSI_U2OS_siTP53BP1_4OHT_BrdU_seq_EDF7d_replicate 1


title: KO_7 3W iWAT

first: Xu

last: Xu

address: 330 Brookline Ave

department: Surgery

institute: Beth Israel Deaconess Medical Center

data_processing:
CLC Genomics workbench 11.0.1
Assembly: CLC Genomics workbench 11.0.1
Supplementary files format and content: excel file include raw counts for each sample

source_name: Inguinal white adipose tissue

extract_protocol:
RNA was harvested using TRIzol™ Reagent (Invitrogen) and purified using RNeasy Mini plus Kit (Qiagen). Approximately 2 μg of total RNA was used for library construction
RNA library for RNA-seq was prepared using TruSeq stranded mRNA library preparation kit

value: Inguinal white adipose tissue

value: Cold exposure at 4C for 3 weeks


title: 0d, seq batch 1, rep1

value: Inflorescences

value: Col-0 (pAP1:AP1-GR ap1cal mutant)

value: 0 days after induction


title: AsiSI_U2OS_siRIF1_BrdU_seq_EDF7d_replicate 1

value: Bone

value: Osteosarcoma

value: Wild-type AsiSI_U2OS

value: siRNA-treated


title: KO_5 3W iWAT


title: BM_K3_bulkRNA

city: changsha

first: Cheng

last: Xing

state: Hunan Province

address: Department of Hematology, the Second Xiangya Hospital, Central South University,

department: Department of Hematology

description: Library name: Sample18

data_processing:
Illumina Casava1.7 software used for basecalling.
Assembly: mm10
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample

source_name: murine bone marrow

extract_protocol:
Total RNA was extracted using the TRIzol reagent (Invitrogen, CA, USA) according to the manufacturer’s protocol.
The libraries were constructed using VAHTS Universal V6 RNA-seq Library Prep Kit according to the manufacturer’s instructions

value: murine bone marrow

value: Fabp4 homozygous knockout

value: sorted from bone marrow


title: BM_K2_bulkRNA

institute: the Second Xiangya Hospital, Central South University,

description: Library name: Sample17


title: KO_6 3W iWAT


title: AsiSI_U2OS_siRIF1_4OHT_BrdU_seq_EDF7d_replicate 2


title: hiPSC 1

description: hiPSC 1

value: hiPSC


title: hiPSC 2

description: hiPSC 2


title: BM_H3_bulkRNA

description: Library name: Sample15

value: Fabp4 heterozygous knockout


title: WT_11 3W iWAT

value: WT


title: BM_K1_bulkRNA

description: Library name: Sample16


title: AsiSI_U2OS_siRIF1_4OHT_BrdU_seq_EDF7d_replicate 1


title: primary MEC 3

description: primary MEC 3

value: primary MEC


title: WT_9 3W iWAT


title: BM_H2_bulkRNA

description: Library name: Sample14


title: AsiSI_U2OS_siCtrl_BrdU_seq_EDF7d_replicate 2


title: primary MEC 2

description: primary MEC 2


title: primary MEC 1

description: primary MEC 1


title: BM_H1_bulkRNA

description: Library name: Sample13


title: KO_2 30C iWAT

value: Thermoneutrality


title: AsiSI_U2OS_siRIF1_BrdU_seq_EDF7d_replicate 2


title: AsiSI_U2OS_siCtrl_BrdU_seq_EDF7d_replicate 1


title: BM_W3_bulkRNA

description: Library name: Sample12

value: Fabp4 wild-type


title: hiPSC 3

description: hiPSC 3


title: KO_1 30C iWAT

value: Inguinal white adipose tissue


title: AsiSI_U2OS_siCtrl_4OHT_BrdU_seq_EDF7d_replicate 2


title: AsiSI_U2OS_siCtrl_4OHT_BrdU_seq_EDF7d_replicate 1


title: BM_W2_bulkRNA

description: Library name: Sample11


title: BM_W1_bulkRNA

description: Library name: Sample10


title: WT_2 30C iWAT


title: KO_7 3W BAT

source_name: Brown adipose tissue

value: Brown adipose tissue

value: Cold exposure at 4C for 3 weeks


title: WT_1 30C iWAT


title: AsiSI_U2OS_Input_yH2AX_ChIP_seq_Figure1c3a_EDF3d4ab_replicate 2

value: No treatment


title: AsiSI_U2OS_Input_yH2AX_ChIP_seq_Figure1c3a_EDF3d4ab_replicate 1

value: Bone


title: K3_bulkRNA

description: Library name: Sample9

value: sorted from vitro bone marrow


title: AsiSI_U2OS_input_yH2AX_ChIP_seq_EDF9gh_replicate 2

value: Osteosarcoma

value: Wild-type AsiSI_U2OS


title: K2_bulkRNA

description: Library name: Sample8

value: murine bone marrow


title: WT_8 3W iWAT


title: KO_6 3W BAT


title: K1_bulkRNA

description: Library name: Sample7

value: Fabp4 homozygous knockout


title: H3_bulkRNA

description: Library name: Sample6


title: KO_5 3W BAT


title: AsiSI_U2OS_Input_ChIP_seq_Figure4d


title: WT_11 3W BAT


title: AsiSI_U2OS_input_yH2AX_ChIP_seq_EDF9gh_replicate 1


title: WT_9 3W BAT


title: AsiSI_U2OS_Input_ChIP_seq_Figure3ab_EDF8ab_replicate 2


title: MCF7_cordycepin_2

city: Nottingham

first: Keith

last: Spriggs

state: Notts

address: University Park

department: Pharmacy

country: United Kingdom

institute: University of Nottingham

description: Cy5 = Subpolysomal, Cy3 = Polysomal

hyb_protocol: Cy3 and Cy5 labelled samples were mixed and added with Agilent Fragmentation Buffer and hybridised at 65C following manufaturer's instructions to a Human Gene Expression 8x60 v2 microarray

scan_protocol: Scanning was done using a G2505C scanner (Agilent Technologies) using the feature extraction and array quality control software provided by the manufacturer

data_processing: Data were uploaded in GeneSpring (Agilent) and normalised.

source_name: MCF-7 cells, treated with 50 uM cordycepin for 30 minutes

label_protocol: Labelling with Cy3 and Cy5 was performed using the Quick Amp Labelling Kit, Two Colors (Agilent). A dye swap was used.

growth_protocol: 2.5 million MCF-7 cells from a subconfluent culture were seeded in p15 plates and incubated in a 37C CO2 incubator for 24 hours.

extract_protocol: Cells were washed with PBS and collected by scraping on ice. Three plates were pooled for each treatment and centrifugated. Cell pellets were lysed in 500 ul lysis buffer and separated on sucrose gradients and the RNA from 12 fractions precipitated with guanidine/HCl and RNA isolated as previously described (Johannes et al 1999, https://doi.org/10.1073/pnas.96.23.13118). Fractions 1-6 (sub-polysomes) and 7-11 (polysomes) were pooled for microarray analysis (fraction 12 did not contain RNA)

treatment_protocol: Three p15 plates as described above were treated with 0.1% DMSO (vehicle control) or 0.1% DMSO and 50 uM cordycepin (cordycepin), incubated for 0.5 hours at 37C in a CO2 incubator.

tag: gender

value: female


title: H1_bulkRNA

description: Library name: Sample4

tag: tissue


title: MCF7_cordycepin_3

description: Cy3 = Subpolysomal, Cy5 = Polysomal

tag: cell type


title: H2_bulkRNA

description: Library name: Sample5


title: AsiSI_U2OS_Input_ChIP_seq_Figure3ab_EDF8ab_replicate 1


title: MCF7_cordycepin_1

description: Cy3 = Subpolysomal, Cy5 = Polysomal


title: AsiSI_U2OS_Input_BrdU_seq_Figure4a_EDF9f_replicate 2


title: W3_bulkRNA

description: Library name: Sample3


title: W2_bulkRNA

description: Library name: Sample2


title: KO_3 3D BAT

value: Cold exposure at 4C for 3 days


title: AsiSI_U2OS_Input_BrdU_seq_Figure4a_EDF9f_replicate 1


title: MCF7_control_2

description: Cy5 = Subpolysomal, Cy3 = Polysomal

source_name: MCF-7 cells, vehicle control


title: KO_2 3D BAT


title: MCF7_cordycepin_4

description: Cy5 = Subpolysomal, Cy3 = Polysomal


title: W1_bulkRNA

description: Library name: Sample1


title: MCF7_control_4

description: Cy3 = Subpolysomal, Cy5 = Polysomal


title: AsiSI_U2OS_Input_BrdU_seq_Figure1c_EDF3d_replicate 2


title: MCF-7 serum control 3

hyb_protocol: Hybridised at 65C in a microarray hybridisation oven according to the manufacturer's protocol (Agilent).

scan_protocol: Agilent  Microarray Scanner, model number G2505C, scan control version A.8.4.1.

data_processing: Standard Agilent Feature Extraction normalization and background correction procedures

source_name: MCF-7 cell cultured in the presence of serum

label_protocol: Labelling was done with Agilent’s one-colour Low Input Quick Amp Labelling Kit (Cy3) according to the manufacturer's instructions. The level of dye incorporation was evaluated by spectrophotometry (Nanodrop ND1000, LabTech, Uckfield, UK). Labeled RNA was fragmented and diluted (v/v) in hybridization buffer.

growth_protocol: MCF-7 cells were seeded at 3 million cells per p15 plate in DMEM with 10%  FBS and glutamine.

extract_protocol: Mackerey-Nagel Nucleospin RNA extraction with a 1 hour DNase incubation

treatment_protocol: 24 hours after seeding, medium was removed from both plates (and kept), the plates washed with PBS. The old medium was put back on one plate (control) and DMEM with glutatmine but without FBS and incubated for 4 hours.


title: MCF7_control_1

description: Cy3 = Subpolysomal, Cy5 = Polysomal


title: KO_1 3D BAT


title: MCF-7 serum control 1


title: AsiSI_U2OS_Input_BrdU_seq_Figure1c_EDF3d_replicate 1


title: MCF7_control_3

description: Cy5 = Subpolysomal, Cy3 = Polysomal


title: AsiSI_U2OS_DMSO_yH2AX_ChIP_seq_EDF9gh_replicate 2

value: DMSO-treated


title: WT_8 3W  BAT

value: WT


title: WT_3 3D BAT


title: Arc-negative NAc nuclei, CPP 5 pairing, homecage

city: New York

first: Marine

last: Salery

state: NY

address: 1425 Madison Ave

institute: Icahn School of Medicine at Mount Sinai

description:
Library name: 06275M
10X Genomics

library_source: transcriptomic single cell

data_processing:
snRNAseq preprocessing: A Cell Ranger (v7.0.0) reference package was generated from the mm10 pre-mRNA mouse genome (GRCm38_v5) that ensured alignment to unspliced pre-mRNAs and mature RNAs. Cell Ranger filtered outputs were analyzed with Seurat v4.3.0 in R v4.2.2. Nuclei containing <900 reads, or <200 or >5000 features (i.e., genes for which at least one read was detected), or >1% of reads mapping to the mitochondrial genome were removed, leaving altogether 12,092 nuclei with a median 2,836 reads per nuclei for further analysis similarly to other previously published datasets 56,57.
Assembly: GRCm38_v5
Supplementary files format and content: HDF5 files for expression matrices and barcodes

molecule: nuclear RNA

source_name: Sorted NAc nuclei

extract_protocol:
Mouse brains were collected after cervical dislocation and bilateral NAc dissection was rapidly performed from 1 mm-thick coronal brain sections using a 14G needle and tissue frozen on dry ice. Bilateral dissections from 16-20 mice were pooled together group-wise into one single sample, which did not allow for the use of pseudobulking analysis strategies (see below). Nuclei suspension was obtained by homogenization of frozen pooled NAc samples in 4 mL of low-sucrose lysis buffer (0.32 M sucrose, 5 mM CaCl2, 3 mM Mg(Ace)2, 0.1 mM EDTA, 10 mM Tris-HCl) using a large clearance then a small clearance pestle of a glass Dounce tissue grinder (Kimble Kontes). The homogenates were filtered in an ultracentrifuge tubes (Beckman Coulter through a 40 μm cell strainer (Pluriselect) into ultracentrifuge tubes (Beckman Coulter), underlaid with 5 mL of high sucrose solution (1.8 M sucrose, 3 mM Mg(Ace)2, 1 mM DTT, 10 mM Tris-HCl). After centrifugation at 107,000 g for 1 h at 4°C in a SW41Ti Swinging-Bucket Rotor (Beckman Coulter, the supernatant was discarded, and nuclei pellets were resuspended in 800 µL of a solution containing 0.5% bovine serum albumin (BSA) in PBS and supplemented with DAPI at 1 µg/mL to allow for nuclei detection. Nuclei were sorted on a BD FACS Aria II three-laser device with a 100 μm nozzle and using BD FACSDiva Software v8.0.2. Gating strategies from a representative sort are visualized in Extended Data Fig. 7. Briefly, debris and doublets were excluded using FSC and SSC filters, nuclei were then selected as DAPI-positive (Violet1-A laser) events, and finally GFP-positive 610 nuclei (Blue1-A laser) were sorted directly into BSA-coated low-binding tubes. 15-18,000 nuclei were recovered for GFP+ samples and 100,000 for GFP- samples.
Following FANS, nuclei were quantified (Countess II, Life Technologies) and ±5,000 per GFP+ sample and ±20,000 per GFP- sample were loaded on a single 10X flow cell GEM well using Chromium Single Cell 3’ Library Construction Kit (10X Genomics). cDNA libraries were prepared according to the manufacturer’s protocol (10X Genomics). Libraries were sequenced at Azenta on a single NovaSeq lane (Illumina) at a depth of ±350 million reads per sample.

value: Sorted NAc nuclei

tag: strain

value: ArcCreERT2 x Ai14

value: pooled male and female

tag: gfp sort

value: NEG

tag: cpp pairings

tag: cpp testing

value: Homecage


title: Arc-positive NAc nuclei, CPP 5 pairing, homecage

description:
Library name: 06275P
10X Genomics

tag: Sex

value: POS


title: AsiSI_U2OS_DMSO_yH2AX_ChIP_seq_EDF9gh_replicate 1


title: MCF-7 serum withdrawal 3

source_name: MCF-7 cell cultured in the absence of serum for four hours


title: WT_2 3D BAT

value: Brown adipose tissue


title: WT_1 3D BAT


title: KO_2 30C BAT

value: Thermoneutrality


title: Arc-positive NAc nuclei, CPP 5 pairing, after CPP test

description:
Library name: 06225P
10X Genomics

value: Test


title: AsiSI_U2OS_DMSO_TIPIN_ChIP_seq_Figure4d_replicate 2

source_name: Bone

value: Bone

value: Osteosarcoma


title: MCF-7 serum withdrawal 2


title: Arc-negative NAc nuclei, CPP 1 pairing, homecage

description:
Library name: 06271M
10X Genomics


title: AsiSI_U2OS_DMSO_TIPIN_ChIP_seq_Figure4d_replicate 1

value: Wild-type AsiSI_U2OS


title: KO_1 30C BAT


title: MCF-7 serum control 2


title: AsiSI_U2OS_DMSO_TIMELESS_ChIP_seq_Figure4d_replicate 2


title: Arc-negative NAc nuclei, CPP 5 pairing, after CPP test

description:
Library name: 06225M
10X Genomics


title: Arc-positive NAc nuclei, CPP 1 pairing, after CPP test

description:
Library name: 06221P
10X Genomics


title: WT_2 30C BAT


title: Arc-positive NAc nuclei, CPP 1 pairing, homecage

description:
Library name: 06271P
10X Genomics


title: AsiSI_U2OS_DMSO_TIMELESS_ChIP_seq_Figure4d_replicate 1


title: WT_1 30C  BAT


title: AsiSI_U2OS_DMSO_BrdU_seq_Figure4a_EDF9f_replicate 2


title: Spleen_CD23plus_Bcells_PBS_Exp3

city: Aurora

first: Shaikh

middle: M

last: Atif

state: CO

address: Research Complex II (RC2): P15-10005 Department of Medicine, Division of Allergy and Clinical Immunology, University of Colorado Anschutz Medical Campus, 12700 E 19th Ave

department: Medicine

institute: University of Colorado

data_processing:
Sequencing data was processed using the Illumina BaseSpace online platform and assessed using FASTQC
The FASTQ Toolkit was used to filter, adaptor trim and quality check trim reads
Reads were aligned to UCSC mm9 genome build using TopHat and read counts (gene expression levels) were obtained using HTSeq
Differential expression analysis was performed using DESeq
Assembly: UCSC mm9
Supplementary files format and content: tab-delimited text file includes raw countrs for each sample

source_name: Spleen

extract_protocol:
RNAeasy micro  kit  (Qiagen) was used for the RNA extraction. RNA quality and integrity were first assessed using an Agilent Tape Station 2200.
The library was constructed using the Illumina TruSeq mRNA library construction kit

treatment_protocol: Mice were exposed to either BeO or PBS

value: Spleen

value: B cells

value: FVB/NDP2 Tg mice

value: PBS


title: AsiSI_U2OS_DMSO_BrdU_seq_Figure4a_EDF9f_replicate 1

value: DMSO-treated


title: Arc-negative NAc nuclei, CPP 1 pairing, after CPP test

description:
Library name: 06221M
10X Genomics

value: Sorted NAc nuclei


title: MCF-7 control 3

source_name: MCF-7 cell treated for two hours with vehicle

growth_protocol: MCF-7 cells were seeded at approximately 2.5 million cells per 15 cm plate in DMEM with 10% FBS, 2 mM glutamine and penicillin/streptomycin and incubated for 24 hours.

extract_protocol: Promega Reliaprep kits using the manufacturer’s instructions

treatment_protocol: Plates were treated with 0.1% DMSO (vehicle, control) or cordycepin 50 uM and incubated for 2 hours.

value: female


title: MCF-7 cordycepin 3

source_name: MCF-7 cell treated for two hours with 50 uM cordycepin


title: MCF-7 control 2


title: CTCF_WT_UN_rep2

city: new york

first: Jane

middle: A

last: Skok

state: NEW YORK

address: Smilow Research Center, Third floor, Room 307, 522 First Avenue

department: Pathology

institute: NYU

description:
Library name: CTCF_WT_UN_rep2
CTCF_WT_UN_rep1_rep2.bin1.rpkm.bw
CTCF_WT_UN_rep1_rep2.peaks.bed

data_processing:
Data were processed using Seq-N-Slide pipeline.
Nextera adaptor were trimmed using TrimGalore.
Reads were aligned against the mouse reference genome (mm10) using the Bowtie2 aligner.
PCR duplicates were removed using Sambamba.
After scaling down each samples to 100M reads, replicates were merged per condition. Narrow peaks were called using MACS2 in pair-end mode with IgG as control for Smc3 ChIP-seq or WT untreated condition (in which FLAG CTCF is not expressed) for CTCF FLAG ChIP-seq to control for unspecific binding. Peaks overlapping ENCODE blacklisted regions were filtered out. Bigwig files were generated using deeptools (bamCoverage) with RPKM normalization (1bp bin).
Assembly: mm10
Supplementary files format and content: Bigwig with RPKM normalization, merged per condition after scaling down to 100M reads
Supplementary files format and content: narrow peaks (except for IgG and WT untreated, q<0.05) using merged replicates

source_name: mESC

growth_protocol: Mouse embryonic stem cells E14Tg2a and all clones derived from these were cultured under feeder-free conditions in 0.1% gelatin coated dishes at 37°C and 5% CO2 in a humidified incubator. The cells were grown in DMEM supplemented with 15% fetal bovine serum , 100 U/ml penicillin - 100 μg/ml streptomycin, 1 X GlutaMax supplement, 1 mM sodium pyruvate, 1 X MEM non-essential amino-acids, 50 μM b-mercaptoethanol, 104 U/ml leukemia inhibitory factor, 3 μM CHIR99021 and 1 μM MEK inhibitor PD0325901. The cells were passaged every alternate day by dissociation with TrypLE.

extract_protocol:
mESCs were dissociated using TrypLE and and double cross linked using 25mM EGS (ethylene glycol bis(succinimidyl succinate)) and 1% formaldehyde. Fixed cells (10 million) were resuspended in 350 μl ice cold lysis buffer (10 mM Tris-HCl (pH 8.0), 100 mM NaCl, 1 mM EDTA (pH 8.0), 0.5 mM EGTA (pH 8.0), 0.1% sodium deoxycholate, 0.5% N-lauroysarcosine and 1X protease inhibitors) and lysed for 10 min by rotating at 4° C. Chromatin was sheared using a bioruptor (Diagenode) for 15 minutes ( 30 sec on, 30 sec off, high output level). FLAG M2 Magnetic Beads were used for FLAG immunoprecipitation. In other cases ( CTCF, Cohesin, IgG) antibodies were bound to protein A magnetic beads by incubation on a rotator for one hour at room temperature.
Samples were washed and tagmentation were performed as per the original ChIPmentation protocol (Schmidl et al., 2015) using 1 μl Tagment DNA Enzyme from the Nextera DNA Sample Prep Kit (Illumina #20034198 ). Chromatin was then eluted and de-crosslinked and DNA was purified using MinElute Reaction Cleanup Kit. Purified DNA was amplified as per the ChIPmentation protocol (Schmidl, Rendeiro et al. 2015) using indexed and non-indexed primers and NEBNext High-Fidelity 2X PCR Master Mix. Library quality and quantity were estimatred using Tapestation and were then sequenced with the Novaseq6000 Illumina technology according to the standard protocols and with around 200 million 150bp paired-end total per sample.

treatment_protocol: For degradation of endogenous CTCF, the auxin-inducible degron was induced by adding 500 μM indole-3-acetic acid (IAA, chemical analog of auxin) to the media. Expression of transgenes was achieved by the addition of doxycycline (Dox, 1 μg/ml) to the media. The cells were treated with IAA and/or Dox for 2 days.

value: mESC

value: WT

value: Untreated

value: replicate 2

tag: antibody

value: CTCF


title: MCF-7 serum withdrawal 1


title: MCF-7 control 1


title: MCF-7 cordycepin 2


title: AsiSI_U2OS_DMSO_4OHT_BrdU_seq_Figure4a_EDF9f_replicate 2


title: CTCF_WT_UN_rep1

description:
Library name: CTCF_WT_UN_rep1
CTCF_WT_UN_rep1_rep2.bin1.rpkm.bw
CTCF_WT_UN_rep1_rep2.peaks.bed

value: replicate 1


title: Spleen_CD23plus_Bcells_PBS_Exp1


title: CTCF_WT_ID_rep2

description:
Library name: CTCF_WT_ID_rep2
CTCF_WT_ID_rep1_rep2.bin1.rpkm.bw
CTCF_WT_ID_rep1_rep2.peaks.bed

value: IAA+Doxyxycline


title: AsiSI_U2OS_DMSO_4OHT_BrdU_seq_Figure4a_EDF9f_replicate 1

value: Bone


title: AsiSI_U2OS_control_yH2AX_ChIP_seq_Figure1c3a_EDF3d4ab_replicate 2

value: Osteosarcoma

value: No treatment


title: MCF-7 cordycepin 1


title: LungBcells_BeO_Exp3

source_name: Lung

value: Lung

value: BeO


title: CTCF_WT_ID_rep1

description:
Library name: CTCF_WT_ID_rep1
CTCF_WT_ID_rep1_rep2.bin1.rpkm.bw
CTCF_WT_ID_rep1_rep2.peaks.bed


title: LungBcells_BeO_Exp2

value: B cells

value: FVB/NDP2 Tg mice


title: totalRNASeq_WT_UN_rep2

description:
Library name: totalRNASeq_WT_UN_rep2
counts.tpm.UN.csv
counts.normalized.UN.csv

data_processing:
Data were processed using Seq-N-Slide pipeline.
The Illumina adaptor and the T overhang were trimmed as per Illumina recommendation using TrimGalore.
Reads were aligned against the mouse reference genome (mm10) using the STAR aligner.
Read count extraction and normalization were performed using the Seq-N-Slide pipeline.
Differentially expressed genes were called using DESeq2 with an adjusted p-value of 0.05 and a fold change cutoff of 1.5
Assembly: mm10
Supplementary files format and content: counts.tpm.csv, comma-separated TPM matrix
Supplementary files format and content: counts.normalized.csv, comma-separated normalized count matrix

extract_protocol:
mESCs were dissociated using TrypLE, washed in 1X PBS, pelletted and 2.5 million cells were used for extracting RNA with RNeasy plus kit (Qiagen #74134) in each case.
RNA quality was checked in Tapestation (Agilent High Sensitivity RNA ScreenTape) and quantified by Nanodrop. 500ng were used for Total RNA libraries preparation using Illumina kit (Illumina Stranded Total RNA Prep, Ligation with Ribo-Zero Plus #20040529). Libraries were then sequenced with the Novaseq6000 Illumina technology according to the standard protocols and with around 100 million 150bp paired-end total per sample.


title: AsiSI_U2OS_control_yH2AX_ChIP_seq_Figure1c3a_EDF3d4ab_replicate 1

value: Wild-type AsiSI_U2OS


title: LungBcells_BeO_Exp1


title: AsiSI_U2OS_control_TIPIN_ChIP_seq_Figure3ab_EDF8a_replicate 2


title: totalRNASeq_WT_UN_rep1

description:
Library name: totalRNASeq_WT_UN_rep1
counts.tpm.UN.csv
counts.normalized.UN.csv


title: Spleen_CD23plus_Bcells_PBS_Exp2

value: Spleen

value: PBS


title: 43D7_2178C

first: Yu-Xin

state: United States

address: 185 Cambridge Street Simches Research Building, CPZN 5.500

department: Center for Genomic Medicine

institute: Massachusetts General Hospital

description:
Gene expression data from Fc-Angptl3 McA cells
McA_Ang3_3, biological rep3

hyb_protocol: Following fragmentation, 41 ul of cDNA were hybridized for 16 hr at 45 C on GeneChip Rat Gene 2.0 ST Array in an Affymetrix GeneChip Hybridization Oven 645. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip Scanner 3000 7G running Affymetrix Gene Command Console ver 3.2.

data_processing: The data were analyzed with using Affymetrix Expression Console ver 1.3.0.187 using Analysis algorithm RMA.

organism: Rattus norvegicus

source_name: Rat hepatoma McA cells with stable expression of Fc-Angptl5

label_protocol: Biotinylated cDNA were prepared according to the standard Affymetrix protocol from 100 ng total RNA using amplification kit WT Plus, Lot # 4264719, followed by labeling 5.5 ug cDNA using the same kit.

growth_protocol: Cells grown under DMEM media with 10% FBS at 37 oC

extract_protocol: RNeasy Mini Kit (Qiagen) according to the manufacturer’s procedures.

treatment_protocol: Stable cells were generated with the expression of Fc tag or Fc-tagged Angptl3.

value: Rat hepatoma cells

value: Fc-Angptl3 cells

tag: growth condition


title: 42D7_2178B

description:
Gene expression data from Fc-Angptl3 McA cells
McA_Ang3_2, biological rep2

source_name: Rat hepatoma McA cells with stable expression of Fc-Angptl4

value: Cells grown under DMEM media with 10% FBS at 37 oC


title: AsiSI_U2OS_control_TIPIN_ChIP_seq_Figure3ab_EDF8a_replicate 1


title: EN3

city: Wuxi

first: 文慧

last: 杨

state: 江苏 Jiangsu

address: 1800 Lihu Avenue

institute: 江南大学 Jiangnan University

data_processing:
The libraries were sequenced on an llumina Novaseq 6000 platform and 150 bp paired-end reads were generated.
Raw reads of fastq format were firstly processed using fastp and the low quality reads were removed to obtain the clean reads.
Then about 50 clean reads for each sample were retained for subsequent analyses. The clean reads were mapped to the reference genome using HISAT2
FPKM  of each gene was calculated and the read counts of each gene were obtained by HTSeq-count . PCA analysis were performed using R (v 3.2.0) to evaluate the biological duplication of samples.
Differential expression analysis was performed using the DESeq. Q value < 0.05 and foldchange > 2 or foldchange < 0.5 was set as the threshold for significantly differential expression gene (DEGs)
Assembly: The known reference gene sequences and annotation files were used as databases, and the expression abundance of the genes encoding each protein in each sample was identified by sequence similarity comparison. The number of reads aligned to the protein-coding gene in each sample was obtained using HTSEQ-COUNT software.
Supplementary files format and content: After reads ressembled by StringTie, gene structure extension and novel transcripts identification were performed by comparing the reference genome and the known annotated genes using Cuffcompare software.

source_name: mesenchymal stem cells

extract_protocol:
Total RNA was extracted from the EMSCs and NPS-EMSCs via the TRIzol reagent (Invitrogen，15596-026).
Then the libraries were constructed using VAHTS Universal V6 RNA-seq Library Prep Kit according to the manufacturer’s instructions.

value: Nasal mucosa

value: Primary cell lines

value: SD

value: NPS-EMSC


title: EN2


title: F3D7_2178F

description:
Gene expression data from Fc control McA cells
McA_Fc_3, biological rep3

source_name: Rat hepatoma McA cells with stable expression of Fc tag

value: Fc control cells


title: GFP-KLF2+ LCM, IgG, rep 2

city: Berkeley

first: Gregory

last: Barton

state: CA

department: Molecular and Cell Biology

institute: UC Berkeley

description: Library name: LCM IgG ctrl 2

data_processing:
Adapter sequence and low-quality bases were trimmed using TrimGalore (v0.6.7) and then mapped to the mouse reference genome (GRCm39) using Bowtie2 (v2.4.2). Peak analysis was performed using SEACR (v1.3) with corresponding merged control samples. The number of reads mapped to spike-in E. coli was used to normalize each sample and the top 1% of peaks are reported. IgG control peaks were used as background
Assembly: Mus musculus transcriptome GRCm38 from Ensembl
Supplementary files format and content: BED file reporting top 1% of SEACR peaks for anti-GFP vs IgG
Library strategy: CUT&Run

source_name: peritoneal cavity

extract_protocol:
CUT&RUN was performed as previously described in (Skene, Henikoff and Henikoff, 2018) with modifications.  Cells were permeabilized with wash buffer containing 0.05% w/v Digitonin (Sigma-Aldrich). Each sample was incubated at 4°C with anti-GFP (Abcam, clone 290) or rabbit IgG (Sigma) at a concentration of 50μg/mL and left to rock overnight. Permeabilized cells were washed and incubated rotating at room temperature for 10 min with pA-MNase (kindly provided by the Henikoff lab) at a concentration of 700ng/mL. After washing, cells were incubated at 0°C and MNase digestion was initiated by addition of CaCl2 to 1.3mM. After 2h, the reaction was stopped by the addition of EDTA and EGTA. Chromatin fragments were released by incubation at 37°C for 10 min. DNA was purified using DNA Clean&Concentrator-5 kit (Zymo).
Libraries were prepared using the SMART-seq2 protocol (Picelli et al., 2014), quantified by Qubit (ThermoFisher), and quality checked by Bioanalyzer (Agilent) before sequencing on an Illumina NovaSeq as paired-ends to a depth of 3-5 million.

value: peritoneal cavity

value: large cavity macrophage

value: GFP-KLF2 knock-in

tag: chip antibody

value: rabbit IgG (Sigma)


title: AsiSI_U2OS_control_TIMELESS_ChIP_seq_Figure3ab_EDF8a_replicate 2

value: Bone

tag: cell line

value: Osteosarcoma

value: No treatment


title: F2D7_2178E

description:
Gene expression data from Fc control McA cells
McA_Fc_2, biological rep2


title: GFP-KLF2+ LCM, IgG, rep 3

description: Library name: LCM IgG ctrl 3


title: EN1


title: 41D7_2178A

description:
Gene expression data from Fc-Angptl3 McA cells
McA_Ang3_1, biological rep1

source_name: Rat hepatoma McA cells with stable expression of Fc-Angptl3


title: AsiSI_U2OS_control_TIMELESS_ChIP_seq_Figure3ab_EDF8a_replicate 1

value: Wild-type AsiSI_U2OS


title: E3

value: EMSC


title: GFP-KLF2+ LCM, anti-GFP, rep 3

description: Library name: LCM anti-GFP 3

value: anti-GFP (Abcam, clone 290)


title: McA_Ang3_3_2172C

hyb_protocol: Following fragmentation, 41 ul of cDNA were hybridized for 16 hr at 45 oC on GeneChip Rat Gene 2.0 ST Array in an Affymetrix GeneChip Hybridization Oven 645. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

growth_protocol: Cells grown under OPTI-MEM media with 2% FBS at 37 oC

value: Rat hepatoma cells

value: Fc-Angptl3 cells


title: AsiSI_U2OS_control_pSIRT1_ChIP_EDF8b_Seq_replicate 2


title: F1D7_2178D

description:
Gene expression data from Fc control McA cells
McA_Fc_1, biological rep1

value: Cells grown under DMEM media with 10% FBS at 37 oC


title: E2

value: Nasal mucosa

value: Primary cell lines


title: GFP-KLF2+ LCM, anti-GFP, rep 2

description: Library name: LCM anti-GFP 2


title: McA_Ang3_2_2172B

value: Cells grown under OPTI-MEM media with 2% FBS at 37 oC


title: AsiSI_U2OS_control_pSIRT1_ChIP_EDF8b_Seq_replicate 1


title: E1

value: SD


title: GFP-KLF2+ LCM, anti-GFP, rep 1

description: Library name: LCM anti-GFP 1

value: peritoneal cavity


title: McA_Ang3_1_2172A


title: McA_Fc_3_2172F

value: Fc control cells


title: celiac ganglion of naive rat

city: Kobe

first: Hirosato

last: Kanda

state: Hyogo

address: 1-3-6 Minatojima, Chuo-Ku

country: Japan

institute: Hyogo Medical University

data_processing:
Ambient RNA counts and empty droplets were removed using CellBender (v.0.3.0). The data was outputted as an HDF5 file after processing with CellBlender.
Doublets were predicted using DoubletFinder package and identified doublets were filtered from the data.
Assembly: rn66
Supplementary files format and content: Filtered_feature_bc_matrix

source_name: whole celiac ganglion

extract_protocol:
The frozen samples were thawed in the ice-cold lysis buffer (Nuclei Extraction Buffer, Miltenyi Biotec), and were dissociated using the gentleMACS Dissociator.
The 10× Chromium libraries were prepared according to manufacturer protocol (10× Genomics) using Chromium Single Cell 3 Reagent Kits (v3.1 Chemistry Dual Index). Briefly, libraries were quantified by Qubit 1x dsDNA HS Assay Kit (Thermo Fisher Q33231) and profiled by High Sensitivity DNA D5000 (Agilent Technologies 5067-4626).

value: whole celiac ganglion

value: Sprague-Dawley

value: male


title: AsiSI_U2OS_control_MCM4_ChIP_EDF8b_Seq_replicate 2

value: Bone

value: Osteosarcoma


title: KLF4 KO AM, rep 2

description: Library name: sample 19

data_processing:
and were aligned with Kallisto v0.43.0 (Bray et al., 2016), using the “-b 100 and -t 4” options to obtain transcript abundances in transcripts per million and estimated counts. The kallisto index used during transcript quantification was built from the Mus musculus transcriptome GRCm38 from Ensembl (ftp://ftp.ensembl.org/pub/release-90/fasta/mus_musculus/cdna/s). Transcript abundances were summarized to gene level using tximport (Soneson et al., 2015).
Assembly: Mus musculus transcriptome GRCm38 from Ensembl
Supplementary files format and content: Hierarchical Data Format 5 files contains run info, abundance esimates, bootstrap estimates, and transcript length information length

source_name: lung

extract_protocol:
extraction protocol, Bone Marrow Macrophage culture and transfer On Day -7, femur, tibia and iliac bones from LysMCre/+Klf2fl/fl, LysM+/+Klf2fl/fl mice were flushed with RPMI (Gibco) and red blood cells were lysed with ACK buffer (Gibco). Cells were counted and 1M cells were plated in 10cm non-TC treated plates in 8 mL RPMI with 10mM HEPES (Gibco), 1mM Sodium Pyruvate (Gibco), 2mM Glutamax (Gibco), 100U/100µg/mLPen/Strep (Gibco), 1.7µL ß-mercaptoethanol (Fisher), 10% FCS (Gibco or Omega) (RP10+), 10% titrated M-CSF 3T3-cell conditioned laboratory-made media. On Day -3, BMM were given an additional 8mL RP10+ with 10% M-CSF. On Day -1, B6.SJL recipient mice were anesthetized with 90mg/kg ketamine + 5mg/kg xyalzine i.p. Upon achieving the appropriate anesthetic level, 5mL of warm PBS was injected slowly into the peritoneal cavity with a 23 gauge needle. Mice were gently rocked and then PBS was recovered with a 21 gauge needle. Mice were kept warm during the duration of the anesthesia and monitored until recovered. On Day 0, BMM were harvested by incubating in 5mL 4mM ETDA in PBS for 20 min in a 37 deg C incubator.  ETDA was quenched by the addition of 7mL RP10+. Cells were counted and resuspended to inject 1x106 cells per recipient mouse in 100µL of RPMI i.p. Cells were harvested by lavage on day 7, stained and sorted on live, single CD45+ cells with a BD FACS Aria Fusion (BD Biosciences). TRIzol LS (Thermo) was added to sorted cells and frozen at -80˚C for RNA extraction and library generation for RNAseq. extraction protocol, Bone Marrow Macrophage culture and transduction. On Day -1, 2.5x106 293T-GP2 retroviral producer cells were plated in 10mL DMEM with 10mM HEPES (Gibco), 1mM Sodium Pyruvate (Gibco), 2mM Glutamax (Gibco), 100U/100µg/mL Pen/Strep (Gibco), 1.7µL B-mercaptoehtanol(Fisher), 10% FCS (Gibco or Omega) (DM10+) in 10cm TC treated plates. On Day 0, 293T-GP2s (Clontech/Takara, RRID:CVCL_WI48) were transfected with 100ng MSCV plasmid (MSCV multiple cloning site IRES puroR 2A mCherry or GFP) and 10ng pVSVg plasmid (Addgene 8454) with 3µL/mL Lipofectamine 2000 (Thermo). Also on Day 0, femur, tibia and iliac bones from C57BL/6 mice were flushed with RPMI (Gibco) and red blood cells were lysed with ACK buffer (Gibco). Cells were counted and 4x106 cells were plated in 10 cm non-TC treated plates in 8 mL RPMI with 10mM HEPES (Gibco), 1mM Sodium Pyruvate (Gibco), 2mM Glutamax (Gibco), 100U/100µg/mL Penicillin/Streptomycin (Gibco), 1.7 µL B-mercaptoethanol (Fisher), 10% FCS (Gibco or Omega) (RP10+), and 10% titrated M-CSF 3T3-cell conditioned laboratory-made media. On Day 1, media was replaced on the 293T-GP2 to 8 mL. On Day 2 viral supernatants were harvested from 293T-GP2s and filtered through 0.45µM PES syringe filter. Bone marrow cultures were harvested, resuspended in 293T-GP2 supernatant supplemented with 10% M-CSF 3T3 cell media and returned to the same 10 cm plate. Media was replaced on 293T-GP2s for repeating of viral infections on Day 3. On Day 4, bone marrow cells are harvested out of plates and resuspended in 8 mL RP10+ with 10% M-CSF 3T3 supe with 5 µg/mL puromycin. Media was again replaced on Day 7 with fresh RP10+ with 10% M-CSF 3T3 supe. Cells were harvested on day 8-10 by incubating in 5mL 4mM ETDA in PBS for 20 min in a 37˚C incubator.  ETDA was quenched by the addition of 7mL RP10+. Cells were counted and 1x105 cells were resuspended in TRIzol (Thermo) and stored at -80˚C for subsequent RNA isolation. extraction protocol, Whole Lung Prep. The lungs were harvested and homogenized into a single-cell suspension with C tubes on a GentleMacs (Milltenyi) with appropriate tissue programs in 0.07mg/mL LiberaseTM and 45µg/mL DNaseI in 2mL HBSS with Ca/Mg. Tissues were incubated 20min at 37˚C and then finished on the GentleMacs. Enzymes were quenched with PBS with 2mM EDTA and 2% FCS on ice and then red blood cells were lysed with room-temperature ACK lysis buffer (Gibco) and passed through a 100μm cell strainer. Cells were sorted for live, single, CD45+CD11b-CD11c+ with a BD FACS Aria.
Total RNA was isolated from cells using TRIzol or TRIzol LS reagent (Invitrogen). Chloroform extraction was performed according to the manufacturer’s protocol. RNA was recovered from the aqueous layer using RNA Clean and Concentrator-5 kit (Zymo Research). RNA was quantified with a Qubit (Invitrogen) and the integrity was evaluated with Agilent Bioanalyzer 2100 (Agilent Technologies). Libraries were prepared using the SMART-seq2 protocol (Picelli et al., 2014). For BMM overexpressing transcription factors, samples were generated from two independent BMM transductions, but RNA was harvested, libraries were generated, and sequencing was all performed concurrently. Samples were sequenced on an Illumina NovaSeq sequencer using paired-end 50 base pair reads.

value: lung

value: alveolar macrophage

value: KLF4 KO


title: AsiSI_U2OS_control_MCM2pS139_ChIP_EDF8b_Seq_replicate 2

extract_protocol:
DNA from cell cultures was isolated size fractionated and subject to exunuclease digestion as described in Aladjem et al. Science 281 1005 1998. and Wang et al. Molecular and Cellular Biology 24:3373-86 2004. For ChipSeq DNA molecules were enriched using antibodies against proteins of interest. For BrdU seq extraction was performed using a protocol modified from Marchal et al. 2018
Samples were eluted and then purified by Monarch PCR & DNA Cleanup Kit (NEBT1030S). 100 ng of samples were used to generate the library. The kits used for the library were NEBNext Ultra II DNA Library Prep Kit for Illumina (NEB E7805S) and NEBNext Multiplex Oligos for Il-lumina (Index Primers Set 1 and Set 2) (NEB E7335S and E7500S).

value: Wild-type AsiSI_U2OS

value: No treatment


title: AsiSI_U2OS_control_MCM4_ChIP_EDF8b_Seq_replicate 1


title: HCC3

city: Shanghai

first: Qin

last: Qi

address: South Wanping road 650

institute: Shanghai University of traditional chinese medicine

data_processing:
Briefly, Paired-end reads were harvested from Illumina HiSeq 4000 sequencer, and were quality controlled by Q30. After 3’ adaptor-trimming and low quality reads removing by cutadapt software (v1.9.3)
clean reads of input libraries were aligned to reference genome (HG19) by STAR software
After that, clean reads of all libraries were aligned to the reference genome by Hisat2 software (v2.0.4). Methylated sites on RNAs (peaks) were identified by MACS software.
Differentially methylated sites were identified by diffReps
GO and Pathway enrichment analysis were performed by the differentially methylated protein coding genes
Assembly: HG19
Supplementary files format and content: excel format (Methylated_RNA_sites.mRNA) and fastq format

source_name: hepatocellular carcinoma tissue

extract_protocol:
m5C RNA immunoprecipitation was performed with the GenSeqTM m5C RNA IP Kit (GenSeq Inc., China) by following the manufacturer’s instructions
Both the input samples without immunoprecipitation and the m5C IP samples were used for RNA-seq library generation with NEBNext® Ultra II Directional RNA Library Prep Kit (New England Biolabs, Inc., USA).
The library quality was evaluated with BioAnalyzer 2100 system (Agilent Technologies, Inc., USA). Library sequencing was performed on an illumina Hiseq instrument with 150bp paired-end reads

value: hepatocellular carcinoma tissue


title: HCC4


title: KLF4 WT AM, rep 2

description: Library name: sample 18

value: KLF4 WT


title: KLF4 WT AM, rep 1

description: Library name: sample 16


title: KLF4 KO AM, rep 1

description: Library name: sample 17


title: GFP-KLF2+ LCM, IgG, rep 1

description: Library name: LCM IgG ctrl 1

value: large cavity macrophage

value: GFP-KLF2 knock-in

value: rabbit IgG (Sigma)


title: HCC2


title: McA_Fc_1_2172D

city: Boston

value: Rat hepatoma cells

value: Cells grown under OPTI-MEM media with 2% FBS at 37 oC


title: AsiSI_U2OS_control_MCM2pS139_ChIP_EDF8b_Seq_replicate 1

data_processing:
BAM files were filtered using alignmentSieve to remove reads shorter than 40bp
For peak calling the MACS2 algorithm was used.
Nascent strand reads were called by comparison to genomic DNA.
Peaks were filtered to accept the top 40% by q-value based on the raw output
Assembly: hg19
Supplementary files format and content: Bed file format showing: AsiSI TADs and random TADs AsiSI cut sites in U2OS NS-seq peaks AsiSI cut sites in LIG4-/- AID RAD21 AsiSI-HCT116 replication timing in U2OS
Supplementary files format and content: BigWig file format of BrdU-seq NS-seq and ChIP-seq


title: WT BMM, GATA6 OE, rep 2

description: Library name: sample 15

source_name: in vitro-derived bone marrow macrophage (BMM)

value: KLF2 WT

value: GATA6 RV


title: AsiSI_U2OS_control_BrdU_seq_Figure1c_EDF3d_replicate 2


title: McA_Fc_2_2172E

value: Fc control cells


title: WT BMM, GATA6 OE, rep 1

description: Library name: sample 14

value: in vitro-derived bone marrow macrophage (BMM)


title: HCC1


title: ANL5

source_name: adjacent noncancerous liver

value: adjacent noncancerous liver


title: AsiSI_U2OS_4OHT_yH2AX_ChIP_seq_Figure1c3a_EDF3d4ab_replicate 2

source_name: Bone

value: Bone

value: Osteosarcoma


title: AsiSI_U2OS_control_BrdU_seq_Figure1c_EDF3d_replicate 1


title: AsiSI_U2OS_4OHT_yH2AX_ChIP_seq_Figure1c3a_EDF3d4ab_replicate 1


title: WT BMM, KLF2 OE, rep 2

description: Library name: sample 13

value: KLF2 RV


title: ANL4


title: HCC5


title: ANL3


title: AsiSI_U2OS_4OHT_TIPIN_ChIP_seq_Figure3ab_EDF8a_replicate 2

value: Wild-type AsiSI_U2OS


title: WT BMM, EV, rep 2

description: Library name: sample 11

value: empty vector


title: WT BMM, KLF2 OE, rep 1

description: Library name: sample 12


title: ANL2


title: AsiSI_U2OS_4OHT_TIPIN_ChIP_seq_Figure3ab_EDF8a_replicate 1


title: AsiSI_U2OS_4OHT_TIMELESS_ChIP_seq_Figure3ab_EDF8a_replicate 2


title: ANL1


title: WT BMM, EV, rep 1

description: Library name: sample 10


title: KLF2 KO BMM, day 7, rep 2

description: Library name: sample 9

value: KLF2 KO

value: day 7


title: AsiSI_U2OS_4OHT_TIMELESS_ChIP_seq_Figure3ab_EDF8a_replicate 1


title: U2OS_replicate _S.merged_EDF3b

value: No treatment


title: U2OS_replicate _G1.merged_EDF3b


title: AsiSI_U2OS_4OHT_pSIRT1_ChIP_EDF8b_Seq_replicate 2


title: AsiSI_U2OS_4OHT_pSIRT1_ChIP_EDF8b_Seq_replicate 1


title: KLF2 WT BMM, day 7, rep 2

description: Library name: sample 6


title: KLF2 WT BMM, day 7, rep 3

description: Library name: sample 7