title: MATa, rad51, DSB 2h, RE-right-inverted, replicate 3

city: Lyon

first: Aurele

last: Piazza

address: 46 Allee d'Italie

country: France

institute: ENS Lyon

description: Library name: CD28

data_processing:
Reads alignement, contact filtering and PCR duplicate removal was performed using the hicstuff (v3.1.2 or 3.2.4) pipeline function with mapping quality set to 20. Hi-C contact matrices in sparse format were binned at 1 kb using hicstuff rebin function and converted to cooler format using hicstuff convert function.
Assembly: S. cerevisiae S288c-R64-2-1 (http://sgd-archive.yeastgenome.org/sequence/S288C_reference/genome_releases/S288C_reference_genome_R64-2-1_20150113.tgz) with the HML, HMR, MAT, and the rDNA repeated regions masked.
Supplementary files format and content: Hi-C contact data in cooler format binned at 1kb

organism: Saccharomyces cerevisiae

growth_protocol: Cells were grown to exponential phase in YP-lactate media containing galactose. For synchronization in G1, cells growin in YP-lactate were treated with alpha-factor for 3 hours. For S-phase cells, G1-arrested cells were washed and released in YP-lactate media containing auxin for 20 minutes. The same protocol was used for depletion of Cdc45-AID and Scc1-AID in S-phase. For cells arrested in mitosis,G1-arrested cells were released in YP-lactate media containing nocodazole for 4 hours. For cells arrested in metaphase upon activation of the DNA damage checkpoint, G1-arrested cells were released in YP-lactate media containing galactose to induce the expression of the HO gene under control of the pGAL1 promoter. It triggers formation of an unrepairable break on chr. V, and samples are collected at 2 and 4 hours post-G1 release. For break induction at MAT, exponential cultures grown in YP-lactate were supplemented to induce expression of the HO gene.

extract_protocol:
Cells were spheroplasted with 0.25 mg/mL Zymolyase 100T at 37°C for 30 minutes, crosslinked with 3 mM EGS (ethylene glycol bis(succinimidyl succinate)) at 30°C for 40 minutes at 100 rpm, and quenched with 400 mM glycine for 5 minutes at 100 rpm.
Hi-C library were generated using the Arima Hi-C+ kit following manufacturer instructions starting from 2-5x10^7 cells. DNA was fragmented in 300-400 bp DNA fragments using Covaris M220 sonicator. Illumina sequencing libraries were prepared using the Thermofisher Collibri ES DNA Library Prep Kit for Illumina Systems with UD indexes following manufacturer's instructions.

treatment_protocol: ~1.5x10^9 cells were crosslinked with 3% formaldehyde for 30 minutes at 120 rpm at room temperature, followed by quenching with 330 mM glycine for 30 minutes at 120 rpm.

value: MATa, ura3::loxP, LYS2, trp1::GAL-HO-hphMX, his3-11,15, leu2-3,112, can1-100, ade2-1, RAD5, rad51::kanMX, RE-right-inverted (RE-leftD)


title: S. pombe, 90%wt+10%ΔmiaA, YES, 30°C, rep3

status: Public on Feb 16 2026

type: SRA

city: Berlin

first: Yu

last: Sun

address: Philippstr. 13

department: Institut für Biologie

country: Germany

institute: Humboldt-Universität zu Berlin

description: Library name: S. pombe_90pwt_rep3

library_source: other

data_processing:
Read alignment was carried out using Bowtie2 with parameters -N 1 -L 6 to allow up to one mismatch per 6 nt seed. To assess reverse transcription-derived misincorporation patterns, the misincorporation rate at each nucleotide position was quantified using CoverageAnalyzer.
Assembly: Reference curation: The reference for S. pombe tRNATyr contains sequences of all unique mature tRNATyr and intron-containing tRNATyr  from GtRNAdb, and both 5’ and 3’ primer sequences were added. For E. coli, sequences of all unique tRNAs were from GtRNAdb, and primer sequences were added.
Supplementary files format and content: The processed data includes the following information: position, refbase, coverage, mm_ratio, a_mism, g_mism, t_mism, c_mism, and arrest_rate.

molecule: other

organism: Schizosaccharomyces pombe

source_name: strain: FY7385, FY7385 tit1DEL

growth_protocol: The S. pombe strains were grown in YES medium with or without 0.1 μM of queuine at 30°C and 140 rpm. The E. coli strains were grown in M9 medium at 37°C or 42°C and 180 rpm.

extract_protocol:
Extraction of small RNAs from cells: Small RNAs were extracted according to the manufacturer’s protocol (PureLink™ miRNA Isolation Kit (Invitrogen)) with some adjustments. Briefly, cells were suspended in 1 ml Trizol (Ambion). The samples were vortexed for 2 min after adding 0.2 ml chloroform and glass beads, and then were centrifuged at 16 000 rcf, 4°C for 15 min. After adding 215 µl ethanol to the upper phase, the samples were transferred to a spin cartridge and centrifuged at 12 000 rcf for 1 min. 700 µl of ethanol was added to the flow-through, and the samples were transferred to a new spin cartridge followed by centrifugation at 12 000 rcf for 1 min. After washing the cartridge with wash buffer, small RNAs were eluted with 50 µl of DEPC-treated water.
For ms2i6A modification detection, in brief, 500 ng of deacylated small RNAs were hybridized with 1 μl of 10 μM tRNATyr stem-loop primer using the following thermocycling program: 95°C for 2 min, 65°C for 30 s, followed by a gradual ramp to 4°C at 5°C per 30 s. After incubation on ice for 1 min, reverse transcription was performed in 20 μl reactions containing 100 μM dA/C/GTP, 12.5 μM dTTP, 100 nM RT-KTq I614Y enzyme, and RT buffer [50 mM Tris-HCl (pH 9.2), 16 mM (NH₄)₂SO₄, 2.5 mM MgCl₂, 0.1% Tween-20], and incubation at 55°C for 1 hour. Following reverse transcription, 5 μl of cDNA was used for PCR amplification in a 50 μl reaction containing 0.5 µM forward and reverse primers, 250 μM dNTPs, 2 mM MgCl2, 1 x Taq buffer with KCl, and 1.25 U Taq polymerase (Thermo Fisher). The thermal cycling conditions were: 96°C for 3 min; 40 cycles of 96°C for 30 s, 50°C for 45 s, and 72°C for 45 s; followed by a final extension at 72°C for 5 min. 3′-end primers included sample-specific barcodes for multiplexing. PCR products were resolved on a 2% agarose gel and purified using the QIAquick Gel Extraction Kit (Qiagen). The purified PCR products were pooled and submitted for Next-generation sequencing. For i6A modification detection, deacylated small RNAs were further treated with 0.5 M I2 for 20 min on ice. Following iodine treatment, saturated Na2S2O3 was added to the reaction mixture until the solution became colorless. Subsequently, saturated Na2CO3 was added dropwise until effervescence ceased. Upon completion of the reaction, small RNAs were purified using the RNA Clean & Concentrator Kit (ZYMO Research) according to the manufacturer’s instructions. Iodine-treated samples were then used for sequencing library preparation following the same protocol as described above for ms2i6A detection.

tag: tissue

value: strain:FY7385, FY7385 tit1DEL

tag: treatment

value: grown in YES medium at 30°C


title: hapo_newborn_cordblood_A0387

type: genomic

city: Chicago

first: Jami

middle: L

last: Josefson

state: Illinois

address: 225 E Chicago Avenue

country: USA

institute: Ann & Robert H. Lurie Children's Hospital of Chicago

description: Illumina Infinium MethylationEPIC BeadChip (850K chip)

hyb_protocol: Genome-wide methylation profiling was conducted with the Infinium MethylationEPIC BeadChip version 1.0 (Illumina, Inc., San Diego, California) array, which interrogates > 850,000 CpG sites at singlenucleotide resolution

scan_protocol: BeadChips were scanned with an Illumina iScan

data_processing:
minfi package in R environment (version 1.40.0)
processed value definition: M values transformed from beta (HAPO_GA_illumina_methylation.xlsx linked to the Series record)

label: Cy3, Cy5

molecule: genomic DNA

organism: Homo sapiens

source_name: newborn cordblood

label_protocol: Standard Illumina Protocol

extract_protocol: DNA was extracted from whole blood that was stored at -80 C and was quantified with the Qubit Fluorometer (Thermo Fisher Scientific, Waltham, Massachusetts)

tag: Sex

value: Female

value: cord clood

tag: developmental stage

value: newborn

tag: cell type

value: whole blood cells


title: Patient BL1042; H3K27ac ChIP

city: Boston

first: Elio

last: Adib

address: 20 Shattuck Street

institute: Brigham and Women's Hospital

description: Library name: BL1042_H3K27ac

library_source: genomic

data_processing:
ChIP-seq reads were aligned to the hg19 genome assembly using Burrows-Wheeler Aligner (bwa) version 0.7.15
Non-uniquely mapped/redundant reads were discarded.
Narrow peaks were called using MACS version 2.1.2 on deduplicated bam files using the following command: macs2 callpeak --SPMR -B -q 0.01 --keep-dup 1 -g hs -f BAMPE --extsize 146 --nomodel -t {treat.bam} -c {input.bam}.
Assembly: hg19
Supplementary files format and content: BigWig and peak text files (BED) were generated

source_name: Primary; Cystectomy; Muscle invasive; T4aN0MX

extract_protocol:
Using a 2 mm2 core needle, one core was extracted from frozen RP tissue blocks in the areas marked on the corresponding slide. Frozen cores were pulverized using the Covaris CryoPrep system.
DNA sequencing libraries were prepared using the ThruPLEX-FD Prep Kit (Rubicon Genomics). Libraries were sequenced on an Illumina HiSeq 4000 to generate 150-bp paired-end reads (Novogene).

tag: antibody

value: H3K27ac antibody, Diagenode C15410206


title: MATa, rad51, DSB 2h, RE-right, replicate 3

description: Library name: CD27

tag: cell line

tag: genotype

value: MATa, ura3::loxP, LYS2, trp1::GAL-HO-hphMX, his3-11,15, leu2-3,112, can1-100, ade2-1, RAD5, rad51::kanMX, RE-right (RE-leftD)


title: hapo_newborn_cordblood_A0389

value: Male


title: S. pombe, 85%wt+15%ΔmiaA, YES, 30°C, rep1

description: Library name: S. pombe_85pwt_rep1


title: Patient BL1041; H3K27ac ChIP

description: Library name: BL1041_H3K27ac

source_name: Primary; Cystectomy; Non-muscle invasive; T1


title: MATa, rad51, DSB 2h, RE-right-inverted, replicate 2

description: Library name: CD26


title: S. pombe, 90%wt+10%ΔmiaA, YES, 30°C, rep2

description: Library name: S. pombe_90pwt_rep2


title: Patient BL1040; H3K27ac ChIP

description: Library name: BL1040_H3K27ac

source_name: Primary; Bladder biopsy; Muscle invasive; T3aN0Mx


title: S. pombe, 90%wt+10%ΔmiaA, YES, 30°C, rep1

description: Library name: S. pombe_90pwt_rep1


title: MATa, rad51, DSB 2h, replicate 4

description: Library name: CD24

value: MATa, ura3::loxP, LYS2, trp1::GAL-HO-hphMX, can1-100, ade2-1, his3-11,15, leu2-3,112, RAD5, rad51::KanMX


title: Patient BL1038; H3K27ac ChIP

description: Library name: BL1038_H3K27ac

source_name: Primary; Cystectomy; Non-muscle invasive; pTisN0


title: S. pombe, 95%wt+5%ΔmiaA, YES, 30°C, rep3

description: Library name: S. pombe_95pwt_rep3


title: MATa, rad51, DSB 2h, RE-right-inverted, replicate 1

description: Library name: CD25


title: MATa, rad51, DSB 2h, RE-right, replicate 2

description: Library name: CD23


title: hapo_newborn_cordblood_A0316


title: S. pombe, 95%wt+5%ΔmiaA, YES, 30°C, rep2

description: Library name: S. pombe_95pwt_rep2


title: hapo_newborn_cordblood_A0373


title: hapo_newborn_cordblood_A0327


title: hapo_newborn_cordblood_A0334


title: Patient BL1039; H3K27ac ChIP

description: Library name: BL1039_H3K27ac

source_name: Primary; Bladder biopsy; Muscle invasive; T3N0


title: hapo_newborn_cordblood_A0305


title: MATa, rad51, DSB 2h, replicate 3

description: Library name: CD21


title: S. pombe, 95%wt+5%ΔmiaA, YES, 30°C, rep1

description: Library name: S. pombe_95pwt_rep1


title: MATa, rad51, DSB 2h, RE-right, replicate 1

description: Library name: CD22


title: Patient BL1037; H3K27ac ChIP

description: Library name: BL1037_H3K27ac

source_name: Metastasis; Lymph node biopsy; Muscle invasive; T3bN0


title: Patient BL1034; H3K27ac ChIP

description: Library name: BL1034_H3K27ac

source_name: Primary; Cystectomy; Muscle invasive; T4bN2


title: Patient BL1020; H3K27ac ChIP

description: Library name: BL1020_H3K27ac

source_name: Primary; Cystectomy; Muscle invasive; T3aN0


title: S. pombe, tit1Δ, YES, 30°C, rep2

description: Library name: S. pombe_tit1Δ_rep2

source_name: strain: FY7385  tit1DEL

value: strain:FY7385  tit1DEL

value: FY7385; leu1-32 ura4-D18 his3-D3 tit1Delta::kanMX


title: hapo_newborn_cordblood_A0301


title: MATalpha, chrIV-680258::RE-right-inverted, asynchronous

description: Library name: CD16

value: MATalpha-inc, ura3::loxP, lys2::LY, can1-100, trp1::GAL-HO-hphMX,  ade2-1, his3::pADH1-OsTIR1-9Myc::HIS3, leu2-3,112 RAD5, chrIV-845464::LY-HOcs, chrIV-680258::RE-right-inverted


title: S. pombe, tit1Δ, YES, 30°C, rep3

description: Library name: S. pombe_tit1Δ_rep3


title: MATa, chrIV-680258::RE-right-inverted, asynchronous

description: Library name: CD15

value: MATa-inc, ura3::loxP, lys2::LY, can1-100, trp1::GAL-HO-hphMX,  ade2-1, his3::pADH1-OsTIR1-9Myc::HIS3, leu2-3,112 RAD5, chrIV-845464::LY-HOcs, chrIV-680258::RE-right-inverted


title: Patient BL1009; H3K27ac ChIP

description: Library name: BL1009_H3K27ac

source_name: Primary; Cystectomy; Muscle invasive; T2N0Mx


title: hapo_newborn_cordblood_A0287


title: S. pombe, tit1Δ, YES+queuine, 30°C, rep3

description: Library name: S. pombe_tit1Δ_q_rep3

value: grown in YES medium with 0.1 μM of queuine at 30°C


title: hapo_newborn_cordblood_A0285


title: hapo_newborn_cordblood_A0281


title: MATalpha, chrIV-680258::RE-right-inverted, DSB chrIV-845464 2h

description: Library name: CD14


title: MATa, chrIV-680258::RE-right-inverted, DSB chrIV-845464 2h

description: Library name: CD13


title: S. pombe, tit1Δ, YES+queuine, 30°C, rep2

description: Library name: S. pombe_tit1Δ_q_rep2


title: hapo_newborn_cordblood_A0276


title: Wild_Type_Jurkat_Cells_Untreated_3

city: Omaha

first: Kate

last: Hyde

state: NE

address: 985802 Nebraska Medical Center

institute: University of Nebraska Medical Center

description: Library name: UT3

library_source: transcriptomic

data_processing:
The original FASTQ format reads were trimmed by fqtrim tool (https://ccb.jhu.edu/software/fqtrim) to remove adapters, terminal unknown bases (Ns) and low quality 3’ regions (Phred score < 30).
For quality control (QC), the low quality 3’ regions were trimmed and only high quality reads with Phred score >=30 were retained.
The QC passed trimmed fastq files were mapped to hg38 reference genome using STAR v2.7.0f aligner and RSEM v1.2.31 to quantifiy the mapped reads
Assembly: hg38
Supplementary files format and content: Tab-delimited text files include raw counts for each Sample
Supplementary files format and content: Tab-delimited text file with raw gene counts for all genes and all samples

molecule: total RNA

source_name: immune cells

growth_protocol: Jurkat cells and CXCR4 KO Jurkat cells were maintained at 500,000 cells/ml of media (1%Pen/Strep/L-glutamine, 10% FBS, 89% ATCC RPMI 1640). 1 million cells were counted and plated in 2ml of media in a 6 well plate, forming one replicate for one condition. Each condition has 3 replicates. CXCR4 KO cells were generated by using the gRNA sequence "GTTCCAGTTTCAGCACATCA" from Liu et al., 2017,  Cell Biosci, PMID: 28904745.

extract_protocol:
24 hours after plating, cells were then harvested. RNA was isolated using TRIzol Reagent and precipitated using isopropanol. RNA was then washed with 75% ethanol and resuspended in RNAse free water. Samples were stored at -80 prior to library construction.
Universal RNA-Seq with NuQuant®+UDI library kit from Tecan Genomics following recommended procedures (Tecan Genomics, Inc., Redwood City, CA)

treatment_protocol: To compare PAMD-Ch17 treated Jurkat cells (PAMD-Ch17 Treated Jurkat Cells 0.6uM) to wild type Jurkat cells (Wild Type Jurkat Cells Untreated), cells were treated with either 0.6uM of PAMD-Ch17 or vehicle for 24 hours. For compaing CXCR4 KO cells to wild type cells, no treatments were performed.

value: immune cells

value: Jurkat

value: human T-cell acute lymphoblastic leukemia


title: Patient BL1010; H3K27ac ChIP

description: Library name: BL1010_H3K27ac

source_name: Primary; Cystectomy; Muscle invasive; T2aN0Mx


title: Patient BL1007; H3K27ac ChIP

description: Library name: BL1007_H3K27ac

source_name: Metastasis; Lymph node biopsy; Muscle invasive; T3aN0Mx


title: S. pombe, tit1Δ, YES, 30°C, rep1

description: Library name: S. pombe_tit1Δ_rep1

value: grown in YES medium at 30°C


title: H23+ADAR1 KD

city: Los Angeles

first: Matthew

last: Krieger

state: CA

address: 10833 Le Conte Avenue

institute: University of California Los Angeles

description:
Library name: Sample 17
mt-h23_adar_kd.bam

data_processing:
Basecalled reads were aligned against the human mitochondrial genome (NCBI Reference Sequence: NC_012920.1) for PC9, H23, H1437 using Minimap2 version 2.17-r941 with the parameters -t 12 -a. Alignments were sorted and indexed using Samtools v1.10 for reference entire reference genome.  BED files were generated from the BAM files using bedtools bamtobed.
Histograms were generated by separating reads in the BED files by strand and normalizing the coverage to the genomic maximum for that sample. Bar graphs were generated by counting all the reads that unambiguously aligned using the FeatureCounts function in the Rsubread package with the following parameters: isGTFAnnotationFile=TRUE, GTF.featureType=c("gene"), GTF.attrType="Name", isLongRead=TRUE, countMultiMappingReads=FALSE, allowMultiOverlap=TRUE, minOverlap=6, useMetaFeatures=FALSE, nthreads=8. Percentages from FeatureCounts for all samples were then used in the creation of bar graphs.
Assembly: NC_012920.1
Supplementary files format and content: Feature count analysis and bam counts

molecule: polyA RNA

extract_protocol:
Cells were seeded to 15cm plates and lysed in NP-40 lysis buffer (Invitrogen) for 30 minutes on ice. Protein A/G beads (Invitrogen) were incubated with J2 antibody overnight at 4°C. Conjugated beads with J2 antibody were then incubated with the lysates for 2 hours at 4°C. The beads were then washed with high-salt PBS buffer (1x PBS, 0.1% Tween, 1M NaCl) once, followed by two washes with a low salt PBS buffer (1x PBS, 0.1% Tween, 0.5M NaCl). The immunoprecipitated samples were eluted from the beads using 1mg/ml Proteinase K (Thermo Fisher) in NP-40 lysis buffer.  The dsRNA was then polyadenylated using the methods provided by E. coli Poly A polymerase ( cat#: M0276L).
PCR-cDNA libraries were prepared from ~100 ng of in vitro polyadenylated dsRNAs using the PCR-cDNA sequencing kit from Oxford Nanopore (ONT, catalog #: SQK-PCB114.24) and pooled as per the manufacturer's instructions. Sequencing was performed using R10.4.1 flow cells on a MinION Mk1B device and sequenced for 24 hours. Basecalling was performed using Dorado (version 7.9.8).

value: Non-Small Cell Lung Carcinoma

value: ADAR1 KD


title: hapo_newborn_cordblood_A0292

value: Female

value: cord clood

value: newborn


title: hapo_newborn_cordblood_A0268

value: whole blood cells


title: S. pombe, tit1Δ, YES+queuine, 30°C, rep1

description: Library name: S. pombe_tit1Δ_q_rep1


title: MATalpha, chrIV-680258::RE-inverted, asynchronous

description: Library name: CD4

value: MATalpha-inc, ura3::loxP, lys2::LY, can1-100, trp1::GAL-HO-hphMX,  ade2-1, his3::pADH1-OsTIR1-9Myc::HIS3, leu2-3,112 RAD5, chrIV-845464::LY-HOcs, chrIV-680258::RE-inverted


title: H23, Rep 5

description:
Library name: Sample 16
mt-h23.bam


title: S. pombe, wt, YES, 30°C, rep3

description: Library name: S. pombe_wt_rep3

source_name: strain: FY7385


title: S. pombe, wt, YES, 30°C, rep2

description: Library name: S. pombe_wt_rep2


title: MATa, chrIV-680258::RE-right, DSB chrV 2h

description: Library name: CD11

value: MATa-inc, ura3::LY-HOcs, lys2::LY, can1-100, trp1::GAL-HO-hphMX,  ade2-1, his3::pADH1-OsTIR1-9Myc::HIS3, leu2-3,112 RAD5, chrIV-680258::RE-right


title: MATa, chrIV-680258::RE-inverted, asynchronous

description: Library name: CD3

value: MATa-inc, ura3::loxP, lys2::LY, can1-100, trp1::GAL-HO-hphMX,  ade2-1, his3::pADH1-OsTIR1-9Myc::HIS3, leu2-3,112 RAD5, chrIV-845464::LY-HOcs, chrIV-680258::RE-inverted


title: PC9+IMT1

description:
Library name: Sample 15
pc9_imt.bam


title: S. pombe, wt, YES, 30°C, rep1

description: Library name: S. pombe_wt_rep1


title: MATalpha, chrIV-680258::RE-right, DSB chrIV-845464 2h

description: Library name: CD2

value: MATalpha-inc, ura3::loxP, lys2::LY, can1-100, trp1::GAL-HO-hphMX,  ade2-1, his3::pADH1-OsTIR1-9Myc::HIS3, leu2-3,112 RAD5, chrIV-845464::LY-HOcs, chrIV-680258::RE-right


title: S. pombe, wt, YES+queuine, 30°C, rep3

description: Library name: S. pombe_wt_q_rep3


title: PC9, Rep 4

description:
Library name: Sample 14
pc9.bam


title: hapo_newborn_cordblood_A0254


title: hapo_newborn_cordblood_A0245


title: H23+IMT1

description:
Library name: Sample 13
h23_imt.bam


title: hapo_newborn_cordblood_A0235

value: Male


title: MATa, chrIV-680258::RE-right, DSB chrIV-845464 2h

description: Library name: CD1

value: MATa-inc, ura3::loxP, lys2::LY, can1-100, trp1::GAL-HO-hphMX,  ade2-1, his3::pADH1-OsTIR1-9Myc::HIS3, leu2-3,112 RAD5, chrIV-845464::LY-HOcs, chrIV-680258::RE-right


title: MATa, rad51, DSB 2h, replicate 2

description: Library name: AD782

value: MATa, ura3::loxP, LYS2, trp1::GAL-HO-hphMX, can1-100, ade2-1, his3-11,15, leu2-3,112, RAD5, rad51::KanMX


title: S. pombe, wt, YES+queuine, 30°C, rep1

description: Library name: S. pombe_wt_q_rep1

value: grown in YES medium with 0.1 μM of queuine at 30°C


title: H1437+IMT1

description:
Library name: Sample 11
h1437_imt.bam


title: S. pombe, wt, YES+queuine, 30°C, rep2

description: Library name: S. pombe_wt_q_rep2


title: H23, Rep 4

description:
Library name: Sample 12
h23.bam


title: hapo_newborn_cordblood_A0233


title: hapo_newborn_cordblood_A0232


title: hapo_newborn_cordblood_A0247


title: H1437, Rep 4

description:
Library name: Sample 10
h1437.bam


title: MATa, metaphase-arrest (DSB chr. V 4h), replicate 4

description: Library name: AD337

value: MATa-inc, ura3::LY-HOcs, lys2::LY, trp1::GAL-HO-hphMX, his3-11,15, can1-100, leu2-3,112, ade2-1, RAD5


title: K-A-DiCre ER, rep1

city: Pune

first: Krishanpal

last: Karmodiya

state: Maharashtra

address: IISER PUNE, Dr. Homi Bhabha Road, Pashan

country: India

institute: IISER Pune

description: Library name: Sample 3

data_processing:
Paired-end HiC library reads were processed (i.e., mapping, filtering, and pairing, and normalization) using Juicer 1.22.01.
Assembly: PlasmoDB v66
Supplementary files format and content: The HiC contact map in a matrix format (.hic files)

organism: Plasmodium falciparum

source_name: Plasmodium falciparum

growth_protocol: All the lines were maintained in 5% hematocrit in RPMI 1640 medium supplemented with 25 mM HEPES, 450 µM hypoxanthine, 24 mM sodium bicarbonate, and 0.5% AlbuMAX II. The parasites were incubated at 37 °C in an atmosphere of 3% oxygen, 4% carbon dioxide, and 93% nitrogen.

extract_protocol:
The cells were crosslinked with 2% formaldehyde and harvested using 0.015% saponin. For the HiC protcol Arima genomics HiC kit was used.
Followed the protocol of Arima genomics HiC library preparation kit.

treatment_protocol: Double synchronized the PfHP1 mutant lines in the 3D7/IG5/DiCre background using 5% sorbitol. The early ring parasites treated for 4 hours with 100nM rapamycin. The parasites were harvested after 48 hours in next cycle.

tag: strain

value: whole organism

tag: time point

value: early ring


title: MATa, S-phase, replicate 4

description: Library name: AD779

value: MATa-inc, ura3::LY-HOcs, lys2::LY, can1::HIS3-LY-Pad, trp1::GAL-HO-hphMX, his3::OsTIR1-9Myc::HIS3, ade2-1, leu2-3,112, RAD5


title: hapo_newborn_cordblood_A0230


title: PC9, Rep 3

description:
Library name: Sample 9
pc9_2.bam

value: Non-Small Cell Lung Carcinoma


title: hapo_newborn_cordblood_A0224


title: E-A-DiCre ER, rep1

description: Library name: Sample 2


title: PC9, Rep 2

description:
Library name: Sample 8
pc9_1.bam


title: PC9, Rep 1

description:
Library name: Sample 7
pc9.sorted.bam


title: hapo_newborn_cordblood_A0220

value: Female


title: MATa, metaphase-arrest (DSB chr. V 2h), replicate 3

description: Library name: AD336


title: MATa, metaphase-arrest (DSB chr. V 4h), replicate 2

description: Library name: AD285

value: MATa-inc, ura3::LY-32x65bp-HOcs, lys2::LY, trp1::GAL-HO-hphMX, his3-11,15, leu2-3,112, can1-100, ade2-1, RAD5


title: L-D-DiCre ER rep3

description:
Library name: Samples 17
Directional RNA-seq

data_processing:
Trimming and QC of the raw data was done using trim galore. The trimmed data was aligned against the P. falciparum reference genome (PlasmoDB_v53) using HISAT2. The aligned files were sorted using samtools which gave bam output files. Raw count files are obtained from the htseq analysis. For the directional RNA sequencing analysis deeptools were used for generating bigwig files for the + strand and -strand.
Assembly: PlasmoDB_v53
Supplementary files format and content: Raw count files in tabular form

extract_protocol:
Ring stage (~10 hours post infection, hpi) parasites were double sorbitol synchronized by 5% sorbitol. The samples were spun down and harvested using 0.015% saponin. The cell pellet was resuspended in Trizol and isolated by Isoprapanol precipitation.
The isolated RNA was subjected to polyA enrichment using NEB polyA mRNA magnetic isolation module (E7490). The library preparation was done using the NEB Ultra II RNA kit (E7770). And  for the DiCre line samples NEBNext Ultra™ II Directional RNA Library Prep with Sample Purification Beads (E7765) was used for the library preparation. The library quality was tested using a DNA high sensitivity kit in Agilent bioanalyzer. The library amount was estimated using Qubit DNA high sensitivity kit. A final pool of 1.7 pM library was loaded on a 75 cycle High output illumina sequencing kit.

value: Plasmodium falciparum


title: H23, Rep 3

description:
Library name: Sample 6
h23_2.bam


title: hapo_newborn_cordblood_A0216

value: cord clood

value: newborn

value: whole blood cells


title: hapo_newborn_cordblood_A0203


title: MATa, metaphase-arrest (DSB 4h) + nocodazole, replicate 2

description: Library name: AD273


title: MATa, metaphase-arrest (DSB chr. V 2h), replicate 1

description: Library name: AD284


title: H23, Rep 2

description:
Library name: Sample 5
h23_1.bam


title: hapo_newborn_cordblood_A0202


title: L-D-DiCre ER rep1

description:
Library name: Samples 15
Directional RNA-seq


title: W-A-DiCre ER rep3

description:
Library name: Samples 14
Directional RNA-seq


title: H23, Rep 1

description:
Library name: Sample 4
h23.sorted.bam


title: Hi-C asynchronous, MATa cells, YEP+lactate+galactose replicate 2

data_processing:
Reads alignement, contact filtering and PCR duplicate removal was performed using the hicstuff (v3.1.2) pipeline function with mapping quality set to 20. Hi-C contact matrices in sparse format were binned at 1 kb using hicstuff rebin function and converted to cooler format using hicstuff convert function.
Assembly: S. cerevisiae S288c-R64-2-1 (http://sgd-archive.yeastgenome.org/sequence/S288C_reference/genome_releases/S288C_reference_genome_R64-2-1_20150113.tgz) with the HML, HMR, MAT, and the rDNA repeated regions masked.
Supplementary files format and content: Hi-C and unfiltered ssHi-C contact data in cooler format binned at 1kb

extract_protocol:
Cells were spheroplasted with 0.25 mg/mL Zymolyase 100T at 37°C for 30 minutes, crosslinked with 3 mM EGS (ethylene glycol bis(succinimidyl succinate)) at 30°C for 40 minutes at 100 rpm, and quenched with 400 mM glycine for 5 minutes at 100 rpm.
Hi-C library were generated using the Arima Hi-C+ kit following manufacturer instructions starting from 2-5x10^7 cells.
DNA was fragmented in 300-400 bp DNA fragments using Covaris M220 sonicator. Illumina sequencing libraries were prepared using the Thermofisher Collibri ES DNA Library Prep Kit for Illumina Systems with UD indexes following manufacturer's instructions.

value: MATa-inc, ura3::loxP, lys2::URA3, trp1::GAL-HO-hphMX, his3-11,15, leu2-3,112, can1-100, ade2-1, RAD5


title: hapo_newborn_cordblood_A0197


title: W-A-DiCre ER rep2

description:
Library name: Samples 13
Directional RNA-seq


title: H1437, Rep 3

description:
Library name: Sample 3
h1437_2.bam


title: Hi-C asynchronous, MATa cells, lactate + Gal 10'


title: W-A-DiCre ER rep1

description:
Library name: Samples 12
Directional RNA-seq


title: hapo_newborn_cordblood_A0188


title: H1437, Rep 2

description:
Library name: Sample 2
h1437_1.bam


title: Hi-C asynchronous, MATa cells, lactate + Glu 10'


title: H1437, Rep 1

description:
Library name: Sample 1
h1437.sorted.bam


title: K-A-DiCre ER rep3

description:
Library name: Samples 11
Directional RNA-seq


title: hapo_newborn_cordblood_A0185


title: Wild_Type_Jurkat_Cells_Untreated_2

description: Library name: UT2

value: immune cells

value: Jurkat

value: human T-cell acute lymphoblastic leukemia


title: Hi-C asynchronous, MATa cells, lactate


title: hapo_newborn_cordblood_A0179

value: Male


title: K-A-DiCre ER rep2

description:
Library name: Samples 10
Directional RNA-seq


title: Hi-C asynchronous chrIV-680258::RE(right), MATalpha cells

value: MATalpha, ura3::loxP, chrIV-845464::LY-HOcs, lys2::LY, trp1::GAL-HO-hphMX, his3::pADH1-OsTIR1-9Myc::HIS3, leu2-3,112, can1-100, ade2-1, RAD5, chrIV-REright-680kb


title: K-A-DiCre ER rep1

description:
Library name: Samples 9
Directional RNA-seq


title: hapo_newborn_cordblood_A0178


title: Wild_Type_Jurkat_Cells_Untreated_1

description: Library name: UT1


title: Hi-C asynchronous chrIV-680258::RE(right), MATa cells

value: MATa, ura3::loxP, chrIV-845464::LY-HOcs, lys2::LY, trp1::GAL-HO-hphMX, his3::pADH1-OsTIR1-9Myc::HIS3, leu2-3,112, can1-100, ade2-1, RAD5, chrIV-REright-680kb


title: E-A-DiCre ER rep3

description:
Library name: Samples 8
Directional RNA-seq


title: Hi-C asynchronous chrIV-680258::RE(full), MATalpha cells

value: MATalpha-inc, ura3::loxP, chrIV-845464::LY-HOcs, lys2::LY, trp1::GAL-HO-hphMX, his3::pADH1-OsTIR1-9Myc::HIS3, leu2-3,112, can1-100, ade2-1, RAD5, chrIV-REfull-680kb


title: Patient BL1046; H3K4me2 ChIP

description: Library name: BL1046_H3K4me2

source_name: Primary; Cystectomy; Muscle invasive; T3bN2

value: H3K4me2 antibody, Millipore C07030


title: hapo_newborn_cordblood_A0172

source_name: newborn cordblood


title: PAMD-Ch17_Treated_Jurkat_Cells_0.6uM_3

description: Library name: T3

value: 0.6uM of PAMD-Ch17


title: PAMD-Ch17_Treated_Jurkat_Cells_0.6uM_2

description: Library name: T2


title: Hi-C asynchronous chrIV-680258::RE(full), MATa cells

value: MATa-inc, ura3::loxP, chrIV-845464::LY-HOcs, lys2::LY, trp1::GAL-HO-hphMX, his3::pADH1-OsTIR1-9Myc::HIS3, leu2-3,112, can1-100, ade2-1, RAD5, chrIV-REfull-680kb


title: hapo_newborn_cordblood_A0165


title: E-A-DiCre ER rep2

description:
Library name: Samples 7
Directional RNA-seq

value: early ring


title: E-A-DiCre ER rep1

description:
Library name: Samples 6
Directional RNA-seq


title: PAMD-Ch17_Treated_Jurkat_Cells_0.6uM_1

description: Library name: T1


title: hapo_newborn_cordblood_A0154

value: Female


title: Hi-C asynchronous, MATa cells, CEN2 inactivation (Gal+Glu 10')

value: MATa, CEN2::pGal1-CEN2-URA3Kl ade2-1 can1-100 his3-11,15 leu2-3,112 lys2 met17 trp1-1 ura3-1 RAD5


title: Wild_Type_Jurkat_Cells_3

description: Library name: JN_3


title: PfHP1-DiCre ER rep3

description:
Library name: Samples 5
Directional RNA-seq

value: Plasmodium falciparum


title: hapo_newborn_cordblood_A0153

value: cord clood

value: newborn


title: hapo_newborn_cordblood_A0151

value: whole blood cells


title: Hi-C asynchronous, MATa cells, CEN3 inactivation (Gal)

value: MATa, ade2-1; can1-100; his3; leu2; lys2; met15; trp1; ura3, CEN3::pGAL1-CEN3-URA3-Klactis; rad5-535


title: Wild_Type_Jurkat_Cells_2

description: Library name: JN_2

value: immune cells

value: Jurkat


title: PfHP1-DiCre ER rep1

description:
Library name: Samples 3
Directional RNA-seq


title: Wild_Type_Jurkat_Cells_1

description: Library name: JN_1

value: human T-cell acute lymphoblastic leukemia


title: Hi-C asynchronous, MATa cells, CEN3 inactivation (Gal+Glu 10')


title: CXCR4_KO2_3

description: Library name: 23DNSCER_3


title: 3D7 LR rep2

description:
Library name: Samples 2
non-directional RNA-seq

value: late ring


title: hapo_newborn_cordblood_A0147

value: Male


title: CXCR4_KO2_2

description: Library name: 23DNSCER_2


title: 3D7 LR rep1

description:
Library name: Samples 1
non-directional RNA-seq


title: Hi-C S-phase, MATa cells, Scc1-depleted

value: MATa-inc, ura3::LY-HOcs, lys2::LY, trp1::GAL-HO-hphMX, can1-100, ade2-1, leu2-3,112, his3::OsTIR1-9Myc::HIS3, SCC1-Pk3-AID::KMX, RAD5

value: Auxin


title: PfHP1-DiCre ER rep2

description:
Library name: Samples 4
Directional RNA-seq


title: Hi-C S-phase, MATa cells, Cdc45-depleted

value: MATa-inc, ura3::LY-Hocs, lys2::LY, trp1::GAL-HO-hphMX,can1::HIS3-L0.6kb, his3::pADH1-OsTIR1-9Myc::HIS3, ade2-1, leu2-3,112, RAD5, CDC45-FlagX5-mini-AID::KanMx4


title: hapo_newborn_cordblood_A0148

description: Illumina Infinium MethylationEPIC BeadChip (850K chip)


title: hapo_newborn_cordblood_A0139


title: CXCR4_KO2_1

description: Library name: 23DNSCER_1


title: hapo_newborn_cordblood_A0124


title: cg6 ER L-D-GFP Input

description: Library name: Sample 20

data_processing:
Trimming and quality control (QC) of the raw data was done using Trim Galore. The trimmed data was aligned against the P. falciparum reference genome (PlasmoDB_v53) using Bowtie2. The aligned files were sorted using samtools which gave bam output files. The peaks were called using MACS2, using the input files as control. The normalized bedgraph files were loaded on IGV (Integrative Genomes Browser) to visualize the enrichment pattern. For the mean tag density and gene body profile seqMINER was used. The heatmaps were generated using Morpheus, Broad Institute.
Assembly: PlasmoDB_v53
Supplementary files format and content: bedgraph (.bedgraph)

source_name: whole organism

extract_protocol:
Cells were crosslinked with 1% formaldehyde and quenched with 2mM Glycine. The samples were sonicated in M220 Covaris sonicator and pulled down using respective antibodies
The sequencing library was prepared using the NEB Ultra II DNA kit (E7645), following the manufacturer's instructions. The prepared library was estimated for the average size using Agilent bioanalyzer or tapestation and for the amount using Qubit fluorometer. A final amount of 1.3 pM library was loaded from the multiplexed pool of all libraries.

treatment_protocol: The ectopic mutant expressing lines were continuously maintained in the 2.5mM  glucosamine from the day of transfection. For the harvesting and expression of the mutants the glucosamine was removed and 1.25 μM Sheild-1 was added to the culture.

value: whole organism

tag: chip antibody

tag: Stage


title: cg6 ER W-A-GFP Input

description: Library name: Sample 19

value: early ring


title: 28hpf_sox17N_ATAC_rep1

city: Coventry

first: Andrew

last: Nelson

address: Gibbet Hill Road

department: School of Life Sciences

country: United Kingdom

institute: University of Warwick

description: Library name: 28hpf_sox17N_ATAC_rep1

data_processing:
ATAC-seq: Reads were trimmed from the 3’ end to a uniform 75 bp using seqtk so that mapping of reads was not impacted by sequencing read length. Adapter sequences were trimmed using Trimmomatic version 0.39 (Bolger et al. 2014). Data quality control and confirmation of adapter removal was performed using FastQC (Andrews 2010). Reads were aligned to the genome reference consortium zebrafish build 11 (GRCz11v97) using Bowtie2 (Langmead and Salzberg 2012) using “Very sensitive” and 2 kb maximum fragment length for paired-end alignments. Samtools (Li et al. 2009) was also used to filter out reads that mapped to the mitochondrial genome, duplicated reads and low-quality reads with a MAPQ score < 22.
Assembly: danRer11
Supplementary files format and content: ATAC-seq processed data are CPM normalised bigWig files of ATAC-seq profiles with biological replicates merged, produced using deepTools bamCoverage.

organism: Danio rerio

source_name: sox17-negative lineages

growth_protocol: Embyos were maintained in E3 embryo medium at 28.5 degrees celcius

extract_protocol:
Cell populations were isolated according to fluorescence profiles using a BD FACSAria Fusion flow cytometer.  ATAC-seq libraries were produced according to "Corces MR, Trevino AE, Hamilton EG, et al. (2017) An improved ATAC-seq protocol reduces background and enables interrogation of frozen tissues. Nature methods 14: 959".
ATAC-seq libraries were produced according to "Corces MR, Trevino AE, Hamilton EG, et al. (2017) An improved ATAC-seq protocol reduces background and enables interrogation of frozen tissues. Nature methods 14: 959".

value: sox17-negative lineages

value: AB

value: FACS isolated


title: Hi-C S-phase,  MATa cells, replicate 1

value: MATa-inc, ura3::LY-HOcs, lys2::LY, can1::HIS3-LY-Pad, trp1::GAL-HO-hphMX, his3::OsTIR1-9Myc::HIS3, ade2-1, leu2-3,112, RAD5


title: hapo_newborn_cordblood_A0116

value: Female

value: cord clood

value: newborn


title: Hi-C asynchronous, MATa cells, YEP+lactate+galactose replicate 4

value: MATa-inc, ura3::loxP, lys2::URA3, trp1::GAL-HO-hphMX, his3-11,15, leu2-3,112, can1-100, ade2-1, RAD5


title: 28hpf_sox17M_ATAC_rep1

description: Library name: 28hpf_sox17M_ATAC_rep1

source_name: hematovascular

value: hematovascular


title: cg6 ER K-A-GFP Input

description: Library name: Sample 18


title: hapo_newborn_cordblood_A0112

value: whole blood cells


title: Hi-C metaphase-arrest (DSB 2h), MATa cells, Scc1-depleted

value: MATa-inc, ura3::LY-HOcs, lys2::LY, trp1::GAL-HO-hphMX, can1-100, his3-11,15, ade2-1, LEU2, his3::OsTIR1-9Myc::HIS3, SCC1-Pk3-AID::KMX, RAD5


title: 28hpf_sox17E_ATAC_rep1

description: Library name: 28hpf_sox17E_ATAC_rep1

source_name: endoderm-enriched

value: endoderm-enriched


title: cg6 ER PfHP1-GFP Input

description: Library name: Sample 17


title: Hi-C rad51D, DSB at MATa 4h

value: MATa, ura3::loxP, lys2::LY, trp1::GAL-HO-hphMX, can1-100, ade2-1, his3-11,15, leu2-3,112, RAD5, rad51::KMX


title: hapo_newborn_cordblood_A0106


title: CTCF_07-729_Bruce-4_rep2

city: New York

first: UkJin

last: Lee

state: NY

address: 413 E 69th St

department: Sanford I. Weill Department of Medicine

institute: Weill Cornell Medicine

description:
Library name: CTCF_07-729_Bruce-4_rep2
Cornell Biotechnology Resource Center EpiGenomics Core

data_processing:
Adapters were trimmed off from paired-end reads using bbduk.sh (v2.4.5) with the following option: ktrim=r ref=adapters rcomp=t tpe=t tbo=t hdist=1 mink=11.
Filtered reads were aligned to the mouse genome (mm10) using bowtie2 (v2.4.5) with the options --local --sensitive-local --no-unal.
PCR duplicates were removed using MarkDuplicates module from picard (v2.27.4) with the following option: --VALIDATION_STRINGENCY=LENIENT.
Bedtools (v2.30.0) was used to remove reads overlapping with blacklist region and convert data to ‘bedgraph’ format. BedGraphToBigWig module from kentUtil was used to convert data to ‘bigWig’ format. Peaks were called with macs2 callpeak with ‘--call-summits’ option.
Assembly: mm10
Supplementary files format and content: ".bigWig" for ChIP-exo tracks. ".bed" for narrow peaks.

organism: Mus musculus

growth_protocol: Bruce-4 cells were cultured at 37˚C on gelatinized plate in serum/2i/LIF medium. Cells were harvested by treating with Trypsin-EDTA for 3 min, washed with PBS, and centrifuged at 300 × g for 5 min at 4˚C. 10,000,000 cells per replicate were fixed with 1% w/v formaldehyde for 10 min at room temperature (RT) on a platform shaker, followed by quenching with 125 mM glycine for 5 minutes under the same conditions. Crosslinked cells were centrifuged at 500 × g for 5 min at 4˚C and were washed twice with ice-cold PBS. After the final wash and centrifuge, the pellet was snap-frozen before extraction.

extract_protocol:
Frozen cell pellets were processed as described previously (Rossi M.J., Nat Commun, 2018, PMID: 30030442).
Libraries were generated with ChIP-exo v6.1 protocol (Rossi M.J., Nat Commun, 2018, PMID: 30030442).

value: Mouse embryonic stem cell

value: CTCF antibody (MilliporeSigma, 07-729)


title: 3D7 LR Input

description: Library name: Sample 16

value: whole organism

value: late ring


title: hapo_newborn_cordblood_A0094


title: Hi-C rad51D, DSB at MATalpha 4h

value: MATalpha, ura3::loxP, lys2::LY, trp1::GAL-HO-hphMX, can1-100, ade2-1, his3-11,15, leu2-3,112, RAD5, rad51::KMX


title: 3T3-L1, SRF, ChIP-seq, TGFβ1-treated

city: Indianapolis

first: Jisun

last: So

state: IN

address: 635 Barnhill Drive

department: Biochemistry and Molecular Biology

institute: Indiana University School of Medicine

description: Library name: Sample 2

data_processing:
For Samples 1-2 (ChIP-seq): Sequence reads were trimmed with fastp and aligned to the mm10 genome using Bowtie2. PCR duplicates and low-quality reads were removed with Samtools. Peak were called with MACS2, merged using Bedops across samples, and quantified with featureCounts. For Samples 3-26 (RNA-seq): Sequence reads were trimmed with fastp and aligned to the mm10 genome using STAR. Filtered reads were assigned to transcriptome and quantified by featureCounts. For Samples 27-30 (snRNA-seq): Sequence reads were processed with Cell Ranger v7.1.0 for demultiplexing, alignment, read filtering, and barcode and UMI counting. Ambient RNA was removed using CellBender v0.3.0.
Assembly: mm10
Supplementary files format and content: txt (raw counts for each sample of ChIP-seq or bulk RNA-seq); tsv (lists of cell barcodes and genes for each sample of snRNA-seq); mtx (expression count matrix for each sample of snRNA-seq)

growth_protocol: For Samples 1-2: 3T3-L1 preadipocytes were maintained in DMEM supplemented with 10% bovine calf serum and 1% penicillin–streptomycin, and differentiated upon confluence with DMEM containing 10% fetal bovine serum (FBS), 5 μg/mL insulin, 500 μM isobutylmethylxanthine, and 1 μM dexamethasone for 48 hours. Cells were then maintained in DMEM supplemented with 10% FBS and 5 μg/mL insulin for another 2 days, followed by maintenance in DMEM with 10% FBS alone for the remainder of the culture period.

extract_protocol:
For Samples 1-2 (ChIP-seq): Cells were homogenized in chilled Douncers and immediatelly cross-linked  with 1% PFA (and quenched with glycine). Chromatin was sheared using a Covaris E220 sonicator, and the fragmented chromatin was incubated with SRF antibody (Santa Cruz, sc-335X) overnight at 4C and immunoprecipitated using protein A/G dynabeads. Following elution, chromatin was reverse cross-linked and purified using AMPure XP beads. For Samples 3-26 (RNA-seq): RNA was extracted from adipose tissue using TRIzol and then purified by on-column DNA digestion. For Samples 27-30 (snRNA-seq): Nuclei were isolated from frozen adipose tissue by pulverizing in liquid nitrogen and homogenizing in chilled Douncers. Next, Hoechst-stained nucleus suspension was subject to sorting to remove debris and multiplets. The nucleus suspension was loaded onto the 10x Genomics Chromium Controller.
For Samples 1-2 (ChIP-seq): Purified DNA was subject to end repair and phosphorylation using the End-It DNA End-Repair Kit, followed by A-tailing with Klenow Fragment and adaptor ligation with Quick Ligase. Then, the libraries were PCR amplified with PfuUltra II Hotstart PCR Master Mix. The DNA fragments were selected based on size using E-Gel EX Agarose Gels and then extracted with MinElute Gel Extraction Kit. For Samples 3-26 (RNA-seq): Extracted RNA (100ng) was processed by NEBNext rRNA Depletion Kit for removing ribosomal RNA. Then, RNA was converted to cDNA using Maxima Reverse Transcriptas and NEBNext mRNA Second Strand Synthesis Kit following manufacturer's protocols. After purification of cDNA based on size, sequencing libraries were generated using Nextera XT DNA Library Preparation Kit and subsequent PCR amplification. For Samples 27-30 (snRNA-seq): Libraries were prepared using the Chromium Single Cell 3' Reagent Kit v3.3, indexed with sample barcodes.

treatment_protocol: For Samples 1-2: For TGFβ1 treatment, differentiated 3T3-L1 cells were treated with 1 ng/mL of TGFβ1.

value: preadipocytes


title: 3D7 ER Input

description: Library name: Sample 15

value: early ring


title: hapo_newborn_cordblood_A0087

value: Male


title: Hi-C rad51D, DSB at MATa 2h


title: 3T3-L1, SRF, ChIP-seq, Control

description: Library name: Sample 1

value: Control


title: cg6 ER L-D-GFP

description: Library name: Sample 14

value: GFP (Abcam, ab290)


title: Hi-C rad51D, DSB at MATalpha 2h


title: hapo_newborn_cordblood_A0084

value: cord clood

value: newborn


title: RAD21_ab992_Bruce-4

description:
Library name: RAD21_ab992_Bruce-4
Cornell Biotechnology Resource Center EpiGenomics Core

value: RAD21 antibody (Abcam, ab992)


title: Hi-C metaphase-arrest (DSB 4h), MATa cells, Cdc45-depleted replicate 2

value: MATa-inc, ura3::LY-Hocs, lys2::LY, trp1::GAL-HO-hphMX, can1-100, his3::pADH1-OsTIR1-9Myc::HIS3, ade2-1, leu2-3,112, RAD5, CDC45-FlagX5-mini-AID::KanMx4

value: Auxin


title: CTCF_07-729_Bruce-4_rep1

description:
Library name: CTCF_07-729_Bruce-4
Cornell Biotechnology Resource Center EpiGenomics Core


title: hapo_newborn_cordblood_A0080

value: Female

value: whole blood cells


title: Hi-C mitotic-arrest (nocodazole), MATa cells

value: MATa-inc, ade2-1 can1-100 his3-11,15 leu2-3,112 RAD5 ura3::loxP, trp1:GAL-HO-HphMX, chrIV765kb::LEU2-HOcs

value: Nocodazole


title: cg6 ER K-A-GFP

description: Library name: Sample 12

value: whole organism


title: hapo_newborn_cordblood_A0072


title: H3K4me3_04-745_Bruce-4

description:
Library name: H3K4me3_04-745_Bruce-4
Cornell Biotechnology Resource Center EpiGenomics Core

value: Mouse embryonic stem cell

value: H3K4me3 antibody (MilliporeSigma, 04-745)


title: cg6 ER PfHP1-GFP

description: Library name: Sample 11


title: Hi-C metaphase-arrest (DSB 4h), MATa cells, Cdc45-depleted replicate 1


title: TNG-BL-nLRC-2

city: Kumamoto City

first: Yen

middle: Xuan

last: Ngo

state: Kumamoto

address: Honjo 2-1-1, Chuo-ku

department: International Research Center for Medical Sciences

country: Japan

institute: Kumamoto University

data_processing:
Sequencing was done in Illumina NextSeq500 generating 8 gz fastq files per samples
Fastq files were imported to CLC GW as paired-end reads and mapped to mouse mm10 genome (ENSEMBL but provided by CLC)
Mapped reads exported, converted into bedgraph for visualization in UCSC browser
Read counts were normalized by calculating number of reads per kilobase per million (RPKM) for each transcript in individual samples using the CLC Genomic Workbench software version 12.0 (Qiagen).
Differentially expressed genes were filtered using fold change and p value < 0.05.
Assembly: mm10
Supplementary files format and content: tab-delimited text files include TPM and RPKM values for each gene in every sample

source_name: Tongue epithelium

extract_protocol:
Tissue was incubated overnight at 4 °C in 0.25% trypsin/EDTA and the next day at 37 °C for 30 minutes. Single-cell suspensions were then filtered, stained with antibodies and sorted by flow cytometry directly into Trizol (Ambion, 10296028) for RNA extraction. RNA quality was measured by Agilent Bioanalyzer RNA 6000 pico kit (5067-1513) and quantity using nanodrop.
Library was synthesized using low input protocol (≤50ng RNA) by SMARTer Stranded Total RNA-Seq Kit v2 – Pico Input Mammalian (Takara) and the library quality was checked by Agilent Bioanalyzer DNA high-sensitivity kit (5067-4626).

treatment_protocol: Doxycycline was mixed in the chow (cat no) for 10 days for oral tissues and 2 weeks for skin, fresh chow was given every week.

value: Tongue epithelium

value: fast-cycling epidermal stem cells

tag: other name

value: Basal layer cells (BL), non-Label retaining cells (nLRCs)

value: K5-tTA/pTRE H2B-GFP

tag: age

value: 2 months old

value: doxycycline 10 days


title: hapo_newborn_cordblood_A0059

value: Male

value: cord clood

value: newborn


title: Hi-C metaphase-arrest (DSB 4h), MATa cells, Cdc45-AID (mock) replicate 2

value: MATa-inc, ura3::LY-Hocs, lys2::LY, trp1::GAL-HO-hphMX, can1-100, his3::pADH1-OsTIR1-9Myc::HIS3, ade2-1, leu2-3,112, RAD5, CDC45-FlagX5-mini-AID::KanMx4

value: DMSO


title: Hi-C metaphase-arrest (DSB 4h), MATa cells, Cdc45-AID (mock) replicate 1


title: hapo_newborn_cordblood_A0054

value: whole blood cells


title: TNG-BL-nLRC-1


title: 3D7 LR H4K8ac

description: Library name: Sample 10

value: late ring


title: TNG-BL-LRC-2

value: slow-cycling epidermal stem cells

value: Basal layer cells (BL), Label retaining cells (LRCs)


title: Hi-C asynchronous, MATa cells, YEP+lactate+galactose replicate 1

value: MATa-inc, ura3::loxP, lys2::URA3, trp1::GAL-HO-hphMX, his3-11,15, leu2-3,112, can1-100, ade2-1, RAD5


title: hapo_newborn_cordblood_A0043

value: Female


title: 3D7 LR H3K9ac

description: Library name: Sample 8

value: whole organism

value: H3K9ac (Millipore, 06-942)


title: TNG-BL-LRC-1

value: Tongue epithelium


title: Hi-C asynchronous, MATa cells, Smc2-depleted

value: MATa, leu2-2 bud4(mutant) cdc15-2; smc2-AID-9myc::NAT; TIR1-9myc::URA3; SPO2051-91-GFP::TRP1; HTA1-mCherry::HPH

value: Auxin


title: hapo_newborn_cordblood_A0041


title: PLT-BL-nLRC-2

source_name: Palate epithelium

value: Palate epithelium

value: fast-cycling epidermal stem cells

value: Basal layer cells (BL), non-Label retaining cells (nLRCs)

value: K5-tTA/pTRE H2B-GFP

value: 2 months old

value: doxycycline 10 days


title: 3D7 LR H3K36me3

description: Library name: Sample 7

value: H3K36me3 (Invitrogen, MA524687)


title: 3D7 LR PfSir2A

description: Library name: Sample 6

value: PfSir2A (in-house)

value: late ring


title: Hi-C asynchronous, MATa cells, Smc2-AID (mock)

value: DMSO


title: hapo_newborn_cordblood_A0063

value: cord clood

value: newborn

value: whole blood cells


title: hapo_newborn_cordblood_A0033

value: Male


title: 3D7 LR PfHP1

description: Library name: Sample 5

value: whole organism

value: PfHP1 (in-house)


title: Hi-C asynchronous, MATa cells, YEP+lactate+galactose replicate 3

value: MATa-inc, ura3::loxP, lys2::URA3, trp1::GAL-HO-hphMX, his3-11,15, leu2-3,112, can1-100, ade2-1, RAD5


title: PLT-BL-nLRC-1

value: Palate epithelium


title: 3D7 LR H3K79me2

description: Library name: Sample 9


title: PLT-BL-LRC-2

value: slow-cycling epidermal stem cells

value: Basal layer cells (BL), Label retaining cells (LRCs)


title: 3D7 ER RNA Pol II

description: Library name: Sample 4

value: RNA Pol II (Abcam, ab5095)

value: early ring


title: Br6032

type: RNA

city: Baltimore

first: Keri

last: Martinowich

state: Maryland

address: 855 N Wolfe St Suite 300

institute: Lieber Institute for Brain Development

hyb_protocol: The next day, hybridization reactions were washed 2x in 0.05% 1xPBS-Tween-20 (Thermo Fisher Scientific, 28320)  and  incubated in 500mL Xenium Post Hybridization Wash Buffer at 37℃ for 30 minutes. After 3 washes of 0.05% 1xPBS-Tween-20, probes were ligated at 37℃ for 2 hours in a reaction consisting of 87.5% Xenium Ligation Buffer, 2.5% Xenium Ligation Enzyme A and 10% Xenium Ligation Enzyme B. After 3 washes of 0.05% 1xPBS-Tween-20, rolling circle products were amplified in a reaction consisting of 90% Xenium Amplification Mix  and 10% Xenium Amplification Enzyme for 2 hours at 30℃. After amplification was completed, slides were washed 2x in TE buffer, 3x in 1xPBS (1mL/wash) and quenched for autofluorescence with 1% Reducing Agent B (10x Genomics) diluted in 1xPBS for 10 minutes at room temperature. Following 3 rinses of 100% Ethanol (Millipore Sigma), slides were dehydrated for 5 minutes at 37℃ and then rehydrated in 1xPBS followed by a 2-minute incubation of 0.05% 1xPBS-Tween-20. Nuclei were then stained in Nuclei Staining Buffer (10x Genomics)and washed 3x in 0.05% 1xPBS-Tween-20. Slides were then stored overnight in the dark at 4℃ and imaged the following day.

scan_protocol: The Xenium instrument was used for automated imaging and onboard processing of the data.

data_processing: Data processed using Xenium Ranger software.

source_name: dorsolateral prefrontal cortex - dlpfc

label_protocol: For probe hybridization, ligation, and amplification, the 10X Genomics protocol: Xenium In Situ Gene Expression was followed (CG000582, Rev E). The probe hybridization solution was then prepared. A custom panel of 300 genes was designed using the 10x Genomics Xenium platform (10X Genomics; Xenium Custom Gene Expression Panel, Part No. 1000563). Details of the custom probe panel design are described in the manuscript. Probe mix was applied to each slide, a cassette lid was applied to each slide cassette and the slides were incubated at 50 ℃ overnight.

growth_protocol: Human dorsolateral prefrontal cortex (dlPFC) was dissected from frozen (-80℃), unfixed postmortem human tissue. 10-micron coronal sections were obtained by cryosectioning. RNAscope smFISH was performed on tissue sections to confirm the inclusion of full laminar organization spanning layer 1 though white matter. Tissue blocks containing these full laminar organization were then cryosectioned to collect 10-micron coronal sections onto microscopy slides for Xenium.

extract_protocol: Xenium slides were fixed and permeabilized according to 10X Genomics’ Xenium In Situ for Fresh Frozen Tissues – Fixation & Permeabilization Protocol (CG000581, Rev C).

value: dorsolateral prefrontal cortex


title: PLT-BL-LRC-1

value: K5-tTA/pTRE H2B-GFP

value: 2 months old

value: doxycycline 10 days


title: 3D7 ER H3K9ac

description: Library name: Sample 3

value: H3K9ac (Millipore, 06-942)


title: hapo_newborn_cordblood_A0020

value: cord clood


title: TL-Bulge-3

source_name: Tail skin epidermis

value: Tail skin epidermis

value: hair follicle stem cells

value: bulge

value: doxycycline 2 weeks


title: 3D7 ER H3K9me3

description: Library name: Sample 2

value: whole organism

value: H3K9me3 (Invitrogen, PA5-31910)


title: hapo_newborn_cordblood_A0014

value: Male

value: newborn

value: whole blood cells


title: TL-BL-nLRC-3

value: fast-cycling epidermal stem cells

value: Basal layer cells (BL), non-Label retaining cells (nLRCs)


title: Br6496

value: dorsolateral prefrontal cortex


title: 3D7 ER PfHP1

description: Library name: Sample 1

value: PfHP1 (in-house)

value: early ring


title: TL-BL-LRC-3

value: slow-cycling epidermal stem cells

value: Basal layer cells (BL), Label retaining cells (LRCs)

value: K5-tTA/pTRE H2B-GFP

value: 2 months old


title: Br2421


title: IgG-Seq Sample IgG48B

city: Jacksonville

first: John

last: Gubatan

state: FL

address: Mayo Clinic Mangurian Building 5220, 4500 San Pablo Rd

institute: Mayo Clinic Florida

description:
Library name: IgG48B
Novogene
IGGSEQ.rds

data_processing:
Analyses of 16S rRNA data were performed using the Quantitative Insights into Microbial Ecology (QIIME) 2 (http://qiime.org), an open-source bioinformatics pipeline for performing analysis of microbiome sequence data as previously described (Boylen et al., 201960).  Briefly, raw sequencing data were demultiplexed using unique barcodes assigned to each sample and then denoised using Dada2 as previously described (Callahan et al., 2016).  Remaining reads were then clustered into Operational Taxonomic Units (OTUs) using Greengenes v13-8 as a reference set to assign taxonomy to each OTU
Assembly: Greengenes v13-8 reference
Supplementary files format and content: Merged IGA-SEQ Phyloseq obejct, Merged IGG-SEQ Phyloseq obejct,
Library strategy: 16S rRNA-seq

source_name: Stool

extract_protocol:
Frozen stool (200 mg) samples from each patient were thawed and dissolved in 1 mL of phosphate buffered saline (Invitrogen, Catalog No. Catalog No. AM9624). Stool was resuspended in 1 mL of 5 mM N-acetyl-cysteine (Thermo Scientific Chemicals, Catalog No. 616-91-1) to break disulfide bonds in mucus and release bacterial cells and then passed through 100 uM filters and centrifuged. The resulting stool pellets were resuspended in 1 mL of PBS and divided into four fractions for downstream experiments (bacterial FACS, whole microbiome 16S, IgA-Seq, and IgG-Seq). For bacterial FACS, stool cell pellets were centrifuged and resuspended in PBS and stained with 1:10,000 SYBR Green (Sigma Aldrich) at room temperature in dark for 20 minutes. Cell pellets were subsequently centrifuged, resuspended in PBS, and stained with 1:250 Anti-Human IgA-APC (REAfinity™, Catalog No. 130-116-879) and 1:250 of Anti-Human IgG-PE (REAfinity™, Catalog No. 130-119-878) and incubated on ice for 20 minutes. Cell pellets were centrifuged and resuspended in FACS buffer and 1:50 Fc block was to each sample and incubated at room temperature for 10 minutes. Bacterial cell pellets were then centrifuged and resuspended in FACS buffer. FACS was used to quantify the proportion of SYBR green positive (live bacterial cells) that were IgA-APC+, IgG-PE+, and IgA+IgG+ double positives.Stool pellets from each patient were processed as previously described. Bacterial cell pellets were resuspended in PBS and separate stool fractions were stained with either 1:250 Anti-Human IgA-APC (REAfinity™, Catalog No. 130-116-879) or 1:250 of Anti-Human IgG-PE (REAfinity™, Catalog No. 130-119-878) and incubated on ice for 20 minutes. Bacterial cell pellets were centrifuged and then washed with MACS buffer.  Anti-PE MicroBeads (Miltenyi Biotec, Catalog No. 130-090-855) were added to IgG fraction and Anti-APC MicroBeads (Miltenyi Biotec, Catalog No. 130-048-801) to IgA fraction. Bacterial cell pellets were then centrifuged, resuspended in MACS buffer, and placed onto OctoMACS™ Separator (Miltenyi Biotec, Catalog No. 130-042-108) columns for magnetic separation. IgA and IgG-bound bacterial fractions were then collected for each sample. Purity of IgA-bound and IgG-bound gut bacteria were above 90% for all samples included in downstream analyses.
DNA from bacterial cell pellets from IgA-bound, IgG-bound, and unfractionated (whole gut microbiome) samples were isolated using the PureLink™ Microbiome DNA Purification Kit (Catalog No. A29790) per manufacturer’s instructions. Bacterial 16S sequencing of the V4 and V5 regions (primer 515F/sequence GTGCCAGCMGCCGCGGTAA, primer 907R/sequence CCGTCAATTCCTTTGAGTTT) were performed at Novogene using 2x250 sequencing on an Illumina MiSeq.

treatment_protocol: Patients with established inflammatory bowel disease (ulcerative colitis or Crohn’s disease) were screened and invited to participate in vitamin D prospective study at Stanford University (IRB 60958) and the University of Copenhagen (IRB 2021-1696). Patients who met inclusion criteria (adult patients (18 years or older) with inflammatory bowel disease (ulcerative colitis or Crohn's disease), low serum vitamin D (25(OH)D ≤ 25 ng/mL, not on vitamin D supplementation at time of recruitment, no prior bowel resections, no antibiotic use in past 3 months) were enrolled. Patients who had prior bowel surgeries (colectomy, small bowel resections), renal dysfunction, history of hypercalcemia, history of HIV (human immunodeficiency virus), history of IgA deficiency, history of common variable immunodeficiency (CVID), or current or recent C. diff infection were excluded from study. All patients provided consent in accordance with Institutional Review Board guidance for each institution as noted above. At the time of enrollment (week 0), patients had blood and stool samples collected. Patients were then treated with 50,000 units of oral vitamin D (ergocalciferol) once per week for 12 weeks. Blood and stool samples were collected at the end of study (week 12). C-reactive protein and fecal calprotectin were measured from week 0 and week 12 blood and stool samples, respectively. Disease activity scores (partial Mayo score for ulcerative colitis, Harvey Bradshaw Index for Crohn’s disease), quality of life scores (short inflammatory bowel disease questionnaire/SIBDQ) were collected at week 0 and week 12.

value: Stool

value: Post-vitamin D


title: IgG-Seq Sample IgG47B

description:
Library name: IgG47B
Novogene
IGGSEQ.rds


title: TL-Bulge-2

value: Tail skin epidermis

value: hair follicle stem cells

value: bulge

value: doxycycline 2 weeks


title: Br5436


title: IgG-Seq Sample IgG46B

description:
Library name: IgG46B
Novogene
IGGSEQ.rds


title: TL-BL-nLRC-2


title: RNA-seq of mus brain in June, biol repl2

city: Fuzhou

first: lanyan

last: lin

state: Fujian

address: 134 Dongjie Road

department: Department of Geriatric Medicine

country: China

institute: Fuzhou University School of Medicine

description:
Library name: 03-E4-15
Column name in gene_count.xls: 22

data_processing:
After quality-filtered, clean reads were aligned to the reference genome using HISAT2 version 2.1.0. Gene-level read counts were quantified with featureCounts version 2.0.6.
Assembly: mm39
Supplementary files format and content: read counts of genes for each sample

source_name: brain

extract_protocol:
Total RNA was extracted from tissue samples using TRIzol reagent (Invitrogen)
Sequencing libraries were prepared following the manufacturer’s protocol with the NEBNext® Ultra™ RNA Library Prep Kit for Illumina® (New England Biolabs). Libraries were sequenced on the Illumina NovaSeq 6000 platform.

value: brain


title: RNA-seq of mus brain in June, biol repl3

description:
Library name: 04-E3-15
Column name in gene_count.xls: 23


title: RNA-seq of mus brain in June, biol repl1

description:
Library name: 03-E3-15
Column name in gene_count.xls: 21


title: TL-BL-LRC-2


title: Br8667


title: RNA-seq of mus brain in May, biol repl4

description:
Library name: 02-E4-15
Column name in gene_count.xls: 20


title: Br1139


title: TL-BL-nLRC-1


title: RNA-seq of mus brain in May, biol repl3

description:
Library name: 02-E3-15
Column name in gene_count.xls: 19


title: IgG-Seq Sample IgG43B

description:
Library name: IgG43B
Novogene
IGGSEQ.rds


title: Br8772


title: IgG-Seq Sample IgG42B

description:
Library name: IgG42B
Novogene
IGGSEQ.rds


title: MATalpha, rad51, DSB 2h, replicate 2

description: Library name: AD770

data_processing:
Reads alignement, contact filtering and PCR duplicate removal was performed using the hicstuff (v3.1.2 or 3.2.4) pipeline function with mapping quality set to 20. Hi-C contact matrices in sparse format were binned at 1 kb using hicstuff rebin function and converted to cooler format using hicstuff convert function.
Assembly: S. cerevisiae S288c-R64-2-1 (http://sgd-archive.yeastgenome.org/sequence/S288C_reference/genome_releases/S288C_reference_genome_R64-2-1_20150113.tgz) with the HML, HMR, MAT, and the rDNA repeated regions masked.
Supplementary files format and content: Hi-C contact data in cooler format binned at 1kb

extract_protocol:
Cells were spheroplasted with 0.25 mg/mL Zymolyase 100T at 37°C for 30 minutes, crosslinked with 3 mM EGS (ethylene glycol bis(succinimidyl succinate)) at 30°C for 40 minutes at 100 rpm, and quenched with 400 mM glycine for 5 minutes at 100 rpm.
Hi-C library were generated using the Arima Hi-C+ kit following manufacturer instructions starting from 2-5x10^7 cells. DNA was fragmented in 300-400 bp DNA fragments using Covaris M220 sonicator. Illumina sequencing libraries were prepared using the Thermofisher Collibri ES DNA Library Prep Kit for Illumina Systems with UD indexes following manufacturer's instructions.

value: MATalpha, ura3::loxP, LYS2, trp1::GAL-HO-hphMX, can1-100, ade2-1, his3-11,15, leu2-3,112, RAD5, rad51::KanMX


title: TL-BL-LRC-1


title: RNA-seq of mus brain in May, biol repl2

description:
Library name: 01-E4-15
Column name in gene_count.xls: 18


title: Br8433


title: IgG-Seq Sample IgG41B

description:
Library name: IgG41B
Novogene
IGGSEQ.rds


title: RNA-seq of mus brain in May, biol repl1

description:
Library name: 01-E3-15
Column name in gene_count.xls: 17


title: BK-Bulge-3

source_name: Back skin epidermis

value: Back skin epidermis


title: Br5639


title: IgG-Seq Sample IgG40B

description:
Library name: IgG40B
Novogene
IGGSEQ.rds


title: BK-GL-3

value: granular layer cells

value: Granular layer cells (GL)


title: RNA-seq of mus brain in April, biol repl4

description:
Library name: 04-E4-10
Column name in gene_count.xls: 16


title: Br5746

value: dorsolateral prefrontal cortex


title: IgG-Seq Sample IgG39B

description:
Library name: IgG39B
Novogene
IGGSEQ.rds


title: RNA-seq of mus brain in April, biol repl3

description:
Library name: 04-E3-10
Column name in gene_count.xls: 15


title: BK-SL-nLRC-3

value: fast-cycling spinous layer cells

value: Spinous layer cells (SL), non-Label retaining cells (nLRCs)


title: IgG-Seq Sample IgG38B

description:
Library name: IgG38B
Novogene
IGGSEQ.rds


title: BK-SL-LRC-3

value: slow-cycling spinous layer cells

value: Spinous layer cells (SL), Label retaining cells (LRCs)


title: RNA-seq of mus brain in April, biol repl2

description:
Library name: 03-E4-10
Column name in gene_count.xls: 14


title: Br5314


title: IgG-Seq Sample IgG37B

description:
Library name: IgG37B
Novogene
IGGSEQ.rds


title: BK-BL-nLRC-3

value: fast-cycling epidermal stem cells

value: Basal layer cells (BL), non-Label retaining cells (nLRCs)

value: K5-tTA/pTRE H2B-GFP

value: 2 months old


title: RNA-seq of mus brain in April, biol repl1

description:
Library name: 03-E3-10
Column name in gene_count.xls: 13


title: Br6437


title: IgG-Seq Sample IgG36B

description:
Library name: IgG36B
Novogene
IGGSEQ.rds

value: Stool

value: Post-vitamin D


title: Br5622


title: BK-BL-LRC-3

value: slow-cycling epidermal stem cells

value: Basal layer cells (BL), Label retaining cells (LRCs)

value: doxycycline 2 weeks


title: IgG-Seq Sample IgG35B

description:
Library name: IgG35B
Novogene
IGGSEQ.rds


title: BK-Bulge-2

value: Back skin epidermis

value: hair follicle stem cells

value: bulge


title: RNA-seq of mus brain in March, biol repl4

description:
Library name: 02-E4-10
Column name in gene_count.xls: 12

value: brain


title: RNA-seq of mus brain in March, biol repl3

description:
Library name: 02-E3-10
Column name in gene_count.xls: 11


title: Br5400

value: dorsolateral prefrontal cortex


title: IgG-Seq Sample IgG34B

description:
Library name: IgG34B
Novogene
IGGSEQ.rds


title: BK-GL-2

value: granular layer cells

value: Granular layer cells (GL)


title: RNA-seq of mus brain in March, biol repl2

description:
Library name: 01-E4-10
Column name in gene_count.xls: 10


title: Br5590


title: IgG-Seq Sample IgG33B

description:
Library name: IgG33B
Novogene
IGGSEQ.rds


title: BK-SL-nLRC-2

value: fast-cycling spinous layer cells

value: Spinous layer cells (SL), non-Label retaining cells (nLRCs)


title: RNA-seq of mus brain in March, biol repl1

description:
Library name: 01-E3-10
Column name in gene_count.xls: 9


title: Br5373


title: BK-SL-LRC-2

value: slow-cycling spinous layer cells

value: Spinous layer cells (SL), Label retaining cells (LRCs)


title: IgG-Seq Sample IgG32B

description:
Library name: IgG32B
Novogene
IGGSEQ.rds


title: IgG-Seq Sample IgG31B

description:
Library name: IgG31B
Novogene
IGGSEQ.rds


title: RNA-seq of mus brain in February, biol repl4

description:
Library name: 04-E4-05
Column name in gene_count.xls: 8


title: Br1113


title: RNA-seq of mus brain in February, biol repl3

description:
Library name: 04-E3-05
Column name in gene_count.xls: 7


title: RNA-seq of mus brain in February, biol repl2

description:
Library name: 03-E4-05
Column name in gene_count.xls: 6


title: Br6432


title: BK-BL-LRC-2

value: K5-tTA/pTRE H2B-GFP

value: 2 months old


title: IgG-Seq Sample IgG30B

description:
Library name: IgG30B
Novogene
IGGSEQ.rds

value: Stool

value: Post-vitamin D


title: Br2719


title: BK-Bulge-1


title: IgG-Seq Sample IgG29B

description:
Library name: IgG29B
Novogene
IGGSEQ.rds


title: IgG-Seq Sample IgG28B

description:
Library name: IgG28B
Novogene
IGGSEQ.rds


title: Br2039


title: RNA-seq of mus brain in February, biol repl1

description:
Library name: 03-E3-05
Column name in gene_count.xls: 5


title: BK-GL-1


title: hapo_newborn_cordblood_A0028

description: Illumina Infinium MethylationEPIC BeadChip (850K chip)

value: Male

value: cord clood

value: newborn

value: whole blood cells


title: TNNAND8_T1(N10)/T2(N10)/T3(N10)/T4(N10) base stem sequence pool, subpopulation P10

city: Darmstadt

first: Daniel

last: Kelvin

address: Merckstrasse 25

department: Centre for Synthetic Biology

institute: Technical University of Darmstadt

description: Library name: P10

data_processing:
Initial data processing performed by Azenta/GENEWIZ.
Assembly: TNNAND1: TGCCTAAAACATACTAGCTTGTCCTTTAATGGTCCTAGAGAGGTGAAGAATACGACCACCTAGGCA; TNNAND8: TGCCTAAAACATACTCGCTTGTCCTTTAATGGTCCTTGAGAGGTGAAGAATACGACCACCTAGGCA
Supplementary files format and content: csv files include the readcount of each sequence discovered in a sample.

extract_protocol:
Plasmid DNA was extracted from yeast using the Yeast Plasmid Miniprep II kit from Zymo Research. The randomized region on the plasmid was amplified via PCR and the product was purified using the Wizard SV Gel and PCR Clean-Up System from Promega.
Yeast libraries were created through homologous recombination by amplifying each sequence pool with primers homologous to the linearized (AgeI+NheI) backbone pCBB06 (Boussebayle et al., 2019) and transforming S. cerevisiae RS453 with with linearized backbone and amplified pool DNA using a high efficiency electroporation protocol (Benatuil et al., 2010).

tag: sample group


title: RNA-seq of mus brain in January, biol repl3

description:
Library name: 02-E3-05
Column name in gene_count.xls: 3


title: TNNAND8_T1(N10)/T2(N10)/T3(N10)/T4(N10) base stem sequence pool, subpopulation P9

description: Library name: P9


title: BK-SL-nLRC-1

value: Back skin epidermis

value: doxycycline 2 weeks


title: IgG-Seq Sample IgG27B

description:
Library name: IgG27B
Novogene
IGGSEQ.rds


title: IgG-Seq Sample IgG26B

description:
Library name: IgG26B
Novogene
IGGSEQ.rds


title: BK-SL-LRC-1


title: RNA-seq of mus brain in June, biol repl4

description:
Library name: 04-E4-15
Column name in gene_count.xls: 24

value: brain


title: IgG-Seq Sample IgG25B

description:
Library name: IgG25B
Novogene
IGGSEQ.rds


title: RNA-seq of mus brain in January, biol repl2

description:
Library name: 01-E4-05
Column name in gene_count.xls: 2


title: BK-BL-nLRC-1

value: fast-cycling epidermal stem cells

value: Basal layer cells (BL), non-Label retaining cells (nLRCs)


title: RNA-seq of mus brain in January, biol repl1

description:
Library name: 01-E3-05
Column name in gene_count.xls: 1


title: IgG-Seq Sample IgG24B

description:
Library name: IgG24B
Novogene
IGGSEQ.rds


title: Cis_3-input

city: Hangzhou

first: Lv

last: Fei

address: The First People's Hospital of Hangzhou, Zhejiang Province

institute: Zhejiang Chinese Medical University

description: Library name: sample12

data_processing:
Raw sequencing reads (FASTQ files) were first processed with fastp to remove adapters and low-quality bases, generating clean reads. Quality control was performed using FastQC. Clean reads were then aligned to the reference genome (e.g., mm10) using HISAT2. Peak calling was performed with exomePeak to identify acetylated regions (peaks) from the IP samples relative to Input. Peaks were annotated to genomic features (e.g., 5’UTR, CDS, 3’UTR). Motif analysis was conducted using HOMER. Differential acetylation analysis between groups was performed with exomePeak. Gene Ontology (GO) and KEGG pathway enrichment analyses were performed on genes harboring peaks or differential peaks.
Assembly: mm10
Supplementary files format and content: Tab-delimited text file
Library strategy: MeRIP-Seq

extract_protocol:
Total RNA was extracted from samples. Ribosomal RNA (rRNA) was depleted from the total RNA to enrich for mRNA and lncRNA. The resulting RNA was chemically fragmented.The fragmented RNA was divided into Input and IP fractions. The IP fraction was incubated with an anti-ac4C antibody for immunoprecipitation. After washing, the immunoprecipitated RNA was eluted.Both IP and Input RNA were used for strand-specific library construction and sequenced on an Illumina platform.
Strand-specific RNA-seq libraries were constructed from both the immunoprecipitated (ac4C-IP) and Input RNA samples. The protocol involved: 1) RNA end repair and 5' phosphorylation, 2) 3' adapter ligation, 3) reverse transcription with dUTP incorporation for strand specificity, 4) 5' adapter ligation, 5) cDNA amplification by PCR, and 6) size selection and purification of the final libraries. Library quality was assessed by Agilent Bioanalyzer, and qualified libraries were sequenced on an Illumina platform (e.g., NovaSeq 6000) to generate paired-end reads.

value: cisplatin-treated

tag: batch

value: input


title: TNNAND1_N6 sequence pool, condition TcNeo, subpopulation positive control (replicate)

description: Library name: TcNeo-plus_replicate


title: TNNAND8_T1(N10)/T2(N10)/T3(N10)/T4(N10) base stem sequence pool, subpopulation P7

description: Library name: P7


title: IgG-Seq Sample IgG23B

description:
Library name: IgG23B
Novogene
IGGSEQ.rds


title: Cis_3-IP

description: Library name: sample11

value: IP


title: TNNAND1_N6 sequence pool, condition TcNeo, subpopulation negative control (replicate)

description: Library name: TcNeo-minus_replicate


title: IgG-Seq Sample IgG22B

description:
Library name: IgG22B
Novogene
IGGSEQ.rds


title: plasma non-exsosomal RNAs at 30 months of age-2

city: Kyoto

first: Norihide

last: Yokoi

state: Kyoto

address: Kitashirakawa Oiwake-cho, Sakyo-ku

department: Graduate School of Agriculture

institute: Kyoto University

description: Library name: 30-Fc-2

data_processing:
The raw data were preprocessed by removing adapter sequences and trimming off low-quality reads using Cutadapt (version 5.0) and Trimmomatic (version 0.39), respectively, retaining high-quality reads of 15-51 bp, which were evaluated using FastQC (version 0.12.1).
Both known and candidate novel miRNAs were identified from the small RNA-seq reads using miRDeep2 software package (Version 2.0.1.2). The small RNA-seq reads were mapped to the Japanese Black cattle whole genome. The mapped reads were sequentially annotated to bovine miRNA precursor and respective mature sequences obtained from the miRBase (version 22.1), using the miRDeep2.pl module.
The miRNA abundance data and differential profiles were analyzed using edgeR package (Version 4.0.16). First, the total read counts were count-per-million (CPM) normalized, and miRNAs with CPM normalized counts greater than 5 in at least 3 of the 9 samples for each EX and FC fractions were selected for downstream analysis.
Assembly: bovine reference genome (ARS-UCD 1.2)
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample
Supplementary files format and content: csv files include CPM normalized values for each Sample

organism: Bos taurus

source_name: plasma

extract_protocol:
A total of nine plasma samples were collected in the morning from jugular veins of 3 steers at approximately 20, 25, and 30 months of age using Venoject II vacuum blood collection tubes (EDTA-2K) (Terumo). Both EX and FC RNAs were extracted from 1 mL of plasma samples using Plasma/Serum Exosome and Free-Circulating RNA Isolation Mini Kit (Norgen Biotek).
Library construction and small RNA-seq were performed on the samples at 51 bp single-ended (> 20 M reads/sample) using Illumina NovaSeq 6000 at Azenta Life sciences.

value: plasma


title: Cis_2-input

description: Library name: sample10


title: TNNAND1_N6 sequence pool, condition TcNeo, subpopulation 8 (replicate)

description: Library name: TcNeo8_replicate


title: IgG-Seq Sample IgG21B

description:
Library name: IgG21B
Novogene
IGGSEQ.rds


title: plasma non-exsosomal RNAs at 30 months of age-1

description: Library name: 30-Fc-1


title: plasma non-exsosomal RNAs at 30 months of age-3

description: Library name: 30-Fc-3


title: Cis_2-IP

description: Library name: sample9


title: IgG-Seq Sample IgG20B

description:
Library name: IgG20B
Novogene
IGGSEQ.rds


title: TNNAND1_N6 sequence pool, condition TcNeo, subpopulation 7 (replicate)

description: Library name: TcNeo7_replicate


title: plasma exsosomal RNAs at 30 months of age-3

description: Library name: 30-Ex-3


title: Cis_1-input

description: Library name: sample8


title: TNNAND1_N6 sequence pool, condition TcNeo, subpopulation 6 (replicate)

description: Library name: TcNeo6-replicate


title: plasma exsosomal RNAs at 30 months of age-2

description: Library name: 30-Ex-2


title: IgG-Seq Sample IgG19B

description:
Library name: IgG19B
Novogene
IGGSEQ.rds


title: Cis_1-IP

description: Library name: sample7


title: TNNAND1_N6 sequence pool, condition TcNeo, subpopulation 5 (replicate)

description: Library name: TcNeo5_replicate


title: IgG-Seq Sample IgG18B

description:
Library name: IgG18B
Novogene
IGGSEQ.rds


title: Ctrl_3-input

description: Library name: sample6

value: control


title: plasma exsosomal RNAs at 30 months of age-1

description: Library name: 30-Ex-1


title: TNNAND1_N6 sequence pool, condition TcNeo, subpopulation 4 (replicate)

description: Library name: TcNeo4_replicate


title: IgG-Seq Sample IgG17B

description:
Library name: IgG17B
Novogene
IGGSEQ.rds


title: plasma non-exsosomal RNAs at 25 months of age-3

description: Library name: 25-Fc-3


title: Ctrl_3-IP

description: Library name: sample5


title: TNNAND1_N6 sequence pool, condition TcNeo, subpopulation 3 (replicate)

description: Library name: TcNeo3_replicate


title: IgG-Seq Sample IgG16B

description:
Library name: IgG16B
Novogene
IGGSEQ.rds


title: plasma non-exsosomal RNAs at 25 months of age-2

description: Library name: 25-Fc-2


title: TNNAND1_N6 sequence pool, condition TcNeo, subpopulation 2 (replicate)

description: Library name: TcNeo2_replicate


title: Ctrl_2-input

description: Library name: sample4


title: plasma non-exsosomal RNAs at 25 months of age-1

description: Library name: 25-Fc-1


title: Ctrl_2-IP

description: Library name: sample3


title: cg6 ER W-A-GFP

description: Library name: Sample 13

value: whole organism

value: GFP (Abcam, ab290)

value: early ring


title: BK-BL-nLRC-2

value: K5-tTA/pTRE H2B-GFP

value: 2 months old


title: IgG-Seq Sample IgG14B

description:
Library name: IgG14B
Novogene
IGGSEQ.rds

value: Stool

value: Post-vitamin D


title: TNNAND1_N6 sequence pool, condition TcNeo, subpopulation 1 (replicate)

description: Library name: TcNeo1_replicate


title: Ctrl_1-input

description: Library name: sample2


title: plasma exsosomal RNAs at 25 months of age-3

description: Library name: 25-Ex-3


title: TNNAND1_N6 sequence pool, condition Neo, subpopulation positive control (replicate)

description: Library name: Neo-plus_replicate

value: TNNAND1_N6 sequence pool, condition Neo


title: IgG-Seq Sample IgG13B

description:
Library name: IgG13B
Novogene
IGGSEQ.rds


title: plasma exsosomal RNAs at 25 months of age-2

description: Library name: 25-Ex-2


title: Ctrl_1-IP

description: Library name: sample1


title: TNNAND1_N6 sequence pool, condition Neo, subpopulation negative control (replicate)

description: Library name: Neo-minus_replicate


title: IgG-Seq Sample IgG12B

description:
Library name: IgG12B
Novogene
IGGSEQ.rds


title: plasma exsosomal RNAs at 25 months of age-1

description: Library name: 25-Ex-1


title: hapo_newborn_cordblood_A0032

description: Illumina Infinium MethylationEPIC BeadChip (850K chip)

data_processing:
minfi package in R environment (version 1.40.0)
processed value definition: M values transformed from beta (HAPO_GA_illumina_methylation.xlsx linked to the Series record)

extract_protocol: DNA was extracted from whole blood that was stored at -80 C and was quantified with the Qubit Fluorometer (Thermo Fisher Scientific, Waltham, Massachusetts)

value: Male

value: cord clood

value: newborn

value: whole blood cells


title: OE-3

city: guangzhou

first: kang

last: Tang

address: No. 1023 South Shatai Road, Baiyun District, Guangzhou, Guangdong, China

institute: Southern Medical University

description: Library name: Sample 9

data_processing:
Raw reads were processed with BBmap (v39.01) and Trimmomatic (v0.39) to remove adapter sequences and low-quality bases. The resulting clean reads were aligned to the GRCm38 reference genome (Ensembl) using HISAT2 (v2.2.1). Gene expression levels were quantified with StringTie (v2.2.1).
Assembly: GRCm38
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample

source_name: SSC cell line

extract_protocol:
For mRNA library preparation, 1 µg of total RNA per sample was used. The mRNA was then fragmented, followed by cDNA synthesis and purification.
The purified cDNA was subjected to end repair, A-tailing, and adapter ligation. cDNA fragments of 200-300 bp were selected, PCR-amplified, and purified to generate the final library. Library quality was assessed using the Agilent 4200 TapeStation. Sequencing was carried out on an Illumina NovaSeq platform with PE150 configuration.

value: SSC cell line

value: Spermatogonial stem cells

value: OE


title: Br6389

value: dorsolateral prefrontal cortex


title: RNA-seq of mus brain in January, biol repl4

description:
Library name: 02-E4-05
Column name in gene_count.xls: 4

value: brain


title: IgG-Seq Sample IgG11B

description:
Library name: IgG11B
Novogene
IGGSEQ.rds


title: TNNAND1_N6 sequence pool, condition Neo, subpopulation 8 (replicate)

description: Library name: Neo8_replicate


title: plasma non-exsosomal RNAs at 20 months of age-3

description: Library name: 20-Fc-3

value: plasma


title: OE-2

description: Library name: Sample 8


title: TNNAND1_N6 sequence pool, condition Neo, subpopulation 7 (replicate)

description: Library name: Neo7_replicate


title: OE-1

description: Library name: Sample 7


title: plasma non-exsosomal RNAs at 20 months of age-2

description: Library name: 20-Fc-2


title: IgG-Seq Sample IgG10B

description:
Library name: IgG10B
Novogene
IGGSEQ.rds


title: TNNAND1_N6 sequence pool, condition Neo, subpopulation 6 (replicate)

description: Library name: Neo6_replicate


title: IgG-Seq Sample IgG9B

description:
Library name: IgG9B
Novogene
IGGSEQ.rds


title: Br5931


title: plasma non-exsosomal RNAs at 20 months of age-1

description: Library name: 20-Fc-1


title: TNNAND1_N6 sequence pool, condition Neo, subpopulation 5 (replicate)

description: Library name: Neo5_replicate


title: IgG-Seq Sample IgG8B

description:
Library name: IgG8B
Novogene
IGGSEQ.rds


title: plasma exosomal RNAs at 20 months of age-3

description: Library name: 20-Ex-3


title: MU-2

description: Library name: Sample 5

value: MU


title: Br5973


title: TNNAND1_N6 sequence pool, condition Neo, subpopulation 4 (replicate)

description: Library name: Neo4_replicate


title: IgG-Seq Sample IgG7B

description:
Library name: IgG7B
Novogene
IGGSEQ.rds


title: plasma exosomal RNAs at 20 months of age-2

description: Library name: 20-Ex-2


title: MU-1

description: Library name: Sample 4


title: TNNAND1_N6 sequence pool, condition Neo, subpopulation 3 (replicate)

description: Library name: Neo3_replicate


title: IgG-Seq Sample IgG6B

description:
Library name: IgG6B
Novogene
IGGSEQ.rds


title: plasma exosomal RNAs at 20 months of age-1

description: Library name: 20-Ex-1


title: 4OHT-3

description: Library name: Sample 3


title: TNNAND1_N6 sequence pool, condition Neo, subpopulation 2 (replicate)

description: Library name: Neo2_replicate


title: IgG-Seq Sample IgG5B

description:
Library name: IgG5B
Novogene
IGGSEQ.rds


title: Whole Stool 16S Sample S48B

description:
Library name: S48B
Novogene

data_processing:
Analyses of 16S rRNA data were performed using the Quantitative Insights into Microbial Ecology (QIIME) 2 (http://qiime.org), an open-source bioinformatics pipeline for performing analysis of microbiome sequence data as previously described (Boylen et al., 201960).  Briefly, raw sequencing data were demultiplexed using unique barcodes assigned to each sample and then denoised using Dada2 as previously described (Callahan et al., 2016).  Remaining reads were then clustered into Operational Taxonomic Units (OTUs) using Greengenes v13-8 as a reference set to assign taxonomy to each OTU
Assembly: Greengenes v13-8 reference
Supplementary files format and content: Merged VD16Seq2.rds Phyloseq object
Library strategy: 16S rRNA-seq

organism: human feces metagenome

tag: patient id


title: 4OHT-2

description: Library name: Sample 2


title: TNNAND1_N6 sequence pool, condition Neo, subpopulation 1 (replicate)

description: Library name: Neo1_replicate


title: IgG-Seq Sample IgG4B

description:
Library name: IgG4B
Novogene
IGGSEQ.rds

tag: tissue


title: Whole Stool 16S Sample S47B

description:
Library name: S47B
Novogene

tag: treatment


title: 4OHT-1

description: Library name: Sample 1


title: TNNAND1_N6 sequence pool, condition Tc, subpopulation positive control (replicate)

description: Library name: Tc-plus_replicate

value: TNNAND1_N6 sequence pool, condition Tc


title: IgG-Seq Sample IgG3B

description:
Library name: IgG3B
Novogene
IGGSEQ.rds


title: Whole Stool 16S Sample S46B

description:
Library name: S46B
Novogene


title: H3K27me3-CKO-2 Cut&tag

city: Chongqing

first: Yuanyuan

last: Liu

address: No. 1 Medical College Road, Yuzhong District, Chongqing, China

institute: Chongqing Medical Journal

description: Library name: Sample-25

data_processing:
Illumina Casava1.7 software used for basecalling.
Assembly: mm10
Supplementary files format and content: BigWig files.
Library strategy: CUT&Tag

source_name: Bone Marrow

extract_protocol:
About 25,000-30,000 HSCs were isolated by FACS and the ATAC-seq was performed following the protocol of Corces et al. About 25,000-30,000 HSCs were isolated by FACS and the CUT&Tag assay was performed.
ATAC-seq: HSCs were lysed and the DNA fragments were broken using the TruePrepTM DNA Library Prep Kit V2 (Vazyme). DNA fragment amplification was performed using KAPA HiFi HotStart Ready Mix (KAPA Biosystems, USA). The Agencourt AMPure XP kit was used to purify cDNA (Beckman Coulter, USA).  Sequencing was performed on the Illumina NovaSeq 6000. CUT&Tag assay: HSCs were harvested and combined with ConA beads (NovoNGS® ConA Beads) and antibodies (H3K27ac, H3K9ac, H3K4me3, IgG and Smarca4), followed by the formation of transposomes using ChiTag Transposome. Transposition fragmentation was performed using constant temperature. DNA extraction was performed using WAHTS DNA Clean Beads (Vazyme). DNA amplification was performed using CUT&Tag 2.0 High-Sensitivity Kit (NovoNGS). Sequencing was performed on the Illumina NovaSeq 6000.

value: Bone Marrow

value: Primary cell

value: Hematopoietic stem cell

value: CKO


title: Whole Stool 16S Sample S45B

description:
Library name: S45B
Novogene

value: Stool

value: Post-vitamin D


title: TNNAND1_N6 sequence pool, condition Tc, subpopulation negative control (replicate)

description: Library name: Tc-minus_replicate


title: TNNAND1_N6 sequence pool, condition Tc, subpopulation 8 (replicate)

description: Library name: Tc8_replicate


title: IgG-Seq Sample IgG2B

description:
Library name: IgG2B
Novogene
IGGSEQ.rds


title: IgG-Seq Sample IgG1B

description:
Library name: IgG1B
Novogene
IGGSEQ.rds


title: Whole Stool 16S Sample S44B

description:
Library name: S44B
Novogene


title: H3K27me3-fl/fl-2 Cut&tag

description: Library name: Sample-23

value: WT


title: TNNAND1_N6 sequence pool, condition Tc, subpopulation 7 (replicate)

description: Library name: Tc7_replicate


title: H3K27me3-CKO-1 Cut&tag

description: Library name: Sample-24


title: IgG-Seq Sample IgG48A

description:
Library name: IgG48A
Novogene
IGGSEQ.rds

value: Pre-vitamin D


title: Whole Stool 16S Sample S43B

description:
Library name: S43B
Novogene


title: H3K27me3-fl/fl-1 Cut&tag

description: Library name: Sample-22


title: TNNAND1_N6 sequence pool, condition Tc, subpopulation 6 (replicate)

description: Library name: Tc6_replicate


title: Whole Stool 16S Sample S42B

description:
Library name: S42B
Novogene


title: IgG-Seq Sample IgG47A

description:
Library name: IgG47A
Novogene
IGGSEQ.rds


title: H3K4me1-CKO-2 Cut&tag

description: Library name: Sample-21


title: TNNAND1_N6 sequence pool, condition Tc, subpopulation 5 (replicate)

description: Library name: Tc5_replicate


title: IgG-Seq Sample IgG46A

description:
Library name: IgG46A
Novogene
IGGSEQ.rds


title: Whole Stool 16S Sample S41B

description:
Library name: S41B
Novogene


title: H3K4me1-CKO-1 Cut&tag

description: Library name: Sample-20


title: TNNAND1_N6 sequence pool, condition Tc, subpopulation 4 (replicate)

description: Library name: Tc4_replicate


title: IgG-Seq Sample IgG45A

description:
Library name: IgG45A
Novogene
IGGSEQ.rds


title: Whole Stool 16S Sample S40B

description:
Library name: S40B
Novogene


title: H3K4me1-fl/fl-2 Cut&tag

description: Library name: Sample-19


title: TNNAND1_N6 sequence pool, condition Tc, subpopulation 3 (replicate)

description: Library name: Tc3_replicate


title: IgG-Seq Sample IgG44A

description:
Library name: IgG44A
Novogene
IGGSEQ.rds


title: Whole Stool 16S Sample S39B

description:
Library name: S39B
Novogene


title: TNNAND1_N6 sequence pool, condition Tc, subpopulation 2 (replicate)

description: Library name: Tc2_replicate


title: H3K4me1-fl/fl-1 Cut&tag

description: Library name: Sample-18


title: Whole Stool 16S Sample S38B

description:
Library name: S38B
Novogene


title: IgG-Seq Sample IgG43A

description:
Library name: IgG43A
Novogene
IGGSEQ.rds


title: H3K4me3-CKO-2 Cut&tag

description: Library name: Sample-17


title: Whole Stool 16S Sample S37B

description:
Library name: S37B
Novogene


title: TNNAND1_N6 sequence pool, condition Tc, subpopulation 1 (replicate)

description: Library name: Tc1_replicate


title: IgG-Seq Sample IgG42A

description:
Library name: IgG42A
Novogene
IGGSEQ.rds


title: H3K4me3-CKO-1 Cut&tag

description: Library name: Sample-16


title: TNNAND1_N6 sequence pool, condition wo, subpopulation positive control (replicate)

description: Library name: wo-plus_replicate

value: TNNAND1_N6 sequence pool, condition wo


title: Whole Stool 16S Sample S36B

description:
Library name: S36B
Novogene


title: IgG-Seq Sample IgG41A

description:
Library name: IgG41A
Novogene
IGGSEQ.rds


title: TNNAND1_N6 sequence pool, condition wo, subpopulation negative control (replicate)

description: Library name: wo-minus_replicate


title: H3K4me3-fl/fl-2 Cut&tag

description: Library name: Sample-15


title: IgG-Seq Sample IgG40A

description:
Library name: IgG40A
Novogene
IGGSEQ.rds


title: Whole Stool 16S Sample S35B

description:
Library name: S35B
Novogene


title: TNNAND1_N6 sequence pool, condition wo, subpopulation 8 (replicate)

description: Library name: _replicate


title: H3K4me3-fl/fl-1 Cut&tag

description: Library name: Sample-14


title: Whole Stool 16S Sample S34B

description:
Library name: S34B
Novogene


title: TNNAND1_N6 sequence pool, condition wo, subpopulation 7 (replicate)

description: Library name: wo7_replicate


title: H3K27ac-CKO-1 Cut&tag

description: Library name: Sample-12


title: IgG-Seq Sample IgG38A

description:
Library name: IgG38A
Novogene
IGGSEQ.rds


title: TNNAND1_N6 sequence pool, condition wo, subpopulation 6 (replicate)

description: Library name: wo6_replicate


title: H3K27ac-fl/fl-2 Cut&tag

description: Library name: Sample-11


title: TNNAND1_N6 sequence pool, condition wo, subpopulation 5 (replicate)

description: Library name: wo5_replicate


title: IgG-Seq Sample IgG36A

description:
Library name: IgG36A
Novogene
IGGSEQ.rds


title: Whole Stool 16S Sample S31B

description:
Library name: S31B
Novogene


title: H3K27ac-fl/fl-1 Cut&tag

description: Library name: Sample-10


title: IgG-Seq Sample IgG35A

description:
Library name: IgG35A
Novogene
IGGSEQ.rds


title: Smarca4-2 Cut&tag

description: Library name: Sample-9


title: TNNAND1_N6 sequence pool, condition wo, subpopulation 4 (replicate)

description: Library name: wo4_replicate


title: Whole Stool 16S Sample S30B

description:
Library name: S30B
Novogene


title: TNNAND1_N6 sequence pool, condition wo, subpopulation 3 (replicate)

description: Library name: wo3_replicate


title: IgG-Seq Sample IgG34A

description:
Library name: IgG34A
Novogene
IGGSEQ.rds


title: Whole Stool 16S Sample S29B

description:
Library name: S29B
Novogene


title: Smarca4-1 Cut&tag

description: Library name: Sample-8


title: TNNAND1_N6 sequence pool, condition wo, subpopulation 2 (replicate)

description: Library name: wo2_replicate


title: IgG-Seq Sample IgG33A

description:
Library name: IgG33A
Novogene
IGGSEQ.rds


title: TNNAND1_N6 sequence pool, condition wo, subpopulation 1 (replicate)

description: Library name: wo1_replicate


title: Whole Stool 16S Sample S28B

description:
Library name: S28B
Novogene


title: IgG-Seq Sample IgG32A

description:
Library name: IgG32A
Novogene
IGGSEQ.rds


title: ATAC-CKO3

description: Library name: Sample-7

data_processing:
Illumina Casava1.7 software used for basecalling.
Assembly: mm10
Supplementary files format and content: BigWig files.


title: MU-3

description: Library name: Sample 6

value: SSC cell line


title: Whole Stool 16S Sample S27B

description:
Library name: S27B
Novogene


title: TNNAND8_T1(N10)/T2(N10)/T3(N10)/T4(N10) base stem sequence pool, subpopulation P8

description: Library name: P8


title: IgG-Seq Sample IgG45B

description:
Library name: IgG45B
Novogene
IGGSEQ.rds


title: IgG-Seq Sample IgG44B

description:
Library name: IgG44B
Novogene
IGGSEQ.rds


title: ATAC-CKO2

description: Library name: Sample-6


title: TNNAND1_N6 sequence pool, condition TcNeo, subpopulation positive control

description: Library name: TcNeo-plus


title: IgG-Seq Sample IgG31A

description:
Library name: IgG31A
Novogene
IGGSEQ.rds


title: Whole Stool 16S Sample S26B

description:
Library name: S26B
Novogene


title: TNNAND1_N6 sequence pool, condition TcNeo, subpopulation negative control

description: Library name: TcNeo-minus


title: ATAC-CKO1

description: Library name: Sample-5


title: W-A-DiCre ER, rep1

description: Library name: Sample 4

data_processing:
Paired-end HiC library reads were processed (i.e., mapping, filtering, and pairing, and normalization) using Juicer 1.22.01.
Assembly: PlasmoDB v66
Supplementary files format and content: The HiC contact map in a matrix format (.hic files)

source_name: Plasmodium falciparum

extract_protocol:
The cells were crosslinked with 2% formaldehyde and harvested using 0.015% saponin. For the HiC protcol Arima genomics HiC kit was used.
Followed the protocol of Arima genomics HiC library preparation kit.

value: whole organism

value: early ring


title: TL-Bulge-1

value: Tail skin epidermis

value: hair follicle stem cells

value: bulge

value: K5-tTA/pTRE H2B-GFP

value: 2 months old

value: doxycycline 2 weeks


title: IgG-Seq Sample IgG30A

description:
Library name: IgG30A
Novogene
IGGSEQ.rds


title: ATAC-WT4

description: Library name: Sample-4

value: Bone Marrow

value: Primary cell


title: Whole Stool 16S Sample S25B

description:
Library name: S25B
Novogene


title: TNNAND1_N6 sequence pool, condition TcNeo, subpopulation 8

description: Library name: TcNeo8


title: IgG-Seq Sample IgG29A

description:
Library name: IgG29A
Novogene
IGGSEQ.rds


title: Whole Stool 16S Sample S24B

description:
Library name: S24B
Novogene


title: ATAC-WT3

description: Library name: Sample-3

value: Hematopoietic stem cell


title: TNNAND1_N6 sequence pool, condition TcNeo, subpopulation 7

description: Library name: TcNeo7


title: IgG-Seq Sample IgG28A

description:
Library name: IgG28A
Novogene
IGGSEQ.rds

value: Stool


title: PfHP1-DiCre ER, rep1

description: Library name: Sample 1


title: L-D-DiCre ER rep2

description:
Library name: Samples 16
Directional RNA-seq

data_processing:
Trimming and QC of the raw data was done using trim galore. The trimmed data was aligned against the P. falciparum reference genome (PlasmoDB_v53) using HISAT2. The aligned files were sorted using samtools which gave bam output files. Raw count files are obtained from the htseq analysis. For the directional RNA sequencing analysis deeptools were used for generating bigwig files for the + strand and -strand.
Assembly: PlasmoDB_v53
Supplementary files format and content: Raw count files in tabular form

extract_protocol:
Ring stage (~10 hours post infection, hpi) parasites were double sorbitol synchronized by 5% sorbitol. The samples were spun down and harvested using 0.015% saponin. The cell pellet was resuspended in Trizol and isolated by Isoprapanol precipitation.
The isolated RNA was subjected to polyA enrichment using NEB polyA mRNA magnetic isolation module (E7490). The library preparation was done using the NEB Ultra II RNA kit (E7770). And  for the DiCre line samples NEBNext Ultra™ II Directional RNA Library Prep with Sample Purification Beads (E7765) was used for the library preparation. The library quality was tested using a DNA high sensitivity kit in Agilent bioanalyzer. The library amount was estimated using Qubit DNA high sensitivity kit. A final pool of 1.7 pM library was loaded on a 75 cycle High output illumina sequencing kit.

value: Plasmodium falciparum


title: Whole Stool 16S Sample S23B

description:
Library name: S23B
Novogene

value: Post-vitamin D


title: ATAC-WT2

description: Library name: Sample-2

value: WT


title: TNNAND1_N6 sequence pool, condition TcNeo, subpopulation 6

description: Library name: TcNeo6


title: Whole Stool 16S Sample S22B

description:
Library name: S22B
Novogene


title: IgG-Seq Sample IgG27A

description:
Library name: IgG27A
Novogene
IGGSEQ.rds

value: Pre-vitamin D


title: MATa, G1-arrest, replicate 3

city: Lyon

first: Aurele

last: Piazza

address: 46 Allee d'Italie

institute: ENS Lyon

description: Library name: AD254

value: MATa-inc, ura3::loxP, LYS2, trp1:GAL-HO-hphMX, ade2-1, can1-100, his3-11,15, leu2-3,112, RAD5 chrIV-765kb::LEU2-Hocs


title: IgG-Seq Sample IgG26A

description:
Library name: IgG26A
Novogene
IGGSEQ.rds


title: ATAC-WT1

description: Library name: Sample-1


title: IgG-Seq Sample IgG25A

description:
Library name: IgG25A
Novogene
IGGSEQ.rds