title: KH105.1_mutCBS-Car2-prom_ESC_CTCF

data_processing:
Fastq files were aligned to the catenated mm10 reference genome with Bowtie2(Langmead and Salzberg, 2012). Reads with a mapq score ≥ 30 were retained, using Samtools. Scaling factor was calculated based on the number of mouse and human reads from input and human reads from the ChIP sample.
Assembly: mm10
Supplementary files format and content: bigWig

extract_protocol:
For crosslinking, ESCs with CTCF site mutation in the Car2 promoter (KH105.1 and KH105.2) were dissociated using TrypLE, resuspended in culture medium and counted. 15e6  ESCs were pelleted at 100g for 5 minutes at RT. Supernatant was discarded and cell pellets were resuspended in 5 mL of 10% FBS prepared in 1X PBS. To this, 5 mL of freshly prepared 2% formaldehyde solution was added to get final formaldehyde concentration of 1%. 2% formaldehyde was diluted from 16% methanol-free formaldehyde in 1X PBS (ThermoFisher 28908). Resuspended cells were incubated on rocker to allow for mixing for 10 minutes at RT. Quenching was performed using 0.125M Glycine prepared in 1X PBS and incubated on rocker for 5 minutes at RT. Tubes were then stored on ice for 15 minutes followed by centrifuging at 100g for 5 minutes at 4° C. Supernatant was discarded and cell pellets were washed twice with 5 mL of ice-cold 1X PBS. Cell pellets were resuspended in 1 mL of ice-cold PBS and transferred to 1.5 ml tubes, centrifuged at 100g for 5 minutes at 4° C. Supernatant was discarded and pellets were snap frozen on dry ice and stored at -70°C. Fixed cells were thawed on ice, resuspended in 1 mL of ice-cold lysis buffer [10 mM Tris HCl pH 7.5, 10 mM NaCl, 0.2% NP-40 (IGEPAL), 0.2% TritonX-100, 1 mM EDTA, 0.5 mM EGTA, supplemented with fresh protease inhibitor] and incubated on ice for 10 minutes. 9.75 x 106 ESC nuclei were transferred to a pre-chilled 1.5 mL tube and 0.25 x 106 crosslinked HEK nuclei were added as spike-in. Nuclei were pelleted at 400g for 5 minutes at 4°C, supernatant discarded and nuclear pellets resuspended in 900 μL of shearing buffer (0.5% SDS, 10 mM Tris HCl pH 7.5, supplemented with fresh protease inhibitor). Chromatin was sheared using Covaris with settings PIP 105, Duty factor 5, Cycles per burst 200, total time 15 minutes. After shearing, samples were collected in pre-chilled 1.5 mL tubes and spun at 13,000 rpm for 5 minutes at 4° C. Supernatant was collected in a fresh tube. 5% sample was removed as Input and stored at -20°C. For immunoprecipitation (IP), 40 μl Dynabeads/ChIP were prepared by washing them once in 1 mL of 1X ChIP incubation buffer (diluted from 5X ChIP incubation buffer in 1X PBS; 5% TritonX-100, 0.75 M NaCl, 5 mM EDTA, 2.5 mM EGTA, 50 mM Tris-Cl pH7.5) and resuspended in the 40 μL of same buffer. For IP, tubes were incubated overnight on end-to-end rocker at 10 rpm, 4°C. Following overnight incubation, beads were collected using magnetic rack and washed sequentially with different wash buffers for 5 minutes each on end-to-end rocker at 10 rpm, 4°C. Beads were washed twice with 500 μL of cold wash buffer 1 (0.1% SDS, 0.1% Sodium deoxycholate, 1% TritonX-100, 0.15 M NaCl, 1 mM EDTA, 0.5 mM EGTA, 10 mM Tris pH 8). Beads were then washed once each with 500 μL of cold wash buffer 2 (0.1% SDS, 0.1% Sodium deoxycholate, 1% TritonX-100, 0.5 M NaCl, 1 mM EDTA, 10 mM Tris pH 8) and 500ul of cold wash buffer 3 [0.25 M LiCl, 0.5% Sodium deoxycholate, 0.5% NP-40 (IGEPAL), 1 mM EDTA, 0.5 mM EGTA, 10 mM Tris pH 8]. Finally, beads were washed twice with 500 μL of cold wash buffer 4 (1 mM EDTA, 0.5 mM EGTA, 10 mM Tris pH 8). For elution, beads were resuspended in 200 μL of elution buffer (1% SDS, 0.1M NaHCO3) and incubated on end-to-end rocker at 10 rpm for 20 minutes, RT. Beads were then separated using magnetic rack and the eluate (supernatant) was transferred to a fresh tube. 5% input samples were thawed on ice and elution buffer was added to bring the volume to 200 μL. To each sample, 2 μL of 1 mg/ml RNaseA was added and incubated at 37°C for 30 minutes. For reverse crosslinking, 8 μL of 5 M NaCL and 5 μL of 10 mg/ml Proteinase K was added and incubated overnight at 65°C. Following reverse crosslinking, DNA was eluted using MinElute kit from Qiagen (28604).
Eluted DNA was quantified using Qubit and libraries were prepared using NEBNext Ultra II DNA library prep kit as per manufacturer’s protocol (E7645S). All of ChIP samples and 4 ng of Input samples were used for library prep. Final library amplification was done for 17 cycles, followed by 0.9X SPRI bead purification (Bulldog Bio CNGS005). Eluted in 10 μL of 10 mM Tris-Cl pH7.5. Entire eluate was run on a 2% E-gel (Invitrogen G401002) and fragments between 200-600bp were excised and eluted using MinElute gel extraction kit (Qiagen 28604). Quality and quantity of libraries were assessed using Qubit and Bioanalyzer High Sensitivity DNA kit.

tag: chip antibody

value: CTCF (Active Motif 61311)


title: Sample_37

status: Public on Nov 27 2025

type: genomic

city: Szczecin

first: Tomasz

middle: K

last: Wojdacz

state: Zachodniopomorskie

address: Unii Lubelskiej 1

department: Independent Clinical Epigenetics Laboratory

country: Poland

institute: Pomeranian Medical University

description: DNA extracted from peripheral blood of healthy women with neither BRCA1 mutation nor epimutation (Controls)

hyb_protocol: Bisulfite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human MethylationEPIC Beadchip using standard Illumina protocol

scan_protocol: Arrays were imaged using BeadArray Reader using standard recommended Illumina scanner setting

data_processing: Data were processed in R, normalized using BMIQ normalization.

label: Cy5 and Cy3

molecule: genomic DNA

organism: Homo sapiens

source_name: Healthy woman with neither BRCA1 mutation nor epimutation (Control)

label_protocol: Standard Illumina Protocol

extract_protocol: The DNA from the whole blood samples was extracted using salting out method.

tag: tissue

value: Peripheral Blood

tag: age

tag: Sex

value: F


title: E14_RNAseq_NPC_dTAG13_24h_rep1

type: SRA

city: San Francisco

first: Karissa

middle: Lynn

last: Hansen

state: CA

address: 555 Mission Bay Blvd S, 312

department: CVRI

country: USA

institute: UCSF

library_source: transcriptomic

data_processing:
Reads were trimmed to 100 base pairs as needed using cutadapt.
Alignment of raw RNA-seq data was produced using STAR version 2.7.7a with default parameters and basic two-pass mapping in mm10. GENCODE VM23 (GRCm38.p6) was used as the reference gene set.
bigWig files were generated using bamCoverage (deepTools) separated by strand with BPM normalization.
Assembly: mm10
Supplementary files format and content: Tab delimited text file includes raw counts for each sample
Supplementary files format and content: bigWigs separated by forward and reverse strand and normalized using BPM

molecule: polyA RNA

organism: Mus musculus

growth_protocol: Parental WT E14Tg2a (karyotype 19, XY, 129/Ola isogenic background) mouse ESCs and subclones were cultured in 2iSL medium [DMEM + GlutaMAX + sodium pyruvate (ThermoFisher 10569044) supplemented with 15% fetal bovine serum, 550 µM 2-mercaptoethanol (ThermoFisher 21985-023), 1X nonessential amino acids (ThermoFisher 11140-050), 104 U of Leukemia Inhibitory Factor (Millipore ESG1107), 1µM PD0325901 (Apex Bio/Fischer A3013-25), and 3µM CHIR99021 (Apex Bio/Fischer A3011-100)]. Cells were maintained at a density of 0.2-1.5 x 105 cells/cm2 by passaging using TrypLE (ThermoFisher 12605010) every 24-48 hours on 0.1% gelatin-coated dishes (Sigma-Aldrich G1890-100G) at 37 °C and 7% CO2. The medium was changed daily when cells were not passaged. Cells were checked for mycoplasma infection every 3-4 months and tested negative.

extract_protocol:
Cells were washed with PBS and lysed directly with 1 mL TRIzol (Thermo Fisher 15596-018), transferred to a 1.5 mL tube, vortexed, and incubated at room temperature for 5 minutes. After incubation, mixture was supplemented with 250 µL Chloroform, vortexed again, and centrifuged at 12,000g at 4ºC for 15 minutes. Upper phase was transferred to a new tube, mixed with an equal volume of isopropanol, and spun at 12,000g at 4ºC for 15 minutes. Pellet was washed with 70% ethanol, air dried, and resuspended in 25 µL water.
100-500ng of DNase-treated total RNA was used as input for polyA+ capture and library preparation using the Illumina Stranded mRNA kit (Illumina 20040532)

treatment_protocol: FKBP12 depletion was triggered using 500 nM of PROTAC dTAG-13 (dTAG) (Sigma-Aldrich SML2601) final, diluted in culture medium. AID depletion was triggered using 500 mM of Indole-3-Acetic Acid sodium salt (IAA, auxin analog) (Tocris Bioscience 7932) final, diluted in culture medium.

tag: cell line

tag: cell type

value: neural progenitor cells

tag: genotype

value: WT

tag: treatment


title: E14_RNAseq_NPC_DMSO_24h_rep4


title: Sample_38


title: E14_RNAseq_ESC_DMSO_24h_rep4

value: embryonic stem cells


title: Sample_36


title: Sample_42

description: DNA extracted from peripheral blood of BRCA1 epimutation carriers

source_name: BRCA1 epimutation carrier


title: OGD_R_treatment_rep1

city: Macao Special Administrative Region of China

first: GAO

middle: SHAN

last: SHAN

address: MACAU UNIVERSITY STREE

country: Macau

institute: MACAU UNIVERSITY

description: Library name: OGD_R1

data_processing:
CLC Genomics Workbench v 11.0.1
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample
Supplementary files format and content: files include FPKM values for each Sample
Assembly: human reference genome (GRCh38)

molecule: total RNA

source_name: hCMEC

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

value: hCMEC


title: E14_RNAseq_ESC_DMSO_24h_rep3


title: Sample_35


title: E14_RNAseq_ESC_DMSO_24h_rep2


title: E14_RNAseq_NPC_DMSO_24h_rep3


title: E14_RNAseq_NPC_DMSO_24h_rep1


title: Sample_39


title: DGP1-OE1, Ck, rep3

city: Yangzhou

first: Mingnan

last: Qu

state: Jiangsu

address: Pazhou Dadao Rd, 17-19

country: China

institute: Yangzhou Univerisity

description:
Library name: DGP1-OE1-3
DGP1-OE1-3

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm8 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata.
Reads Per Kilobase of exon per Megabase of library size (FPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Data filtering steps.Prior to assembly, the low quality reads(1,reads containing sequencing adaptors; 2,reads containing sequencing primer;3, nucleotide with q quality score lower than 20 )were removed .software CutAdapter,parameters -o 5 -p 100.
Read alignment software,software HISAT ,version 2.0 ,parameters -l fr-firststrand -mi 20 -mx 500000 -p 2 -b dta -q phred33-quals -x 9.
Perform expression level for mRNAs by calculating FPKM.stimate the expression levels of all transcripts.software StringTie ,version 1.3.0,parameters -b dta -q phred33-quals.
Assembly: msu7.0
Supplementary files format and content: FPKM values for each Sample.

organism: Oryza sativa

source_name: leaf

growth_protocol: All the plant materials  were grown in 1/2MS medium under normal conditions.

extract_protocol:
Total RNA was extracted from rice leaves using a Trelief® RNApre Pure Plant Kit (tsingke, code: TSP411) according to the manufacturer’s instructions.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: The leaves of 3-week-old rice plants were collected.

value: leaf

value: leaf cells


title: OGD_treatment_rep2

description: Library name: OGD2


title: KH105.2_mutCBS-Car2-prom_ESC_CTCF

library_source: genomic


title: Sample_33


title: Fresh tumor, B16F10 tumor bearing mice treated with M44 vaccine and TIGIT antibody

city: Nanjing

first: Chun

last: Lu

address: No. 8 Xuefu Road, Pukou

institute: Nanjing University

description: 10X Genomics

library_source: transcriptomic single cell

data_processing:
Raw reads of scRNA-seq were aligned and quantified with the CellRanger pipeline (v5.0.1, 10X Genomics) against GRCm38 reference genome to generate a matrix of unique molecular identifier (UMI) counts by cell barcodes.
UMI data were imported into Seurat (v4.1.1) for downstream analysis.
Assembly: GRCm38
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Fresh tumor

extract_protocol:
The tumors were sliced into roughly 1 mm3 pieces and placed in RPMI-1640 medium containing 2% FBS. The tissues were then subjected to enzymatic digestion using the MACS Tumor Dissociation Kit (Miltenyi Biotec, #130-096-730, DE) on a gentleMACS Dissociator for 40 min, following the manufacturer's instructions. The dissociated cells were then filtered with 70 μm cell strainers, centrifuged and resuspended in MACS buffer (Miltenyi Biotec, #130-091-221, DE). After counting, CD45 (TIL) MicroBeads (Miltenyi Biotec, #130-110-618, DE) were used for isolating the CD45+ immune cells for scRNA-seq.
The CD45+ immune cell suspensions were added to Chromium microfluidic chips and barcoded with a 10X Chromium Controller (10X Genomics, Shanghai Genechem Co.,Ltd). RNA from the barcoded cells was subsequently reverse-transcribed into cDNA. The cDNA was processed with a Chromium Single Cell 3’ v2 reagent kit (10X Genomics) to construct sequencing libraries according to the manufacturer’s instructions

value: Fresh tumor

value: CD45+ immune cells


title: Sample_34


title: OGD_treatment_rep1

description: Library name: OGD1


title: DGP1-OE1, Ck, rep2

description:
Library name: DGP1-OE1-2
DGP1-OE1-2


title: Fresh tumor, B16F10 tumor bearing mice treated with M44 vaccine

description: 10X Genomics


title: Sample_32


title: DGP1-OE1, Ck, rep1

description:
Library name: DGP1-OE1-1
DGP1-OE1-1


title: ZH11, Ck, rep3

description:
Library name: ZH11-3
ZH11-3


title: HEK293 shControl heat shock 42°C 30 min rep2

city: Chapel Hill

first: Jonathan

middle: C

last: Schisler

state: NC

address: MBRB, Rm 2340C

department: McAllister Heart Institute

institute: The University of North Carolina at Chapel Hill

description:
Library name: SHCTL42-2
Control HEK293 cells after acute heat shock

data_processing:
Raw FASTQ files were quality-checked using FastQC v0.11.9. Adapter sequences and low-quality bases (Phred < 20) were trimmed from the 3′ ends using Trim Galore! v0.6.7 (Cutadapt wrapper).
The resulting 50 bp single-end reads were aligned to the human reference genome GRCh38.p13 (primary assembly) using STAR v2.7.8a in 2-pass mode with Ensembl gene annotations (release 105).
Gene-level quantification was performed in Partek® Flow® v10.0 using the Partek E/M algorithm. Only uniquely mapping reads that overlapped annotated exons were counted.
Differential expression analysis was performed in Partek Flow using DESeq2 with median-of-ratios normalization.
Normalization and log2 transformation performed in Partek® Flow® v10.0 using recommended Total Count method followed by Add pseudocount 0.001 (equivalent to log2(CPM + 0.0001)). This is Partek's default recommended pipeline for raw count data from Quantify to annotation model (Partek E/M).
Assembly: GRCh38.p13 (Ensembl release 105)
Supplementary files format and content: raw_counts.txt: tab-delimited matrix of raw gene counts (rows = genes, columns = library names exactly matching above, first column = Ensembl gene ID)
Supplementary files format and content: log2cpm_filtered.txt: tab-delimited matrix of log2(CPM + 0.001) values for 15,475 filtered genes (rows = genes, columns = library names exactly matching above, first column = Ensembl gene ID). Lowly expressed genes were filtered out (removed if < 1 count per million in fewer than 30% of samples) prior to CPM calculation, normalization, and log2 transformation with pseudocount 0.0001.

growth_protocol: HEK293 cells (ATCC CRL-1573) were cultured in Dulbecco’s Modified Eagle Medium (DMEM) supplemented with 10% fetal bovine serum, 100 U/mL penicillin, and 100 µg/mL streptomycin at 37°C in a humidified atmosphere containing 5% CO₂. Stable knockdown cell lines expressing shRNA against STUB1 (shSTUB1/shCHIP) or non-targeting control shRNA (shCTL) were maintained under selection with 2–5 µg/mL puromycin.

extract_protocol:
Immediately after the treatment timepoint, culture medium was aspirated and cells were lysed directly on the plate by addition of RLT buffer (QIAGEN). Total RNA was then extracted using the RNeasy Mini Kit (QIAGEN cat. no. 74104) with on-column DNase I digestion (QIAGEN RNase-Free DNase Set, cat. no. 79254) according to the manufacturer’s instructions, including the optional β-mercaptoethanol step in RLT for complete denaturation. RNA concentration and purity were assessed by NanoDrop; integrity was confirmed by Agilent Bioanalyzer 2100 (RIN ≥ 8.0 for all samples).
Polyadenylated mRNA was purified from 500–1000 ng total RNA and sequencing libraries were prepared using the Illumina TruSeq RNA Sample Preparation Kit v2 (cat. no. RS-122-2001 or RS-122-2002) following the manufacturer’s low-throughput protocol. Libraries were amplified for 15 PCR cycles and size-selected for ~200–300 bp inserts. Final library quantity and quality were assessed by Qubit and Agilent Bioanalyzer. Indexed libraries were pooled equimolarly (6-plex per lane) and clustered using the Illumina cBot. Sequencing was performed single-end 50 cycles on an Illumina HiSeq 2500 using v3 or v4 chemistry at the University of North Carolina High-Throughput Sequencing Facility (HTSF).

treatment_protocol: Cells were seeded at ~50–60% confluence 24–48 h prior to experiment. For heat-shock samples, culture plates were sealed with paraffin film and submerged in a precision water bath pre-set to 42°C (±0.1°C) for exactly 30 minutes. Immediately after the 30-minute heat shock, cells were lysed directly on the plate by addition of RLT buffer (QIAGEN RNeasy kit) — no recovery period at 37°C was allowed. Control plates (37°C) were lysed in parallel by direct addition of RLT buffer.

value: embryonic kidney cell

value: non-targeting control shRNA

value: heat shock 42°C 30 minutes


title: HEK293 shControl heat shock 42°C 30 min rep3

description:
Library name: SHCTL42-3
Control HEK293 cells after acute heat shock


title: Fresh tumor, B16F10 tumor bearing mice treated with saline

description: 10X Genomics


title: Fresh tumor 5, B16F10 tumor bearing mice treated with M44 vaccine

description: RNA-seq

data_processing:
Reads were mapped to the mouse genome Mus musculus GRCm39 release-109 using STAR (V.2.7.8) and quantified by featureCounts (V.1.6.4)
To normalize gene length and sequencing depth, TPM (transcripts per million) were used to measure gene or transcript expression levels.
Assembly: GRCm39
Supplementary files format and content: comma-separated values (csv) file includes raw counts for each sample
Supplementary files format and content: comma-separated values (csv) file includes TPM for each sample

extract_protocol:
Fresh tumor tissue was frozen in liquid nitrogen after dissection and then stored at -80 ℃. RNA was extracted from the tumors using the RNeasy Plus Mini Kit (Cat#74134, Qiagen, DE).
RNA libraries for RNA-seq were prepared using Illumina TruseqTM RNA sample prep Kit following manufacturer's protocols.

value: Mouse melanoma cells

value: M44 vaccine


title: HEK293 shControl heat shock 42°C 30 min rep1

description:
Library name: SHCTL42-1
Control HEK293 cells after acute heat shock


title: OGD_treatment_rep3

description: Library name: OGD3


title: ZH11, Ck, rep2

description:
Library name: ZH11-2
ZH11-2


title: Sample_30


title: HEK293 shControl 37°C control rep3

description:
Library name: SHCTL37-3
Control HEK293 cells, basal conditions

value: none (37°C control)


title: ZH11, Ck, rep1

description:
Library name: ZH11-1
ZH11-1


title: Fresh tumor 4, B16F10 tumor bearing mice treated with M44 vaccine

description: RNA-seq


title: HEK293 shControl 37°C control rep2

description:
Library name: SHCTL37-2
Control HEK293 cells, basal conditions


title: DSID65 Fetal membranes (twin B)

city: Chicago

first: William

last: Ackerman

state: Illinois

address: 820 South Wood Street, MC 808, Dept. of Obstetrics & Gynecology

department: Obstetrics and Gynecology

institute: University of Illinois Chicago College of Medicine

description: Library name: DSID65_FM_twB

data_processing:
Sequenced reads were mapped to the SILVA 132 database using QIIME2-2017.2. An operational taxonomic units (OTU) table was generated which contained the OTUs identified in each sample along with the number of sequence reads and the taxonomic classification of each OTU. The classification was further collapsed at either genera, family, order or phylum level for subsequent analyses using the MicrobialAnalyst web-based platform. Because blood samples were expected to have low number of reads, we thought it more important to be inclusive of low abundance taxa even if these could represent sequencing errors, therefore the default R code was modified to exclude the abundance filters. The Chao-1 index (measure of α-diversity) was used to estimate OTU richness in different types of samples. Enrichment of taxa between groups was further analyzed by LEfSe (linear discriminant analysis effect size) and EdgeR methods built within the platform. These computational algorithms designed primarily for highly multidimensional data, employ a combination of statistical tests to extract features (e.g. OTU) that show significant differences in abundance (enrichment) in different samples while accounting for the effect size of the differences.
Assembly: SILVA_132 reference database
Supplementary files format and content: OTU counts for each sample (tab delimited) and corresponding OTU table

organism: human metagenome

source_name: full thickness amniochorion

extract_protocol:
All specimens were collected using sterile gloves, and all procedures were carried out under strict sterile conditions. For sequencing of 16S RNA genes and microbial community analysis, genomic DNA was extracted and the 16S rRNA amplified using V4 primers. 16S amplicon multiplex libraries were sequenced on Illumina platform at the Sequencing Facility of the Argonne National Laboratory.
Genomic DNA was amplified using primers targeting the V4 region of the 16S rRNA gene with Illumina overhang adapters. Amplicon PCR was performed with KAPA HiFi HotStart ReadyMix under the following conditions: 95 °C for 3 min; 25 cycles of 95 °C for 30 s, 55 °C for 30 s, 72 °C for 30 s; final extension at 72 °C for 5 min. PCR products were purified using AMPure XP beads (0.8× ratio). Dual indices and Illumina sequencing adapters were added in a second PCR (8 cycles) using Nextera XT index primers, followed by another AMPure XP bead cleanup. Libraries were quantified with Qubit and validated for size using Bioanalyzer. Equimolar pooling was performed prior to sequencing on an Illumina MiSeq platform (paired-end).

value: full thickness amniochorion


title: Sample_27

value: Peripheral Blood


title: HEK293 shSTUB1 heat shock 42°C 30 min rep3

description:
Library name: SHCHIP42-3
HEK293 cells with STUB1 knockdown after acute heat shock

value: STUB1 knockdown (stable shRNA)


title: Fresh tumor 1, B16F10 tumor bearing mice treated with M44 vaccine

description: RNA-seq


title: Fresh tumor 5, B16F10 tumor bearing mice treated with saline

description: RNA-seq

value: saline


title: Sample_28

value: F


title: Sample_29


title: HEK293 shControl 37°C control rep1

description:
Library name: SHCTL37-1
Control HEK293 cells, basal conditions


title: Sample_31


title: Sample_25


title: Fresh tumor 2, B16F10 tumor bearing mice treated with M44 vaccine

description: RNA-seq


title: DSID65 Placenta (twin A)

description: Library name: DSID65_PLAC_twA

source_name: villous placental tissue

value: villous placental tissue


title: Sample_24


title: DSID63 Placenta

description: Library name: DSID63_PLAC


title: Sample_23


title: DSID63 Fetal membranes

description: Library name: DSID63_FM


title: Fresh tumor 3, B16F10 tumor bearing mice treated with saline

description: RNA-seq


title: Fresh tumor 3, B16F10 tumor bearing mice treated with M44 vaccine

description: RNA-seq


title: Fresh tumor 2, B16F10 tumor bearing mice treated with saline

description: RNA-seq


title: HEK293 shSTUB1 37°C control rep3

description:
Library name: SHCHIP37-3
HEK293 cells with STUB1 knockdown, basal conditions


title: HEK293 shSTUB1 heat shock 42°C 30 min rep2

description:
Library name: SHCHIP42-2
HEK293 cells with STUB1 knockdown after acute heat shock


title: DSID65 Placenta (twin B)

description: Library name: DSID65_PLAC_twB


title: DSID62 Placenta

description: Library name: DSID62_PLAC


title: DSID65 Fetal membranes (twin A)

description: Library name: DSID65_FM_twA


title: Sample_22


title: HEK293 shSTUB1 heat shock 42°C 30 min rep1

description:
Library name: SHCHIP42-1
HEK293 cells with STUB1 knockdown after acute heat shock


title: Fresh tumor 4, B16F10 tumor bearing mice treated with saline

description: RNA-seq


title: Fresh tumor 1, B16F10 tumor bearing mice treated with saline

description: RNA-seq


title: DSID62 Fetal membranes

description: Library name: DSID62_FM


title: Sample_26


title: Recql4 mutant, day 9

city: Meblourne

first: Alistair

middle: Morgan

last: Chalk

state: VIC

address: 1G Royal Parade

department: Bioinformatics

country: Australia

institute: WEHI

data_processing:
CRISPR screen analysis was performed using CRISPR-Beta-Binomial package (CB2 ) (v 1.3.0). To measure differences in sgRNA levels, CB2 combines a beta-binomial model with a modified Student’s t-test. Next, to estimate gene-level significance, a Fisher’s combined probability test was conducted. Raw reads were mapped to the broadgpp_brie_crispr library with run_sgrna_quant() and read counts were normalised with get_CPM(). Gene level statistics were calculated using measure_gene_stats(). Annotation with ENSEMBL was performed with biomaRt.
Assembly: mm10
Supplementary files format and content: CB2_Recql4_Screen_count_data.tsv
Library strategy: DNA-seq of PCR amplified integrated sgRNA

source_name: cell line

extract_protocol:
Genomic DNA was extracted from the cell pellets using the Gentra Puregene kit (Qiagen). The extracted DNA was quantified on a Nanodrop spectrophotometer.
DNA libraries were generated by PCR amplification of the integrated sgRNA constructs (as described in https://portals.broadinstitute.org/gpp/public /resources/protocols).

value: cell line

value: Myeloid cell line

value: R26-CreERT2 Recql4fl/R347X

value: tamoxifen


title: Sample_20


title: Input 2

city: Sendai

first: Masayuki

last: Yamamoto

state: Miyagi

address: 2-1 Seiryo-cho, Aoba-ku

country: Japan

institute: Tohoku University Graduate School of Medicine

description: Library name: Sample 6

data_processing:
Illumina bcl2fastq v2.15.0 software used for basecalling.
Raw sequenced reads were mapped into hg38 using BWA 0.7.17.
Peaks were called with MACS2 version 2.2.7.1
Assembly: GRCm38/hg38
Supplementary files format and content: bed files were generated using MACS.

growth_protocol: HMC3 cells (CRL-3304) were maintained in Eagle’s Minimum Essential Medium (EMEM; 051-07615, FUJIFILM Wako) supplemented with 10% fetal bovine serum, 1 mM sodium pyruvate, non-essential amino acids, 70 mg/L penicillin G, and 100 mg/L streptomycin (FUJIFILM Wako). Cells were cultured in a humidified incubator at 37°C with 95% humidity and 5% CO₂.

extract_protocol:
The cells were fixed with 1% formaldehyde for 10 min at room temperature and subsequently quenched with 0.125-M glycine. ChIP was performed with anti-Nrf2 antibody (Cell Signaling Technology; D1Z9C).The antibody incubation were pereformed overnight at 4 °C.
The DNA libraries were prepared from 2 ng of ChIP and input samples quantified with a Qubit Fluorometer (Life Technologies), using the NEB kit. Libraries were prepared for sequencing following standard Illumina protocols.

treatment_protocol: HMC3 cells were treated with CDDO-Im (30 nM) for 4 hours.


title: Recql4 mutant, day 4


title: DSID58 Placenta

description: Library name: DSID58_PLAC


title: Input 1

description: Library name: Sample 5


title: Sample_21


title: DSID58 Fetal membranes

description: Library name: DSID58_FM


title: HEK293 shSTUB1 37°C control rep2

description:
Library name: SHCHIP37-2
HEK293 cells with STUB1 knockdown, basal conditions


title: Recql4 mutant, day 0


title: CDDO-Im_ChIP 2

description: Library name: Sample 4

value: NRF2 (Cell Signaling Technology; D1Z9C)


title: Sample_18

description: DNA extracted from peripheral blood of women with neither BRCA1 mutation nor epimutation prior BC diagnosis

source_name: Woman with neither BRCA1 mutation nor epimutation prior BC diagnosis


title: DSID57 Placenta

description: Library name: DSID57_PLAC


title: Sample_17


title: Veh_ChIP 2

description: Library name: Sample 2


title: DSID57 Fetal membranes

description: Library name: DSID57_FM


title: Veh_ChIP 1

description: Library name: Sample 1


title: Sample_15


title: Recql4 control, day 0

value: R26-CreERT2 Recql4fl/+


title: Recql4 control, day 4


title: DSID50 Placenta

description: Library name: DSID50_PLAC


title: DSID50 Fetal membranes

description: Library name: DSID50_FM


title: input_H, 5~6 year-old, rep2

city: Alar City, Xinjiang Uygur Autonomous Region

first: linlin

last: pei

state: Aral

address: Alar City Happy Road Street

institute: Tarim university

description: Library name: sample 4

data_processing:
MeTDiff software was used to identify m6A-enriched peaks in each m6A IP sample, with the INPUT sample as a control.Differential methylation peaks (DMPs) between groups were detected using MeTDiff (parameter: FRAGMENT_LENGTH = 200. Screening criteria: p < 0.05, fc > 1.5) and annotated using ChIPseeker software.Differentially expressed genes (DEGs) were analysed using DESeq2 software (screening criteria: q < 0.05, foldchange > 2 or foldchange < 0.5). GO and KEGG enrichment analyses of DMPs and DEGs were performed by the hypergeometric distribution test to determine the biological function or pathway that the gene where the peak is located primarily affects. GO analyses were performed using tools provided by the Gene Ontology Consortium (http://www.geneontology.org). KEGG analysisKEGG analysis was performed using tools provided by Kyoto Encyclopedia of Genes and Genomes (https://www.genome.jp/kegg/). A Python (v.2.7.12) script was used to correlate the content of the two histologies and to compare both transcription and methylation levels.
Assembly: GCF_016772045.1
Supplementary files format and content: D.peak.mRNA.annotation.xls
Supplementary files format and content: H.peak.mRNA.annotation.xls

organism: Ovis aries

source_name: ovarian tissue

extract_protocol:
Total RNA was extracted from ovarian tissues using Trizol lysis (Invitrogen, CA, USA). Additionally, genomic DNA was removed using the rDNAIR-free enzyme (TaKara). The genomic DNA was extracted and analyzed using a Bioanalyzer 2100 (Agilent Technologies, Santa Clara, CA, USA) and a NanoDrop 2000 (Thermo Fisher Scientific, Waltham, MA, USA) to verify RNA quality. Qualified RNA used for sequencing library construction had an OD 260/280 ratio of ≥ 1.8, a RIN of ≥ 8, and exhibited significantly brighter 28S bands compared to 18S bands. The RNA concentration of all samples was 200 ng/μL.
Quality-qualified RNA was used for library construction according to the TruSeq stranded total RNA kit (Illumina, San Diego, CA).High-throughput sequencing was performed using the Illumina NovaSeq 6000 sequencing platform (OE Biotech Co., Ltd., Shanghai, China).

value: ovarian tissue

value: 5-6 years

tag: rip antibody

value: none (input)


title: Sample_19


title: HEK293 shSTUB1 37°C control rep1

description:
Library name: SHCHIP37-1
HEK293 cells with STUB1 knockdown, basal conditions

value: embryonic kidney cell


title: DSID47 Placenta

description: Library name: DSID47_PLAC


title: CDDO-Im_ChIP 1

description: Library name: Sample 3


title: Sample_16


title: Sample_14


title: Sample_13


title: Recql4 DKO rescue, day 9

description: Recql4 DKO rescue, day 9

data_processing:
CRISPR screen analysis was performed using CRISPR-Beta-Binomial package (CB2 ) (v 1.3.0). To measure differences in sgRNA levels, CB2 combines a beta-binomial model with a modified Student’s t-test. Next, to estimate gene-level significance, a Fisher’s combined probability test was conducted. Raw reads were mapped to the broadgpp_brie_crispr library with run_sgrna_quant() and read counts were normalised with get_CPM(). Gene level statistics were calculated using measure_gene_stats(). Annotation with ENSEMBL was performed with biomaRt.
Assembly: mm10
Supplementary files format and content: CB2_Recql4_dropout_Screen_count_data.tsv : Tab seperated count data calculated using CB2.
Supplementary files format and content: CB2_Recql4_dropout_Screen_count_data_cpm.tsv : Tab seperated counts-per-million count data calculated using CB2.

extract_protocol:
Genomic DNA was extracted from the cell pellets using the Gentra Puregene kit (Qiagen). The extracted DNA was quantified on a Nanodrop spectrophotometer.
DNA libraries were generated by PCR amplification of the integrated sgRNA constructs (as described in https://portals.broadinstitute.org/gpp/public /resources/protocols).
DNA-seq of PCR amplified integrated sgRNA

tag: day

value: R26-CreERT2 Recql4-/- sgKlhdc3


title: DSID47 Fetal membranes

description: Library name: DSID47_FM

value: full thickness amniochorion


title: input_D, 1~2 year-old, rep1

description: Library name: sample 2

value: 1-2 years


title: DSID45 Placenta

description: Library name: DSID45_PLAC


title: Recql4 RRE control, day 5

description: Recql4 RRE control, day 5

value: R26-CreERT2 Recql4-/- sgKlhdc3 mCherry-Recql4


title: Recql4 control, day 9


title: IP_D, 1~2 year-old, rep1

description: Library name: sample 1

data_processing:
MeTDiff software was used to identify m6A-enriched peaks in each m6A IP sample, with the INPUT sample as a control.Differential methylation peaks (DMPs) between groups were detected using MeTDiff (parameter: FRAGMENT_LENGTH = 200. Screening criteria: p < 0.05, fc > 1.5) and annotated using ChIPseeker software.Differentially expressed genes (DEGs) were analysed using DESeq2 software (screening criteria: q < 0.05, foldchange > 2 or foldchange < 0.5). GO and KEGG enrichment analyses of DMPs and DEGs were performed by the hypergeometric distribution test to determine the biological function or pathway that the gene where the peak is located primarily affects. GO analyses were performed using tools provided by the Gene Ontology Consortium (http://www.geneontology.org). KEGG analysisKEGG analysis was performed using tools provided by Kyoto Encyclopedia of Genes and Genomes (https://www.genome.jp/kegg/). A Python (v.2.7.12) script was used to correlate the content of the two histologies and to compare both transcription and methylation levels.
Assembly: GCF_016772045.1
Supplementary files format and content: D.peak.mRNA.annotation.xls
Supplementary files format and content: H.peak.mRNA.annotation.xls
Library strategy: MeRIP-seq


title: Recql4 DKO rescue, day 5

description: Recql4 DKO rescue, day 5


title: Sample_12

value: Peripheral Blood


title: IP_H, 5~6 year-old, rep2

description: Library name: sample 3


title: Sample_11

value: F


title: NIPBL-FKBP mESC-derived gastruloids +dTAG at 96h replicate 2

description: Library name: NIPBL_gast_96_rep2

data_processing:
ATAC-seq reads underwent mapping using bwa mem v0.7.17-r1188123 to the mm10 mouse reference genome assembly. Reads that were uniquely mapped and not assigned to mitochondrial DNA, with MAPQ > 10, were retained through selection using SAMtools v1.12.  Duplicate reads were then removed using the Picard v2.25.6 “MarkDuplicates” function.
To decipher the cell type compositions within bulk ATAC-seq samples from both control and NIPBL-depleted gastruloids, a previously published single-cell ATAC-seq atlas of gastruloid development was used (Braccioli et al, 2025). Initially, pseudobulk ATAC-seq profiles for each cell type (cluster) were generated from single-cell data by summing counts in each peak across all cells belonging to the same clusters. Subsequently, read counts of DMSO and dTAG treated bulk samples within the same peak set utilized in the single-cell data were generated. These bulk and pseudobulk counts were then concatenated, normalized using the median of ratios normalization method implemented in DESeq2 v1.30.1147, and transformed using the variance stabilizing transform (VST).
Independent component analysis (ICA) was employed to decipher the contributions of constituent cell types in the bulk samples. ICA was conducted on VST-transformed and zero-centered pseudobulk counts using the FastICA algorithm, implemented in the “icafast” function from the ica R package. The number of components was set to 7 with a maximum of 100 algorithm iterations. The source signal estimates and the unmixing matrix obtained from ICA were then applied to the VST-transformed bulk count matrix to deconvolve the cell type contributions. Finally, cell type proportion estimates were derived by setting the negative contributions to zero and normalizing contributions to the sum of the contributions for each sample.
Assembly: mm10
Supplementary files format and content: BigWig files with ATAC-seq signal - Compressed, indexed, binary files for visualizing continuous genomic data.

growth_protocol: Before the aggregation of gastruloids, NIPBL-FKBP ESCs were maintained in 2i-LIF medium, comprising a mixture of 50% DMEM/F12 (Thermo Fisher Scientific 11320-033) and 50% Neurobasal media (Thermo Fisher Scientific 21103-049). This medium was supplemented with 0.5X N2 (Thermo Fisher Scientific 17502-048), 0.5X B27 + retinoic acid (Thermo Fisher Scientific 17504-044), 0.05% BSA (Thermo Fisher Scientific), 3 μM CHIR99021 (BioConnect), 1 μM PD03259010 (BioConnect), 2 mΜ Glutamine (Thermo Fisher Scientific), 1.5 × 10-4 M 1-thioglycerol (Sigma-Aldrich), 100 U/mL LIF (BioConnect, GFM200-5), and 50 U/mL penicillin-streptomycin (Thermo Fisher Scientific). These cells were cultured on gelatin-coated 10 cm petri dishes within a humidified incubator set at 5% CO2 and 37ºC. The protocol for gastruloid culture followed previously established methods (71). Briefly, gastruloids were formed through the aggregation of ESCs in differentiation medium (N2B27). This medium consisted of a mix of DMEM/F12 and Neurobasal medium, supplemented with 2mΜ Glutamine, β-mercaptoethanol, and 50 U/mL penicillin-streptomycin. U-bottom 96-well plates (Thermo Fisher Scientific) were employed for culture, and the process was conducted in a humidified incubator maintained at 5% CO2 and 37ºC. Cell dissociation was carried out in N2B27 medium using a serological pipette in conjunction with a 200 µL pipette tip. Subsequently, 3.75×104 cells were transferred into N2B27 medium, resulting in a final volume of 5 mL. Each well received a 40 µL aliquot of this suspension, containing approximately 300 cells. After 48 hours, 150 µL of N2B27 medium containing 3 μM CHIR99021 was added using the Hamilton Star R&D liquid handling platform.

extract_protocol:
At 120 hours, gastruloids were fixed with 4% formaldehyde for 30 minutes at RT (Sigma-Aldrich), underwent a single wash with PBS, and were subsequently stored at 4ºC. Gastruloids were dissociated into a single-cell suspension through gentle trypsinization and frozen with the addition of 10% DMSO and 10% fetal bovine serum. These samples were then stored at -70ºC until further use.
The Tn5 protein purification was carried out by the NKI protein facility as previously described (Braccioli et al., 2025). Transposon annealing was achieved by combining 10 µL of 10X TE buffer with 45 µL each of 100 µM Tn5MErev oligonucleotides and 100 µM corresponding Tn5ME-A and Tn5ME-B oligonucleotides. The adapter solution was then subjected to incubation at 95ºC for 10 minutes followed by gradual cooling to 4ºC at a rate of 0.1ºC per second. For transposome formation, the annealed adapters were diluted with an equal volume of H2O. This resulting adapter solution was mixed with 0.2 mg/mL Tn5 at a 1:20 ratio and incubated for 1 hour at 37ºC. The transposomes were either utilized immediately for tagmentation or stored at -20ºC for up to 2 weeks. A total of 50,000 cells were collected in cold PBS and lysed using a 2X lysis buffer (1M Tris-HCl pH 7.5, 5M NaCl, 1M MgCl2, 10% IGEPAL). Following centrifugation, the resulting pellet was treated with 2X TD buffer and 2 µL of transposon mix. PCR amplification was performed twice using KAPA HiFi HotStart ReadyMix (Roche) and P5 and P7 indexed primers (please refer to the oligonucleotide list). Fragments ranging from 200 to 700 bp were purified using AMPure XP beads (Beckman Coulter), and the DNA quality was assessed through Bioanalyzer High Sensitivity DNA analysis (Agilent). ATAC-seq oligos available in Supplementary Table S1.

treatment_protocol: Degradation of proteins tagged with the FKBP degron [FKBP12-F36V] was induced by adding dTAG-13 (abbreviated dTAG; Sigma Cat, SML2601) to a final concentration of 500 nM (from a 1000X filter-sterilized stock diluted in DMSO) at the specified time point. Starting from the subsequent day, the culture medium was refreshed with fresh N2B27 medium daily.

value: embryonic stem cell-derived gastruloid

value: dTAG13 at 96h


title: Recql4 RRE control, day 9

description: Recql4 RRE control, day 9

value: cell line

value: Myeloid cell line


title: Recql4 RRE control, day 2

description: Recql4 RRE control, day 2


title: DSID42 Placenta

description: Library name: DSID42_PLAC

value: villous placental tissue


title: NIPBL-FKBP mESC-derived gastruloids +dTAG at 72h replicate 2

description: Library name: NIPBL_gast_72_rep2

value: dTAG13 at 72h


title: Sample_9


title: DSID42 Fetal membranes

description: Library name: DSID42_FM


title: Recql4 RRE control, day 0

description: Recql4 RRE control, day 0


title: Sample_10


title: DSID41 Placenta

description: Library name: DSID41_PLAC


title: DSID41 Fetal membranes

description: Library name: DSID41_FM


title: Sample_7


title: NIPBL-FKBP mESC-derived gastruloidsDMSO treated replicate 2

description: Library name: NIPBL_gast_NT_rep2

value: DMSO


title: Sample_8


title: Recql4 DKO rescue, day 0

description: Recql4 DKO rescue, day 0


title: NIPBL-FKBP mESC-derived gastruloids +dTAG at 96h replicate 1

description: Library name: NIPBL_gast_96_rep1


title: NIPBL-FKBP mESC-derived gastruloids +dTAG at 72h replicate 1

description: Library name: NIPBL_gast_72_rep1


title: naive CD4+ T cells, Nudt21 KO2, 0H

city: shanghai

first: Xingli

last: Zhang

address: 280 Chongqing South Rd

institute: Shanghai Jiao Tong University School of Medicine

data_processing:
Transcriptomic reads from the RNA-Seq experiments were mapped to a reference genome (mm10) using Bowtie.
Differentially expressed genes were subsequently analyzed using the DAVID bioinformatics platform and IPA.
The well-established algorithm DaPars (https://github.com/ZhengXia/DaPars) was used to identify the alternative proximal polyA site and calculate the Percentage of Distal polyA site Usage Index (PDUI) for each transcript
Assembly: mm10
Supplementary files format and content: txt file include  FPKM values for each gene in samples

source_name: naive CD4+ T cells

growth_protocol: Naïve CD4+ T cells were sorted from spleen and lymph nodes and cultured with anti-CD3/CD28 for 0hr or 48hr in 1640 medium.

extract_protocol:
Total RNA was extracted using Trizol Reagent (Invitrogen) following standard protocols and subjected to RNA-Seq performed by Novogene. Paired-end RNA-Seq was performed to yield more than 100 million reads per sample, which allowed us to obtain not only transcript expression but also alternative PAS usage.Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: anti-CD3/CD28 for 0hr or 48hr

tag: strain

value: sorted naive CD4+ T cells

value: no treatment


title: DSID38 Placenta (twin B)

description: Library name: DSID38_PLAC_twB


title: Sample_6


title: DSID45 Fetal membranes

description: Library name: DSID45_FM


title: DSID38 Fetal membranes (twin B)

description: Library name: DSID38_FM_twB


title: Sample_5


title: NIPBL-FKBP mESC-derived gastruloids +dTAG at 48h replicate 2

description: Library name: NIPBL_gast_48_rep2

value: dTAG13 at 48h


title: NIPBL-FKBP mESC-derived gastruloids +dTAG at 48h replicate 1

description: Library name: NIPBL_gast_48_rep1


title: Recql4 DKO rescue, day 2

description: Recql4 DKO rescue, day 2


title: naive CD4+ T cells, Nudt21 WT2, 0H

value: wild type


title: DSID38 Placenta (twin A)

description: Library name: DSID38_PLAC_twA


title: naive CD4+ T cells, Nudt21 WT1, 0H


title: NIPBL-FKBP mESC-derived gastruloids DMSO treated replicate 1

description: Library name: NIPBL_gast_NT_rep1


title: DSID38 Fetal membranes (twin A)

description: Library name: DSID38_FM_twA


title: Sample_3


title: DSID36 Placenta

description: Library name: DSID36_PLAC


title: CD201+CD150+KSL wild-type cultured HSC CUT&Tag H3K4me3

city: Oxford

first: Catherine

last: Chahrour

address: MRC Weatherall Institute of Molecular Medicine

country: United Kingdom

institute: University of Oxford

description: Library name: mHSC-wt-1_H3K4me3

data_processing:
FASTQ files were quality checked using FastQC version v0.12.1.
Adapter sequences were removed and low quality reads were trimmed using trim_galore version 0.6.10 using the following parameters: --2colour 20.
Reads were aligned to the reference genome mm39 using Bowtie2 (v2.5.1)
Bigwigs were produced using deeptools bamCoverage (v3.5.1) with RPKM normalisation.
Assembly: mm39
Supplementary files format and content: tsv file containing raw counts
Library strategy: CUT&Tag

source_name: Bone Marrow

extract_protocol:
FACS sorted cells were pelleted at 300 x g for 10 mins at RT before resuspending in 1 ml NE1 buffer (20 mM HEPES-KOH pH 7.9, 10 mM KCl, 0.5 mM spermidine, 0.1% Triton X-100, 20% glycerol, 1× Complete Protease Inhibitor [EDTA-free]) and incubating on ice for 10 mins. Nuclei were pelleted at 500 x g for 10 mins at 4 C before resuspending in 0.1% formaldehyde and incubating at RT for 2 mins, followed by quenching with 78 mM Glycine and pelleting the nuclei at 500 x g for 10 mins at 4°C. Nuclei were resuspended in Wash Buffer (20 mM HEPES pH 7.5, 150 mM NaCl, 0.5 mM spermidine, 1× Roche Complete Protease Inhibitor [EDTA-free]) and counted by trypan blue staining. Concanavalin A (Con A) beads were activated by washing (2x) with 1 ml Concanavalin Activation Buffer (20 mM HEPES-KOH pH 7.9, 10 mM KCl, 1 mM CaCl₂, 1 mM MnCl₂). For each antibody/sample combination, 5 ul of activated ConA beads were added to 5x104 . Nuclei were incubated with 0.5 ul of primary antibody (antibodies listed in Supplementary Table 3) in 25 ul of antibody buffer (0.1% BSA, 2 mM EDTA in Wash Buffer) for either 1 hr at RT or overnight at 4oC. Nuclei were then incubated with 25 ul of 1:100 secondary antibody (typically Guinea Pig anti-Rabbit IgG) for 30 mins at RT. Nuclei were washed with 200 ul Wash Buffer and incubated with 25 ul 1:20 pAG-Tn5 (EpiCypher) in WB-300 (300 mM NaCl in Wash Buffer) for 1hr at RT. Nuclei were washed (x2) with 200 ul of WB-300 to remove unbound pAG-Tn5 and then incubated at 37oC for 1hr in 50 ul Tagmentation buffer (10 mM MgCl₂ in WB-300). Tagmentation was halted by washing with 50 ul TAPS Wash Buffer (10 mM TAPS pH 8.5, 0.2 mM EDTA) before lysing the nuclei with 5 ul SDS-ProK Buffer (1% SDS, 10 mM TAPS pH 8.5, Thermolabile Proteinase K) and incubating for 1 hr at 37oC and 1hr at 58oC. SDS was neutralised with 15 ul 6% Triton and tagmented DNA amplified with NEBNext Ultra II Q5 Master Mix and indexed primers (thermal profile: 58 °C 5 min, 72 °C 5 min, 98 °C 5 min, [98 °C 10 sec, 60 °C 10 sec, 72 °C 1 min] ×12). Libraries were cleaned with Agencourt AMPure XP beads.
Libraries were cleaned with Agencourt AMPure XP beads.

value: Bone Marrow

value: Primary cells

value: Runx2 WT

value: H3K4me3 Active Motif (39159)


title: naive CD4+ T cells, Mettl3 KO3, 0H


title: CD201+CD150+KSL wild-type cultured HSC CUT&Tag Runx2

description: Library name: mHSC-wt-1_Runx2

value: Anti-RUNX2 Abcam (ab236639)


title: naive CD4+ T cells, Mettl3 KO1, 0H


title: DSID31 Placenta

description: Library name: DSID31_PLAC


title: naive CD4+ T cells, Mettl3 WT3, 48H

value: anti-CD3/CD28 for 48hr


title: Sample_2

value: Peripheral Blood

value: F


title: Sample_1


title: DSID31 Fetal membranes

description: Library name: DSID31_FM

value: full thickness amniochorion


title: DSID36 Fetal membranes

description: Library name: DSID36_FM


title: screen_dim_biorep2_rep5

city: Rehovot

first: Noam

last: Stern-Ginossar

address: 234 herzel

department: Molecular Genetics

country: Israel

institute: Weizmann Institute

description: Second biological replicate (infection number 2) and fifth technical replicate (PCR replicate) of  THP1 monocytes overexpressing PDGFRa transduced with the Gecko genome-wide CRISPR-screen library  and were infected with HCMV-GFP for two days and sorted to the dim population

data_processing:
for sgRNA libraries, MAGeCK v0.5.6 was used to count sgRNA from FASTQ files  for rna-seq libraries, The reads were trimmed to remove linker by using cutadapt. Reads aligned to hg19 based rRNA and tRNA reference were removed. Then reads were aligned to combined reference of the host and the virus. The alignments of the rna-seq data were made with Bowtie1. The alighment of the Slam-seq were mad with STAR and the mutation rate T->C analysis was mad with GRAND-slam. Assembly: Host: Human hg19 (GRCh37)
Assembly: hg19 (GRCh37)
Supplementary files format and content: comma-deliminated raw read count
Library strategy: CRISPR-screen

source_name: THP1 Monocyte

growth_protocol: THP1 cells were grown in RPMI CD14 monocytes were grown in x-vivo and macrophages were grown in rpmi

extract_protocol:
RNA was extracted in TRIZOL , DNA was extracted using blood kit
slam-seq  was constructed  according to Jürges, C et al., 2018 RNA-seq library was constructed according to Shishkin, A. A. et al. 2015 CRISPR screen library was constructed using blood kit and nested PCR according to Sanjana, N. E. et al., 2014

treatment_protocol: differentiated cells were treated with PMA for three days

value: THP1 Monocyte


title: screen_dim_biorep2_rep4

description: Second biological replicate (infection number 2) and foutrh technical replicate (PCR replicate) of  THP1 monocytes overexpressing PDGFRa transduced with the Gecko genome-wide CRISPR-screen library  and were infected with HCMV-GFP for two days and sorted to the dim population


title: CD201-CD150-KSL wild-type cultured HPC RNA-seq replicate 3

description: Library name: HPC-wt-rep3

data_processing:
FASTQ files were quality checked using FastQC version v0.12.1.
Adapter sequences were removed and low quality reads were trimmed using trim_galore version 0.6.10 using the following parameters: --2colour 20.
Reads were aligned to the reference genome mm39 using STAR v2.7.11a with the following parameters: --quantMode TranscriptomeSAM GeneCounts --outSAMunmapped Within --outSAMattributes Standard.
RNA-seq alignments were quantified using featureCounts v2.0.6 with the following parameters: -s 2 -p --countReadPairs -t exon -g gene_id.
Assembly: mm39
Supplementary files format and content: tsv file containing raw counts

extract_protocol:
Messenger RNA was purified from total RNA using poly-T oligo-attached magnetic beads. After fragmentation, the first strand cDNA was synthesized using random hexamer primers followed by the second strand cDNA synthesis.
The library was ready after end repair, A-tailing, adapter ligation, size selection, amplification, and purification. The library was checked with Qubit and real-time PCR for quantification and bioanalyzer for size distribution detection.

value: CD201-CD150-cKit+Sca1+Lineage- hematopoietic progenitor cells


title: naive CD4+ T cells, Mettl3 WT2, 48H


title: CD201-CD150-KSL wild-type cultured HPC RNA-seq replicate 2

description: Library name: HPC-wt-rep2


title: naive CD4+ T cells, Nudt21 KO1, 0H


title: CD201-CD150-KSL wild-type cultured HPC RNA-seq replicate 1

description: Library name: HPC-wt-rep1


title: naive CD4+ T cells, Mettl3 WT3, 0H


title: DSID26 Fetal membranes

description: Library name: DSID26_FM


title: CD201-CD150-KSL Runx2-homozygous knockout cultured HPC RNA-seq replicate 3

description: Library name: HPC-hom-rep3

value: Runx2 homozygous KO


title: screen_dim_biorep2_rep3

description: Second biological replicate (infection number 2) and third technical replicate (PCR replicate) of  THP1 monocytes overexpressing PDGFRa transduced with the Gecko genome-wide CRISPR-screen library  and were infected with HCMV-GFP for two days and sorted to the dim population


title: Sample_4

data_processing: Data were processed in R, normalized using BMIQ normalization.

extract_protocol: The DNA from the whole blood samples was extracted using salting out method.


title: naive CD4+ T cells, Mettl3 WT1, 48H


title: CD201-CD150-KSL Runx2-homozygous knockout cultured HPC RNA-seq replicate 2

description: Library name: HPC-hom-rep2


title: naive CD4+ T cells, Mettl3 WT2, 0H


title: screen_dim_biorep2_rep1

description: Second biological replicate (infection number 2) and first technical replicate (PCR replicate) of  THP1 monocytes overexpressing PDGFRa transduced with the Gecko genome-wide CRISPR-screen library  and were infected with HCMV-GFP for two days and sorted to the dim population


title: CD201-CD150-KSL Runx2-homozygous knockout cultured HPC RNA-seq replicate 1

description: Library name: HPC-hom-rep1


title: naive CD4+ T cells, Mettl3 WT1, 0H


title: DSID25 Fetal membranes

description: Library name: DSID25_FM


title: screen_dim_biorep1_rep3

description: First biological replicate (infection number 1) and third technical replicate (PCR replicate) of  THP1 monocytes overexpressing PDGFRa transduced with the Gecko genome-wide CRISPR-screen library  and were infected with HCMV-GFP for two days and sorted to the dim population


title: CD201-CD150-KSL Runx2-heterozygous knockout cultured HPC RNA-seq replicate 3

description: Library name: HPC-het-rep3

value: Runx2 heterozygous KO


title: DSID22 Placenta

description: Library name: DSID22_PLAC

value: villous placental tissue


title: PLCPRF5-siSCR_3, Day 2

city: 양산시

first: Susmita

last: Sen

address: 경남 양산시 물금읍 범어리 2762-1

department: Department of Anatomy

country: South Korea

institute: Pusan National University

description:
Library name: Sample 6
Sequenced using MGI DNBSEQ-T7 instrument

data_processing:
The trimmed reads were mapped to human reference (hg38) using STAR aligner (ver. 2.7.3)
The raw TPM values were calculated by RSEM (ver. 1.3.3)
Differentially expressed genes were identified by calculating normalized count with DESeq2
Assembly: hg38
Supplementary files format and content: The csv files contain normalized counts of transcripts. This values were calculated by DESeq2 to identify DEGs
Supplementary files format and content: TPM values were calcuated by RSEM and stored in tsv files

source_name: Liver

growth_protocol: PLCPRF5 cells were cultured using RPMI media-supplemented with 10% FBS and antibiotics (P/S), and kept in a 5% CO2 at 37 degree C.

extract_protocol:
Cells were kept observing after siRNA transfection to check for the cell status, and 48 hours later, cells were harvested using Rneasy mini kit (Qiagen). 3ug of total RNA was used for the construction of the seuencing libraries.
RNA libraries were prepared for RNA sequencing based on the manusfactor's instructions. The adapter contamination were trimmed by Cutadapt and the trimmed read were further processed by Trimomatic to filter out low quality reads.

treatment_protocol: Cells were seeded onto 6 well plate and 24 hours later, they were transfected using 100nM (pre-optimized concentration) of siRNAs

value: Liver

value: Hepatocellular carcinoma liver cells

value: Control

value: siRNA transfection


title: PLCPRF5-siSCR_2, Day 2

address: 경남 양산시 물금읍 범어리 2762-1

description:
Library name: Sample 5
Sequenced using MGI DNBSEQ-T7 instrument


title: screen_dim_biorep1_rep1

description: First biological replicate (infection number 1) and first technical replicate (PCR replicate) of  THP1 monocytes overexpressing PDGFRa transduced with the Gecko genome-wide CRISPR-screen library  and were infected with HCMV-GFP for two days and sorted to the dim population


title: DSID22 Fetal membranes

description: Library name: DSID22_FM


title: DSID26 Placenta

description: Library name: DSID26_PLAC


title: CD201-CD150-KSL Runx2-heterozygous knockout cultured HPC RNA-seq replicate 1

description: Library name: HPC-het-rep1

value: Bone Marrow

value: Primary cells


title: PLCPRF5-siSCR_1, Day 2

address: 경남 양산시 물금읍 범어리 2762-1

description:
Library name: Sample 4
Sequenced using MGI DNBSEQ-T7 instrument


title: screen_dim_biorep1_rep2

description: First biological replicate (infection number 1) and second technical replicate (PCR replicate) of  THP1 monocytes overexpressing PDGFRa transduced with the Gecko genome-wide CRISPR-screen library  and were infected with HCMV-GFP for two days and sorted to the dim population


title: PLCPRF5-siCOPG1_3, Day 2

address: 경남 양산시 물금읍 범어리 2762-1

description:
Library name: Sample 3
Sequenced using MGI DNBSEQ-T7 instrument


title: screen_bright_biorep2_rep4

description: Second biological replicate (infection number 2) and foutrh technical replicate (PCR replicate) of  THP1 monocytes overexpressing PDGFRa transduced with the Gecko genome-wide CRISPR-screen library  and were infected with HCMV-GFP for two days and sorted to the bright population


title: screen_dim_biorep2_rep2

description: Second biological replicate (infection number 2) and second technical replicate (PCR replicate) of  THP1 monocytes overexpressing PDGFRa transduced with the Gecko genome-wide CRISPR-screen library  and were infected with HCMV-GFP for two days and sorted to the dim population


title: DSID21 Fetal membranes

description: Library name: DSID21_FM


title: DSID25 Placenta

description: Library name: DSID25_PLAC


title: CD201+CD150+KSL wild-type cultured HSC RNA-seq replicate 3

description: Library name: mHSC-wt-rep3

value: Runx2 WT


title: CD201+CD150+KSL wild-type cultured HSC RNA-seq replicate 2

description: Library name: mHSC-wt-rep2


title: PLCPRF5-siCOPG1_2, Day 2

address: 경남 양산시 물금읍 범어리 2762-1

description:
Library name: Sample 2
Sequenced using MGI DNBSEQ-T7 instrument


title: DSID19 Placenta

description: Library name: DSID19_PLAC


title: screen_bright_biorep2_rep3

description: Second biological replicate (infection number 2) and third technical replicate (PCR replicate) of  THP1 monocytes overexpressing PDGFRa transduced with the Gecko genome-wide CRISPR-screen library  and were infected with HCMV-GFP for two days and sorted to the bright population


title: CD201+CD150+KSL wild-type cultured HSC RNA-seq replicate 1

description: Library name: mHSC-wt-rep1


title: PLCPRF5-siCOPG1_1, Day 2

address: 경남 양산시 물금읍 범어리 2762-1

description:
Library name: Sample 1
Sequenced using MGI DNBSEQ-T7 instrument


title: screen_bright_biorep2_rep2

description: Second biological replicate (infection number 2) and second technical replicate (PCR replicate) of  THP1 monocytes overexpressing PDGFRa transduced with the Gecko genome-wide CRISPR-screen library  and were infected with HCMV-GFP for two days and sorted to the bright population


title: DSID19 Fetal membranes

description: Library name: DSID19_FM


title: CD201+CD150+KSL Runx2-homozygous knockout cultured HSC RNA-seq replicate 3

description: Library name: mHSC-hom-rep3


title: 5637 cells, siYKT6-3

city: Wuhan

first: Yu

last: Xiao

address: Donghu Road 169

department: Department of Urology

institute: Zhongnan Hospital of Wuhan University

description:
Library name: sample6
Column name in All_reads_counts.txt: si_3

data_processing:
Raw sequencing reads were quality-filtered using fastp (version 0.23.0). Cleaned reads were aligned to the Homo sapiens reference genome (GRCh38, NCBI) with subsequent quantification of exonic reads mapped to annotated genes using featureCounts (Subread-1.5.1; Bioconductor).
Assembly: GRCh38
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample

growth_protocol: 5637 cells were maintained in RPMI 1640 supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37℃.

extract_protocol:
Total RNAs were extracted using TRIzol Reagent (Invitrogen, cat. NO 15596026）following the methods. A total of 2 μg of high-quality RNA was used for the construction of sequencing libraries.
KCTM Stranded mRNA Library Prep Kit for Illumina® (Catalog NO. DR08402, Wuhan Seqhealth Co., Ltd. China) following the manufacturer’s instruction

value: bladder cancer cell

value: YKT6 knockdown

tag: batch


title: CD201-CD150-KSL Runx2-heterozygous knockout cultured HPC RNA-seq replicate 2

description: Library name: HPC-het-rep2


title: CD201+CD150+KSL Runx2-homozygous knockout cultured HSC RNA-seq replicate 2

description: Library name: mHSC-hom-rep2


title: DSID21 Placenta

description: Library name: DSID21_PLAC


title: DSID18 Placenta

description: Library name: DSID18_PLAC


title: screen_bright_biorep2_rep5

description: Second biological replicate (infection number 2) and fifth technical replicate (PCR replicate) of  THP1 monocytes overexpressing PDGFRa transduced with the Gecko genome-wide CRISPR-screen library  and were infected with HCMV-GFP for two days and sorted to the bright population


title: CD201+CD150+KSL Runx2-homozygous knockout cultured HSC RNA-seq replicate 1

description: Library name: mHSC-hom-rep1


title: screen_bright_biorep1_rep3

description: First biological replicate (infection number 1) and third technical replicate (PCR replicate) of  THP1 monocytes overexpressing PDGFRa transduced with the Gecko genome-wide CRISPR-screen library  and were infected with HCMV-GFP for two days and sorted to the bright population


title: 5637 cells, siYKT6-1

description:
Library name: sample4
Column name in All_reads_counts.txt: si_1


title: DSID18 Fetal membranes

description: Library name: DSID18_FM


title: DSID16 Placenta

description: Library name: DSID16_PLAC


title: CD201+CD150+KSL Runx2-heterozygous knockout cultured HSC RNA-seq replicate 3

description: Library name: mHSC-het-rep3


title: screen_bright_biorep1_rep2

description: First biological replicate (infection number 1) and second technical replicate (PCR replicate) of  THP1 monocytes overexpressing PDGFRa transduced with the Gecko genome-wide CRISPR-screen library  and were infected with HCMV-GFP for two days and sorted to the bright population


title: 5637 cells, siYKT6-2

description:
Library name: sample5
Column name in All_reads_counts.txt: si_2


title: screen_bright_biorep1_rep1

description: First biological replicate (infection number 1) and first technical replicate (PCR replicate) of  THP1 monocytes overexpressing PDGFRa transduced with the Gecko genome-wide CRISPR-screen library  and were infected with HCMV-GFP for two days and sorted to the bright population


title: CD201+CD150+KSL Runx2-heterozygous knockout cultured HSC RNA-seq replicate 2

description: Library name: mHSC-het-rep2


title: 5637 cells, siNC-2

description:
Library name: sample2
Column name in All_reads_counts.txt: NC_2

value: WT


title: 5637 cells, siNC-3

description:
Library name: sample3
Column name in All_reads_counts.txt: NC_3


title: THP1_PDGFRa_3hpl

description: THP1 monocytes overexpressing PDGFRa were infected with HCMV and labeled with 4sU 3 hr post infection for 3 hr and procced to slam-seq treatment and sequencing to detect newly synthesized RNA.

data_processing:
for sgRNA libraries, MAGeCK v0.5.6 was used to count sgRNA from FASTQ files  for rna-seq libraries, The reads were trimmed to remove linker by using cutadapt. Reads aligned to hg19 based rRNA and tRNA reference were removed. Then reads were aligned to combined reference of the host and the virus. The alignments of the rna-seq data were made with Bowtie1. The alighment of the Slam-seq were mad with STAR and the mutation rate T->C analysis was mad with GRAND-slam. Assembly: Host: Human hg19 (GRCh37)
Assembly: hg19 (GRCh37)
Supplementary files format and content: comma-deliminated raw read count
Library strategy: Slam-seq


title: DSID12 Placenta

description: Library name: DSID12_PLAC


title: CD201+CD150+KSL Runx2-heterozygous knockout cultured HSC RNA-seq replicate 1

description: Library name: mHSC-het-rep1


title: DSID16 Fetal membranes

description: Library name: DSID16_FM


title: 5637 cells, siNC-1

description:
Library name: sample1
Column name in All_reads_counts.txt: NC_1


title: DSID12 Fetal membranes

description: Library name: DSID12_FM


title: EA18.1_RNAseq_NPC_dTAG13_24h_rep6

description:
Library name: KHRNA97
KHRNA97

data_processing:
Reads were trimmed to 100 base pairs as needed using cutadapt.
Alignment of raw RNA-seq data was produced using STAR version 2.7.7a with default parameters and basic two-pass mapping in mm10. GENCODE VM23 (GRCm38.p6) was used as the reference gene set.
bigWig files were generated using bamCoverage (deepTools) separated by strand with BPM normalization.
Assembly: mm10
Supplementary files format and content: Tab delimited text file includes raw counts for each sample
Supplementary files format and content: bigWigs separated by forward and reverse strand and normalized using BPM

extract_protocol:
Cells were washed with PBS and lysed directly with 1 mL TRIzol (Thermo Fisher 15596-018), transferred to a 1.5 mL tube, vortexed, and incubated at room temperature for 5 minutes. After incubation, mixture was supplemented with 250 µL Chloroform, vortexed again, and centrifuged at 12,000g at 4ºC for 15 minutes. Upper phase was transferred to a new tube, mixed with an equal volume of isopropanol, and spun at 12,000g at 4ºC for 15 minutes. Pellet was washed with 70% ethanol, air dried, and resuspended in 25 µL water.
100-500ng of DNase-treated total RNA was used as input for polyA+ capture and library preparation using the Illumina Stranded mRNA kit (Illumina 20040532)

value: neural progenitor cells


title: THP1_PDGFRa_2hpl


title: screen_bright_biorep2_rep1

description: Second biological replicate (infection number 2) and first technical replicate (PCR replicate) of  THP1 monocytes overexpressing PDGFRa transduced with the Gecko genome-wide CRISPR-screen library  and were infected with HCMV-GFP for two days and sorted to the bright population


title: Immortalized myeloid cell line, Recql4 -/- Klhdc3 -/- replicate 3

data_processing:
fastq to unmapped bam was performed using picard v2.23.9.
mark adapters was performed using picard v2.23.9.
Mapping to mm10 was performed using baw-mem (v0.7.15).
Replication timing analysis was performed using TIGER as previously described (https://pubmed.ncbi.nlm.nih.gov/33704387/)
Assembly: mm10
Supplementary files format and content: recql4_Raw_data.txt : Raw counts
Supplementary files format and content: recql4_Smoothed_data.txt : Smoothed counts.

source_name: Immortalized myeloid cell line

growth_protocol: Immortalized myeloid cell lines (HoxB8) selected in GM-CSF were maintained in IMDM with 10% fetal bovine serum (FBS), antibiotics and glutamine. Cells were cultured with 5% CO2 at 37C.

extract_protocol:
DNA isolated with Gentra PureGene DNA isolation kit
Libraries (DNBseq Normal DNA library construction) and QC were performed by BGI Pty Ltd
whole genome sequencing library (DNBSEQ PE150); PE150bp; sequenced aiming for 30x coverage of mouse genome

treatment_protocol: WT and Recql4-/-Klhdc3-/- genotypes; proliferating cultures were collected for DNA isolation

value: Immortalized myeloid cell line

value: Recql4 -/- Klhdc3 -/-


title: DSID10 Placenta (twin B)

description: Library name: DSID10_PLAC_twB

data_processing:
Sequenced reads were mapped to the SILVA 132 database using QIIME2-2017.2. An operational taxonomic units (OTU) table was generated which contained the OTUs identified in each sample along with the number of sequence reads and the taxonomic classification of each OTU. The classification was further collapsed at either genera, family, order or phylum level for subsequent analyses using the MicrobialAnalyst web-based platform. Because blood samples were expected to have low number of reads, we thought it more important to be inclusive of low abundance taxa even if these could represent sequencing errors, therefore the default R code was modified to exclude the abundance filters. The Chao-1 index (measure of α-diversity) was used to estimate OTU richness in different types of samples. Enrichment of taxa between groups was further analyzed by LEfSe (linear discriminant analysis effect size) and EdgeR methods built within the platform. These computational algorithms designed primarily for highly multidimensional data, employ a combination of statistical tests to extract features (e.g. OTU) that show significant differences in abundance (enrichment) in different samples while accounting for the effect size of the differences.
Assembly: SILVA_132 reference database
Supplementary files format and content: OTU counts for each sample (tab delimited) and corresponding OTU table


title: THP1_monocytes_3hpl

description: THP1 monocytes were infected with HCMV and labeled with 4sU 3 hr post infection for 3 hr and procced to slam-seq treatment and sequencing to detect newly synthesized RNA.

value: THP1 Monocyte


title: EA18.1_RNAseq_NPC_dTAG13_24h_rep5

description:
Library name: KHRNA96
KHRNA96


title: Immortalized myeloid cell line, Recql4 -/- Klhdc3 -/- replicate 2


title: DSID10 Fetal membranes (twin B)

description: Library name: DSID10_FM_twB

value: full thickness amniochorion


title: THP1_monocytes_2hpl

description: THP1 monocytes were infected with HCMV and labeled with 4sU 3 hr post infection for 2 hr and procced to slam-seq treatment and sequencing to detect newly synthesized RNA.


title: EA18.1_RNAseq_NPC_DMSO_24h_rep6

description:
Library name: KHRNA94
KHRNA94


title: Immortalized myeloid cell line, Recql4 -/- Klhdc3 -/- replicate 1


title: Immortalized myeloid cell line, WT replicate 3


title: THP1_macrophages_3hpl

description: THP1 macrophages were infected with HCMV and labeled with 4sU 3 hr post infection for 3 hr and procced to slam-seq treatment and sequencing to detect newly synthesized RNA.

source_name: THP1 Monocyte-derived macrophage

value: THP1 Monocyte-derived macrophage


title: DSID10 Fetal membranes (twin A)

description: Library name: DSID10_FM_twA


title: EA18.1_RNAseq_NPC_DMSO_24h_rep5

description:
Library name: KHRNA93
KHRNA93


title: EA18.1_RNAseq_NPC_dTAG13_24h_rep4

description:
Library name: KHRNA95
KHRNA95


title: DSID10 Placenta (twin A)

description: Library name: DSID10_PLAC_twA

value: villous placental tissue


title: Immortalized myeloid cell line, WT replicate 1


title: Immortalized myeloid cell line, WT replicate 2


title: DSID08 Placenta

description: Library name: DSID08_PLAC


title: primary_CD14_monocytes_3hpl

description: Primary CD14 monocytes were infected with HCMV and labeled with 4sU 3 hr post infection for 3 hr and procced to slam-seq treatment and sequencing to detect newly synthesized RNA.

source_name: Primary CD14+ Monocyte

value: Primary CD14+ Monocyte


title: primary_CD14_monocytes_unlabeled

description: Primary CD14 monocytes were procced to slam-seq treatment and sequencing to serve as a control for newly synthesized RNA.


title: DSID08 Fetal membranes

description: Library name: DSID08_FM


title: DSID05 Placenta

description: Library name: DSID05_PLAC


title: primary_CD14_monocytes_2hpl

description: Primary CD14 monocytes were infected with HCMV and labeled with 4sU 3 hr post infection for 2 hr and procced to slam-seq treatment and sequencing to detect newly synthesized RNA.


title: celMBD2_F1gfpmbd2CC_RNAseq_2

city: Hong Kong

first: Wing Yee Karen

last: Yuen

address: 4S15, Kadoorie Biological Science building, The University of Hong Kong, Pok Fu Lam Road

department: School of Biological Sciences

country: Hong Kong

institute: The University of Hong Kong

description:
Library name: celMBD2_F1gfpmbd2CC_RNAseq_2
Column name in CelMBD2CC_TPM.csv: GFPMBD2F1CC_R2

data_processing:
Sequencing reads were filtered for adapter sequence, low quality sequence and retaining reads with read length ≥ 40bp, using Cutadapt with parameter --max-n 0.05 and followed by fastp --unqualified_percent_limit 50 --qualified_quality_phred 12 --disable_adapter_trimming --n_base_limit 50 --length_required 40. Reads were mapped to the reference genome WBcel235 using STAR v2.7.9a and gene counts were obtained with the built-in counting option --quantMode.
The Transcripts Per Million (TPM) value for each gene was calculated using RSEM v1.3.3.
Assembly: WBcel235
Supplementary files format and content: The Transcripts Per Million (TPM) value for each gene in all samples calculated using RSEM v1.3.3 in CSV format.

organism: Caenorhabditis elegans

source_name: whole adult organism

growth_protocol: All experiments were then performed on young adult worms (3 days post hatching) obtained by bleach synchronization. L1 larvae were fed with OP50 E. coli and grown on standard conditions at 20°C.

extract_protocol:
Total RNA was isolated using TRIzol-chloroform extraction, followed by isopropanol precipitation. To remove DNA, RNA was treated with TURBO DNA-free™ Kit (Ambion, Cat.#AM1907).
The samples were submitted to the Centre for PanorOmic Sciences (CPOS, HKU LKS Faculty of Medicine) for library preparation with KAPA Hyper Prep Kit following manufacturer protocol.

treatment_protocol: P0 homozygous coiled-coil domain deletion mutants were obtained by manually picking worms without the GFP balancer born from bleaching the heterozygous stock. F1 homozygous coiled-coil domain deletion mutants were obtained by manually picking worms born from bleaching the P0 homozygous coiled-coil domain deletion mutants.

value: whole adult organism

tag: developmental stage

value: adult

value: Synchronized young adult homozygous coiled coil domain deletion mutant worms sired by homozygous coiled coil domain deletion mutant


title: DSID05 Fetal membranes

description: Library name: DSID05_FM


title: primary_CD14_macrophages_3hpl

description: Primary CD14 macrophages were infected with HCMV and labeled with 4sU 3 hr post infection for 3 hr and procced to slam-seq treatment and sequencing to detect newly synthesized RNA.

source_name: Primary CD14+ Monocyte-derived macrophage


title: celMBD2_F1gfpmbd2CC_RNAseq_1

description:
Library name: celMBD2_F1gfpmbd2CC_RNAseq_1
Column name in CelMBD2CC_TPM.csv: GFPMBD2F1CC_R1


title: EA18.1_RNAseq_NPC_DMSO_24h_rep4

description:
Library name: KHRNA92
KHRNA92


title: DSID02 Placenta

description: Library name: DSID02_PLAC


title: M. tuberculosis H37Rv pstA1 deletion mutant 60 min biological replicate 3

city: Baltimore

first: Petros

last: Karakousis

state: MD

address: 1550 Orleans Street

department: Medicine

institute: Johns Hopkins University School of Medicine

description:
Library name: pstA1del_60min_rep3
column name in raw_counts_all_samples.csv pstA1_RIF_60min_3

data_processing:
Raw reads were quality assessed using FastQC v0.12.1
Reads were aligned to M. tuberculosis H37Rv reference genome (GCF_000195955.2) using Bowtie2 v2.5.1
Gene counts were quantified using featureCounts (Subread v2.0.0)
Assembly: GCF_000195955.2 (ASM19595v2)
Supplementary files format and content: CSV file containing gene counts matrix with genes as rows and samples as columns

organism: Mycobacterium tuberculosis H37Rv

source_name: Mycobacterium tuberculosis

growth_protocol: Mycobacterium tuberculosis samples were cultured in 7H9 Middlebrook broth supplemented with 10% OADC enrichment, 0.2% glycerol and 0.05% Tween-80 at 37°C with shaking to mid-log phase (OD600 ~0.5).

extract_protocol:
Bacterial pellets (15 mL culture) were resuspended in TRIzol with 0.1 mm zirconia beads and lysed using a Precellys Evolution homogenizer (3 cycles, 30 seconds at 7,400 rpm). RNA was extracted with chloroform, precipitated with ethanol, and purified on RNeasy columns (Qiagen) with on-column DNase I digestion.
RNA libraries were prepared using NEBNext Ultra II Directional RNA Library Prep Kit with polyA selection following manufacturer's protocols. Libraries were sequenced on Illumina NovaSeq X Plus platform (2×150 bp paired-end reads).

treatment_protocol: Bacterial RNA was extracted from mid-log phase cultures pre-rifampin treatment (0 minutes) and following exposure to sub-inhibitory rifampin (7.5 ng/ml, 1/4 MIC) for 30 or 60 minutes.

value: Mycobacterium tuberculosis

value: pstA1 deletion mutant

value: rifampin 7.5 ng/ml 60 min


title: M. tuberculosis H37Rv pstA1 deletion mutant 60 min biological replicate 1

description:
Library name: pstA1del_60min_rep1
column name in raw_counts_all_samples.csv pstA1_RIF_60min_1


title: celMBD2_P0gfpmbd2CC_RNAseq_2

description:
Library name: celMBD2_P0gfpmbd2CC_RNAseq_2
Column name in CelMBD2CC_TPM.csv: GFPMBD2P0CC_R2

value: Synchronized young adult homozygous coiled coil domain deletion mutant worms


title: primary_CD14_macrophages_2hpl

description: Primary CD14 macrophages were infected with HCMV and labeled with 4sU 3 hr post infection for 2 hr and procced to slam-seq treatment and sequencing to detect newly synthesized RNA.

value: Primary CD14+ Monocyte-derived macrophage


title: THP1_macrophages_2hpl

description: THP1 macrophages were infected with HCMV and labeled with 4sU 3 hr post infection for 2 hr and procced to slam-seq treatment and sequencing to detect newly synthesized RNA.


title: M. tuberculosis H37Rv pstA1 deletion mutant 30 min biological replicate 3

description:
Library name: pstA1del_30min_rep3
column name in raw_counts_all_samples.csv pstA1_RIF_30min_3

value: rifampin 7.5 ng/ml 30 min


title: DSID02 Fetal membranes

description: Library name: DSID02_FM

extract_protocol:
All specimens were collected using sterile gloves, and all procedures were carried out under strict sterile conditions. For sequencing of 16S RNA genes and microbial community analysis, genomic DNA was extracted and the 16S rRNA amplified using V4 primers. 16S amplicon multiplex libraries were sequenced on Illumina platform at the Sequencing Facility of the Argonne National Laboratory.
Genomic DNA was amplified using primers targeting the V4 region of the 16S rRNA gene with Illumina overhang adapters. Amplicon PCR was performed with KAPA HiFi HotStart ReadyMix under the following conditions: 95 °C for 3 min; 25 cycles of 95 °C for 30 s, 55 °C for 30 s, 72 °C for 30 s; final extension at 72 °C for 5 min. PCR products were purified using AMPure XP beads (0.8× ratio). Dual indices and Illumina sequencing adapters were added in a second PCR (8 cycles) using Nextera XT index primers, followed by another AMPure XP bead cleanup. Libraries were quantified with Qubit and validated for size using Bioanalyzer. Equimolar pooling was performed prior to sequencing on an Illumina MiSeq platform (paired-end).


title: M. tuberculosis H37Rv pstA1 deletion mutant 30 min biological replicate 2

description:
Library name: pstA1del_30min_rep2
column name in raw_counts_all_samples.csv pstA1_RIF_30min_2


title: Kasumi3_macrophages_rep2

description: uninfectedprimary Kasumi3 monocytes that treated for three days with PMA to generate macrophages were sequenced

data_processing:
for sgRNA libraries, MAGeCK v0.5.6 was used to count sgRNA from FASTQ files  for rna-seq libraries, The reads were trimmed to remove linker by using cutadapt. Reads aligned to hg19 based rRNA and tRNA reference were removed. Then reads were aligned to combined reference of the host and the virus. The alignments of the rna-seq data were made with Bowtie1. The alighment of the Slam-seq were mad with STAR and the mutation rate T->C analysis was mad with GRAND-slam. Assembly: Host: Human hg19 (GRCh37)
Assembly: hg19 (GRCh37)
Supplementary files format and content: comma-deliminated raw read count

source_name: Kasumi3 Monocyte-derived macrophage

value: Kasumi3 Monocyte-derived macrophage


title: M. tuberculosis H37Rv pstA1 deletion mutant 30 min biological replicate 1

description:
Library name: pstA1del_30min_rep1
column name in raw_counts_all_samples.csv pstA1_RIF_30min_1


title: DSID01 Placenta

description: Library name: DSID01_PLAC


title: Kasumi3_macrophages_rep1


title: DSID01 Fetal membranes

description: Library name: DSID01_FM


title: M. tuberculosis H37Rv pstA1 deletion mutant 60 min biological replicate 2

description:
Library name: pstA1del_60min_rep2
column name in raw_counts_all_samples.csv pstA1_RIF_60min_2


title: M. tuberculosis H37Rv pstA1 deletion mutant untreated biological replicate 3

description:
Library name: pstA1del_0min_rep3
column name in raw_counts_all_samples.csv pstA1_ctrl_3

value: untreated 0 min


title: SspA/HDM_rep3

city: Charlestown

first: Jin Mo

last: Park

state: MA

address: 149 Thirteenth Street

department: Cutaneous Biology Research Center

institute: Massachusetts General Hospital

description:
Library name: Sample 6
D.SH_3

data_processing:
Basecalls were performed using  bcl2fastq v2.20.0.422 (Illumina).
Read alignment was performed on the mm10 assembly of the mouse genome using the genome mapper STAR for RNA-Seq.
Normalized values and differential gene expression were calculated by DEseq2 algorithm.
Assembly: mm10
Supplementary files format and content: The file is in a txt format and contains normalized counts.

source_name: Skin

growth_protocol: 8-week-old C57BL/6 mice were maintained in a specific-pathogen-free condition.

extract_protocol:
Trizol Reagent (Thermo Fisher Scientific) and PureLink RNA Mini Kit (Thermo Fisher Scientific)
TruSeq Stranded mRNA Sample Preparation Kits (Illumina)

treatment_protocol: Shaved and depilated back skin of mice was subjected to topical treatment with SspA (3 micrograms of staphylococcal protease V8) and HDM (10 micrograms). This SspA and HDM application was repeated one more time 3 days later. This condition resulted in edema, epidermal hyperproliferation, and immune cell infiltration at the affected skin area. The mice were sacrificed 7 days after the first SspA and HDM treatment for skin collection and RNA isolation. RNA isolated from shaved and depilated skin without SspA and HDM treatment was analyzed for comparison.

value: Skin

value: Whole skin tissue

value: Wild-type

value: SspA/HDM


title: celMBD2_gfpmbd2_RNAseq_2

description:
Library name: celMBD2_gfpmbd2_RNAseq_2
Column name in CelMBD2CC_TPM.csv: GFPMBD2_R2

value: Synchronized gfp::mbd-2 young adult worms


title: celMBD2_P0gfpmbd2CC_RNAseq_3

description:
Library name: celMBD2_P0gfpmbd2CC_RNAseq_3
Column name in CelMBD2CC_TPM.csv: GFPMBD2P0CC_R3


title: M. tuberculosis H37Rv pstA1 deletion mutant untreated biological replicate 2

description:
Library name: pstA1del_0min_rep2
column name in raw_counts_all_samples.csv pstA1_ctrl_2


title: Kasumi3_monocytes_rep2

description: uninfectedprimary Kasumi3 monocytes were sequenced

source_name: Kasumi3 Monocyte

value: Kasumi3 Monocyte


title: celMBD2_gfpmbd2_RNAseq_1

description:
Library name: celMBD2_gfpmbd2_RNAseq_1
Column name in CelMBD2CC_TPM.csv: GFPMBD2_R1

value: whole adult organism


title: M. tuberculosis H37Rv pstA1 deletion mutant untreated biological replicate 1

description:
Library name: pstA1del_0min_rep1
column name in raw_counts_all_samples.csv pstA1_ctrl_1


title: celMBD2_F1mbd2_RNAseq_2

description:
Library name: celMBD2_F1mbd2_RNAseq_2
Column name in CelMBD2_TPM.csv: F1_R2

treatment_protocol: P0 homozygous null mutants were obtained by manually picking worms without the GFP balancer born from bleaching the heterozygous stock. F1 homozygous null mutants were obtained by manually picking worms born from bleaching the P0 homozygous null mutants.

value: hku11[C27A12.10::exon 1 STOP/ hT2[bli-4(e937) let-?(q782) qIs48] (null mutation of MBD2 with early stop codon at exon1)

value: adult

value: Synchronized young adult homozygous null mutant worms sired by homozygous null mutant


title: SspA/HDM_rep1

description:
Library name: Sample 4
D.SH_1


title: primary_CD14_macrophages_rep2

description: uninfectedprimary CD14 monocytes that treated for three days with PMA to generate macrophages were sequenced

source_name: Monocyte-derived macrophage

value: Monocyte-derived macrophage


title: primary_CD14_macrophages_rep1


title: celMBD2_P0gfpmbd2CC_RNAseq_1

description:
Library name: celMBD2_P0gfpmbd2CC_RNAseq_1
Column name in CelMBD2CC_TPM.csv: GFPMBD2P0CC_R1


title: M. tuberculosis H37Rv wild-type rifampin 60 min biological replicate 3

description:
Library name: WT_60min_rep3
column name in raw_counts_all_samples.csv WT_RIF_60min_3

value: Mycobacterium tuberculosis

value: H37Rv wild-type

value: rifampin 7.5 ng/ml 60 min


title: Control_rep3

description:
Library name: Sample 3
D.Un_3

value: Untreated


title: celMBD2_P0mbd2_RNAseq_2

description:
Library name: celMBD2_P0mbd2_RNAseq_2
Column name in CelMBD2_TPM.csv: P0_R2

value: Synchronized young adult homozygous null mutant worms sired by heterozygous null mutant


title: celMBD2_gfpmbd2_RNAseq_3

description:
Library name: celMBD2_gfpmbd2_RNAseq_3
Column name in CelMBD2CC_TPM.csv: GFPMBD2_R3


title: M. tuberculosis H37Rv wild-type rifampin 60 min biological replicate 2

description:
Library name: WT_60min_rep2
column name in raw_counts_all_samples.csv WT_RIF_60min_2


title: primary_CD14_monocytes_rep2

description: uninfectedprimary CD14 monocytes were sequenced

value: Primary CD14+ Monocyte


title: celMBD2_F1mbd2_RNAseq_1

description:
Library name: celMBD2_F1mbd2_RNAseq_1
Column name in CelMBD2_TPM.csv: F1_R1


title: primary_CD14_monocytes_rep1


title: celMBD2_P0mbd2_RNAseq_1

description:
Library name: celMBD2_P0mbd2_RNAseq_1
Column name in CelMBD2_TPM.csv: P0_R1


title: Control_rep2

description:
Library name: Sample 2
D.Un_2

value: Skin


title: Control_rep1

description:
Library name: Sample 1
D.Un_1

value: Whole skin tissue


title: THP1_PDGFRa_rep2

description: uninfected thp1 monocytes overexpressing PDGFRa were sequenced

value: THP1 Monocyte


title: M. tuberculosis H37Rv wild-type rifampin 60 min biological replicate 1

description:
Library name: WT_60min_rep1
column name in raw_counts_all_samples.csv WT_RIF_60min_1


title: Kasumi3_monocytes_rep1


title: myocardial tissue, 6d of post mortem interval, rep3

city: Busan

first: Jungho

last: Kim

address: 57, Oryundae-ro, Geumjeong-gu, Busan, Republic of Korea

department: Department of Clinical Laboratory Science, College of Health Sciences

institute: Catholic University of Pusan

description: Library name: 6d_f

data_processing:
Illumina Casava1.8 software used for basecalling.
A quality control of raw sequencing data was performed using FastQC (Simon, 2010).   method using Python “conorm” package 1.2.0.
Adapter and low-quality reads were removed using trimmomatic-0.39 and cutadapt 2.8. Then the trimmed reads were mapped to the reference genome using STAR-2.5.3a. The quantification of reads was processed using COMPSRA. The Read Counts were processed based on TMM + CPM normalization
The Read Counts were processed based on TMM + CPM normalization method using Python “conorm” package 1.2.0.
Assembly: mmu
Supplementary files format and content: tab-delimited text files include read count values for each Sample

source_name: myocardial tissue

extract_protocol:
RNA was harvested using Trizol reagent. 500 ng of total RNA was used for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using NEBNext Multiplex Small RNA Library Prep kit standard protocols.

value: myocardial tissue

value: 6d of post mortem interva


title: M. tuberculosis H37Rv wild-type rifampin 30 min biological replicate 2

description:
Library name: WT_30min_rep2
column name in raw_counts_all_samples.csv WT_RIF_30min_2

value: rifampin 7.5 ng/ml 30 min


title: THP1_PDGFRa_rep1


title: celMBD2_N2_RNAseq_1

description:
Library name: celMBD2_N2_RNAseq_1
Column name in CelMBD2_TPM.csv: N2_R1

value: whole adult organism

value: N2 (wildtype)

value: Synchronized wildtype young adult worms


title: celMBD2_N2_RNAseq_2

description:
Library name: celMBD2_N2_RNAseq_2
Column name in CelMBD2_TPM.csv: N2_R2

value: adult


title: M. tuberculosis H37Rv wild-type rifampin 30 min biological replicate 1

description:
Library name: WT_30min_rep1
column name in raw_counts_all_samples.csv WT_RIF_30min_1


title: M. tuberculosis H37Rv wild-type rifampin 30 min biological replicate 3

description:
Library name: WT_30min_rep3
column name in raw_counts_all_samples.csv WT_RIF_30min_3


title: SspA/HDM_rep2

description:
Library name: Sample 5
D.SH_2

value: Wild-type

value: SspA/HDM


title: myocardial tissue, 6d of post mortem interval, rep1

description: Library name: 6d_d


title: myocardial tissue, 6d of post mortem interval, rep2

description: Library name: 6d_e


title: THP1_macrophages_rep1

description: uninfected thp1 monocytes were treated with PMA for three days to generate macropahges were sequenced

value: THP1 Monocyte-derived macrophage


title: THP1_macrophages_rep2


title: celMBD2_input_replicate1

description: Library name: celMBD2_input1

data_processing:
The reads were first filtered for adapter sequence and low-quality reads, retaining only reads with read length ≥ 30bp. Low Quality was defined as reads with more than 5% unknown bases (“N”) and/or reads having more than 50% of bases with quality value <= 11 were filtered out. Clean reads were mapped to the reference genome WBcel235 using BWA (Version 0.7.17.5) with default parameters. Samtools view was used to remove unmapped reads and retain only properly paired mapped reads (-f 2 -F 4) with a minimum mapping quality of 30.
The 2 replicates with Samtools sorted alignments were merged. Duplicated reads were marked and removed using Picard (V2.18.2) MarkDuplicates with "REMOVE_DUPLICATES=true". The read counts of both ChIP and input files were then normalized with CPM (count per million)) with Deeptools bamCompare, normalized ChIP read counts were divided by normalized input read counts to get the ratio of the number of reads and generated the processed Bigwig files for coverage plots.
Assembly: WBcel235
Supplementary files format and content: Bigwig file obtained from merging the replicates and calculating CPM normalized read counts of ChIP over input.

growth_protocol: All the newly constructed strains were outcrossed with N2 for at least 3 times.  All experiments were then performed on young adult worms (3 days post-hatching) obtained by bleach synchronization. L1 larvae were fed with OP50 E. coli and grown on standard conditions at 20°C.

extract_protocol:
Worm droplets in PBS frozen in liquid nitrogen were grinded into fine powder, followed by fixing in 1.1% formaldehyde in PBS. The fixation was quenched and further lysis was performed by adding MNase buffer supplemented with 0.2% NP-40 and 0.5% sodium deoxycholate. DNA is digested with Mnase at 37°C for 20 minutes. Then chromatin was solubilized by adding EDTA and Triton X-100 to a final concentration of 10 mM and 1%, nutated at 4°C for 2 hr. Two volumes of cold 150 mM NaCl FA buffer supplemented with 1% Triton™ X-100 + 0.1% sodium deoxycholate + 0.1% sarkosyl was added, followed by sonication with a Covaris M220 model (duty factor 20%, average power 8, cycles per burst 200, 60 s per cycle, total 5 cycles) to liberate chromatin. Immunoprecipitation of GFP::3xFLAGMBD-2 was performed anti-FLAG antibody-conjugated magnetic beads (MCE Cat# HY-K0207) overnight at 4°C. 5% of the protein was stored as input. The antibody/protein/DNA complexes were then eluted by Elution buffer (1%SDS/0.1M NaHCO3). The beads were then magnetized and the eluate was retrieved. The eluate was further subjected to RNase A and proteinase K treatment. Reverse crosslink was performed in 0.2 M NaCl salt at 65°C overnight in the thermomixer. The DNA was purified with PCR Purification Kit (QIAGEN, Cat. 28106).
The samples were submitted to the Centre for PanorOmic Sciences (CPOS, HKU LKS Faculty of Medicine) for library preparation with KAPA Hyper Prep Kit following manufacturer protocol.

treatment_protocol: Synchronized young adult worms (Day3 post-hatching) were obtained from bleaching GFP::3xFLAG::MBD-2 worms and growing in liquid culture (M9 buffer) supplemented with OP50 E. coli bacteria as food source. Synchronization was performed with bleaching worms for embryos and allowing hatching in M9 buffer overnight before adding food source.

value: Young adult


title: myocardial tissue, 0h of post mortem interval, rep3

description: Library name: 0h_c

value: 0h of post mortem interval


title: M. tuberculosis H37Rv wild-type untreated biological replicate 3

description:
Library name: WT_0min_rep3
column name in raw_counts_all_samples.csv WT_ctrl_3

value: Mycobacterium tuberculosis

value: H37Rv wild-type

value: untreated 0 min


title: celMBD2_ChIPseq_replicate2

description: Library name: celMBD2_ChIP2


title: THP1_monocytes_rep2

description: uninfected thp1 monocytes were sequenced


title: M. tuberculosis H37Rv wild-type untreated biological replicate 2

description:
Library name: WT_0min_rep2
column name in raw_counts_all_samples.csv WT_ctrl_2


title: THP1_monocytes_rep1


title: myocardial tissue, 0h of post mortem interval, rep2

description: Library name: 0h_b


title: M. tuberculosis H37Rv wild-type untreated biological replicate 1

description:
Library name: WT_0min_rep1
column name in raw_counts_all_samples.csv WT_ctrl_1


title: celMBD2_ChIPseq_replicate1

description: Library name: celMBD2_ChIP1


title: Transplant Patient Blood B cell Memory

status: Public on Nov 26 2025

city: Birmingham

first: Alexander

last: Rosenberg

state: AL

address: 1720 2nd Ave. South

institute: University of Alabama at Birmingham

data_processing:
Joined paired-end reads were assembled and quality filtered as follows sequences <200bp were removed, sequences with any basepairs with a phred score of <=Q10, >5bp with <=Q20 and >15bp of <=Q30 were removed
Sequences were annotated using IMGT/High-Vquest v3.5.30
Annotated sequences were grouped and assigned "lineageIDs" based on identical V-gene & J-gene annotation, NT_CDR3 length and NT_CDR3 similarity of >85%
Data processinig scripts available at DOI 10.5281/zenodo.8039145
Assembly: IMGT/V-QUEST reference directory release 202243-1
Supplementary files format and content: CSV files of IMGT/High-Vquest annotations from "2_, 4_ & 8_" files with additiional metadata including isotype and lineage grouping IDs

source_name: Blood

extract_protocol:
B cell subsets were sorted directly into lysis buffer (Norgen Single Cell RNA Purification Kit, Cat #51800) with 1% mercaptoethanol, lysates were snap frozen on dry ice and stored at -80°C. Total cellular RNA was extracted from bulk sorted B cell and ASC subsets according to the manufacturer’s protocol.
cDNA preparation was performed (BioRad iScipt, Cat #1708891) per manufacturer’s instructions, and DNA amplicon products where generated using Ig-specific variable and constant gene primers. Samples were indexed (Nextera Index Kit, Illumina), purified, quantitated (KAPPA Library Quantitation Kit, Roche) and pooled into libraries. Following generation, libraries were denatured per manufacturer instructions (Illumina) and loaded onto a 600-cycle V3 MiSEQ cartridge (Illumina) for sequencing.

value: Blood

value: B cell Memory

value: Transplant


title: Transplant Patient Kidney B cell Memory 50k Cells

source_name: Kidney

value: Kidney

value: B cell Memory (50k Cells)


title: myocardial tissue, 0h of post mortem interval, rep1

description: Library name: 0h_a

value: myocardial tissue


title: Transplant Patient Kidney B cell Memory 10k Cells

value: B cell Memory (10k Cells)


title: Transplant Patient Blood B cell Antibody Secreting Cells

value: B cell Antibody Secreting Cells


title: Transplant Patient Kidney B cell Double Negative 50k Cells

value: B cell Double Negative (50k Cells)


title: celMBD2_input_replicate2

description: Library name: celMBD2_input2

value: whole adult organism


title: Transplant Patient Kidney B cell Double Negative 10k Cells

value: B cell Double Negative (10k Cells)


title: Healthy Control Brain Dead Organ Donor Small Bowel B cell Memory

source_name: Small Bowel

value: Small Bowel

value: Healthy


title: Transplant Patient Kidney B cell Antibody Secreting Cells 10k Cells

value: B cell Antibody Secreting Cells (10k Cells)


title: Transplant Patient Kidney B cell Antibody Secreting Cells 50k Cells

value: B cell Antibody Secreting Cells (50k Cells)


title: Healthy Control Brain Dead Organ Donor Blood B cell Memory


title: Healthy Control Brain Dead Organ Donor Lung B cell Memory

source_name: Lung

value: Lung


title: cell-free DNA from Alzheimer's patient 33

type: other

city: Pamplona

first: Maite

last: Mendioroz

address: Calle Irunlarrea, 3

department: Neuroepigenetics

country: Spain

institute: Miguel Servet Foundation - Navarrabiomed

hyb_protocol: cfDNA was bisulfite converted, restored and hybridized to the Illumina Infinium® MethylationEPIC BeadChip microarray (850 K) using standard Illumina protocols.

scan_protocol: Arrays were imaged using the Illumina HiScan System (Illumina) using standard Illumina protocols.

data_processing:
The EPIC array methylation data were fully preprocessed using the minfi package (v.1.32.0) in the R software environment (v.4.0.2). Normalization was performed using the ssNoob and BMIQ methods.
normalized_beta_values.csv

label: Cy3, Cy5

molecule: other

source_name: plasma cell-free DNA

label_protocol: Standard Illumina protocol

extract_protocol: cfDNA was isolated from 2 mL plasma by using QIAmp Circulating Nucleic Acid Kit (QIAGEN, Redwood City, CA, USA), following the manufacturer’s protocol.

value: plasma cell-free DNA

value: Female

tag: apoe genotype

value: Alzheimer


title: cell-free DNA from Alzheimer's patient 34

value: Male


title: cell-free DNA from Alzheimer's patient 35


title: cell-free DNA from Alzheimer's patient 32