title: Maternal side placenta tissue of participant A005


title: Cas12a-SLCxSLC_sublib1_week1_v0_rep3

status: Public on Jun 19 2024

type: SRA

city: Vienna

first: Giulio

last: Superti-Furga

address: Lazarettgasse 14

country: Austria

institute: CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences

description: Combinatorial Cas12a library

library_source: other

data_processing:
read trimming (Cas9 libraries only): Read1 reads were trimmed using cutadapt (Galaxy Version 4.8+galaxy1) to remove up- and downstream flanking sequences. The two gRNAs from read1 and read2 were then joined using FASTQ Joiner (Galaxy Version 2.0.1.1+galaxy0) before mapping to the reference sequences.
read mapping: MAGeCK count (Galaxy Version 0.5.9.2.4).
Assembly: Human NCBI genome build 36
Supplementary files format and content: tab-delimited raw gRNA pair count tables
Library strategy: Amplicon-Seq

molecule: other

organism: Homo sapiens

source_name: cell line

growth_protocol: For standard culture conditions, HCT116 cells were grown in RPMI (R8758 Sigma) supplemented with 10% Fetal Bovine Serum (10270-106, Lot 42F8381K, Gibco) and Penicillin-Streptomycin (15140-122, Gibco)

extract_protocol:
For the Cas12a-Metal-SLCxSLC, Cas12a- and Cas9-SLCxEnzymes, and Cas12a- and Cas9-SLCxSLC, gDNA was purified from 2x10e7 (QIAamp DNA Mini Kit), 1.7x10e7 (QIAGEN Genomic-tip 100/G) or 2.2x10e8 cells (QIAGEN Genomic-tip 500/G), respectively. gDNA from Cas12a- and Cas9-SLCxSLC screens was digested with restriction enzymes to improve PCR amplification of sgRNA regions. Up to 1.5 mg gDNA was digested with 200 U PacI (Cas12a-SLCxSLC) or 100 U PacI and 100 U XbaI (Cas9-SLCxSLC) (all NEB) for 48 hours.
sgRNA sequences from Cas12a library gDNA samples were amplified with barcoded FW and RV primer that introduce Illumina adapter and read1 sequencing primer binding sites. Up to 1.2 mg gDNA was used as template in 12 ml volume (divided in 96 x 125 µl PCRs) in the following program: 98°C for 30 sec.; 5 cycles: 98°C for 10 sec., 61°C for 30 sec, 72°C for 30 sec; 19 cycles: 98°C for 10 sec., 72°C for 1 min.; 72°C for 2 min. For the samples of the metal transporter and SLC family-wide sub-screen 1, Q5 Polymerase (NEB) was used, SLC vs SLC sub-screen 2-4 and SLC vs metabolic enzymes samples were processed with self-purified Pfu-Sso7d polymerase  and Phusion HF buffer (NEB). Primer sequences are shown in Supplementary Table SX. PCR products we double size selected with DNA purification bads and multiplexed for Illumina sequencing. sgRNA sequences from Cas9 library gDNA samples were first amplified with staggered FW and RV primer that contain partial Illumina adapter sequences at the 5’ end using the same PCR program as above. Up to 1.2 mg gDNA was used as template (125 µg/125 µl volume PCR) and amplified with self-purified Pfu-Sso7d polymerase. An aliquot of the pooled amplified PCR products was double size selected with DNA purification bads and purified fragments were barcoded in a second PCRs (98°C for 30 sec; 6-8 cycles: 98°C for 10 sec., 61°C for 30 sec, 72°C for 30 sec; 72°C for 2 min). PCR products we double size selected with DNA purification bads and multiplexed for Illumina sequencing.

treatment_protocol: Cas9 pools were cultivated in standard media (glu) or in hypoxia (hyp) conditions (1% oxygen), if indicated. Cas12a pools were cultivated in standard media (glu), under hypoxia (hyp), in presence of 50 mM antimycin (ant) or in  low glucose media with galactose (gal) replacement (week 1-3: 20% glucose/80% galactose, week 3-4: 100% galactose, week 4-5: 10% glucose/90% galactose), if indicated. Treatments were started after one (Cas12a samples) or two (Cas9 samples) weeks after transduction. Cells from Cas12-SLCxSLC and Cas9-SLCxSLC samples were cultured in the presence of 100 U/ml Nystatin (Merck, #N3503-5MU) to prevent fungal contaminations.

tag: tissue

value: cell line

tag: cell line

value: HCT116 (RRID:CVCL_0291) subclone (RESOLUTE #CE06WS-Q)

tag: cell type

value: Human colorectal carcinoma cell line

tag: genotype

value: Contains lentiviral enCas12 expression contruct pRDA_174 (Addgene #136476)

tag: treatment


title: Fetal side placenta tissue of participant A005

type: genomic

city: Philadelphia

first: Jagadeesh

last: Puvvula

state: Pennsylvania

address: 423 Guardian Drive

department: Department of Biostatistics, Epidemiology, and Informatics

country: USA

institute: University of Pennsylvania

hyb_protocol: Bisulfite conversion of the DNA was performed using the EZ DNA Methylation Kit (Zymo Research, Irvine, CA), and DNA methylation levels were measured using Infinium HumanMethylation450K BeadChip (Illumina, San Diego, CA) using standard protocol

scan_protocol: Arrays were imaged using BeadArray Reader (HiScan) and following the standard recommended Illumina scanner setting.

data_processing: Raw methylation data was processing using the minfi bioconductor package. Quality control steps includes, removing samples with >5% high detection p-values (p-value >1e-7) and probes failed in one or more samples with the same cut-off. Background correction with dye-bias normalization was performed using normal-exponential out-of-band method. Bias from type-2 prob values was normalized using beta-mixture quantile normalization methods. Additionally, batch effects were corrected using an empirical Bayes framework. We also removed the CpGs located on sex chromosomes, enriched at single-nucleotide polymorphisims, and those prone to cross-reativity.

label: Cy3 and Cy5

molecule: genomic DNA

source_name: Pregnant individual at delivery visit

label_protocol: Standard Illumina Protocol

extract_protocol: DNA was extracted using a DNeasy Blood and Tissue kit with RNase A, following the manufacturer's protocols. DNA was then prepared for the array following the Illumina Infinium HD Assay Methylation Protocol Guide

value: Fetal side placenta tissue


title: Cas12a-SLCxSLC_sublib1_week2_rep1

description: Combinatorial Cas12a library


title: Cord blood mono nuclear cells of participant A005

value: Cord blood mono nuclear cells


title: Maternal side placenta tissue of participant A004

value: Maternal side placenta tissue


title: Cas12a-SLCxSLC_sublib1_week1_v0_rep2

description: Combinatorial Cas12a library


title: Cas12a-SLCxSLC_sublib1_week1_v0_rep1

description: Combinatorial Cas12a library


title: Cord blood mono nuclear cells of participant A004


title: Fetal side placenta tissue of participant A004


title: Maternal side placenta tissue of participant A003


title: Fetal side placenta tissue of participant A003


title: Maternal side placenta tissue of participant A002


title: Fetal side placenta tissue of participant A002


title: Cord blood mono nuclear cells of participant A002


title: Cord blood mono nuclear cells of participant A006


title: Maternal side placenta tissue of participant A001


title: Fetal side placenta tissue of participant A001


title: DSBs_IMR90_untreated_2

city: Mainz

first: Maurice

last: Scheuren

address: Anselm-Franz-von-Bentzel-Weg 7

department: Division of Anthropology, Faculty of Biology, Institute of Organismic and Molecular Evolution

country: Germany

institute: Johannes Gutenberg-University Mainz

library_source: genomic

data_processing:
The generated NGS reads were scanned for the first and second barcode sequences, allowing for one mismatch, subsequently the enclosed UMI and adjacent sequence were extracted. The resulting sequences were mapped to the GRCh38 reference genome using Bowtie2 in PE mode with options ‘—local -N 1 –fr’ and then converted to bed-format using SAMtools. To obtain unique DSB events, PCR duplicates were singularized by identifying alignments that share a starting position within a ± 6 bp of range and a Hamming distance < 1 regarding the UMI. The resulting DSB positions were depleted from blacklisted regions using BEDTools intersect and the reference ‘GRCh38-blacklist.v2.bed’ (https://github.com/igordot/reference-genomes/blob/master/GRCh38/blacklist.v2.bed). To subsequently identify genomic regions enriched in DSBs, a topological-based workflow was developed as a model-free method, following the proposal by Mitra and colleagues (2020). Therefore, we identified local maxima in the genome wide DSB distribution. In summary, BEDTools coverage with the option ‘-counts’ was used to calculate DSB coverage over 100 bp sliding 1 kb bins of GRCh38. The resulting smoothed DSB distribution was used to identify local maxima within the distribution using 'scipy.signal.find_peaks' from the SciPy package. The replicates’ resulting local maxima were used to identify common maxima through BEDTools intersect. These common local maxima were centered into a 1 kb overlapping shared 'peak' and were subsequently referred to as recurrent DSB clusters (RDCs).
Assembly: hg38
Supplementary files format and content: BED file with each unique DSB event per sample

source_name: lung

growth_protocol: IMR90 cells were cultured in Dulbecco's modified Eagle's medium supplemented with 10 % fetal bovine serum (Thermo Fisher Scientific) at 37 °C and 5 % CO2.

extract_protocol:
Briefly, isolated sperm heads from a total ejaculate or roughly 2 x 106 cultured IMR90 cells were resuspended in 1X PBS and mixed with an equal volume of 1.5 % low melting point agarose before being drawn up with a syringe. To start, approximately 20 µl of gel was submerged in buffer (75 mM NaCl, 25 mM EDTA; pH 8) supplemented with dithiothreitol to achieve a final concentration of 1 mM and incubated for 1 h at room temperature. Next, the buffer was exchanged with lysis buffer (25 mM EDTA, 1 % SDS; pH 8) supplemented with 1 µl of Proteinase K and incubated overnight (15-19 h) at room temperature. The following day, the genomic DNA was blunted using the Quick Blunting Kit (New England Biolabs). Agarose was digested using β-Agarase I (New England Biolabs) prior to Adapter ligation. Next, the adapter containing the RNA polymerase promoter was ligated with T4 DNA ligase (New England Biolabs) and incubated overnight (15-19 h) at 16 °C. Unligated adapters were removed using gel electrophoresis and the gDNA was recovered using the QIAquick Gel Extraction Kit (Qiagen). The isolated gDNA was fragmented using Covaris S-series with 'Duty Factor 10 %, Intensity 4 and Burst 200' for 80 sec. The in vitro transcription reaction was carried out at 37 °C overnight (15-19 h) using the HiScribe T7 Quick High Yield RNA Synthesis Kit (New England Biolabs). The resulting RNA was polyadenylated with E. coli Poly(A) Polymerase (New England Biolabs), reverse transcribed using the Biozym cDNA Synthesis Kit (Biozym), and then amplified using PCR with the Taq PCR Core Kit (Qiagen).
The NEBNext Ultra II DNA PCR-free Library Prep Kit for Illumina (New England Biolabs) was used to prepare and sequence the PCR-free libraries employing a PE150 strategy on a NovaSeq 6000.

treatment_protocol: To inhibit DNA-Pkc activity in the IMR90 cells, AZD7648 (MedChemExpress) was dissolved in DMSO and added to the medium at a final concentration of 1 µM, while an equivalent volume of DMSO was added to the control medium. After 48 h of incubation, the cells were harvested for further processing.

value: lung

value: female lung fibroblast

value: DMSO control


title: Samples 4-5, PBMC, post treatment, Adalimumab non-responder (GEX)

city: Maribor

first: Mario

middle: Smode

last: Gorenjak

address: Taborska ulica 8

country: Slovenia

institute: Faculty of Medicine, University of Maribor

description:
10X Multiplex library
S004_001_post_NR, CMO tags: 301|302|303|304
S005_014_post_NR, CMO tags: 305|306|307|308
S004_001_post_NR_filtered_barcodes.tsv.gz
S004_001_post_NR_filtered_features.tsv.gz
S004_001_post_NR_filtered_matrix.mtx.gz
S005_014_post_NR_filtered_barcodes.tsv.gz
S005_014_post_NR_filtered_features.tsv.gz
S005_014_post_NR_filtered_matrix.mtx.gz

library_source: transcriptomic single cell

data_processing:
The obtained raw sequencing .fastq.gz files were assessed for quality using fastq.gzC 0.11.9 software prior to downstream analysis. Obtained data was pre-processed using CellRanger 7.0.0 software with intron mode (10X Genomics) to demultiplex, align the reads to GRCh38 reference genome, cell barcode processing and gene counting. Supplementary_files_format_and_content: Filtered feature barcode matrices (Market Exchange Fromat - MEX) with .mtx file extension, cell barcodes and features with .tsv file extension (https://www.10xgenomics.com/support/software/cell-ranger/latest/analysis/outputs/cr-outputs-mex-matrices).
Assembly: GRCh38-2020-A (10X Genomics)
Supplementary files format and content: Tab separated values and Matrix Market Exchange format matrices
Supplementary files format and content: barcodes.tsv.gz; cell barcodes
Supplementary files format and content: features.tsv.gz; gene Ids
Supplementary files format and content: matrix.mtx.gz; gene expression count data

molecule: polyA RNA

source_name: Peripheral venous blood

extract_protocol:
Peripheral venous blood was collected into K2EDTA tubes (Vacutainer BD, Franklin Lakes, NJ, USA). The PBMCs were isolated using density gradient centrifugation with Lympholyte H Cell Separation Medium (Cedarlane, Burlington, ON, Canada) and SepMate 50 centrifuge tubes (StemCells Technologies, Vancouver, BC, Canada). The remaining platelets and erythrocytes were removed using the low-speed centrifugation and red blood cell lysis, respectively. The isolated PBMCs were stored in liquid nitrogen at a density of 1-10E6 cells/mL. A combination of 10% dimethyl sulfoxide (Sigma-Aldrich, Bur-lington, MA, USA) and 40% heat-inactivated fetal bovine serum (Gibco, ThermoFisher Scientific, Waltham, MA, USA) was used as the cryopreservation medium. The cell concentration was determined using the CytoSmart automated cell counter (Corning Inc., Corning, NY, USA). To perform scRNA-seq the 10X Chromium System (10X Genomics, Pleasanton, CA, USA) was used. First, the cryopreserved PBMCs were thawed and washed in Dulbecco's Phosphate-Buffered Saline supplemented with 5% FBS to remove the cryopreservation medium. The quality of the cell samples was confirmed using the trypan blue exclusion and viability of all samples was >90%. 2E6 cells per sample were used for the library preparation.
Samples 001 and 002 were processed as single reactions using Chromium Next Gem Single Cell 3' Kit v3.1 (PN-1000269), Chromium Next GEM Chip G Single Cell Kit (PN-1000127), and Dual Index Kit TT Set A (PN-1000215; all 10X Genomics) according to the manufacturer’s instructions (CG000315 Rev E). Other samples were processed as multiplexed reactions, with three samples per reaction, using Chromium Next Gem Single Cell 3' Kit v3.1 (PN-1000269), 3’ Feature Barcode Kit (PN-1000262), Dual Index Kit TT Set A (PN-1000215) and Dual Index Kit NN Set A (PN-1000243; all 10X Genomics). For the multiplexed samples, the cells were first CMO labelled using 3’CellPlex Kit Set A (PN-1000261, 10X Genomics) according to the manufacturer’s instructions (CG000391 Rev B). All samples were loaded onto the Chromium Controller Instrument (10X Ge-nomics) to generate gel bead-in-emulsions (GEM). Next, complementary DNA (cDNA) libraries were constructed. GEM–reverse transcription (RT) was performed in a C1000 deepwell block thermocycler (BioRad, Hercules, CA, USA). The cDNA was purified using Dynabeads MyOne Silane Beads (Thermo Fisher Scientific) and amplified following the recommendations in the 10X Genomics protocol CG000315 Rev E, for single reaction samples, and protocol CG000388 Rev C, for multiplex reaction samples. The product was subsequently purified using the SPRIselect Reagent Kit (B23318, Beckman Coulter, Brea, CA, USA,). Next, 3’ Gene Expression Libraries were constructed using the Chromium Single-Cell 3′ Library Construction Kit (PN-1000196). For the multiplexed samples Cell Multiplexing Libraries were additionally generated using Dual Index Kit NN Set A (PN-1000243) and 3’Feature Barcode Kit (PN-1000262). Library quality control was performed using the Agilent Bioanalyzer 2100 and using High Sensitivity DNA Kit (Agilent, Santa Clara, CA, USA). The prepared libraries were sequenced with Illumina NovaSeq pair-end 150bp at GENEWIZ (GENEWIZ Germany GmbH, Leipzig, Germany) with an average sequencing depth of >100 million reads per library yielding approximate average of 28,600 reads per cell.

value: Peripheral venous blood

tag: patients

value: PBMC

value: Ustekinumab

tag: phenotype

value: Adalimumab non-responder

tag: library type

value: mRNA


title: Samples 4-5, PBMC, post treatment, Adalimumab non-responder (CMO)

value: CMO


title: DSBs_IMR90_untreated_1


title: Sample 2, PBMC, pre treatment, Adalimumab responder (GEX)

description:
10X Single GEM well library
S002_016_pre_RE (GEX)
S002_016_pre_RE_filtered_barcodes.tsv.gz
S002_016_pre_RE_filtered_features.tsv.gz
S002_016_pre_RE_filtered_matrix.mtx.gz

value: Naive

value: Adalimumab responder


title: Samples 1-3, PBMC, post treatment, Adalimumab responder (GEX)

description:
10X Multiplex library
S001_010_post_RE, CMO tags: 309|310|311|312
S002_016_post_RE, CMO tags: 301|302|303|304
S003_008_post_RE, CMO tags: 305|306|307|308
S001_010_post_RE_filtered_barcodes.tsv.gz
S001_010_post_RE_filtered_features.tsv.gz
S001_010_post_RE_filtered_matrix.mtx.gz
S002_016_post_RE_filtered_barcodes.tsv.gz
S002_016_post_RE_filtered_features.tsv.gz
S002_016_post_RE_filtered_matrix.mtx.gz
S003_008_post_RE_filtered_barcodes.tsv.gz
S003_008_post_RE_filtered_features.tsv.gz
S003_008_post_RE_filtered_matrix.mtx.gz

value: Adalimumab


title: Samples 1-3, PBMC, post treatment, Adalimumab responder (CMO)


title: DSBs_IMR90_AZD7648treated_1

value: Treatment with AZD7648


title: DSBs_IMR90_AZD7648treated_2


title: Cord blood mono nuclear cells of participant A001


title: DSBs_Spermatozoa_2

source_name: sperm

value: sperm


title: Fetal side placenta tissue of participant A033

value: Fetal side placenta tissue


title: DSBs_Spermatozoa_1


title: Maternal side placenta tissue of participant A070


title: Maternal side placenta tissue of participant A052


title: Cord blood mono nuclear cells of participant A003

value: Cord blood mono nuclear cells


title: Flag:GTPBP8 in HEK293 biol rep 2

city: Nashville

first: James

last: Marks

state: Tennessee

address: 638A Robinson Research Building

institute: NIAMS/NIH

data_processing:
Illumina Nova-seq 6000 or Nextseq550 platform was used for sequencing
Basecalling was done using bcl2fastq V2.17.1
The reads were aligned to the hg38 genome using PARalyzer
normalized reads and clusters were combined in a csv file
Assembly: hg38
Supplementary files format and content: PARalyzer output

growth_protocol: HEK293 cells were cultured in DMEM media supplemented with 10% Fetal Bovine Serum and 1% Penicillin-Streptomycin.

extract_protocol:
Whole cell lysates were prepared. First Flag-GTPBP8 and V5-AUH proteins were enriched by immunoprecipitation with Flag or V5 beads. After washing the beads, RNase T1 digestion was performed, 3´ends of the RNA fragments were dephosphorylated using CIP, and RNA was fluorescently 3´end-labeled using T4 Rnl2(1–249)K227Q, followed by dephosporylation with T4 PNK. RNA-protein complexes were separated by SDS-PAGE and excised. After proteinase K treatment, RNA was extracted and 5' end labelled with T4 RNA ligase. Following small RNA cDNA library preparation was performed.
Ligation products were reverse transcribed and amplified by PCR.

treatment_protocol: Cells were treated with 50 ng/ml doxycycline for 48 hrs and 16 h before cell harvesting cells were treated with  4-thiouridine (4SU)  at a final concentration of 100 μM. Just before harvesting cells were crosslinked with 312 nm UV-light for 5 min.

tag: ip molecule

value: Flag

value: WT dox inducible

value: 4SU and 312 UV light


title: Flag:GTPBP8 in HEK293 biol rep 1


title: OLD Biological Rep 2, Passage 8

city: Stanford

first: Vittorio

last: Sebastiano

state: California

address: 265 Campus Drive

department: OB-GYN/Reproductive, Perinatal and Stem Cell Biology Research

institute: Stanford University

description:
Whole Genome Ezymatic Conversion
ALL_fibropass.hmr.txt
OLD3_allPs.hmr.txt

data_processing:
Trimming (Trimgalore)
Mapping (Bismark)
Conversion to methpipe/DNMTools formatted SAM using DNMTools
Duplicate reads removed, individual CpG coverage/average methylation calculated for symmetrical CpGs, using methpipe. Symmetrical CpG counts were then converted to bigwig format with wigToBigWig function
Low methylated regions (LMRs) calculated from symmetrical CpG counts file using hmr function in methpipe.
Assembly: hg38
Supplementary files format and content: bigwig files containing methylation pecentage per symmetric CpG in UCSC format
Supplementary files format and content: hmr files are genomic coordinates of low methylated regions for either all neonatal passages merged (NEO2_allPs.hmr.txt), all old passages merged (OLD3_allPs.hmr.txt), or all neonatal and old passages merged (ALL_fibropass.hmr.txt).

source_name: dermal fibroblasts

growth_protocol: All fibroblasts were thawed in passage 2 (P2) and maintained in Human Dermal Fibroblast Media (#116-500, Cell Applications). Media was refreshed every other day and fibroblasts were passaged using Tryple Select (12563011,Gibco) when culture dishes were >80% confluent. Cell pellets were frozen down every passage (P2-P8) to establish a large database of samples.

extract_protocol:
DNA from neonatal and old fibroblast cells was extracted using the GeneJET genomic DNA extraction kit (Thermo Scientific, Cat.n.K0721). DNA samples were quantified by Qubit 2.0 Fluorometer (Invitrogen, Carlsbad, CA).
WGBS library preparation and sequencing reactions were conducted at Novogene Corporation Inc (Sacramento, CA, USA).
Whole Genome Enzymatic Conversion

value: dermal fibroblasts

tag: age (years)

tag: passage


title: Sample 1, PBMC, pre treatment, Adalimumab responder (GEX)

description:
10X Single GEM well library
S001_010_pre_RE (GEX)
S001_010_pre_RE_filtered_barcodes.tsv.gz
S001_010_pre_RE_filtered_features.tsv.gz
S001_010_pre_RE_filtered_matrix.mtx.gz

value: Peripheral venous blood


title: Cord blood mono nuclear cells of participant A063


title: OLD Biological Rep 2, Passage 5


title: NEO Biological Rep 2, Passage 8

description:
Whole Genome Ezymatic Conversion
ALL_fibropass.hmr.txt
NEO2_allPs.hmr.txt

source_name: foreskin fibroblasts

value: foreskin fibroblasts


title: OLD Biological Rep 2, Passage 2


title: Maternal side placenta tissue of participant A044

value: Maternal side placenta tissue


title: Fetal side placenta tissue of participant A045


title: NEO Biological Rep 2, Passage 5


title: Cord blood mono nuclear cells of participant A021


title: CD4 T-cell, donor 43, aged 17

description:
IP
EZH2_CD4_pooled_ENCinp_fe.bw
none

data_processing:
Trimming (Trimgalore)
mapping (Bowtie2)
Callpeak ran on merged replicates for each tissue/passage (MACS2) using Inp (control) and IP to find fold enrichment. CD4 samples have no Inp file, online ENCODE file ENCFF918OQM.bam was used instead.
bigwig file called (bedGraphToBigWig)
Assembly: hg38
Supplementary files format and content: bigwig file containing fold enrichment signal track for either neonatal P2 merged, old P2 merged or CD4 samples (all donors) merged

source_name: CD4 T-cells

growth_protocol: All fibroblasts were thawed in passage 2 (P2) and maintained in Human Dermal Fibroblast Media (#116-500, Cell Applications). Media was refreshed every other day and fibroblasts were passaged using Tryple Select (12563011,Gibco) when culture dishes were >80% confluent.

extract_protocol:
ChIP experiments were performed on chromatin extracts according to the manufacturer's protocol (ChIP-IT High sensitivity, Active Motif, Cat.n. 53040) and chromatin sheared using the Bioruptor system (Bioruptor Plus, diagenode, Cat.n. B01020001) between 30-45 cycles (each cycle 30 sec ON/ 30 sec OFF high voltage).
ChIP-Seq library preparation and sequencing reactions were conducted at Novogene Corporation Inc (Sacramento, CA, USA).

value: CD4 T-cells

tag: chip antibody

value: Ezh2 (D2C9) XP® Rabbit mAb, Cell Signaling, Cat. n. 5246

tag: age

tag: passage number


title: CD4 T-cell, donor 48, aged 17

description:
IP
EZH2_CD4_pooled_ENCinp_fe.bw
none


title: NEO Biological Rep 2, Passage 2


title: Fetal side placenta tissue of participant A052


title: Cord blood mono nuclear cells of participant A044


title: Flag:GTPBP8 in HEK293 biol rep 3


title: Maternal side placenta tissue of participant A021


title: Old Biological Rep 3, Passage 2

description:
IP
OLD_P2_Merged_fe.bw
O3P2_peaks.narrowPeak


title: Fetal side placenta tissue of participant A063


title: CD4 T-cell, donor 32, aged 23

description:
IP
EZH2_CD4_pooled_ENCinp_fe.bw
none


title: Maternal side placenta tissue of participant A037


title: Maternal side placenta tissue of participant A035


title: Maternal side placenta tissue of participant A063


title: Maternal side placenta tissue of participant A049


title: Cord blood mono nuclear cells of participant A059


title: Old Biological Rep 1, Passage 2

description:
IP
OLD_P2_Merged_fe.bw
O1P2_peaks.narrowPeak


title: Neonatal Biological Rep 2, Passage 2

description:
IP
NEO_P2_Merged_fe.bw
N2P2_peaks.narrowPeak


title: Neonatal Biological Rep 1, Passage 2

description:
IP
NEO_P2_Merged_fe.bw
N1P2_peaks.narrowPeak


title: Fetal side placenta tissue of participant A032


title: Cord blood mono nuclear cells of participant A047


title: Old Biological Rep 3, Passage 2, input

description:
Input/Control
OLD_P2_Merged_fe.bw
O3P2_peaks.narrowPeak


title: Maternal side placenta tissue of participant A061


title: Cord blood mono nuclear cells of participant A052


title: Fetal side placenta tissue of participant A044


title: Maternal side placenta tissue of participant A075


title: Old Biological Rep 1, Passage 2, input

description:
Input/Control
OLD_P2_Merged_fe.bw
O1P2_peaks.narrowPeak


title: Old Biological Rep 2, Passage 2, input

description:
Input/Control
OLD_P2_Merged_fe.bw
O2P2_peaks.narrowPeak


title: Cord blood mono nuclear cells of participant A020


title: Neonatal Biological Rep 2, Passage 2, input

description:
Input/Control
NEO_P2_Merged_fe.bw
N2P2_peaks.narrowPeak


title: Neonatal Biological Rep 1, Passage 2, input

description:
Input/Control
NEO_P2_Merged_fe.bw
N1P2_peaks.narrowPeak


title: Old Biological Rep 2, Passage 2

description:
IP
OLD_P2_Merged_fe.bw
O2P2_peaks.narrowPeak


title: Cord blood mono nuclear cells of participant A033


title: Cord blood mono nuclear cells of participant A075


title: Fetal side placenta tissue of participant A060


title: rnaseq_t7_WIZ-g6_R3

city: Basel

first: Alejandro

last: Reyes

address: Fabrikstrasse 22

department: Data Sciences

country: Switzerland

institute: Novartis Institutes For BioMedical Research

library_source: transcriptomic

data_processing:
Gene and isoform level quantifications of RNA-seq data were done using the software salmon version 1.0.0, using as reference the cDNA catalogue of human hg38 transcripts as downloaded from ENSEMBL
processed data files format and content: Text files containing the results of the transcript-level quantifications of the software salmon (extension .sf).

molecule: total RNA

source_name: blood

extract_protocol:
RNA was extracted using the Zymo quick-RNA 96 kit according to manufacturer‚Äôs protocol.
NGS libraries were prepared from 250 ng total RNA using the Illumina TruSeq Stranded mRNA Sample Preparation kit (Illumina, #20020595), according to the manufacturers instructions

value: blood

value: CD34+ derived erythroblasts


title: Maternal side placenta tissue of participant A041


title: Fetal side placenta tissue of participant A066


title: rnaseq_t7_WIZ-g6_R2


title: Maternal side placenta tissue of participant A018


title: rnaseq_t7_WIZ-g18_R3


title: rnaseq_t7_WIZ-g18_R2


title: Maternal side placenta tissue of participant A065


title: Fetal side placenta tissue of participant A041


title: Cord blood mono nuclear cells of participant A045


title: rnaseq_t7_WIZ-g18_R1


title: Cord blood mono nuclear cells of participant A018


title: rnaseq_t7_untreated_R2

value: untreated


title: rnaseq_t7_untreated_R1


title: Fetal side placenta tissue of participant A021


title: Fetal side placenta tissue of participant A035


title: Maternal side placenta tissue of participant A032


title: rnaseq_t7_UNC0642_R2


title: Fetal side placenta tissue of participant A018


title: rnaseq_t7_EHMT2-g8_R3


title: rnaseq_t7_UNC0642_R1


title: rnaseq_t7_UNC0642_R3


title: Fetal side placenta tissue of participant A059


title: Fetal side placenta tissue of participant A049


title: rnaseq_t7_EHMT2-g8_R2


title: Cord blood mono nuclear cells of participant A066


title: rnaseq_t7_EHMT2-g8_R1


title: Fetal side placenta tissue of participant A061


title: rnaseq_t7_EHMT2-g18_R3


title: Cord blood mono nuclear cells of participant A032


title: Maternal side placenta tissue of participant A020


title: Cord blood mono nuclear cells of participant A049


title: Maternal side placenta tissue of participant A059


title: rnaseq_t7_untreated_R3


title: rnaseq_t7_WIZ-g6_R1


title: Cord blood mono nuclear cells of participant A035


title: rnaseq_t7_EHMT2-g18_R1


title: rnaseq_t7_dWIZ-2_R3


title: rnaseq_t7_dWIZ-2_R2


title: Maternal side placenta tissue of participant A066


title: rnaseq_t7_dWIZ-2_R1


title: Fetal side placenta tissue of participant A020


title: rnaseq_t7_DMSO_R3

value: DMSO


title: Fetal side placenta tissue of participant A047


title: rnaseq_t7_DMSO_R2


title: rnaseq_t7_DMSO_R1


title: Fetal side placenta tissue of participant A037


title: rnaseq_t7_ctrl-g0135_R3


title: Fetal side placenta tissue of participant A070


title: Maternal side placenta tissue of participant A033


title: rnaseq_t7_ctrl-g0135_R2


title: rnaseq_t7_ctrl-g0135_R1


title: Fetal side placenta tissue of participant A065


title: Fetal side placenta tissue of participant A075


title: rnaseq_t7_EHMT2-g18_R2


title: rnaseq_t7_ctrl-g0111_R1


title: rnaseq_t7_ctrl-g0111_R2


title: Cord blood mono nuclear cells of participant A060


title: rnaseq_t0_WIZ-g6_R1


title: Cord blood mono nuclear cells of participant A061


title: Cord blood mono nuclear cells of participant A065


title: rnaseq_t0_WIZ-g6_R2


title: Maternal side placenta tissue of participant A047


title: Maternal side placenta tissue of participant A045


title: rnaseq_t7_ctrl-g0111_R3


title: Maternal side placenta tissue of participant A080 (2)


title: rnaseq_t0_WIZ-g18_R3


title: rnaseq_t0_WIZ-g6_R3


title: Maternal side placenta tissue of participant A080 (1)


title: Fetal side placenta tissue of participant A080


title: rnaseq_t0_WIZ-g18_R1


title: Maternal side placenta tissue of participant A060


title: Maternal side placenta tissue of participant A079


title: rnaseq_t0_untreated_R2


title: Fetal side placenta tissue of participant A079


title: Maternal side placenta tissue of participant A078


title: rnaseq_t0_untreated_R1


title: rnaseq_t0_UNC0642_R3


title: RNA-seq of E. coli wt cells in stationary phase 45°C -Replicate 2

city: Wuhan

first: binguang

last: ma

address: No.1,Shizishan Street, Hongshan

country: China

institute: Huazhong Agricultural University

data_processing:
CLC Genomics Workbench v 11.0.1
Sequence reads were trimmed for adaptor sequence/low-quality sequence using CLC genomic benchwork (parameter- Quality limit: 0.05)
Trimmed sequence reads were mapped to GrCM38/mm10 using CLC genomic benchwork (parameters- mismath cost: 2 insertion cost: 3 deletion cost: 3 length fraction: 0.8 similarity fraction: 0.8)
Read count extraction and normalization were performed using CLC genomic benchwork
Assembly: E. coli MG1655 GenBank: U00096.2,total length : 4639675 bp
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

organism: Escherichia coli str. K-12 substr. MG1655

source_name: WT

growth_protocol: E. coli cells were grown at  37°C or 45°C in Lennox Broth (LB) . The cultures were grown to early logarithmic phase or stationary phase.

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.
After the RNA samples passed the detection, magnetic beads with Oligo(dT) were used to enrich eukaryotic mRNA (if prokaryotes were prokaryotes, the mRNA was enriched by removing rRNA through the kit). Then mRNA was fragmented into fragments by fragmentation buffer. A strand of cDNA was synthesized by using mRNA as template and random Hexamers with six bases. Then buffer, dNTPs (dTTP in dNTP was replaced by dUTP) and DNA Polymerase I and RNase H were added to synthesize the double-stranded cDNA. AMPure XP Beads were used to purify the double-stranded cDNA, and USER enzyme was used to degrade the second strand of cDNA containing U. The purified double-stranded cDNA was repaired at the end, A tail was added, and sequencing adaptor was connected. Then AMPure XP beads were used for fragment size selection. Finally, PCR amplification was performed and AMPure XP beads were used to purify the PCR products to obtain the final library. After the construction of the library, Qubit 2.0 was used for preliminary quantification, and then Agilent 2100 was used to detect the size of the inserted fragments of the library. After the inserted fragments met the expectations, Q-PCR method was used to accurately quantify the effective concentration of the library to ensure the quality of the library.

treatment_protocol: The resuscitated E. coli culture medium was inoculated 1:100 into LB medium and cultured at 37 ° C. When the OD600 of culture medium reached 2 (1.5 h), the culture medium of normal temperature group was kept at 37℃, and the culture medium of heat treatment group was kept at 50℃ water bath for 1 min and 20 s to increase the temperature to 45℃, and then the culture medium was kept at 45℃. Before heat treatment, 10 min and 2.5 h after heat treatment, 1 mL was sampled from the normal temperature group and the heat treatment group, respectively, to prepare 3C library

tag: strain

value: WT

value: F- lambda- ilvG- rfb-50 rph-1


title: RNA-seq of E. coli wt cells in stationary phase 45°C -Replicate 1


title: rnaseq_t0_UNC0642_R2


title: RNA-seq of E. coli wt cells in early logarithmic phase 45°C -Replicate 3


title: Cord blood mono nuclear cells of participant A078


title: RNA-seq of E. coli wt cells in early logarithmic phase 45°C -Replicate 2


title: Fetal side placenta tissue of participant A077

value: Fetal side placenta tissue


title: rnaseq_t0_UNC0642_R1


title: RNA-seq of E. coli wt cells in early logarithmic phase 45°C -Replicate 1


title: RNA-seq of E. coli wt cells in stationary phase 37°C -Replicate 2


title: rnaseq_t0_WIZ-g18_R2


title: Maternal side placenta tissue of participant A077


title: rnaseq_t0_EHMT2-g8_R3


title: RNA-seq of E. coli wt cells in stationary phase 37°C -Replicate 3


title: Cord blood mono nuclear cells of participant A077

value: Cord blood mono nuclear cells


title: rnaseq_t0_EHMT2-g8_R2


title: RNA-seq of E. coli wt cells in stationary phase 37°C -Replicate 1


title: RNA-seq of E. coli wt cells in early logarithmic phase 37°C -Replicate 3


title: rnaseq_t0_untreated_R3


title: RNA-seq of E. coli wt cells in early logarithmic phase 37°C -Replicate 1


title: rnaseq_t0_EHMT2-g8_R1


title: RNA-seq of E. coli wt cells in early logarithmic phase 37°C -Replicate 2


title: RNA-seq of E. coli wt cells in stationary phase 45°C -Replicate 3


title: 3C-seq of E. coli wt cells in stationary phase 45°C -Replicate 2

data_processing:
Iterative alignment, Min-leght=20, step=5, bowtie2 --very-sensitive
Filtering, Mapping quality=30, no ambiguous reads
Assignment to restriction fragment
Removal of un-informative events (uncuts, loops etc) as described in Cournac et al. BMC 2012.
Binning at 5kb
Assembly: E. coli MG1655 GenBank: U00096.2,total length : 4639675 bp
Supplementary files format and content: contact maps (2D array of 929 5kb-bins x 929 5kb-bins)

extract_protocol:
Fresh formaldehyde solution with a final concentration of 7% (1%, 3%, 5% and 7% were used in the comparison experiment of formaldehyde) was added to 1mL of E. coli culture medium, and the chromosomes were fixed by incubating at room temperature for 30 min and then incubating at 4℃ for 30 min. The excess formaldehyde was quenched by adding 2.5 M glycine solution and incubating at 4 ° C for 30 min. Centrifugation was performed at 3500 g for 10 min at 4 ° C and the supernatant was removed. The precipitate can be stored in refrigerator at -80℃ or digested directly. 10 μL protease inhibitors and 200 μL Ready-Lyse were added to each tube of precipitate, and the precipitate was resuspended and incubated for 30 min at room temperature. Centrifugation was performed at 3500 g for 10 min at 4 ° C and the supernatant was removed. The precipitate obtained can be directly used for the next enzyme digestion, or it can be quick-frozen with liquid nitrogen and stored in the refrigerator at -80℃ for about a week for subsequent experiments. The fixed precipitated product was resuspended with 100 μL of 1×TE Buffer, and 5 μL of 10%SDS was added and incubated for 20 min at room temperature to obtain the lysate solution of bacteria. If it is to use frozen precipitation products need to be placed on ice in advance to thaw. Each 100 μL lysate solution was mixed with 50 μL 20% TritonX-100, 100 μL Cut Smart Buffer, 710 μL ultra-pure water and 40 μL limiting enzyme HpaII (or Hpy4CHIV). When configuring the digestion buffer, it is best to perform the operation on ice and limit the enzyme to the last addition. The digested buffer system was incubated at 37℃ for 6 h (treated for 3 h, 5 h, and 6 h respectively in the enzyme digestion time experiment) to fully fragment the DNA, and then 50 μL 10% SDS was added to quench the excess restriction enzymes. Before joining, the digested solution was cooled on ice for a period of time, ensuring that the temperature did not exceed 16 °C. Because the connection system requires a lot of dilution, it is best to also cool ultrapure water on ice to below 16 ° C. To each 1 mL of enzymatic solution, 100 μl BSA, 1 mL 20% TritonX-100, 2 mL T4 Ligation Buffer, 1.6 mL ultrapure water, and 10 μl T4 DNA ligase were mixed thoroughly. At this stage, after all other solutions have been added, let cool on ice for a few minutes before adding the ligase. The connecting system was placed in a water bath in an incubator at 16℃ for 4 hours and then 200 μL 0.5 M EDTA was added and mixed. Proteinase K was added to the mixture and the final concentration of 100 ug/mL was incubated overnight at 58 ° C to digest the protein in the solution. The obtained mixed solution was thoroughly mixed with an equal volume of phenol chloroform isoamyl alcohol DNA extract and centrifuged at 12000 g for 10 min. The top layer of nucleic acid solution was transferred to a new EP tube and 1/10 volume of 3 M sodium acetate pH = 5.2, an appropriate amount of Glycogen and twice the ice-cold absolute ethanol were added for mixing. The supernatant was removed after centrifugation at 12000 g at 4 ° C for 15 min. The precipitate was redissolved with 100 μL of 1×TE Buffer and RNaseA was added and incubated for 30 min at 37 ° C for RNA degradation.
After the DNA samples passed the test, the Covaris ultrasonic crushing instrument was used to randomly interrupt the library, and then the whole library preparation was completed through the steps of end repair, adding A-tail, adding sequencing adaptor, purification, PCR amplification and so on. After the construction of the library, Qubit 2.0 was used for preliminary quantification and dilution of the library, and then Agilent 2100 was used to detect the inserted fragments of the library. After the size of the inserted fragments met the expectation, Q-PCR method was used to accurately quantify the effective concentration of the library to ensure the quality of the library.
3C-seq

value: thermal stress


title: Cord blood mono nuclear cells of participant A073


title: rnaseq_t0_EHMT2-g18_R3


title: Maternal side placenta tissue of participant A072


title: 3C-seq of E. coli wt cells in stationary phase 45°C -Replicate 1


title: 3C-seq of E. coli wt cells in early logarithmic phase 45°C -Replicate 2


title: Fetal side placenta tissue of participant A078


title: rnaseq_t0_EHMT2-g18_R2


title: 3C-seq of E. coli wt cells in early logarithmic phase 45°C -Replicate 1


title: Fetal side placenta tissue of participant A072


title: rnaseq_t0_EHMT2-g18_R1


title: rnaseq_t0_dWIZ-2_R3


title: 3C-seq of E. coli wt cells in stationary phase 37°C -Replicate 1


title: Cord blood mono nuclear cells of participant A069


title: 3C-seq of E. coli wt cells in early logarithmic phase 37°C -Replicate 1


title: rnaseq_t0_dWIZ-2_R2


title: 3C-seq of E. coli wt cells in early logarithmic phase 37°C -Replicate 2


title: Fetal side placenta tissue of participant A069


title: Maternal side placenta tissue of participant A068


title: Fetal side placenta tissue of participant A068


title: R. torques VIII-239 glucose biol rep 2

city: Ann Arbor

first: Gabriel

last: Vasconcelos Pereira

state: Michigan

address: 1150 W. Medical Center Dr.

institute: University of Michigan

description:
rRNA depleted, mRNA
NP-1 Rt8 G2

data_processing:
Quality check and trim performed using Trimmomatic v0.39
Reads were aligned to the R. torques genome using BowTie2 v2.3.5.1.
Reads mapping to gene features were counted using htseq-count (release_0.11.1)
Differential expression analysis was performed with the edgeR v3.34.0 package in R v.4.0.2 (with the aid of Rstudio v1.3.1093)
Assembly: JBBJJQ000000000
Supplementary files format and content: RPKM file

organism: [Ruminococcus] torques VIII-239

source_name: bacterial cell

growth_protocol: R. torques VIII-239 was grown anaerobically at 37ºC to mid-log phase in YCFA medium with 5 mg/ml glucose or 5 mg/ml mucin O-glycans.

extract_protocol:
Samples were treated with 500 uL buffer (200 mM NaCl, 200 mM Tris, 20 mM EDTA at pH 8), 210 uL of 20% SDS, and 500 uL phenol:choloroform:isoamyl alcohol (125:24:1, pH 4.3) and was bead beat for 3 minutes. Samples were precipitated with isopropanol, purified with the RNeasy Mini Kit,treated with DNase (NEB), and re-purified wtih the RNeasy Mini Kit. rRNA was depleted with the MICROBEExpress Bacterial mRNA Enrichment Kit (ThermoFisher).
Samples were multiplexed for sequencing on the Illumina NovaSeq X platform at the University of Michigan Sequencing Core.

treatment_protocol: Cultures were grown in a 96-well plate in 200 uL cultures. To increase biomass, each biological replicate was split into 12 replicate wells pooled at sample collection (each biological replicate included final culture volume of 2.4 mL). At collection, cells were pelleted, resuspended in 1 mL RNAprotect (Qiagen), and frozen at -80C until extraction.

value: bacterial cell

value: wildtype

value: 5 mg/ml glucose


title: R. torques VIII-239 glucose biol rep 1

description:
rRNA depleted, mRNA
NP-1 Rt8 G1


title: Cord blood mono nuclear cells of participant A068


title: 3C-seq of E. coli wt cells in early logarithmic phase-0 37°C -Replicate 2


title: 3C-seq of E. coli wt cells in stationary phase 37°C -Replicate 2


title: 3C-seq of E. coli wt cells in early logarithmic phase-0 37°C -Replicate 1


title: Maternal side placenta tissue of participant A069


title: R. torques VIII-239 mucin o-glycans biol rep 2

description:
rRNA depleted, mRNA
NP-1 Rt8 M2

value: 5 mg/ml mucin O-glycans


title: Fetal side placenta tissue of participant A067


title: R. torques VIII-239 mucin o-glycans biol rep 3

description:
rRNA depleted, mRNA
NP-1 Rt8 M3


title: rnaseq_t0_dWIZ-2_R1


title: BLISS_shCDK12_OHT_rep1

city: Milano

first: Stefano

last: Campaner

address: Via adamello 16

department: Center for Genomic Science

country: Italy

institute: fondazione Istituto italiano di tecnologia

data_processing:
Data were analysed according to the sBLISS-seq protocol (Bouwman, B.A.M., Agostini, F., Garnerone, S. et al. Genome-wide detection of DNA double-strand breaks by in-suspension BLISS. Nat Protoc 15, 3894–3941 (2020). https://doi.org/10.1038/s41596-020-0397-2)
Assembly: hg19
Library strategy: SBLISS-seq

extract_protocol:
Cells were fixed with 2%PFA and processed according to the publised sBLISS protocol (Bouwman, B.A.M., Agostini, F., Garnerone, S. et al. Genome-wide detection of DNA double-strand breaks by in-suspension BLISS. Nat Protoc 15, 3894–3941 (2020). https://doi.org/10.1038/s41596-020-0397-2)
Libraries were prepared according to the published sBLISS-seq protocol

value: shCDK12 OHT


title: rnaseq_t0_ctrl-g0135_R3


title: rnaseq_t0_DMSO_R2


title: V5:AUH in HEK293

value: WT dox inducible

value: 4SU and 312 UV light


title: rnaseq_t0_ctrl-g0135_R1


title: R. torques VIII-239 mucin o-glycans biol rep 1

description:
rRNA depleted, mRNA
NP-1 Rt8 M1


title: R. torques VIII-239 glucose biol rep 3

description:
rRNA depleted, mRNA
NP-1 Rt8 G3


title: shcSNX5 cells, rep 1

city: Taoyuan

first: Yi-Tung

last: Chen

address: No.259, Wenhua 1st Rd., Guishan Dist.

country: Taiwan

institute: Chang Gung University

data_processing:
Partek® Flow® Genomic Analysis Software
Sequence reads were trimmed for adaptor sequence/low-quality sequence using Partek® Flow® Genomic Analysis Software
Trimmed sequence reads were mapped to hg38 using Partek® Flow® Genomic Analysis Software
Read count extraction and normalization were performed using Partek® Flow® Genomic Analysis Software
Assembly: hg38
Supplementary files format and content: tab-delimited text files include raw read counts for each Sample

source_name: SAS

growth_protocol: SAS cells were maintained in DMEM supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
RNA was harvested using Trizol (Invitrogen). 1.0 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using TruSeq strandard mRNA Library Prep Kit following manufacturer's protocols.

value: SAS

value: Oral cancer cell line

value: viral infection


title: Ctrl cells, rep 1


title: rnaseq_t0_DMSO_R1

value: blood

value: CD34+ derived erythroblasts


title: BLISS_shCDK12_OHT_rep2


title: rnaseq_t0_DMSO_R3

value: DMSO


title: rnaseq_t0_ctrl-g0135_R2


title: Ctrl cells, rep 2

value: WT


title: Cord blood mono nuclear cells of participant A067


title: Maternal side placenta tissue of participant A067

value: Maternal side placenta tissue


title: Ctrl cells, replicate 1

extract_protocol:
RNA was harvested using Trizol (Invitrogen). 1.0 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using TruSeq RNA Exome Library Prep Kit following manufacturer's protocols.

tag: shRNA

value: shLuc


title: Maternal side placenta tissue of participant A064


title: rnaseq_t0_ctrl-g0111_R1


title: rnaseq_t0_ctrl-g0111_R3


title: Fetal side placenta tissue of participant A064

value: Fetal side placenta tissue


title: Pol2_SerP2_siLuc

data_processing:
Read filtering with fastx toolkit version 0.0.13.2: fastq_masker -Q33 -q 20 -r -N -v
Alignment to hg9 with bwa version 0.6.2; bwa aln -t 16 reffile fastqfile| bwa samse -n 1 reffile - fastqfile | samtools view -q 1 -ut reffile - |samtools sort - bamfile
read duplicates were removed
Assembly: hg19
Supplementary files format and content: *.bw: bigWig files of the alignments

extract_protocol:
Cells were fixed with 1% formaldehyde for 10 min and quenched with 0.125 m glycine for 5 min at room temperature. Cells were washed twice with PBS and resuspended in LB1 buffer (50 mm HEPES pH 7.5, 140 mm NaCl, 1 mm EDTA, 10% Glycerol, 0.5% NP-40, 0.25% Triton X-100) for 10 min on ice. After centrifugation, nuclei were extracted resuspending cells at room temperature for 10 min in LB2 buffer (10 mm Tris-HCl pH 8, 200 mm NaCl, 1 mm EDTA, 0.5 mm EGTA). The extracted nuclei were finally resuspended in LB3 buffer (10 mm Tris-HCl pH 8, 100 mm NaCl, 1 mm EDTA, 0.5 mm EGTA, 0.1% Na-Deoxycholate, 0.5% N-lauroylsarcosine) and sonicated in order to obtain DNA fragments of 300–100 bp. The lysate from 50 × 10E6 cells was incubated with 10 μg of RNA PolIIS2p antibody (ChromoTek, E310) previously bound to protein G Dynabeads (Invitrogen) in PBS+0.5% bovine serum albumin. After the incubation with the antibody, beads were collected using the DynaMag magnet, washed six times with 1 ml of RIPA buffer (50 mm HEPES pH 7.5, 500 mm LiCl, 1 mm EDTA, 1% NP-40, 0.7% Na-Deoxycholate) and once with 1 ml of TE 1X+50 mm NaCl. De-crosslinking was performed overnight at 65 °C with 150 μl of TE 1X+2% SDS. For cells fixed with glutaraldehyde, de-crosslinking was performed with 150 μl of TE+1% SDS+100 mm NaHCO3. Samples were first treated for 1 h with RNaseA at 37 °C, then Proteinase K was added and the de-crosslink reaction was incubated overnight at 65 °C. DNA was purified with PCR Qiaquick columns (Qiagen) and quantified using PicoGreen (Invitrogen) or QUBIT (Invitrogen).
Libraries were prepared for Illumina sequencing using a standard protocol consisting in blunting, addition of dA overhangs, ligation of Illumina adapters, selection on gel and PCR with index primers

tag: antibody

value: siLuc


title: shSTAU1 cells, replicate 2


title: Cord blood mono nuclear cells of participant A064

tag: tissue

value: Cord blood mono nuclear cells


title: Ctrl cells, replicate 2

tag: cell line


title: CUTNRUN-CTCF_DMSO_t4_R2

data_processing:
CUT&RUN data were mapped to the human reference genome hg38 using bowtie version 2.4.5. Data were normalized using the library size normalization from DESeq2. For each CUT&RUN sample, sequenced fragments were grouped according to their size into transcription factor fraction (< 120bp) and histone fractions (> 120bp). For WIZ and H3K9me2 CUT&RUN data, where global directional shifts were seen upon dWIZ-2 treatment, were renormalized using Drosophila melanogaster genome spike ins.
processed data files format and content: Normalized coverage tracks formatted as bigwigs.
Library strategy: CUT&RUN

extract_protocol:
Detail description of the extraction protocol can be found in the Supplementary Material of Ting et al.
The protocol was CUTNRUN, as described in the Ting et al paper.

tag: cell type


title: Fetal side placenta tissue of participant A062


title: RNA_seq_siCDK12_OHT_rep3

data_processing:
Read filtering with fastx toolkit 0.0.13.2: fastq_masker -Q33 -q 20 -r N -v
alignment with tophat version 2.0.8: tophat -r 170 -p 8 --no-novel-juncs --no-novel-indels --library-type fr-unstranded --transcriptome-index transcriptome_index reffile fastq_file_R1 fastq_file_R2
Removing duplicate reads: samtools rmdup -sS bamfile
Quantifying read counts over features with featureCounts v. 1.4.5-p1: featureCounts -T 2 -p -P -a gtffile
Idendifying Differentially Expressed Genes (DEG) using DESeq2 R Bioconductor package
Assembly: hg19
Supplementary files format and content: tab-delimited text file containing gene symbols/IDs, output of DESeq2 for each condition (siCDK12, OHT, siCDK12+OHT) vs control and raw and library-normalized counts

extract_protocol:
RNA was extracted with the RNeasy MinElute Spin columns from Qiagen according to the manufacturer and eluted in 14µl of RNase free water.
Libraries for RNA-Seq were prepared with the TruSeq RNA Sample Preparation Kits v2 (Illumina) following manufacturer instruction (except for skipping the first step of mRNA purification with poly-T oligo-attached magnetic beads)


title: Maternal side placenta tissue of participant A062


title: Cord blood mono nuclear cells of participant A062


title: CUTNRUN-CTCF_DMSO_t4_R1


title: shcSNX5 cells, rep 2

tag: genotype


title: Pol2_SerP2_siCDK12

tag: treatment


title: rnaseq_t0_ctrl-g0111_R2


title: RNA_seq_siCDK12_OHT_rep4


title: RNA_seq_siLuc_OHT_rep3


title: Maternal side placenta tissue of participant A058


title: RNA_seq_siCDK12_OHT_rep1


title: shSTAU1 cells, replicate 1


title: CUTNRUN-WIZ_t2_dWIZ-2_R3


title: RNA_seq_siCDK12_OHT_rep2


title: Fetal side placenta tissue of participant A058


title: RNA_seq_siLuc_OHT_rep2


title: CUTNRUN-WIZ_t2_dWIZ-2_R2


title: RNA_seq_siCDK12_rep3


title: RNA_seq_siLuc_OHT_rep1


title: RNA_seq_siCDK12_rep2


title: RNA_seq_siCDK12_rep4


title: CUTNRUN-WIZ_t2_dWIZ-2_R1


title: CUTNRUN-WIZ_t2_DMSO_R3


title: Cord blood mono nuclear cells of participant A058


title: RNA_seq_siCDK12_rep1


title: RNA_seq_siLuc_rep3


title: Maternal side placenta tissue of participant A056


title: CUTNRUN-WIZ_t2_DMSO_R2


title: RNA_seq_siLuc_rep2


title: Cord blood mono nuclear cells of participant A056


title: RNA_seq_siLuc_rep1


title: Fetal side placenta tissue of participant A056


title: CUTNRUN-WIZ_t2_DMSO_R1


title: Cas12a-Metal-SLCxSLC_input_rep3

description: Combinatorial Cas12a library

organism: synthetic construct

source_name: Plasmid

extract_protocol:
For the Cas12a-Metal-SLCxSLC, Cas12a- and Cas9-SLCxEnzymes, and Cas12a- and Cas9-SLCxSLC, gDNA was purified from 2x10e7 (QIAamp DNA Mini Kit), 1.7x10e7 (QIAGEN Genomic-tip 100/G) or 2.2x10e8 cells (QIAGEN Genomic-tip 500/G), respectively. gDNA from Cas12a- and Cas9-SLCxSLC screens was digested with restriction enzymes to improve PCR amplification of sgRNA regions. Up to 1.5 mg gDNA was digested with 200 U PacI (Cas12a-SLCxSLC) or 100 U PacI and 100 U XbaI (Cas9-SLCxSLC) (all NEB) for 48 hours.
sgRNA sequences from Cas12a library gDNA samples were amplified with barcoded FW and RV primer that introduce Illumina adapter and read1 sequencing primer binding sites. Up to 1.2 mg gDNA was used as template in 12 ml volume (divided in 96 x 125 µl PCRs) in the following program: 98°C for 30 sec.; 5 cycles: 98°C for 10 sec., 61°C for 30 sec, 72°C for 30 sec; 19 cycles: 98°C for 10 sec., 72°C for 1 min.; 72°C for 2 min. For the samples of the metal transporter and SLC family-wide sub-screen 1, Q5 Polymerase (NEB) was used, SLC vs SLC sub-screen 2-4 and SLC vs metabolic enzymes samples were processed with self-purified Pfu-Sso7d polymerase  and Phusion HF buffer (NEB). Primer sequences are shown in Supplementary Table SX. PCR products we double size selected with DNA purification bads and multiplexed for Illumina sequencing. sgRNA sequences from Cas9 library gDNA samples were first amplified with staggered FW and RV primer that contain partial Illumina adapter sequences at the 5’ end using the same PCR program as above. Up to 1.2 mg gDNA was used as template (125 µg/125 µl volume PCR) and amplified with self-purified Pfu-Sso7d polymerase. An aliquot of the pooled amplified PCR products was double size selected with DNA purification bads and purified fragments were barcoded in a second PCRs (98°C for 30 sec; 6-8 cycles: 98°C for 10 sec., 61°C for 30 sec, 72°C for 30 sec; 72°C for 2 min). PCR products we double size selected with DNA purification bads and multiplexed for Illumina sequencing.

value: Plasmid


title: Cas12a-Metal-SLCxSLC_input_rep2

description: Combinatorial Cas12a library


title: CUTNRUN-IgG_t4_dWIZ-2_R1


title: Maternal side placenta tissue of participant A055

extract_protocol: DNA was extracted using a DNeasy Blood and Tissue kit with RNase A, following the manufacturer's protocols. DNA was then prepared for the array following the Illumina Infinium HD Assay Methylation Protocol Guide


title: Cas12a-Metal-SLCxSLC_input_rep1

description: Combinatorial Cas12a library


title: Fetal side placenta tissue of participant A055


title: st17 wnt/chd-IBET explants rep 3

city: Evanston

first: Paul

middle: Benjamin

last: Huber

state: Illinois

address: 2205 Tech Drive

department: Molecular Biosciences

institute: Northwestern University

data_processing:
Seqeunce files were trimmed for adaptors and low quality reads using fastp v.0.23.2 using default parameters
Trimmed sequence reads were mapped to Xl9.2 (Xenopus genome) using STAR v.2.6.0
Read counts were obtained using htseq v.1.99.2
Assembly: Xl9.2
Supplementary files format and content: Raw read counts from htseq are listed in excel  spreadsheet
Supplementary files format and content: Deseq results are listed in excel spreadhseet

organism: Xenopus laevis

source_name: animal pole explant

extract_protocol:
Total RNA was extracted in Trizol and precipated using LiCl treament
Libraries were prepared using the NEB Next Ultra II directional RNA library prep kit using manufacturer's protocol

value: animal pole explant

tag: Stage

value: neural crest-reprogrammed

value: wild type

value: IBET st 9 to st 17


title: Cas12a-Metal-SLCxSLC_week5_rep3

description: Combinatorial Cas12a library

data_processing:
read trimming (Cas9 libraries only): Read1 reads were trimmed using cutadapt (Galaxy Version 4.8+galaxy1) to remove up- and downstream flanking sequences. The two gRNAs from read1 and read2 were then joined using FASTQ Joiner (Galaxy Version 2.0.1.1+galaxy0) before mapping to the reference sequences.
read mapping: MAGeCK count (Galaxy Version 0.5.9.2.4).
Assembly: Human NCBI genome build 36
Supplementary files format and content: tab-delimited raw gRNA pair count tables
Library strategy: Amplicon-Seq

value: cell line

value: HCT116 (RRID:CVCL_0291) subclone (RESOLUTE #CE06WS-Q)

value: Human colorectal carcinoma cell line

value: Contains lentiviral enCas12 expression contruct pRDA_174 (Addgene #136476)


title: st17 wnt/chd-IBET explants rep 2


title: CUTNRUN-IgG_t4_DMSO_R1

value: blood

value: CD34+ derived erythroblasts


title: CUTNRUN-H3K9me2_t4_dWIZ-2_R3


title: Maternal side placenta tissue of participant A054

data_processing: Raw methylation data was processing using the minfi bioconductor package. Quality control steps includes, removing samples with >5% high detection p-values (p-value >1e-7) and probes failed in one or more samples with the same cut-off. Background correction with dye-bias normalization was performed using normal-exponential out-of-band method. Bias from type-2 prob values was normalized using beta-mixture quantile normalization methods. Additionally, batch effects were corrected using an empirical Bayes framework. We also removed the CpGs located on sex chromosomes, enriched at single-nucleotide polymorphisims, and those prone to cross-reativity.


title: st17 wnt/chd-IBET explants rep 1


title: Fetal side placenta tissue of participant A054


title: st17 uninjected-IBETexplants rep 3

value: epidermal


title: Cas12a-Metal-SLCxSLC_week5_rep1

description: Combinatorial Cas12a library


title: CUTNRUN-H3K9me2_t4_dWIZ-2_R2


title: CUTNRUN-H3K9me2_t4_dWIZ-2_R1


title: Maternal side placenta tissue of participant A053

value: Maternal side placenta tissue


title: st17 uninjected-IBET explants rep 2


title: Cas12a-Metal-SLCxSLC_week4_rep3

description: Combinatorial Cas12a library


title: Cas12a-Metal-SLCxSLC_week4_rep2

description: Combinatorial Cas12a library


title: CUTNRUN-H3K9me2_t4_DMSO_R3

value: DMSO


title: Fetal side placenta tissue of participant A053

value: Fetal side placenta tissue


title: Cas12a-Metal-SLCxSLC_week5_rep2

description: Combinatorial Cas12a library


title: st17 uninjected-IBET explants rep 1


title: CUTNRUN-H3K9me2_t4_DMSO_R1


title: Maternal side placenta tissue of participant A051


title: CUTNRUN-H3K9me2_t4_DMSO_R2


title: Fetal side placenta tissue of participant A051


title: Cas12a-Metal-SLCxSLC_week4_rep1

description: Combinatorial Cas12a library


title: Cas12a-Metal-SLCxSLC_week1_rep2

description: Combinatorial Cas12a library


title: Cas12a-Metal-SLCxSLC_week1_rep3

description: Combinatorial Cas12a library


title: CUTNRUN-H3K9ac_t4_dWIZ-2_R2


title: Fetal side placenta tissue of participant A048


title: st17 wnt/chd-DMSO explants rep 2

value: DMSO st 9 to st 17


title: st17 wnt/chd-DMSO explants rep 1


title: CUTNRUN-H3K9ac_t4_dWIZ-2_R3


title: Cord blood mono nuclear cells of participant A048

value: Cord blood mono nuclear cells


title: Cas9-SLCxEnzyme_input_rep2

description: Combinatorial Cas9 library

value: Plasmid


title: st17 uninjected-DMSO explants rep 2

value: animal pole explant


title: st17 uninjected-DMSO explants rep 3


title: Maternal side placenta tissue of participant A046


title: Cas9-SLCxEnzyme_input_rep3

description: Combinatorial Cas9 library


title: CUTNRUN-H3K9ac_t4_dWIZ-2_R1


title: CUTNRUN-H3K9ac_t4_DMSO_R3


title: Fetal side placenta tissue of participant A046


title: st17 uninjected-DMSO explants rep 1


title: CUTNRUN-H3K9ac_t4_DMSO_R2


title: Cas12a-Metal-SLCxSLC_week1_rep1

description: Combinatorial Cas12a library


title: st17 wnt/chd-DMSO explants rep 3

value: neural crest-reprogrammed


title: Maternal side placenta tissue of participant A048


title: st13 wnt/chd-IBET explants rep 3

value: wild type

value: IBET st 9 to st 13


title: Cas9-SLCxSLC_input_rep2

description: Combinatorial Cas9 library


title: CUTNRUN-H3K9ac_t4_DMSO_R1


title: Maternal side placenta tissue of participant A043


title: CUTNRUN-WIZ_t2_dWIZ-2_R4


title: st13 wnt/chd-IBET explants rep 2


title: Cas9-SLCxSLC_input_rep1

description: Combinatorial Cas9 library


title: Fetal side placenta tissue of participant A043


title: Cord blood mono nuclear cells of participant A043


title: st13 wnt/chd-IBET explants rep 1


title: Cas12a-SLCxEnzyme_input_rep3

description: Combinatorial Cas12a library


title: CUTNRUN-WIZ_t4_dWIZ-2_R3


title: CUTNRUN-WIZ_t4_dWIZ-2_R2


title: Cas12a-SLCxEnzyme_input_rep2

description: Combinatorial Cas12a library


title: st13 uninjected-IBETexplants rep 3


title: CUTNRUN-WIZ_t4_dWIZ-2_R1


title: st13 uninjected-IBET explants rep 2


title: Fetal side placenta tissue of participant A042


title: Cas12a-SLCxEnzyme_input_rep1

description: Combinatorial Cas12a library


title: Maternal side placenta tissue of participant A042


title: st13 uninjected-IBET explants rep 1


title: Cas9-SLCxEnzyme_input_rep1

description: Combinatorial Cas9 library


title: Cas12a-SLCxSLC_sublib3_4_input_rep3

description: Combinatorial Cas12a library


title: Cas12a-SLCxSLC_sublib3_4_input_rep2

description: Combinatorial Cas12a library


title: Maternal side placenta tissue of participant A040


title: Fetal side placenta tissue of participant A040


title: CUTNRUN-WIZ_t4_DMSO_R3


title: Cord blood mono nuclear cells of participant A042


title: st13 wnt/chd-DMSO explants rep 2

description:
uninjDMSOvsWntCHDdmso_st13
wntchdDMSOvsWNTCHDibet_st13

value: DMSO st 9 to st 13


title: CUTNRUN-WIZ_t4_DMSO_R2


title: st13 wnt/chd-DMSO explants rep 1


title: Cas12a-SLCxSLC_sublib2_input_rep3

description: Combinatorial Cas12a library


title: CUTNRUN-WIZ_t4_DMSO_R1


title: st13 uninjected-DMSO explants rep 3

description:
uninjDMSOvsWntCHDdmso_st13
uninjDMSOvsUNINJibet_st13


title: Cas12a-SLCxSLC_sublib2_input_rep2

description: Combinatorial Cas12a library


title: EdU_HU_seq_shCDK12_OHT_rep3

data_processing:
Read filtering with fastx toolkit version 0.0.13.2: fastq_masker -Q33 -q 20 -r -N -v
Alignment to hg19 with bwa version 0.6.2; bwa aln -t 16 reffile fastqfile| bwa samse -n 1 reffile - fastqfile | samtools view -q 1 -ut reffile - |samtools sort - bamfile
Spike-ins were aligned using mm10 genome assembly
Replicates of the same condition were merged after alignment and spike-in normalization to a single BAM file for the analyses
Peak calling was carried out with epic2 with the following options: -gn hg19 --gaps-allowed 10 --bin-size 400
Assembly: hg19
Supplementary files format and content: *.bed.gz: genomic regions (peaks) called from the merge of the triplicates
Supplementary files format and content: *.bw: bigWig files of the merged replicates

extract_protocol:
Methanol fixed cells were permeabilized with 0.2% Triton-X in PBS and EdU was coupled to a cleavable biotin-azide linker (Azide-PEG(3+3)-S-S-biotin) using the Click-IT chemistry (Macheret M. and Halazonetis T., Nature protocol 2019). DNA was then purified by phenol-chloroform extraction and ethanol precipitation and subjected to EdU-labelled DNA isolation according to the published protocol (Macheret M and Halazonetis T., Nature protocol 2019).
HT-Chip-seq library preparation


title: EdU_HU_seq_shCDK12_OHT_rep2


title: Cord blood mono nuclear cells of participant A039


title: st13 uninjected-DMSO explants rep 2


title: Cas12a-SLCxSLC_sublib2_input_rep1

description: Combinatorial Cas12a library


title: CUTNRUN-WIZ_t2_DMSO_R4


title: Fetal side placenta tissue of participant A039


title: st9 wnt/chd explants rep 3

value: blastula animal pole

value: wnt/chd injected


title: st13 wnt/chd-DMSO explants rep 3


title: EdU_HU_seq_shCDK12_rep3


title: EdU_HU_seq_shCDK12_OHT_rep1


title: Cas12a-SLCxSLC_sublib1_input_rep2

description: Combinatorial Cas12a library


title: Maternal side placenta tissue of participant A036


title: EdU_HU_seq_shCDK12_rep2


title: st9 wnt/chd explants rep 2


title: Fetal side placenta tissue of participant A036


title: Cord blood mono nuclear cells of participant A036


title: st9 wnt/chd explants rep 1


title: Cas12a-SLCxSLC_sublib1_input_rep1

description: Combinatorial Cas12a library


title: EdU_HU_seq_shCDK12_rep1


title: Maternal side placenta tissue of participant A039


title: st9 uninjected explants rep 3

value: uninjected


title: Cas12a-SLCxSLC_sublib1_input_v0_rep3

description: Combinatorial Cas12a library


title: Fetal side placenta tissue of participant A031


title: Cas12a-SLCxSLC_sublib1_input_v0_rep2

description: Combinatorial Cas12a library


title: st9 uninjected explants rep 2


title: st13 uninjected-DMSO explants rep 1


title: Cas12a-SLCxSLC_sublib1_input_rep3

description: Combinatorial Cas12a library


title: Cord blood mono nuclear cells of participant A031


title: st9 uninjected explants rep 1


title: Maternal side placenta tissue of participant A028


title: Tumor, D&M, 5

city: Columbus

first: Katherine

middle: E

last: Miller

state: OH

address: 700 Children's Dr.

department: Institute for Genomic Medicine

institute: Nationwide Children's Hospital

data_processing:
RNA-Seq reads were aligned using STAR (STAR_2.6.1c) to a concatenated reference comprised of the Homo sapiens (GRCh38.p12 assembly) and Mus musculus (GRCm38.p6 assembly) genomes.
The resulting alignments were separated into species-specific bam files, converted back to fastq files and processed through individual human and mouse pipelines
Assembly: GRCh38.p12 assembly and GRCm38.p6 assembly

organism: Homo sapiens/Mus musculus xenograft

source_name: tumor

growth_protocol: All animal studies were performed in accordance with protocols approved by the New York Medical College Institutional Animal Care and Use Committee.

extract_protocol:
Total RNA was extracted from tumors using RNeasy mini kit (Qiagen) after homogenization of tumors by Tumor Dissociation Kit (Miltenyi Biotec) combined with the gentleMACS Dissociator.
Library was constructed using RNA as input using Illumina TruSeq Stranded Total RNA library preparation kit

treatment_protocol: Control (PBS and IgG) or DOX (0.5 mg/kg, once every 3 days for 5 times, i.v.)  or MAG (150 mg/animal, once per day for 12 days, i.p.) or DOX combined with MAG were injected.

value: tumor

value: doxorubicin + magrolimab


title: Fetal side placenta tissue of participant A028


title: EdU_HU_seq_shNT_rep3

value: shNT


title: st13 TSA explants rep 1

value: epidermal

value: TSA 2 cell to stage 13


title: Tumor, D&M, 4


title: EdU_HU_seq_shNT_OHT_rep1


title: Cord blood mono nuclear cells of participant A028


title: Cas12a-SLCxSLC_sublib1_input_v0_rep1

description: Combinatorial Cas12a library


title: EdU_HU_seq_shNT_rep2


title: Tumor, D&M, 3


title: Maternal side placenta tissue of participant A031

value: Maternal side placenta tissue


title: Maternal side placenta tissue of participant A027


title: st13 TSA explants rep 2


title: EdU_HU_seq_shNT_rep1


title: Tumor, D&M, 2


title: EdU_HU_seq_shNT_OHT_rep2


title: EdU_HU_seq_shNT_OHT_rep3


title: EU_seq_shCDK12_OHT_rep3

data_processing:
Read filtering with fastx toolkit 0.0.13.2: fastq_masker -Q33 -q 20 -r N -v
reads alignment with STAR v. 2.7.5c
Quantifying read counts over features with featureCounts v. 1.4.5-p1: featureCounts -T 2 -p -P -a gtffile
Assembly: hg19
Supplementary files format and content: count_matrix.xls: tab-delimited text file containing raw counts for each gene
Supplementary files format and content: EU_seq_shNT_OHT_rep3.bw: bigwig of EU_seq_shNT_OHT_rep3 sample
Supplementary files format and content: EU_seq_shCDK12_OHT_rep3.bw: bigwig of EU_seq_shCDK12_OHT_rep3 sample

extract_protocol:
RNA was then extracted and purified using the Quick-RNATM Miniprep Kit (Zymo Research, cat. #R1055) according to the manufacturer’s instructions. Nascent RNA was biotinylated and purified starting from 50 μg of total RNA. EU was coupled to a cleavable biotin-azide linker (Azide-PEG(3+3)-S-S-biotin) (kind gift from Thanos Halazonetis) using the Click-IT chemistry as shown below: 50 μg of RNA (40 μg of human EU-labelled RNA and 10 μg of murine EU-labelled RNA) were mixed with the same volume of 2X Click-IT reaction cocktail (171 mM Tris-HCl pH 8, 8 mM CuSO4, 200 mM sodium-L-ascorbate, 0,1 mM biotin–azide) and incubated for 30 minutes at RT with gentle shaking. RNA was precipitated and the EU-labelled RNA was then isolated using 50 μl of Dynabeads MyOne streptavidin C1 (Invitrogen, Cat. No. 65001) each sample, that were washed before use two times with Binding and Washing Buffer 1X (5 mM Tris-HCl pH 7.5, 0.5 mM EDTA, 1 M NaCl, 0.5% Tween-20), followed by two washes with solution A (0.1 M NaOH, 0.05 M NaCl) and two washes with solution B (0.1 M NaCl). After washing, the beads were resuspended to twice the original volume with Binding and Washing Buffer 2X. RNase OUT (1:100, Invitrogen, Cat. No. 10777-019) was added to RNA and then samples were heated at 70°C for 5 minutes and placed back on ice to remove secondary structures. Then EU-labelled RNA was mixed with an equal volume of washed beads (100 µL) and incubated for 30 minutes on a rotating wheel at room temperature. The RNA-beads complex was then washed three times with Binding and Washing Buffer 1X and once with RNase free-water. Finally, the EU-labelled RNA was eluted by incubating the streptavidin beads with 55 μl of 2% β -mercaptoethanol (Calbiochem, Cat. No. 444203) in 10 mM Tris-HCl pH. 8 for 1 h at room temperature. 5 μl of each sample were used for Qubit quantification (RNA HS assay kit; Thermofisher, Cat. No. Q32852).
TruSeq Stranded Total RNA Gold (Illumina, Cat. No. 20020598)


title: Fetal side placenta tissue of participant A027

value: Fetal side placenta tissue


title: st9 TSA explants rep 2

value: TSA 2 cell to stage 9


title: st13 DMSO explants (control for TSA) rep 1

value: DMSO 2 cell to stage 13


title: Maternal side placenta tissue of participant A026


title: Tumor, D&M, 1


title: Tumor, MAG, 5

value: magrolimab


title: st9 TSA explants rep 1

value: animal pole explant


title: EU_seq_shCDK12_OHT_rep2


title: Tumor, MAG, 4


title: EU_seq_shCDK12_OHT_rep1


title: st13 DMSO explants (control for TSA) rep 2

value: wild type


title: Fetal side placenta tissue of participant A026


title: st9 DMSO explants (control for TSA) rep 1

value: DMSO 2 cell to stage 9


title: st9 DMSO explants (control for TSA) rep 2


title: EU_seq_shNT_OHT_rep2


title: EU_seq_shNT_OHT_rep3


title: Cord blood mono nuclear cells of participant A026

value: Cord blood mono nuclear cells


title: Tumor, MAG, 3


title: Tumor, MAG, 2


title: Cas12a-SLCxSLC_sublib3_4_input_rep1

description: Combinatorial Cas12a library

value: Plasmid


title: Maternal side placenta tissue of participant A025


title: EU_seq_shNT_OHT_rep1


title: Fetal side placenta tissue of participant A025


title: Tumor, MAG, 1


title: st13 IBET explants rep 2

value: IBET 2 cell to stage 13


title: EU_seq_shCDK12_rep3


title: Cord blood mono nuclear cells of participant A025


title: Tumor, DOX, 5

value: doxorubicin


title: st13 DMSO explants (control for IBET) rep 2


title: Maternal side placenta tissue of participant A024


title: EU_seq_shCDK12_rep2


title: Tumor, DOX, 4

value: tumor


title: st13 DMSO explants (control for IBET) rep 1


title: EU_seq_shCDK12_rep1


title: Tumor, DOX, 3


title: Fetal side placenta tissue of participant A024


title: st9 IBET explants rep 2

value: blastula animal pole

value: IBET 2 cell to stage 9


title: EU_seq_shNT_rep3

value: shNT


title: Tumor, DOX, 2


title: Cord blood mono nuclear cells of participant A024


title: st9 IBET explants rep 1


title: EU_seq_shNT_rep2


title: st9 DMSO explants (control for IBET) rep 2


title: EU_seq_shNT_rep1


title: Tumor, DOX, 1


title: Maternal side placenta tissue of participant A016


title: Tumor, Control, 5


title: st13 IBET explants rep 1

value: epidermal


title: BLISS_shCDK12_rep2


title: Cord blood mono nuclear cells of participant A016


title: st9 DMSO explants (control for IBET) rep 1


title: Cab39l_KO, Cab39l knockout, scRNAseq

city: Houston

first: Bogdan

middle: A

last: Czerniak

state: TX

address: 1515 Holcombe

department: Pathology

institute: UT MD Anderson Cancer Center

description: 10x Genomics

data_processing:
Raw sequencing data (fastq file) was demultiplexed and analyzed using 10X Genomics Cell Ranger software v 3.0.2 utilizing standard default settings and the cellranger count command to generate html QC metrics and cloupe files for each sample.
Assembly: mm10
Supplementary files format and content: Tab-seperated values files and matrix files

organism: Mus musculus

source_name: Cab39l knockout tissue

extract_protocol:
The bladders were harvested after ligating the urethra and injecting 50 µl of 0.25% Trypsin in PBS. The cells were incubated in Trypsin at 37°C for 30 minutes. The urothelial cell clusters and tissue fragments were removed by passing the cell suspension through the 70µm cell strainer. The red blood cells were removed by Ficoll gradient centrifugation. The collected single cell suspensions were washed twice with PBS containing 0.04% BSA and resuspended in 200µl of PBS.
Library preparation steps were carried out by running ThermoFisher Qubit HS dsDNA Assay along with Agilent HS DNA Bioanalyzer for concentration and quality assessments. Equal amounts of each uniquely-indexed sample library were pooled together. The resultant pool was verified for concentration via qPCR using a KAPA Biosystems KAPA Library Quantification Kit.

value: Cab39l knockout tissue


title: BLISS_shCDK12_rep1


title: Tumor, Control, 4


title: Maternal side placenta tissue of participant A015

value: Maternal side placenta tissue


title: Lpar6_KO, Lpar6 knockout, scRNAseq

description: 10x Genomics

source_name: Lpar6 knockout tissue

value: Lpar6 knockout tissue


title: Tumor, Control, 3


title: BLISS_shNT_rep2


title: Fetal side placenta tissue of participant A015

value: Fetal side placenta tissue


title: NU_wt, Wild type, scRNAseq

description: 10x Genomics

source_name: wild type urothelial tissue

value: wild type urothelial tissue


title: BLISS_shNT_rep1


title: Tumor, Control, 1


title: Tumor, Control, 2


title: Red_Flesh_Mesocarp_RepC_R201

status: Public on Jun 18 2024

city: Beuacouzé

first: Jean-Marc

last: Celton

address: 42 ue Georges Morel

country: France

institute: IRHS

description:
CB_vs_CR-CG-overallMethylation.bed
CB_vs_CR-CHG-overallMethylation.bed
CB_vs_CR-CHH-overallMethylation.bed

data_processing:
The quality of paired end sequencing reads (100 bp) generated from WGBS was evaluated with FastQC (version 0.11.9). The Trimmomatic (v0.39) software was used to remove adaptor sequences and poor quality bases using the given parameters “LEADING:3, TRAILING:3, MINLEN:80, ILLUMINACLIP:adapter:2:30:10”. The reference genome GDDH13 v1.1 was converted (C to T and G to A) by ‘bismark\_genome\_preparation’ tool within Bismark (v0.24.0). Subsequently, trimmed sequencing reads were aligned to the converted genome version using bowtie2. The resulting aligned BAM files were then processed to remove duplicates with the deduplicate\_bismark tool. Methylation extraction was performed on the deduplicated reads with bismark\_methylation\_extractor tool to generate the context-specific methylation-states (CpG, CHG and CHH) at the individual cytosine-level for each sample with the following parameters “-p --parallel 4 --bedGraph --CX\_context --cytosine\_report --comprehensive --gzip”. From this extraction, a genome-wide cytosine report was generated. The R package methylkit (v1.26.0) was used to compare the methylomes between red and white fruit flesh. Pairwise comparison was conducted with two and three semi-biological replicates, respectively. Methylation levels at cytosines in CpG, CHG or CHH contexts were initially calculated using the ‘methRead’ function with mincov=4. The ‘tileMethylCounts’ function was used to summarize methylated and unmethylated base counts over tiling windows across the genome with the parameters ‘win.size=100, step.size=100, cov.bases=4’. The ‘unite’ function was used to merge and retain only bases that were covered in tiled regions of all replicates with the destrand = FALSE parameter. Subsequently, the differential methylation statistics were calculated with ‘calculateDiffMeth’ function and ‘getMethylDiff’ function was used to select the DMRs for CpG, CHG, and CHH contexts that satisfied the following parameters ‘minDiff=25 q-value=0.05’. The command 'bedtools closest' from Bedtools (v2.27.1) with the parameter '-Db' was employed on the GDDH13 annotated genes to identify and retrieve the nearest gene to each DMR.
Assembly: GDDH13 v1.1
Supplementary files format and content: .bed files

organism: Malus domestica

source_name: Treatment 3

growth_protocol: This analysis included three semi-biological replicates of RF and WF mesocarps (fruits from different trees) from red-flesh cultivar, cv. 'R201' (plantation year : 2013). The transition stage between fully red fruits and heterogeneously pigmented fruits was targeted during fruit development (84 Days After Full Bloom - DAFB).\\

extract_protocol:
Total DNA was extracted from fruit mesocarp according to the method detailed by CTAB protocol detailed by Porebski et al, 1997
The library construction method and sequencing process are carried out according to the following steps: 1. Take genome DNA samples for quality control; 2. Fragmented genome DNA to the mean size of 200-350bp; 3. Blunt-ending and 3'-end dAaddition; 4. Methlated adaptor ligation; 5. Bisulfite conversion with EZ DNA Methylation-Gold kit (ZYMO); 6. PCR amplification; 7. Library quality control; 8. Library circularization; 9. The library was amplified to make DNA nanoball (DNB); 10. Sequencing on DNBSEQ (DNBSEQ Technology) platform.

treatment_protocol: Distinction between red-flesh and white-flesh mesocarps from same fruits

value: Red-Flesh Mesocarp


title: White_Flesh_Mesocarp_RepB_R201

source_name: Control 2

value: White-Flesh Mesocarp


title: Fetal side placenta tissue of participant A016

source_name: Pregnant individual at delivery visit


title: Red_Flesh_Mesocarp_RepB_R201

source_name: Treatment 2


title: White_Flesh_Mesocarp_RepA_R201

source_name: Control 1


title: White_Flesh_Mesocarp_RepC_R201

source_name: Control 3


title: scRNA_GEX_CD34_29_NCKO

city: Regensburg

first: Alexander

last: Fischer

address: Franz-Josef-Strauß-Allee 11

institute: Leibniz Institute for Immunotherapy

data_processing:
single cell sequencing data was pre-processed and mapped using the CellRanger pipeline (10X genomics). The standard .tsv output files were used for downstream analyses.
The R Seurat package (v. 4.0.5) was used to demultiplex by hashtag antibody barcode information. Filtering for a minimum of 750 counts and 250 different genes and a maximum percentage of 5% mitochondrial genes was applied
Data was normalized using the NormalizeData function of Seurat with the LogNormalize option and a cell-level normalization scale factor of 10000. For data integration, the Harmony package (v. 0.1.0) was utilized using RunHarmony.
Single cell clustering and cluster identification was performed using Seurat’s RunUMAP, FindNeighbors and FindClusters functions with “harmony” as reduction method. Marker genes by cluster were determined using FindAllMArkers with minimum percentage of cells set to 25% and a logFC requirement of 0.5
Significance of cluster distribution differences between SA2KO and control was tested using the scCODA python library (v. 0.1.8) applying the Dirichlet-multinomial Bayesian model test
Assembly: GRCh38.p10
Supplementary files format and content: zipped, tab-separated file containing the cell-associated barcodes (*barcodes.tsv) generated by CellRanger.
Supplementary files format and content: zipped, tab-separated matrix (market exchange (MEX) format) containing the counts for each feature generated by CellRanger. Each element of the matrix is the number of UMIs associated with a feature (row) and a barcode (column).
Supplementary files format and content: zipped, tab-separated file containing the Features corresponding to row indices for the matrix. For each feature, the feature ID and name are stored in the first and second column of the (unzipped) features.tsv.gz file, respectively. The third column identifies the type of feature, i.e. Gene Expression or Multiplexing Capture.
Supplementary files format and content: .rds (R object) file containing the final integrated Seurat object containing all samples. Can be used to reproduce clustering etc.
Supplementary files format and content: comma separated file containing statistical results from scCODA cluster distribtution analysis

source_name: cord blood

growth_protocol: CD34+ HSPCs were enriched from fresh cord blood samples on the day of birth using the CD34 MicroBead kit (Miltenyi biotec). Cells were expanded for 2-3d in serum-free Stem Span media (Stem Cell Technologies) supplemented with human recombinant cytokines (Peprotech): SCF (0.1ng/mL), FLT3 (0.1ng/mL), IL6 (0.004ng/mL), TPO (0.025ng/mL) and StemRegenin1 (7500nmol/mL, Stem Cell technologies) as well as Penicillin/Streptomycin.

extract_protocol:
Cells were stained with DNA-barcoded TotalSeq-B hashtag antibodies (Biolegend). After Hashtag antibody staining (10ng/µL, 30min, 4°C), HSPCs of control and KO of the same donor were flowcytometry sorted for viability combining 10,000 propidium iodide negative cells per condition stained with compatible hashtag antibodies. Cells were loaded onto the 10X Genomics chromium platform according to manufacturers instructions.
Libraries were generated witht the Chromium Next GEM Single Cell 3ʹ Reagent Kit v3.1 according to manufacturer’s instructions with 14 cycles for PCR steps. Feature barcode libraries represeting the hashtag barcodes were addtionally generated from the same cDNA using the 10x 3' Feature Barcode Kit.

treatment_protocol: Cells were transfected using the Neon electroporation system (Invitrogen, 1400V, 20ms, 2 pulses) at a density of 10,000 viable cells/µL with ribonucleoprotein complexes of guide RNA and Cas9 protein ( Cas9 (Alt-R™ S.p. HiFi Cas9 Nuclease V3, IDT)  and Cas9 electroporation enhancer (IDT). Cells were kept in antibiotics-free media after transfection and harvested after 14 d.

value: cord blood

value: HSPC


title: scRNA_GEX_CD34_31_NCKO


title: Tdo2high MFs CM-treated 4T1-LM3 cells_1

city: Chongqing

first: yong

middle: can

last: liu

address: No.1, Yi-Xue-Yuan Road, Yu-zhong District, Chongqing 400016, China.

institute: Chongqing medical university

data_processing:
The sequencing data was filtered with SOAPnuke  by  Removing reads containing sequencing adapter;
Removing reads whose low-quality base ratio (base quality less than or equal to 15) is more than 20%
Removing reads whose unknown base ('N' base) ratio is more than 5%, afterwards clean reads were obtained and stored in FASTQ format
Assembly: GRCm38
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

extract_protocol:
Total RNA was extracted from the tissues using Trizol (Invitrogen, Carlsbad, CA, USA) according to manual instruction.
total RNA was qualified and quantified using a Nano Drop and Agilent 2100 bioanalyzer (Thermo Fisher Scientific, MA, USA). The RNA library construction and subsequent RNA sequencing were performed by BGI-Shenzhen, China. First-strand cDNA was generated using random hexamer-primed reverse transcription, followed by a second-strand cDNA synthesis. afterwards, A-Tailing Mix and RNA Index Adapters were added by incubating to end repair. The cDNA fragments obtained from previous step were amplified by PCR, and products were purified by Ampure XP Beads, then dissolved in EB solution. The product was validated on the Agilent Technologies 2100 bioanalyzer for quality control. The double stranded PCR products from previous step were heated denatured and circularized by the splint oligo sequence to get the final library. The single strand circle DNA (ssCir DNA) was formatted as the final library.

value: Murine mammary carcinoma cell

value: Conditioned medium


title: Control CM-treated 4T1-LM3 cells_3


title: Suspension_p25_biol rep 1

city: Bron

first: Bertrand

middle: Pierre-Yves

last: PAIN

address: 18, Avenue du  Doyen Lépine

institute: U1208, INSERM

description: Susp P25-1

data_processing:
FastQ files were collected and preprocessed with fastp 0.20.1, which enabled UMI preprocessing and polyA trimming.
The trimmed fastQ files were aligned with STAR 2.7.6a using the Chlorocebus sabaeus genome assembly (ChlSab1.1) with annotation 101.
PCR duplicates were then removed using UMI-Tools 1.0.1.
Using quant3p, 3’ annotations were extended before being counted by HTSeq.
DEGs were analyzed using RNA-seq DRaMA with EdgeR.
Assembly: Chlorocebus sabaeus genome assembly (ChlSab1.1) with annotation 101.
Supplementary files format and content: Xcell file with all of the DEGs

organism: Chlorocebus sabaeus

source_name: kidney

growth_protocol: Adherent Vero cells (ATCC CCL-81) were passaged  in a serum-free and chemically defined in-house medium in T-flasks. Cells were incubated in a humidified incubator with 5% CO2 at 37°C. Suspension Vero cells were derived from adherent cells and cultivated in a serum-free and chemically defined in-house medium developed for suspension cells on a shaker with agitation and incubated in a humidified incubator with 5% CO2 at 37°C.

extract_protocol:
Total RNAs were prepared by Trizol extraction using standard protocols
RNA libraries were prepared for sequencing using standard Illumina protocols for 3' mRNA sequencing

treatment_protocol: Frozen cell pellets

value: kidney

value: Vero

value: Epithelial cell

tag: group

value: Suspension

tag: time point


title: Control CM-treated 4T1-LM3 cells_2


title: Suspension_p25_biol rep 2

description: Susp P25-2


title: Control CM-treated 4T1-LM3 cells_1


title: Suspension_p15_biol rep 2

description: Susp P15-2


title: Suspension_p15_biol rep 3

description: Susp P15-3


title: Suspension_p15_biol rep 1

description: Susp P15-1


title: Suspension_p5_biol rep 3

description: Susp P5-3


title: Suspension_p5_biol rep 2

description: Susp P5-2


title: EZH2KO CLP2

city: Beijing

first: Ziyi

last: Wang

address: Litang Road 168, Changping District, Beijing

institute: Beijing Tsinghua Changgung Hospital

data_processing:
Sequence reads were trimmed for adaptor sequence/low-quality sequence using Trimmomatic (version 0.36) (parameter- ILLUMINACLIP:{adaptor.fa}:2:30:10  -phred33 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 HEADCROP:0 MINLEN:36 PE)
Clean Reads were further treated with UMI_soft (in-house) to eliminate duplication bias introduced in library preparation and sequencing on using UMI. （Default Parameter developed by Wuhan Seqhealth Co., Ltd.）
The de-duplicated consensus sequences were mapped to GRCh38 using STAR software (version 2.5.3a) (parameters- --outSAMtype BAM SortedByCoordinate)
Read count extraction and normalization were performed using featureCounts（Version 1.5.1）（parameter -T 10 -d 30 -D 1000 -C -s 1 -t {exon} -g {geneid} --primary -O -a {gff_annotation_file}）
Assembly: GRCh38
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

source_name: lung

extract_protocol:
RNA was harvested using TRIzol Reagent (Invitrogen, cat. NO 15596026）. 2 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using KC-DigitalTM Stranded mRNA Library Prep Kit for Illumina® (Catalog NO. DR08502, Wuhan Seqhealth Co., Ltd. China) following manufacturer's protocols.

value: lung

value: EZH2 knockout

value: cecal ligation and puncture


title: EZH2KO sham2

value: Close the abdomen directly after laparotomy


title: Suspension_p5_biol rep 1

description: Susp P5-1


title: EZH2KO sham3


title: EZH2KO CLP3


title: EZH2KO CLP1


title: Red_Flesh_Mesocarp_RepA_R201

source_name: Treatment 1


title: EZH2KO sham1


title: CLP3

value: WT


title: Tdo2high MFs CM-treated 4T1-LM3 cells_2


title: Adherent_p25_biol rep 3

description: Adh P25-3

value: Adherent


title: Adherent_p25_biol rep 2

description: Adh P25-2


title: Tdo2high MFs CM-treated 4T1-LM3 cells_3


title: Suspension_p25_biol rep 3

description: Susp P25-3


title: CLP2


title: CLP1


title: Adherent_p25_biol rep 1

description: Adh P25-1


title: Adherent_p15_biol rep 2

description: Adh P15-2


title: sham3


title: sham1


title: Adherent_p15_biol rep 1

description: Adh P15-1


title: sham2


title: Adherent_p5_biol rep 3

description: Adh P5-3


title: Adherent_p5_biol rep 2

description: Adh P5-2


title: S.unvax.SA.d10.4

city: Seattle

first: Kevin

last: Urdahl

state: Washington

address: 307 Westlake Ave N #500

department: Global Infectious Disease

institute: Seattle Children's Research Institute

description: Lung parenchymal cells were selected for 10X Genomics scRNAseq using IV labelling and FACSAria II sorting.

data_processing:
The Seurat R package was used for initial QC filtering and integration. First. a filtering step was applied across all samples. requiring all passing cells to have UMIs mapped to at least 500 distinct genes. and fewer than 5% of UMIs mapped to mitochondrial genes. Genes detected in fewer than 3 cells per mouse were excluded from further analysis. The Seurat integration pipeline56 was then applied to correct for batch effects and align cells across conditions including all combinations of mouse strain. Mtb strain. time post challenge. and CoMtb status.
Initial cell type assignment was performed using the CellTypist python package.57 As CellTypist does not have an available cell type model suitable for mouse lung or mouse immune cells. we created a de novo mouse lung immune cell type model using two published mouse cell atlases. namely the Tabula Muris58 and scMCA59 resources. Cell type labels were harmonized between both sources (e.g. macrophage -> Macrophage) and both datasets were filtered to retain immune and lung-associated cell types. excluding cells specific to other organs. The CellTypist python package was then used to train a mouse lung cell type model based on this combined resource. This model was then used to assign cell types to count-normalized log transformed data on a per-cell level from mouse lung scRNAseq samples. using the python scanpy60 package to normalize total counts per cell to 10.000 and log transform as required by CellTypist.
Assembly: mm10-2020-A (10X Genomics)
Supplementary files format and content: R Seurat object containing raw and normalized counts, per-sample and per-cell metadata, cell type label assignments, calculated UMAP and PCA co-ordinates.

source_name: Lung

extract_protocol:
After one round of washing with ice-cold DPBS. cells were resuspended to 1000 cells/ml in DPBS. and 8000 cells were inputted into the 10X Genomics pipeline following the manufacturer’s recommendations.
Per 10x protocol

treatment_protocol: We performed single-cell RNA sequencing (scRNAseq) and flow cytometry analysis of lungs from Mtb-infected SP140-/- C57Bl/6 mice with and without CoMtb (10^4 CFU of Mtb injected i.d. 8 weeks prior to aerosol Mtb infection) 10days after conventional dose (50-100 CFU) Mtb infection. Single cell suspensions were generated from lung samples prior to Mtb infection and at days 10. 17 and 34 post-Mtb infection. Cells were resuspended in 200 ul MACS buffer (PBS containing 2.5% FBS plus 1 mM EDTA). filtered through a 70 um filter. and run on a FACS AriaII (BD) sorter. To collect parenchymal cells for single-cell RNA sequencing. alveolar macrophages (AM. SiglecF+CD11c+) were sorted separately into one collection tube to account for autofluorescence in the IV label channel. and all other IV-negative cells were sorted into another collection tube. After sorting. the two populations were combined and counted on a hemocytometer.

value: Lung

tag: mtb strain

tag: timepoint


title: S.unvax.SA.d10.3


title: Adherent_p5_biol rep 1

description: Adh P5-1


title: S.unvax.SA.d10.1


title: S.cotb.SA.d10.1

value: CoMtb


title: ChIP_CD34_17_2_SA2_529_1252_PU1

description:
CD34_PU1.peaks.ann.txt
raw data cannot be deposited online

data_processing:
Sequences wer aligned to the human reference genome (GRCh38.p10) using bowtie2 (v. 2.4.5) in very sensitive mode
Samtools (v.1.6) was used to remove lower quality alignments with mapQ=<10 and sorting
HOMER style tagDirectories were generated using HOMER makeTagDirectory (-checkGC and -unique). For AML samples, tag directories were corrected for copy number varations based on FreeC output genereated from DNA-Input-Sequencing data.
Bigwig coverage tracks  were generated using HOMER’s makeUCSCfile function. For HSPC RAD21/CTCF/MED12/PU1/H3K27ac data sets, BigWigs were aditionally scaled based on median coverage across the top 5% common peaks detected in all samples.
For focal peaks, HOMER was used to call peaks (factor mode; -fdr 0.00001 -tbp). For region peaks, i.e. H3K27ac, HOMER was used for peak calling in region mode (-fdr 0.00001, -size 250, -L 0 -F 5 -minDist 350, -tbp -ntagThreshold 10). In case of AMLs, peak calling was performed in individual tag directories, in case of HSPCs condition-merged tag directories were used. For each data set, peak files of all conditions/groups were merged and filtered for low-mappability and blacklisted regions to generate reference peak sets. Subsequently, the individual samples were annotated to combined peak set to obtain peak coverage tables for each data set separetely.
Annotation tables with peak coverage were used for differential analysis using DESeq2 or edgeR to calculate differential Peak Coverage between controls and associated cohesin deficient samples. For H3K27ac data sets, counts were additionally normalized  for length and GC content using offsets generated by the cqn R package, which were implemented in edgeR. For STAG1 and STAG2 HPSC datasets differential analysis was performed using HOMER’s getDiffExpression.pl routine with the -batch, -rlog and -normtotal options enabled. The same applies to RAD21 ChIP-seq in RAD21 KD HSPCs.
Assembly: GRCh38.p10
Supplementary files format and content: bigWig coverage track files for individual samples
Supplementary files format and content: tab-delimited file containing peak coordinates and coverage counts for each sample (HOMER annotation output)
Supplementary files format and content: tab-delimited file containing peak coordinates and DESeq2 or edgeR statistics for differential peak testing

growth_protocol: CD34+ HSPCs were enriched from fresh cord blood samples on the day of birth using the CD34 MicroBead kit (Miltenyi biotec). Cells were expanded for 7d in serum-free Stem Span media (Stem Cell Technologies) supplemented with human recombinant cytokines (Peprotech): SCF (0.1ng/mL), FLT3 (0.1ng/mL), IL6 (0.004ng/mL), TPO (0.025ng/mL) and StemRegenin1 (7500nmol/mL, Stem Cell technologies) as well as Penicillin/Streptomycin.

extract_protocol:
Cells were fixated using 0.5M DSG and 1% formaldehyde. Chromatin was sheared using Branson Sonifier 250. ChIP was performed with lysate of 2 Mio cells using a target specific antibody (anti-RAD21ab992 (abcam), anti-H3K27ac ab4729 (abcam), anti-CTCF 2899S (Cell Signaling), anti-STAG2 (custom produced), anti-STAG1 (custom produced), anti-MED12 (custom produced), anti-PU.1 sc352 (santa cruz)) and ProteinA Dynbeads. After de-crosslinking and proteinase K digest, DNA was purified using Monarch PCR & DNA clean-up kit (NEB).
Libraries were generated using the NEBNextUltra II DNA Library Prep Kit for Illumina with all available input material and 11 PCR cycles for amplification.

treatment_protocol: To obtain AML cells, PBMCS were extracted from bone marrow or whole blood samples of patients using Lymphoprep at the timepoint of first diagnosis and viably frozen. For knockdown experiments with healthy cells, HSPCs were transfected using the Neon electroporation system (Invitrogen, 1400V, 20ms, 2 pulses) at a density of 60,000 viable cells/µL with 1.33µg of chemically modified siRNAs (Axiolabs) per mio cells. Cells were kept in antibiotics-free media after transfection and harvested after 4d.

value: wt


title: ChIP_CD34_20_5_SA2_529_1252_PU1

value: cord blood


title: ChIP_CD34_14_2_SA2_529_1252_PU1

value: HSPC


title: ChIP_CD34_14_3_siCtrl_PU1

value: siCtrl


title: B.unvax.none.d0.4

treatment_protocol: We performed single-cell RNA sequencing (scRNAseq) and flow cytometry analysis of lungs from Mtb-infected animals with and without CoMtb (10^4 CFU of Mtb injected i.d. 8 weeks prior to aerosol Mtb infection) immediately pre-infection and at 10. 17 and 34 days after CD infection. Single cell suspensions were generated from lung samples prior to Mtb infection and at days 10. 17 and 34 post-Mtb infection. Cells were resuspended in 200 ul MACS buffer (PBS containing 2.5% FBS plus 1 mM EDTA). filtered through a 70 um filter. and run on a FACS AriaII (BD) sorter. To collect parenchymal cells for single-cell RNA sequencing. alveolar macrophages (AM. SiglecF+CD11c+) were sorted separately into one collection tube to account for autofluorescence in the IV label channel. and all other IV-negative cells were sorted into another collection tube. After sorting. the two populations were combined and counted on a hemocytometer.


title: ChIP_CD34_22_3_siCtrl_PU1


title: ChIP_CD34_24_2_siCtrl_PU1


title: ChIP_CD34_22_3_siCtrl_MED12

description: raw data cannot be deposited online


title: B.unvax.none.d0.3


title: B.unvax.none.d0.2


title: Adherent_p15_biol rep 3

description: Adh P15-3


title: B.unvax.SA.d34.4


title: ChIP_CD34_28_6_siCtrl_MED12

description: raw data cannot be deposited online


title: B.unvax.SA.d34.3


title: B.unvax.SA.d34.2


title: ChIP_CD34_24_2_siCtrl_MED12

description: raw data cannot be deposited online


title: B.unvax.none.d0.1


title: B.unvax.SA.d17.4


title: S.unvax.SA.d10.2


title: ChIP_CD34_22_2_SA2_529_1252_PU1


title: ChIP_CD34_18_4_siCtrl_MED12

description: raw data cannot be deposited online


title: B.unvax.SA.d17.3


title: ChIP_CD34_14_4_Mock_MED12

description: raw data cannot be deposited online

value: Mock


title: S.cotb.SA.d10.4


title: B.unvax.SA.d17.2


title: S.cotb.SA.d10.3