title: CD138-, AL8, rep1, TCR

description: Library name: BRI-2079

data_processing:
Raw FASTQ files were processed by Cell Ranger 6.1.1 using GRCh38-2020-A and cellranger-vdj- GRCh38-alts-ensembl-5.0.0 as references for the mapping of transcript counts and immune receptor calls respectively. Count matrices for transcripts and V(D)J sequences were generated simultaneously using cellranger multi.
Demultiplexing: Each barcoded cell was genotyped for a panel of human SNPs with minor allele frequency smaller than 5% (Fairley et al., 2019) through Cellsnp-lite. Subsequently, Vireo was used to infer the genotypes of each original group of samples included in each CD138- library. Whenever two libraries included overlapping identities, a distance matrix was computed to verify that the algorithm had independently learned the same genotypes in both. The genotypes associated to the cells from the CD138+ fractions, which had weaker coverage of SNPs were elucidated by treating the genotypes inferred in the CD138- libraries as ground truths and computing maximum likelihood estimates from these. Barcodes that were not given a singlet assignment by Vireo were not discarded from the embedding but excluded from comparisons across individuals or conditions.
Ambient RNA correction: SoupX was used to compute ambient RNA profiles for each library. These profiles were used to compute corrected count matrices, which were in turn converted to integer values through randomized rounding. Corrected counts were employed for differential gene expression and gene set enrichment analyses.
Cells expressing more than 5% mitochondrial transcripts or fewer than 500 total transcripts were excluded as low quality cells. Barcodes not included in the filtered count matrix generated by CellRanger were deemed empty droplets and discarded. Cells expressing more than 10,000 total transcripts were considered potential doublets and also excluded.
Doublet detection: Scrublet (0.2.3) was used, under default parameters, to detect barcodes corresponding to doublets. Barcodes labeled as doublets were excluded from all analyses. Further removal of plasma cell doublets was required as a second step as described below.
Annotation of CD138- cells: After filtering, CD138- libraries were concatenated and its transcriptomes were projected to the reference map constructed by Zeng et al. through its associated software package BoneMarrowMap. Each cell was assigned low-dimensional embedding coordinates, a cell state label, a pseudotime, and a mapping score based on its proximity to cells from the reference.
Identification of CD138+ plasma cells: CD138+ and CD138- fractions were concatenated and jointly embedded. Cells were annotated through CellTypist31 using the model Immune_All_AddPIP as a reference. Leiden clustering (resolution = 1.5) was performed on all cells, and cells from clusters whose modal identity was neither “Plasma cells” nor “Plasmablasts” were excluded. Subsequently, a panel of marker genes corresponding to blood populations was selected as identifiers of contamination. Expression thresholds for these markers were computed through an iterative method. For each gene, cell states among CD138- cells were ranked by average expression. A baseline set of reference states, starting with the four highest-ranked states, was established to differentiate true expression against background. Additional states were then sequentially considered for inclusion, with the requirement that each new state added must enhance the true positive rate (TPR) while maintaining a false positive rate (FPR) of 5% against non-reference states. The process was concluded when the inclusion of further states ceased to improve the TPR, thus defining the optimal reference states and the associated expression thresholds for each gene. These thresholds were used to determine anomalous expression in plasma cell clusters.  Subsequently, cells from clusters that had anomalously high expression of any marker marker genes corresponding to other blood populations (see Fig. S4A) were identified manually and excluded. Clusters where more than 50% of the cells were considered doublets during genetic demultiplexing or had mitochondrial transcript fractions above 5% were also discarded (Fig S4B). Surviving barcodes were re-embedded and re-clustered, and the obtained clusters were subjected to another round of filtering (Fig. S4C & S4D). Lastly, individual cells with expression of any contamination marker above its respective threshold were discarded.
Definition of plasma cell subsets: An scVI model with 30 latent variables was trained on the identified plasma cells to construct a batch-integrated embedding of plasma cell subsets. Leiden clustering was performed on the nearest neighbors graph (k = 15) computed from the learned latent variables (resolution = 0.4). Clusters primarily represented by cells from one or two AL patients were named after the overrepresented individual(s). Clusters with significant representation from individuals across both conditions were assigned the prefix "PC".
Assembly: GRCh38-2020-A and cellranger-vdj-GRCh38-alts-ensembl-5.0.0
Supplementary files format and content: Raw counts (tsv.gz): library identity, barcode, and raw counts for all cells included in each sample after SoupX correction.
Supplementary files format and content: Immune receptor repertoires (.airr): data associated with each filter-passing cell in each sample.
Supplementary files format and content: Library barcodes and metadata (.csv): library identity, barcode, donor/patient identity, annotation, and associated metadata for all cells across CD138- (CD138-_barcodes_and_metadata.csv) and CD138+ (CD138+_barcodes_and_metadata.csv) libraries
Library strategy: TCR-Seq


title: siCont_8Cell_024

status: Public on Mar 18 2025

type: SRA

city: Munich

first: Tamas

last: Schauer

address: Feodor-Lynen-Straße 21

department: Institute of Epigenetics and Stem Cells

country: Germany

institute: Helmholtz Zentrum München

description:
binary.siCont_8Cell.txt
RT.siCont_8Cell.bedgraph

library_source: genomic

data_processing:
library strategy: Single-cell Repli-seq
Sequencing reads were aligned to the GRCm38 genome using bowtie2 (version 2.5.1) 59 with the parameters --local --no-unal --no-mixed --no-discordant. Reads were filtered by mapping quality using samtools with the parameter -q 20. Read duplicates were removed using picard MarkDuplicates (version 3.0.0) with the parameter -REMOVE_DUPLICATES true. Using bedtools intersect (version 2.31.0), read counts were obtained for contiguous 50kb genomic bins.
The window counts were first normalised to RPM (reads per million). Aiming to correct for the mappability biases intrinsic to the genomic regions, for each bin its respective average of all samples within the same condition was calculated. Outlier regions were then masked, specifically the windows of the lower 5th percentile and the upper 1st percentile values. To correct for low mappability, the windows were segmented with the R package copynumber (version 1.38.0, R version 4.2.3) to keep the segments with the highest 95% of values. The data were centred by the mean and scaled by the interquartile range for each cell and smoothed using a median filter with a running window width of 15 windows, followed by a segmentation with the R package copynumber. Finally, using the function normalmixEM from R package mixtools (version 2.0.0), the segmented values were used to fit a mixture model with two components to identify replicated and non-replicated window populations.
To obtain replication timing values and to correct for potential sampling bias of cells, we calculated the fraction of replicated cells in overlapping intervals of the genome-wide replication score with interval size of 35% and increment of 4.33% (e.g. 0-35%, 4.33-39.33% etc.) for each genomic bin. The average of these 16 intervals served as replication timing value that was used for downstream analyses.
Assembly: GRCm38
Supplementary files format and content: tab-separated txt file with binary replication status
Supplementary files format and content: bedgraph file with replication timing values

molecule: genomic DNA

organism: Mus musculus

source_name: 8-cell embryo

growth_protocol: Zygotes were collected from the oviduct and cumulus cells were removed upon brief incubation in M2 media containing hyaluronidase. Zygotes were placed in drops of KSOM and cultured at 37 ºC with 5% CO2 until they reached 4-cell, 8-cell and morula stage.

extract_protocol:
Early stage zygotes were collected and cultured until they reached the S-phase at each developmental stage, based on their time after hCG injection. Embryos were collected at different time points to achieve sampling over the entire S-phase. Zona pellucida was removed by exposure to acid Tyrode and each blastomere was dissociated by gentle pipetting after trypsin treatment.
Individual blastomeres were placed into 8-strip PCR tubes containing lysis buffer and extracted DNA was fragmented by heat incubation. Fragmented DNA was tagged by the universal primer (5’-TGTGTTGGGTGTGTTTGGKKKKKKKKKKNN-3’) and amplified with WGA primer sets which have individual barcode. Amplified DNA was purified by the QIAquick 96 PCR Purification Kit (QIAGEN) and concentration was determined by the NanoDrop (Thermo Scientific). Equal amount of DNA from each samples (up to 96 samples) were pooled and 1ug of them was ligated with the illumina adaptors using the NEBNext Ultra II DNA Library Prep Kit (NEB). Illumina sequence (NEBNext Multiplex Oligos for Illumina; NEB) were added to the adaptor- ligated samples by the PCR. Clean up and size selection of the PCR product was done using SPRIselect (Beckman Coulter) and the quality of the library was confirmed by 2100 Bioanalyzer with the High Sensitivity DNA Kit (Agilent).

treatment_protocol: 20 μM siControl (Dharmacon, D-001210-01) or 20 μM siRif1 (Dharmacon, D-040028-01) were injected into zygotes at 17-18 hours post-hCG injection and embryos were cultured until 4-cell, 8-cell and morula stage, respectively.

tag: tissue

value: 8-cell embryo

tag: genotype

value: (C57BL/6J xCBA) x DBA/2J

tag: treatment

value: siControl


title: CD138-, AL5_AL6_AL7_HD5, rep2, BCR

city: Boston

first: Nicolas

middle: Alejandro

last: Gort-Freitas

state: MA

address: 200 Longwood Ave

department: Systems Biology

country: USA

institute: Harvard Medical School

description: Library name: BRI-2071

library_source: transcriptomic

data_processing:
Raw FASTQ files were processed by Cell Ranger 6.1.1 using GRCh38-2020-A and cellranger-vdj- GRCh38-alts-ensembl-5.0.0 as references for the mapping of transcript counts and immune receptor calls respectively. Count matrices for transcripts and V(D)J sequences were generated simultaneously using cellranger multi.
Demultiplexing: Each barcoded cell was genotyped for a panel of human SNPs with minor allele frequency smaller than 5% (Fairley et al., 2019) through Cellsnp-lite. Subsequently, Vireo was used to infer the genotypes of each original group of samples included in each CD138- library. Whenever two libraries included overlapping identities, a distance matrix was computed to verify that the algorithm had independently learned the same genotypes in both. The genotypes associated to the cells from the CD138+ fractions, which had weaker coverage of SNPs were elucidated by treating the genotypes inferred in the CD138- libraries as ground truths and computing maximum likelihood estimates from these. Barcodes that were not given a singlet assignment by Vireo were not discarded from the embedding but excluded from comparisons across individuals or conditions.
Ambient RNA correction: SoupX was used to compute ambient RNA profiles for each library. These profiles were used to compute corrected count matrices, which were in turn converted to integer values through randomized rounding. Corrected counts were employed for differential gene expression and gene set enrichment analyses.
Cells expressing more than 5% mitochondrial transcripts or fewer than 500 total transcripts were excluded as low quality cells. Barcodes not included in the filtered count matrix generated by CellRanger were deemed empty droplets and discarded. Cells expressing more than 10,000 total transcripts were considered potential doublets and also excluded.
Doublet detection: Scrublet (0.2.3) was used, under default parameters, to detect barcodes corresponding to doublets. Barcodes labeled as doublets were excluded from all analyses. Further removal of plasma cell doublets was required as a second step as described below.
Annotation of CD138- cells: After filtering, CD138- libraries were concatenated and its transcriptomes were projected to the reference map constructed by Zeng et al. through its associated software package BoneMarrowMap. Each cell was assigned low-dimensional embedding coordinates, a cell state label, a pseudotime, and a mapping score based on its proximity to cells from the reference.
Identification of CD138+ plasma cells: CD138+ and CD138- fractions were concatenated and jointly embedded. Cells were annotated through CellTypist31 using the model Immune_All_AddPIP as a reference. Leiden clustering (resolution = 1.5) was performed on all cells, and cells from clusters whose modal identity was neither “Plasma cells” nor “Plasmablasts” were excluded. Subsequently, a panel of marker genes corresponding to blood populations was selected as identifiers of contamination. Expression thresholds for these markers were computed through an iterative method. For each gene, cell states among CD138- cells were ranked by average expression. A baseline set of reference states, starting with the four highest-ranked states, was established to differentiate true expression against background. Additional states were then sequentially considered for inclusion, with the requirement that each new state added must enhance the true positive rate (TPR) while maintaining a false positive rate (FPR) of 5% against non-reference states. The process was concluded when the inclusion of further states ceased to improve the TPR, thus defining the optimal reference states and the associated expression thresholds for each gene. These thresholds were used to determine anomalous expression in plasma cell clusters.  Subsequently, cells from clusters that had anomalously high expression of any marker marker genes corresponding to other blood populations (see Fig. S4A) were identified manually and excluded. Clusters where more than 50% of the cells were considered doublets during genetic demultiplexing or had mitochondrial transcript fractions above 5% were also discarded (Fig S4B). Surviving barcodes were re-embedded and re-clustered, and the obtained clusters were subjected to another round of filtering (Fig. S4C & S4D). Lastly, individual cells with expression of any contamination marker above its respective threshold were discarded.
Definition of plasma cell subsets: An scVI model with 30 latent variables was trained on the identified plasma cells to construct a batch-integrated embedding of plasma cell subsets. Leiden clustering was performed on the nearest neighbors graph (k = 15) computed from the learned latent variables (resolution = 0.4). Clusters primarily represented by cells from one or two AL patients were named after the overrepresented individual(s). Clusters with significant representation from individuals across both conditions were assigned the prefix "PC".
Assembly: GRCh38-2020-A and cellranger-vdj-GRCh38-alts-ensembl-5.0.0
Supplementary files format and content: Raw counts (tsv.gz): library identity, barcode, and raw counts for all cells included in each sample after SoupX correction.
Supplementary files format and content: Immune receptor repertoires (.airr): data associated with each filter-passing cell in each sample.
Supplementary files format and content: Library barcodes and metadata (.csv): library identity, barcode, donor/patient identity, annotation, and associated metadata for all cells across CD138- (CD138-_barcodes_and_metadata.csv) and CD138+ (CD138+_barcodes_and_metadata.csv) libraries

molecule: polyA RNA

organism: Homo sapiens

source_name: Bone marrow

extract_protocol:
Bone marrow aspirates were obtained from patients with newly diagnosed AL amyloidosis seen at our center between 2019 and 2023. Healthy samples were obtained from discarded surgical material of patients undergoing primary, elective total hip arthroplasty, according to a Brigham and Women’s Hospital IRB approved protocol. Samples were processed within 2 hours from collection. Bone marrow mononuclear cells (BMMC) were separated by Ficoll Paque PLUS (Sigma) according to protocol and plasma cells were enriched by CD138-positive selection with anti-CD138 magnetic activated cell separation microbeads (Miltenyi Biotec). Viable CD138 positive and negative fractions were resuspended in FBS with 10% DMSO or Bambanker (Bulldog Bio) and stored in liquid nitrogen until the day of analysis.
10X Chromium Next GEM Single Cell 5’ reagent kits and BCR/TCR amplification kits were used for joint transcriptional and immune profiling of bone marrow samples. For the CD138+ samples, a combined profiling of BCR and 5’RNA was performed. For CD138- samples, a combined profiling of BCR, TCR, and 5’RNA was performed. The samples were aggregated into a fewer number of fraction-specific pools and loaded at a concentration of 20,000 cells per lane. The resulting libraries were sequenced on Illumina NovaSeq S1.

value: Bone marrow

tag: disease state

value: Healthy & diseased (AL)

tag: enrichment


title: siCont_8Cell_032


title: CD138-, AL8, rep1, GEX

description: Library name: BRI-2078

library_source: transcriptomic single cell

value: Diseased (AL)


title: siCont_8Cell_020


title: siCont_8Cell_021


title: siCont_8Cell_019


title: CD138-, AL5_AL6_AL7_HD5, rep2, TCR

description: Library name: BRI-2070


title: siCont_8Cell_018


title: CD138-, AL5_AL6_AL7_HD5, rep2, GEX

description: Library name: BRI-2069


title: siCont_8Cell_017


title: siCont_8Cell_016


title: CD138+, AL1_AL2_HD1_HD2, rep1, BCR

description: Library name: BRI-2091


title: CD138-, AL8_AL9, rep1, TCR

description: Library name: BRI-2082


title: CD138-, AL5_AL6_AL7_HD5, rep1, GEX

description: Library name: BRI-2066


title: CD138-, AL3_AL4, rep2, BCR

description: Library name: BRI-2062


title: CD138-, AL3_AL4, rep2, TCR

description: Library name: BRI-2061


title: siCont_8Cell_015


title: siCont_8Cell_014


title: siCont_8Cell_013


title: CD138-, AL3_AL4, rep2, GEX

description: Library name: BRI-2060


title: CD138-, AL3_AL4_HD3, rep1, TCR

description: Library name: BRI-2058


title: CD138-, AL3_AL4_HD3, rep1, BCR

description: Library name: BRI-2059


title: siCont_8Cell_010


title: siCont_8Cell_009


title: siCont_8Cell_011


title: CD138-, AL1_AL2_HD1, rep2, TCR

description: Library name: BRI-2048


title: siCont_8Cell_012


title: siCont_4Cell_055

description:
binary.siCont_4Cell.txt
RT.siCont_4Cell.bedgraph

source_name: 4-cell embryo

value: 4-cell embryo


title: CD138-, AL3_AL4_HD3, rep1, GEX

description: Library name: BRI-2057


title: CD138-, AL5_AL6_AL7_HD5, rep1, BCR

description: Library name: BRI-2068


title: CD138-, AL1_AL2_HD1, rep1, BCR

description: Library name: BRI-2046


title: siCont_4Cell_053


title: siCont_4Cell_052


title: CD138-, AL1_AL2_HD1, rep1, TCR

description: Library name: BRI-2045


title: siCont_4Cell_051


title: CD138-, AL1_AL2_HD1, rep1, GEX

description: Library name: BRI-2044


title: CD138-, AL1_AL2_HD1, rep2, GEX

description: Library name: BRI-2047


title: CD138-, AL5_AL6_AL7_HD5, rep1, TCR

description: Library name: BRI-2067


title: siCont_4Cell_056


title: siCont_4Cell_050


title: CD138+, AL3, rep1, TCR

description: Library name: ALpos_bcr


title: CD138+, AL3, rep1, GEX

description: Library name: ALpos_gex


title: CD138+, HD8, rep1, TCR

description: Library name: HDpos_bcr

value: Healthy


title: siCont_4Cell_049


title: siCont_4Cell_048


title: CD138+, HD8, rep1, GEX

description: Library name: HDpos_gex


title: siCont_4Cell_046


title: siCont_4Cell_045


title: siCont_4Cell_044


title: CD138-, AL3, rep1, TCR

description: Library name: ALneg_tcr


title: CD138-, AL3, rep1, BCR

description: Library name: ALneg_bcr


title: siCont_4Cell_054


title: CD138-, AL1_AL2_HD1, rep2, BCR

description: Library name: BRI-2049


title: siCont_4Cell_043


title: siCont_4Cell_042


title: CD138-, HD8, rep1, TCR

description: Library name: HDneg_tcr


title: siCont_4Cell_041


title: CD138-, AL3, rep1, GEX

description: Library name: ALneg_gex


title: siCont_4Cell_040


title: CD138-, HD8, rep1, BCR

description: Library name: HDneg_bcr


title: siCont_4Cell_039


title: CD138-, HD8, rep1, GEX

description: Library name: HDneg_gex


title: siCont_4Cell_047


title: siCont_4Cell_037


title: siCont_4Cell_038


title: siCont_4Cell_036


title: siCont_4Cell_035


title: SiNET8, snRNA-seq

city: Rehovot

first: Einav

last: Somech

address: Hertzel 234

country: Israel

institute: Weizmann

description: Library name: Sample 9

data_processing:
After sequencing, raw data were processed to ensure high data quality. The raw sequencing data were converted to counts of unique molecular identifiers (UMI) and further normalized to transcripts per million (TPM) values. To facilitate comparative analysis across samples, these TPM values were divided by 10 (since the actual transcript complexity is estimated to be around 100,000 rather than the 1 million used in standard TPM calculations). The resulting values were log2-transformed and centered for each gene across the tumors to derive relative expression. For the analysis of absolute expression levels, the raw UMI counts were used. Low-quality cells were excluded based on the number of detected genes, using thresholds of 1000 detected genes for nuclei-seq and 700 for scRNA-seq to retain lymphocytes. Filtering was also applied to retain only genes where the logged row-means per gene across all cells passed a threshold of 4.5. The final processed dataset ranged from 287 to 10,802 cells per sample, ensuring that high-quality data were used for subsequent analysis.
Assembly: GRCh38
Supplementary files format and content: csv files, and matrix files

molecule: nuclear RNA

source_name: small intestine

extract_protocol:
Fresh tumors were collected directly from the operating room during surgery. The tumors were washed in ice-cold HBSS and minced using Noyes spring scissors. Tumor dissociation was performed using a tumor dissociation kit (Miltenyi Biotec) in a GentleMACS Octo-dissociator on low-speed settings. A single-cell suspension was obtained by passing the dissociated slurry through a 60-100 micron cell strainer, followed by RBC removal using an RBC lysis buffer (Roche). Dead cell removal was performed following the manufacturer’s protocol, and cells were assessed for viability and density using Trypan blue. For frozen tumors, nuclei isolation was achieved using either ST-based buffers or the EZ-lysis method (Sigma). Tissue was cut into pieces and homogenized in ice-cold buffer, followed by nuclei isolation through centrifugation. The resulting nuclei were washed, resuspended, and filtered through a 40 μm cell strainer.
Library construction was carried out using the Chromium Next GEM Single Cell 3′ GEM, Library & Gel Bead Kit v3.1 for fresh tumor/single-cell libraries and the Chromium Next GEM Single 5′ GEM for frozen tumor/single-nuclei libraries. Cells or nuclei were emulsified with reagents and single gel beads containing barcoded oligonucleotides, encapsulated into nanoliter-sized droplets for reverse transcription (RT). After RT, cDNA amplification, fragmentation, and adapter/sample index attachment were performed. Libraries from two 10x channels were pooled and sequenced on one lane of an Illumina NovaSeq-6000, using an sp-100 kit or four libraries pooled together on two lanes with an S1-100 kit. Paired-end reads were used: Read 1 (26 nt), Read 2 (55 nt), Index 1 (8 nt), and Index 2 (0 nt).

value: small intestine

tag: cell type

value: Neuroendocrine tumor cells


title: SiNET6, snRNA-seq

description: Library name: Sample 7


title: SiNET10, snRNA-seq

description: Library name: Sample 11


title: SiNET7, snRNA-seq

description: Library name: Sample 8


title: siCont_4Cell_034


title: siCont_4Cell_033


title: SiNET3, scRNA-seq

description: Library name: Sample 4

molecule: total RNA


title: SiNET9, snRNA-seq

description: Library name: Sample 10


title: SiNET2, scRNA-seq

description: Library name: Sample 3


title: SiNET1, scRNA-seq

description: Library name: Sample 2


title: siCont_4Cell_030


title: siCont_4Cell_032


title: siCont_4Cell_029


title: siCont_4Cell_028


title: Si-ADENO, scRNA-seq

description: Library name: Sample 1


title: DAOY cells with Hira loss-of-function treated with SAG_3

city: Warsaw

first: Weronika

last: Skarzynska

address: Banacha 2c

country: Poland

institute: Centre of New Technologies

description: Library name: HIRA_KO_PLUS_SAG_3

data_processing:
RNASeq raw data was analysed using salmon in the unmapped mode. Differential expression was quantified using tximport and DSeq2
Assembly: GR.Ch38.p14
Supplementary files format and content: csv

source_name: DAOY

extract_protocol:
Daoy control and Hira KO cells were starved for 48 h with 500 nM SAG. Next RNA was isolated with the use of Universal RNA Purification Kit (EURx).
RNA 3’ mRNA-seq libraries were constructed using QuantSeq 3’ mRNA-Seq Library Prep Kit reagents FWD for Illumina (Lexogen, cat. no. 015.96) and Lexogen i7 6 nt Index Set adapters (7001–7096; Lexogen, cat. no. 044.96). The manufacturer’s protocol was followed, starting with 500 ng of supplied RNA and using 11 cycles of enrichment by amplification. The resulting 3’ mRNA-seq libraries were subjected to fragment length control using an Agilent Bioanalyzer 2100 and High Sensitivity DNA kit reagents (Agilent, cat. no. 5067 − 4626). Library concentration was then determined by qPCR using the Kapa Library Quantification kit (Kapa Biosciences, cat. no. KK4824). The manufacturer’s protocols were followed. Sequencing was carried out on an Illumina NovaSeq 6000 instrument using NovaSeq 6000 S1 Reagent Kit (200 cycles) reagents (Illumina, cat. no. 20012864), in pair-end read mode 2 × 100 cycles using the manufacturer’s recommended standard procedure with 1% addition of Phix control library (Illumina, cat. no. FC-110-3001).

tag: cell line

value: DAOY


title: DAOY cells with Hira loss-of-function treated with SAG_1

description: Library name: HIRA_KO_PLUS_SAG_1


title: DAOY cells with Hira loss-of-function treated with SAG_2

description: Library name: HIRA_KO_PLUS_SAG_2


title: siCont_4Cell_027


title: siCont_4Cell_026


title: SiNET5, snRNA-seq

description: Library name: Sample 6


title: DAOY cells with Hira loss-of-function treated with DMSO_3

description: Library name: HIRA_KO_MINUS_SAG_3


title: DAOY cells with Hira loss-of-function treated with DMSO_2

description: Library name: HIRA_KO_MINUS_SAG_2


title: siCont_4Cell_025


title: SiNET4, snRNA-seq

description: Library name: Sample 5


title: siCont_4Cell_024


title: DAOY cells treated with SAG_3

description: Library name: Control_PLUS_SAG_3


title: DAOY cells with Hira loss-of-function treated with DMSO_1

description: Library name: HIRA_KO_MINUS_SAG_1


title: siCont_4Cell_023


title: siCont_4Cell_021


title: DAOY cells treated with SAG_2

description: Library name: Control_PLUS_SAG_2


title: DAOY cells treated with SAG_1

description: Library name: Control_PLUS_SAG_1


title: DAOY cells treated with DMSO_3

description: Library name: Control_MINUS_SAG_3


title: siCont_4Cell_019


title: DAOY cells treated with DMSO_2

description: Library name: Control_MINUS_SAG_2


title: siCont_4Cell_020


title: siCont_4Cell_031


title: siCont_4Cell_018


title: siCont_4Cell_017


title: DAOY cells treated with DMSO_1

description: Library name: Control_MINUS_SAG_1


title: Human neutrophil, Microplastic 3

city: Seoul

first: Koung-Min

last: Park

address: 5-26, Sinchon-ro 4-gil

country: South Korea

institute: Yonsei university college of medicine

description: Library name: hPMN_MP3

data_processing:
Illumina GATK software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence(using fastp), then mapped to GRCh38 whole genome using STAR
Calculation mapped reads using salmon
CPM + TMM calculation using conorm
Assembly: GRCh38
Supplementary files format and content: tab-delimited text files include Read count values for each Sample

source_name: Human blood

growth_protocol: Neutrophils were collected from the blood of healthy donors by histopaque-1119 and -1077.

extract_protocol:
RNA was extracted using a TaKaRa RNAiso Plus.
RNA libraries were prepared for sequencing using the NEBNext Ultra II Directional RNA-Seq Kit standard protocols.

treatment_protocol: One group was 1 × 106 cells/ml human neutrophils cultured for 6 h after treatment with polystyrene MPs (10 μg), and the other group served as control in 6 well plate.

value: Human blood

value: neutrophil

value: polystyrene microplastic


title: siCont_4Cell_016


title: Human neutrophil, Microplastic 2

description: Library name: hPMN_MP2


title: siCont_4Cell_015


title: Human neutrophil, Control 3

description: Library name: hPMN_C3


title: siCont_4Cell_014


title: Human neutrophil, Control 2

description: Library name: hPMN_C2


title: siCont_4Cell_013


title: Human neutrophil, Control 1

description: Library name: hPMN_C1


title: siCont_4Cell_022


title: siCont_4Cell_012


title: siCont_4Cell_011


title: siCont_4Cell_010


title: siCont_4Cell_009


title: M2macrophage&PE&Day28_1

city: Palo Alto

first: Qi

last: Gao

state: CA

address: 240 Pasteur Dr., BMI building Room 0200E, Department of Orthopaedic Surgery, Stanford University, BMI building Room 0200E, Stanford University

institute: Stanford University

description: Library name: M2plusd28_1

data_processing:
featureCounts v1.5.0-p3 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene. FPKM, expected number of Fragments Per Kilobase of transcript sequence per Millions base pairs sequenced, considers the effect of sequencing depth and gene length for the reads count at the same time, and is currently the most commonly used method for estimating gene expression levels.
Reference genome and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built using Hisat2 v2.0.5 and paired-end clean 1 reads were aligned to the reference genome using Hisat2 v2.0.5. We selected Hisat2 as the mapping tool for that Hisat2 can generate a database of splice junctions based on the gene model annotation file and thus a better mapping result than other non-splice mapping tools.
Supplementary files format and content: csv files include FPKM values for each Sample

source_name: Mesechemal stem cell, Human umbilical vein endothelial cells, macrophages

extract_protocol:
TRIzol™ Reagent (Life Technologies, UK) was applied to extract total RNA from the contracts and then treated with chloroform. mRNA was isolated from the aqueous phase by sequentially adding isopropyl alcohol and 75% ethanol. RNA concentration and quality measurements were taken using NanoDrop. Library preparation, quality control and sequencing were performed by Novogene Co., Ltd.
Messenger RNA was purified from total RNA using poly-T oligo-attached magnetic beads. After fragmentation, the first strand cDNA was synthesized using random hexamer primers, followed by the second strand cDNA synthesis. The library was checked with Qubit and real-time PCR for quantification and bioanalyzer for size distribution detection. Quantified libraries will be pooled and sequenced on Illumina platforms, according to effective library concentration and data amount.

value: Day 28 with M2 macrophage with Polyethylene particles


title: M2macrophage&PE&Day21_3

description: Library name: M2plusd21_3

value: Mesechemal stem cell, Human umbilical vein endothelial cells, macrophages

value: Day 21 with M2 macrophage with Polyethylene particles


title: M2macrophage&PE&Day28_3

description: Library name: M2plusd28_3


title: M2macrophage&PE&Day28_2

description: Library name: M2plusd28_2


title: M2macrophage&PE&Day21_1

description: Library name: M2plusd21_1


title: siRif1_8Cell_055

description:
binary.siRif1_8Cell.txt
RT.siRif1_8Cell.bedgraph

value: 8-cell embryo


title: siRif1_8Cell_056

value: (C57BL/6J xCBA) x DBA/2J


title: M2macrophage&PE&Day21_2

description: Library name: M2plusd21_2


title: M2macrophage&PE&Day14_3

description: Library name: M2plusd14_3

value: Day 14 with M2 macrophage with Polyethylene particles


title: siRif1_8Cell_054


title: siRif1_8Cell_053


title: siRif1_8Cell_052


title: siRif1_8Cell_051


title: M2macrophage&PE&Day14_1

description: Library name: M2plusd14_1


title: M2macrophage&PE&Day14_2

description: Library name: M2plusd14_2


title: siRif1_8Cell_049


title: M2macrophage&PE&Day7_1

description: Library name: M2plusd7_1

value: Day 7 with M2 macrophage with Polyethylene particles


title: siRif1_4Cell_055

description:
binary.siRif1_4Cell.txt
RT.siRif1_4Cell.bedgraph


title: M1macrophage&PE&Day28_2

description: Library name: M1plusd28_2

value: Day 28 with M1 macrophage with Polyethylene particles


title: siRif1_4Cell_056


title: M1macrophage&PE&Day28_3

description: Library name: M1plusd28_3


title: siRif1_4Cell_053


title: siRif1_4Cell_054


title: M1macrophage&PE&Day28_1

description: Library name: M1plusd28_1


title: M1macrophage&PE&Day21_3

description: Library name: M1plusd21_3

value: Day 21 with M1 macrophage with Polyethylene particles


title: siRif1_4Cell_052

value: 4-cell embryo


title: M1macrophage&PE&Day21_2

description: Library name: M1plusd21_2


title: siRif1_4Cell_051


title: M1macrophage&PE&Day21_1

description: Library name: M1plusd21_1


title: M1macrophage&PE&Day14_3

description: Library name: M1plusd14_3

value: Day 14 with M1 macrophage with Polyethylene particles


title: siRif1_4Cell_050


title: M1macrophage&PE&Day14_2

description: Library name: M1plusd14_2


title: M1macrophage&PE&Day14_1

description: Library name: M1plusd14_1


title: siRif1_8Cell_048


title: siRif1_8Cell_046


title: M2macrophage&PE&Day7_3

description: Library name: M2plusd7_3


title: siRif1_8Cell_047


title: M1macrophage&PE&Day7_3

description: Library name: M1plusd7_3

value: Day 7 with M1 macrophage with Polyethylene particles


title: siRif1_4Cell_049


title: M1macrophage&PE&Day7_1

description: Library name: M1plusd7_1


title: siRif1_8Cell_050


title: M2macrophage&PE&Day7_2

description: Library name: M2plusd7_2


title: siRif1_8Cell_045


title: M1macrophage&PE&Day7_2

description: Library name: M1plusd7_2


title: siRif1_8Cell_043


title: siRif1_8Cell_042


title: M2macrophage&Day28_2

description: Library name: M2d28_2

value: Day 28 with M2 macrophage


title: M2macrophage&Day28_1

description: Library name: M2d28_1


title: M2macrophage&Day28_3

description: Library name: M2d28_3


title: siRif1_8Cell_041


title: M2macrophage&Day21_3

description: Library name: M2d21_3

value: Day 21 with M2 macrophage


title: siRif1_8Cell_040


title: M2macrophage&Day21_2

description: Library name: M2d21_2


title: siRif1_8Cell_039


title: M2macrophage&Day21_1

description: Library name: M2d21_1


title: M2macrophage&Day14_2

description: Library name: M2d14_2

value: Day 14 with M2 macrophage


title: siRif1_8Cell_038


title: siRif1_8Cell_044


title: M2macrophage&Day14_1

description: Library name: M2d14_1


title: siRif1_8Cell_036


title: M2macrophage&Day14_3

description: Library name: M2d14_3


title: siRif1_8Cell_037


title: siRif1_8Cell_034


title: M2macrophage&Day7_3

description: Library name: M2d7_3

value: Day 7 with M2 macrophage


title: M2macrophage&Day7_1

description: Library name: M2d7_1


title: siRif1_8Cell_032


title: siRif1_8Cell_031


title: siRif1_8Cell_035


title: M2macrophage&Day7_2

description: Library name: M2d7_2


title: siRif1_8Cell_030


title: M1macrophage&Day28_3

description: Library name: M1d28_3

value: Day 28 with M1 macrophage


title: M1macrophage&Day28_1

description: Library name: M1d28_1


title: siRif1_8Cell_029


title: M1macrophage&Day28_2

description: Library name: M1d28_2


title: M1macrophage&Day21_3

description: Library name: M1d21_3

value: Day 21 with M1 macrophage


title: M1macrophage&Day21_2

description: Library name: M1d21_2

value: Mesechemal stem cell, Human umbilical vein endothelial cells, macrophages


title: siRif1_8Cell_027


title: M1macrophage&Day21_1

description: Library name: M1d21_1


title: siRif1_8Cell_025


title: M1macrophage&Day14_3

description: Library name: M1d14_3

value: Day 14 with M1 macrophage


title: M1macrophage&Day14_2

description: Library name: M1d14_2


title: siRif1_8Cell_024

value: 8-cell embryo


title: siRif1_8Cell_023

value: (C57BL/6J xCBA) x DBA/2J


title: siRif1_8Cell_022


title: siRif1_8Cell_028


title: siRif1_8Cell_020


title: siRif1_8Cell_021


title: M1macrophage&Day7_3

description: Library name: M1d7_3

value: Day 7 with M1 macrophage


title: M1macrophage&Day7_1

description: Library name: M1d7_1


title: M1macrophage&Day14_1

description: Library name: M1d14_1


title: siRif1_8Cell_018


title: siRif1_8Cell_026


title: MDA-MB-231 Cell Library 1KB3 ESAM+ 2 0809

city: Austin

first: Daylin

last: Morgan

state: Texas

address: 107 W Dean Keeton St

department: BME

institute: The Univeristy of Texas at Austin

description: Library name: 1KB3-EP2-0809

data_processing:
All data was processed using https://github.com/brocklab/pycashier. Paired-end reads were merged into contingous sequences using "pycashier merge". Then barcode sequences were extracted, corrected and filtered with "pycashier extract".
Supplementary files format and content: all processed data is tsvs with 5 columns: barcode, count, sample, percent, sample, n_samples

source_name: breast

extract_protocol:
DNA was extracted from frozen cell pellets containg 1e6 cells using the Invitrogen PureLink Genomic DNA kit (ThermoFisher, K182001) according to manufacturer’s instructions.
Amplification steps were performed following published ClonMapper barcode amplification procedures (up-to-date web protocol: https://docs.brocklab.com/clonmapper, published protocol:https://doi.org/10.1007/978-1-0716-1811-0_8).

treatment_protocol: Cells were seeded in a 24-well at 50,000 cells per well then treated with varying doses of doxorubicin for 48 hours. Samples were allowed to recover and expanded until they reached ~5e6 cells.

value: breast

value: TNBC

value: Twice FACS sorted ESAM+


title: MDA-MB-231 Cell Library 1KB3 ESAM+ 0801

description: Library name: 1KB3-EP-0801

value: FACS sorted ESAM+


title: siRif1_8Cell_015


title: MDA-MB-231 Cell Library 1KB3 ESAM- 2 0729

description: Library name: 1KB3-EN2-0809

value: Twice FACS sorted ESAM-


title: MDA-MB-231 Cell Library 1KB3 ESAM- 0729

description: Library name: 1KB3-EN-0729

value: FACS sorted ESAM-


title: siRif1_8Cell_017


title: siRif1_8Cell_033


title: siRif1_8Cell_016


title: M1macrophage&Day7_2

description: Library name: M1d7_2


title: siRif1_8Cell_013


title: MDA-MB-231 Cell Library 1KB3 0810

description: Library name: 1KB3-810


title: MDA-MB-231 Cell Library 1KB3 ESAM- 0801

description: Library name: 1KB3-EN-0801


title: MDA-MB-231 Cell Library 1KB3 0719

description: Library name: 1KB3-0719


title: MDA-MB-231 Cell Library 1KB3 0729

description: Library name: 1KB3-0729


title: siRif1_8Cell_012


title: siRif1_8Cell_014


title: siRif1_8Cell_011


title: siRif1_8Cell_010


title: MDA-MB-231 Cell Library 1KB3 Dox-400-5 [scRNA-seq]

description: Library name: B6

data_processing:
All samples were processed using cellranger v8.0.1 and aligned to GRCh38 using "cellranger count".
Supplementary files format and content: For each sample there are three outputs per sample of the filtered_feature_bc_matrix as generated by cellranger count.
Supplementary files format and content: For all samples there is a combined anndata object with normalized counts and metadata.

extract_protocol: Cells were loaded into wells of a Chromium A Chip and libraries were prepared using 10X Genomics 3' Single Cell Expression (v3.1) protocol.

value: 400nM Dox


title: MDA-MB-231 Cell Library 1KB3 0712

description: Library name: 1KB3-0712


title: siRif1_8Cell_009


title: MDA-MB-231 Cell Library 1KB3 ESAM+ 0729

description: Library name: 1KB3-EP-0729


title: siRif1_8Cell_019


title: MDA-MB-231 Cell Library 1KB3 Dox-400-4 [scRNA-seq]

description: Library name: B5


title: siRif1_8Cell_007


title: siRif1_8Cell_006


title: siRif1_8Cell_008


title: siRif1_8Cell_005


title: MDA-MB-231 Cell Library 1KB3 Dox-400-1 [scRNA-seq]

description: Library name: B2


title: MDA-MB-231 Cell Library 1KB3 Dox-250-1 [scRNA-seq]

description: Library name: A1

value: 250nM Dox


title: MDA-MB-231 Cell Library 1KB3 Dox-250-4 [scRNA-seq]

description: Library name: A4


title: siRif1_8Cell_003


title: siRif1_8Cell_002


title: siRif1_8Cell_001


title: MDA-MB-231 Cell Library 1KB3 Pretreatment 2 [scRNA-seq]

description: Library name: PT-2

value: pretreament


title: MDA-MB-231 Cell Library 1KB3 Dox-550-30HR [scRNA-seq]

description: Library name: Dox

value: 550nM Dox


title: siRif1_4Cell_048

value: 4-cell embryo


title: siRif1_8Cell_004


title: MDA-MB-231 Cell Library 1KB3 Pretreatment 1 [scRNA-seq]

description: Library name: PT-1

value: initial


title: siRif1_4Cell_046


title: 150SI2

city: Shijiazhuang

first: Jia'xiang

last: Wu

address: Shijiazhuang 050011,China

country: China

institute: The Fourth Hospital of Hebei Medical University

description: Library name: Sample 5

data_processing:
Some of the original sequences obtained by sequencing will contain sequencing adapter sequences and low-quality sequences. In order to ensure the quality of information analysis data, we filter the original sequences to obtain high-quality Clean Reads, and then perform subsequent analysis. Subsequent analysis is based on Clean Reads. Thus, to get high quality clean reads, reads were further filtered by Cutadapt (https://cutadapt.readthedocs.io/en/stable/,version:cutadapt-1.9).The data processing steps are as follows: (1) Remove reads contaminated by adapters (the number of bases contaminated by adapters in reads is greater than 5bp. For double-end sequencing, if one end is contaminated by adapters, the reads at both ends are removed); (2) Remove low-quality reads (the bases with quality values Q≤19 in the reads account for more than 50% of the total bases. For double-end sequencing, if one end is a low-quality read, the reads at both ends will be removed); (3) Remove reads with an N ratio greater than 5% (for double-end sequencing, if one end contains an N ratio greater than 5%, the reads at both ends will be removed).
The filtered sequencing sequences of each sample were aligned with the reference genome to locate them to the genome. We used the HISAT2 (https://daehwankimlab.github.io/hisat2/, version:hisat2-2.2.1) package to align the reads of all samples with the reference genome of the studied species. HISAT2 is an upgraded version of TopHat2, which uses the improved BWT algorithm (Sirén et al. 2014) to convert the reference genome into an index, achieving faster speed and less resource consumption.
The mapped reads of each sample were assembled using StringTie (http://ccb.jhu.edu/software/stringtie/,version:stringtie-2.1.6) with default parameters. HTSeq (http://www-huber.embl.de/users/anders/HTSeq/doc/overview.html) was used to count the number of reads mapped to each gene and estimate the expression level of each gene. The FPKM (Fragments Per Kilobase Millon Mapped Reads) method was used to calculate the gene expression.
Assembly: Homo_sapiens.GRCh38
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

extract_protocol:
Total RNA was extracted using Trizol reagent (Invitrogen, CA, USA) according to the manufacturer's instructions. Total RNA was tested by Annoroad Gene Technology Corporation (Beijing) using the following methods: sample purity was tested using a NanoPhotometer® spectrophotometer (Thermo Fisher); RNA integrity and concentration were tested using the RNA Nano 6000 Assay Kit of the Bioanalyzer 2100 system (Agilent Technologies, CA, USA). Total RNA samples that met the requirements were selected for construction of sequencing libraries.
After the total RNA sample is qualified, it is purified according to the characteristics of mRNA from different sources. The 3' end of eukaryotic mRNA has a polyA tail structure, and magnetic beads with Oligo (dT) are selected for enrichment and purification; prokaryotic mRNA does not have this characteristic, and a kit is selected to remove rRNA to obtain more effective information. Fragmentation Buer is added to the purified mRNA to make its fragments into short fragments. Then, the fragmented RNA is used as a template, and random primers are used for reverse transcription to achieve the synthesis of the first strand of cDNA, and the 2nd Strand Marking Buer and 2nd Strand/End Repair Enzyme Mix are added to synthesize the second strand of cDNA. After end repair, addition of base A, addition of sequencing adapters, the target fragment is recovered by magnetic bead screening, and PCR amplification is performed to complete the entire library preparation. After the library construction was completed, Qubit3.0 was used for preliminary quantification, and the library was diluted to 1 ng/ul. Then, the insert size of the library was detected using Agilent2100. When the insert size met expectations, the effective concentration of the library was accurately quantified (library effective concentration>10nM) using Bio-RAD CFX 96 fluorescence quantitative PCR instrument and Bio-RAD KIT iQ SYBR GRN to ensure the quality of the library. The qualified library was sequenced using the Illumina platform. The sequencing strategy was PE150.

value: Human esophageal squamous cell carcinoma cells


title: siRif1_4Cell_045


title: siRif1_4Cell_047


title: siRif1_4Cell_043


title: MCF7 cells,  treated with CM obtained from PreNeu (cm-PreNeu), 72h, biological replicate 2, experiment 2

city: Bellinzona

first: Marco

last: Bolis

address: Via Francesco Chiesa

country: Switzerland

institute: IOR Institute of Oncology Research

description:
Library name: MCF7_cmPreNeu_biorep2_experiment_B
Column name in rawcounts_experiment_B.txt: MCF7_plus_cmPreNeu_p329
rawcounts_experiment_B.txt

data_processing:
Quality of sequencing reads was evaluated using FastQC (v.0.11.9) (https://www.bioinformatics.babraham.ac.uk/projects/fastqc/).
Sequences were mapped to the GRCh38 assembly of the human genome using STAR (v.2.6.1c). Alignments were conducted in 2-pass mode and soft-clipping of reads was allowed. Quantification of gene-counts using gencode-based annotations were performde by STAR v2.6.1c (experiment_1) or RSEM v1.3.3 (experiment_2).
Downstream analysis was performed in R using DESeq2 (v1.28.1).
Assembly: GRCh38
Supplementary files format and content: tab delimited txt files contain raw counts for each sample

extract_protocol:
RNA extraction was performed using RNeasy Mini Kit (250) (74106, Qiagen), following the manufacturer’s instructions.
10-100 ng total RNA was treated with the NEBNext® Poly(A) mRNA Magnetic Isolation Module. Library construction was performed with the NEBNext® Ultra II Directional RNA Library Prep Kit for Illumina®, according to the manufacturer’s protocol.

value: cancer cell-line

value: cm-PreNeu

tag: batch


title: siRif1_4Cell_042

value: (C57BL/6J xCBA) x DBA/2J


title: siRif1_4Cell_044


title: MDA-MB-231 Cell Library 1KB3 Dox-250-6 [scRNA-seq]

description: Library name: A6


title: 150NC1

description: Library name: Sample 1


title: MCF7 cells,  treated with CM obtained from LOX-1+ neutrophils (cm-LOX1), 72h, biological replicate 2, experiment 2

description:
Library name: MCF7_cmLOX1_biorep2_experiment_B
Column name in rawcounts_experiment_B.txt: MCF7_plus_cmLOX1_p329
rawcounts_experiment_B.txt


title: 150SI3

description: Library name: Sample 6


title: siRif1_4Cell_040


title: MCF7 cells,  treated with CM obtained from LOX-1+ neutrophils (cm-LOX1), 72h, biological replicate 1, experiment 2

description:
Library name: MCF7_cmLOX1_biorep1_experiment_B
Column name in rawcounts_experiment_B.txt: MCF7_plus_cmLOX1_p105
rawcounts_experiment_B.txt


title: siRif1_4Cell_039


title: siRif1_4Cell_038


title: RNA-seq_HGC27_shUSP47_rep1

city: Shanghai

first: Aixia

last: Song

address: Dong'an Road

institute: Fudan University

description: Library name: Sample 3

data_processing:
Raw reads were trimmed followed by mapping to the hg19 or mm10 genome using STAR v2.7.5c with the parameter ‘‘--outSAMtype BAM SortedByCoordinate --twopassMode Basic --outFilterMismatchNmax 3’’.
Low mapping quality reads and PCR duplicates were removed using SAMtools v1.9 96 and Picard v2.23.3 (https://broadinstitute.github.io/picard/). Calculation of the normalization factor was performed in the same way as described in ChIP-Rx.
Strand-specific normalized bigwigs were generated by deeptools v3.5.0.97 To identify differentially expressed genes, we collected the counts per gene by the featureCounts tool from the Rsubread R package v2.0.1.103 Differential expression analysis was then performed using DESeq2 R package v1.26.0.
Assembly: hg19
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample

growth_protocol: Human HGC27 cells were grown in  RPMI 1640 (Gibco) supplemented with 10% FBS (Yeasen) and 1 × Penicillin-Streptomycin (Thermo) at 37 °C, 5% CO2.

extract_protocol:
RNA was isolated with TRIzol. 1 ug of total RNA was used for the construction of sequencing libraries.
Libraries were prepared according to  ABclonal's instructions accompanying the ABclonal Stranded mRNA-seq Lib Prep Module for Illumina (ABclonal, RK20349). Libraries were sequenced on the Illumina NovaSeq 6000 following the manufacturer's protocols.

treatment_protocol: HGC27 cells were infected with lentivirus that expressed either scrambled shRNA (shScr) or USP47-targeting shRNA (shUSP47).

value: gastric carcinoma cell line

value: USP47 shRNA

value: infected with lentivirus


title: 150NC3

description: Library name: Sample 3


title: siRif1_4Cell_036


title: T47D, teton_sgZHX2, Hypoxia, replicate 3

city: Wuhan

first: gao

last: chuan

state: Hubei province

address: bayi road

department: College of life science

institute: Wuhan university

data_processing:
The RNA sequencing data were initially subjected to quality evaluation using FastQC. Subsequent alignment of the data was performed against the human genome (hg38) using hisat2, employing the default settings. For quantification of transcripts, featureCounts was utilized, and DESeq2 was employed for the analysis of differentially expressed transcripts.
Assembly: hg38
Supplementary files format and content: tab-delimited text file includes raw counts for eatch Sample

source_name: Breast

growth_protocol: The T47D cell line was maintained in RPMI medium supplemented with 10% fetal bovine serum and 1% penicillin–streptomycin. Post-lentivirus infection, cells were selected using either hygromycin (200 μg/ml) or puromycin (2 μg/ml), based on the vector's resistance marker. All cells were maintained at 37°C in 5% CO2 incubator. Hypoxia treatments were conducted in a Baker Ruskinn's InvivO2 400 hypoxia workstation.

extract_protocol:
RNA was extracted from T47D cells utilizing the FastPure Cell/Tissue Total RNA Isolation Kit.
The quality of the total RNA was assessed using an Agilent 2100 Bioanalyzer. This was followed by two rounds of polyA+ RNA selection, after which the mRNA was converted into cDNA. Illumina sequencing adapters and barcodes were added to the cDNA through PCR amplification. The indexed libraries were subsequently normalized and pooled. Finally, 150 bp paired-end sequencing was conducted on the Illumina Nova-seq platform, following the recommended protocol.

value: Breast

value: Tumor cell


title: 150SI1

description: Library name: Sample 4


title: RNA-seq_HGC27_Control shRNA_rep2

description: Library name: Sample 2

value: Control shRNA


title: RNA-seq_HGC27_shUSP47_rep2

description: Library name: Sample 4


title: siRif1_4Cell_035


title: siRif1_4Cell_037


title: RNA-seq_HGC27_Control shRNA_rep1

description: Library name: Sample 1


title: T47D, teton_sgZHX2, Hypoxia, replicate 2


title: T47D, teton_sgZHX2, Hypoxia, replicate 1


title: 150NC2

description: Library name: Sample 2


title: MCF7 cells,  treated with CM obtained from PreNeu (cm-PreNeu), 72h, biological replicate 1, experiment 2

description:
Library name: MCF7_cmPreNeu_biorep1_experiment_B
Column name in rawcounts_experiment_B.txt: MCF7_plus_cmPreNeu_p105
rawcounts_experiment_B.txt

value: breast


title: siRif1_4Cell_033


title: siRif1_4Cell_032


title: siRif1_4Cell_041


title: T47D, teton_control, Hypoxia, replicate 3


title: siRif1_4Cell_031


title: T47D, teton_control, Hypoxia, replicate 2


title: siRif1_4Cell_030


title: T47D, teton_control, Hypoxia, replicate 1


title: T47D, sgZHX2, Hypoxia, replicate 3


title: siRif1_4Cell_029


title: siRif1_4Cell_034


title: siRif1_4Cell_027


title: siRif1_4Cell_026


title: T47D, sgCtrl, Hypoxia, replicate 3


title: T47D, sgZHX2, Hypoxia, replicate 1


title: T47D, sgCtrl, Hypoxia, replicate 2


title: siRif1_4Cell_025


title: T47D, sgCtrl, Hypoxia, replicate 1


title: T47D, shZHX2, SA, hypoxia,replicate 2


title: siRif1_4Cell_028


title: T47D, sgZHX2, Hypoxia, replicate 2


title: siRif1_4Cell_021


title: siRif1_4Cell_024


title: siRif1_4Cell_020


title: T47D, shZHX2, PA, hypoxia,replicate 3


title: T47D, shZHX2, PA, hypoxia,replicate 1


title: T47D, shZHX2, WT, hypoxia,replicate 3


title: siRif1_4Cell_019


title: T47D, shZHX2, PA, hypoxia,replicate 2


title: siRif1_4Cell_017


title: siRif1_4Cell_016


title: T47D, shZHX2, WT, hypoxia,replicate 1


title: siRif1_4Cell_014


title: siRif1_4Cell_015


title: T47D, shZHX2, vector, hypoxia,replicate 3


title: siRif1_4Cell_023


title: siRif1_4Cell_022


title: T47D, shZHX2, SA, hypoxia,replicate 3


title: T47D, shZHX2, vector, hypoxia,replicate 2


title: T47D, shZHX2, SA, hypoxia,replicate 1


title: siRif1_4Cell_011


title: siRif1_4Cell_012


title: HL-60, ATRA+palbociclib, rep2

city: Jena

first: Tino

last: Schenk

state: Thüringen

address: Am Klinikum 1

department: KIM II

institute: University Hospital Jena

description: Library name: 2_ATRA+palbociclib

data_processing:
usegalaxy.eu (HISAT2, htseq-count )
Assembly: hg38
Supplementary files format and content: tab-delimited txt file for all samples

source_name: blood

growth_protocol: RPMI + 10%FCS

extract_protocol:
Quick-RNA™ Miniprep Kit
TruSeq RNA Library preparation (polyA)

treatment_protocol: 3h, 100nM ATRA, 500nM palbociclib

value: blood

value: myeloid

value: wt

value: ATRA + palbociclib


title: HL-60, ATRA+palbociclib, rep3

description: Library name: 3_ATRA+palbociclib


title: HL-60, ATRA+palbociclib, rep1

description: Library name: 1_ATRA+palbociclib


title: T47D, shZHX2, vector, hypoxia,replicate 1


title: siRif1_4Cell_018

value: 4-cell embryo


title: HL-60, palbociclib, rep3

description: Library name: 3_palbociclib

value: palbociclib


title: T47D, shCtrl, vector, hypoxia,replicate 3


title: siRif1_4Cell_010


title: HL-60, palbociclib, rep2

description: Library name: 2_palbociclib


title: T47D, shZHX2, WT, hypoxia,replicate 2


title: T47D, shCtrl, vector, hypoxia,replicate 2


title: HL-60, palbociclib, rep1

description: Library name: 1_palbociclib


title: HL-60, ATRA, rep2

description: Library name: 2_ATRA

value: ATRA


title: T47D, shCtrl, vector, hypoxia,replicate 1


title: HL-60, ATRA, rep3

description: Library name: 3_ATRA


title: siRif1_4Cell_009


title: siRif1_4Cell_008


title: HL-60, untreated, rep3

description: Library name: 3_Untreated

value: untreated


title: T47D, Hypoxia, PA, Flag, replicate 8

data_processing:
raw fastq data were initially processed to remove adaptor sequences using Cutadapt with parameters [-u 10 -u -15 -U 10 -U -15 -m 30]. The cleaned reads were aligned to the human reference genome (GRCh38, Ensemble release 100) using bowtie2 with default settings. Peak identification was performed using MACS2 with input data as controls. Replicates of ChIP-seq data were pooled for downstream analysis.
Assembly: hg38
Supplementary files format and content: Peak

extract_protocol:
1×107 of T47D cells were fixed using 1% formaldehyde for 10 minutes and quenched with 125 mM glycine for 5 minutes (cells treated under hypoxia were fixed in hypoxia chamber). Post-fixation, cells were washed twice with cold PBS supplemented with protease inhibitors. Cells were lysed using LB1 buffer (50 mM HEPES-KOH pH 7.5, 140 mM NaCl, 1 mM EDTA, 10% glycerol, 0.5% NP-40, 0.25% Triton X-100) followed by LB2 (10 mM Tris-HCl pH 8.0, 200 mM NaCl, 1 mM EDTA, 0.5 mM EGTA) and LB3 (10 mM Tris-HCl pH 8.0, 100 mM NaCl, 1 mM EDTA, 0.5 mM EGTA, 0.1% sodium deoxycholate, 0.5% N-lauroylsarcosine) buffers. Nuclei were collected and sonicated using Bioruptor sonicator (15 cycles, 30 s on and 30 s off). After Triton X-100 treatment (1% final concentration), supernatants were collected post-centrifugation (20,000g, 10 min, 4 °C) and incubated with antibody-bounddynabeads for approximately 8 hours at 4 °C. Following washing, chromatin-protein complexes bound to beads were eluted, crosslinks reversed overnight at 65 °C, and treated with RNase (1 hour at 37 °C) and protease K (2 hours at 55 °C).
DNA was recovered using PCR purification kit and subjected to library preparation using the NEBNext Ultra II kit, following the manufacturer’s instructions.

tag: chip antibody

value: Hypoxia


title: siRif1_4Cell_013

value: (C57BL/6J xCBA) x DBA/2J


title: HL-60, untreated, rep2

description: Library name: 2_Untreated


title: HL-60, untreated, rep1

description: Library name: 1_Untreated


title: T47D, Hypoxia, PA, Flag, replicate 7


title: siRif1_4Cell_007


title: a_Gal1_ChIP_2_16824

city: Barcelona

first: Neus

last: Martínez

address: Dr.Aiguader 88

department: Cancer

country: Spain

institute: Hospital del Mar Medical Research Institute

description: instrument model: sanger/illumina 1.9

data_processing:
We analyzed ChIP-seq data using The Galaxy Project platform (https://usegalaxy.org). Quality of immunoprecipitated DNA reads was determined by Fast Quality Control Report (FastQC) tool, those reads with >30 score were considered proper for the analysis. Selected reads were mapped with Bowtie2 tool using Homo Sapiens b38 (hg38) as a reference genome. Aligned reads from Gal1 IP were used as ChIP-seq Tag File, a 10-5 p-value cutoff was applied for peak detection, and an upper MFOLD range of 32 was determined to build the MACS peak calling model and to select regions with a high-confidence enrichment ratio against background (ChIP-seq IgG IP control File).
Assembly: hg38
Supplementary files format and content: bedgraph, bigwig

source_name: HPSC

growth_protocol: HPSC (2∙106) were seeded in 150 mm plates and kept growing for 48 h in 10% FBS DMEM at 37 ºC and 5% CO2.  Each IP was incubated with 5 μg of Gal1 antibody kindly given by Dr. Gabius (Institut für Physiologische Chemie, Tierärztliche Fakultät, Ludwig- Maximilians-Universität, Munich, Germany) or with 5 μg of irrelevant anti-rabbit IgGs, used as an unspecific binding control. Immunoprecipitated DNA and protein complexes where eluted by adding 100 μl of elution buffer (0.1 M Na2CO3, 1% SDS diluted in distillated water) to each sample and incubating them for 1h at 800 rpm and 37 ºC. DNA was purified using MinElute® PCR Purification kit (QIAGEN) and eluted in 20 μl for ChIP-sequencing (ChIP-seq)

extract_protocol:
Cells were fixed with 1% formaldehyde solution during 10 min at RT, and quenched with 0.125 M glycine during 5min at RT. Nuclei were collected at 800 x g, 4 ºC for 5 min and lysed with nuclear lysis buffer (50 mM Tris-HCl pH 8.1, 10 mM EDTA pH 8, 1% SDS; supplemented with protease inhibitors cocktail). DNA was sonicated obtaining 200-500 bp fragments. Sonicated samples were 10 times diluted with dilution buffer (16.7 mM Tris-HCl pH 8.1, 167 mM NaCl, 1.2 mM EDTA pH 8, 1% Triton X-100, 0.01% SDS; supplemented with protease inhibitors cocktail).
High sensitivity quality control (Qubit), DNA libraries (Bioanalyzer, Agilent Technologies) and DNA sequencing (Sanger) were performed by Genomics Unit (Centre of Genomic Regulation (CRG), PRBB, Barcelona).

value: HPSC

value: human pancreatic stellate cells


title: a_IgGs_ChIP_2_16823

description: instrument model: sanger/illumina 1.9


title: siRif1_4Cell_006


title: siRif1_4Cell_005


title: T47D, Hypoxia, PA, Flag, replicate 5


title: Handling_5h30min_CRS1_v9

city: Zürich

first: Pierre-Luc

last: Germain

address: Winterthurerstrasse 190

department: D-HEST Institute for Neuroscience

institute: ETH Zürich

description: Library name: CRS1_v9

data_processing:
Transcript-level quantification was performed with Kallisto using the GENCODE M17 annotation.
Counts from protein-coding transcripts were aggregated for gene-level quantification.
Assembly: GRCm38
Supplementary files format and content: bulkRNA_GeneCounts.csv.zip : a matrix of counts per gene symbol.
Supplementary files format and content: bulkRNA.SE.rds.zip : A R SummarizedExperiment containing the gene counts, metadata, and DEA results.

source_name: Ventral hippocampus

extract_protocol:
One snap-frozen ventral hippocampus per animal was homogenized in 500 µl Trizol (Invitrogen 15596018) using metal beads (Qiagen 69989) in a tissue lyser bead mill (Qiagen, Germany) at 4°C for 2 min at 20 Hz. RNA was extracted according to the manufacturer’s recommendations.
The CRS1 experiment was prepared using the Illumina TruSeq stranded RNA kit, while the other libraries were prepared at Novogene using the NEBNext® Ultra RNA Library Prep Kit.

value: Ventral hippocampus

tag: Sex

value: female

tag: ars timepoint

value: Handling


title: HL-60, ATRA, rep1

description: Library name: 1_ATRA


title: PKI_BCC_4

city: Bethesda

first: Ramiro

last: Iglesias-Bartolome

address: 37 Convent Drive

department: LCMB

institute: NIH/NCI

description: Library name: Sample 21

data_processing:
Basecalling RTA 3.9.25, Illumina instrument run time analysis software
Demultiplexing, Bcl2fastq v2.20
Filtering (Adaptor and quality), Cutadapt 1.18
Alignment, STAR 2.7.0f
Counts were calculated in PartekFlow v12. No batch effect was observed so batch correction was not necessary and all controls were pooled together. Differential expression analysis against control mice was performed with Partek Flow GSA algorithm
Assembly: mm10
Supplementary files format and content: "Gene_counts.txt" contains the raw gene counts without normalization
Supplementary files format and content: "Normalized_counts_TMM.txt" contains TMM normalized counts

source_name: skin

extract_protocol:
RNA was isolated and processed using RNeasy Plus Mini Kit (Qiagen) according to manufacturer’s instructions. Cells were lysed using the Precellys lysing kit (Bertin Instruments).
Illumina® Stranded mRNA ligation Prep

treatment_protocol: Keratinocytes were isolated from BCC mice and their respective controls: SmoM2 mice 29 days post-tumor induction, Gnas-eKO mice 42 days post-tumor induction, and PKI mice 57 days post-tumor induction. Tail skin was removed from mice, cleaned using 10% iodine in PBS and washed with sterile PBS several times. Each tail was cut into pieces and then incubated overnight at 4°C in 2.5 parts of 0.25% trypsin (Gibco 15050-057) and 1 part of 5U/mL dispase (Stem Cell Technologies 07913). The next day, the epidermis was scraped from the dermis and minced in 0.25% trypsin with EDTA (Gibco 25200056). Trypsin was neutralized in DMEM with 10% FBS and cells were strained in a 100μm cell strainer followed by a 40μm cell strainer. After centrifugation at 500G for 8 minutes cells were lysed in RLT Lysis buffer from the RNeasy Plus Mini Kit.

value: skin

value: Tail keratinocytes

value: C


title: T47D, Hypoxia, PA, Flag, replicate 6

value: Breast

value: Tumor cell


title: Handling_45min_CRS1_v8

description: Library name: CRS1_v8

value: male


title: siRif1_4Cell_004

data_processing:
library strategy: Single-cell Repli-seq
Sequencing reads were aligned to the GRCm38 genome using bowtie2 (version 2.5.1) 59 with the parameters --local --no-unal --no-mixed --no-discordant. Reads were filtered by mapping quality using samtools with the parameter -q 20. Read duplicates were removed using picard MarkDuplicates (version 3.0.0) with the parameter -REMOVE_DUPLICATES true. Using bedtools intersect (version 2.31.0), read counts were obtained for contiguous 50kb genomic bins.
The window counts were first normalised to RPM (reads per million). Aiming to correct for the mappability biases intrinsic to the genomic regions, for each bin its respective average of all samples within the same condition was calculated. Outlier regions were then masked, specifically the windows of the lower 5th percentile and the upper 1st percentile values. To correct for low mappability, the windows were segmented with the R package copynumber (version 1.38.0, R version 4.2.3) to keep the segments with the highest 95% of values. The data were centred by the mean and scaled by the interquartile range for each cell and smoothed using a median filter with a running window width of 15 windows, followed by a segmentation with the R package copynumber. Finally, using the function normalmixEM from R package mixtools (version 2.0.0), the segmented values were used to fit a mixture model with two components to identify replicated and non-replicated window populations.
To obtain replication timing values and to correct for potential sampling bias of cells, we calculated the fraction of replicated cells in overlapping intervals of the genome-wide replication score with interval size of 35% and increment of 4.33% (e.g. 0-35%, 4.33-39.33% etc.) for each genomic bin. The average of these 16 intervals served as replication timing value that was used for downstream analyses.
Assembly: GRCm38
Supplementary files format and content: tab-separated txt file with binary replication status
Supplementary files format and content: bedgraph file with replication timing values

extract_protocol:
Early stage zygotes were collected and cultured until they reached the S-phase at each developmental stage, based on their time after hCG injection. Embryos were collected at different time points to achieve sampling over the entire S-phase. Zona pellucida was removed by exposure to acid Tyrode and each blastomere was dissociated by gentle pipetting after trypsin treatment.
Individual blastomeres were placed into 8-strip PCR tubes containing lysis buffer and extracted DNA was fragmented by heat incubation. Fragmented DNA was tagged by the universal primer (5’-TGTGTTGGGTGTGTTTGGKKKKKKKKKKNN-3’) and amplified with WGA primer sets which have individual barcode. Amplified DNA was purified by the QIAquick 96 PCR Purification Kit (QIAGEN) and concentration was determined by the NanoDrop (Thermo Scientific). Equal amount of DNA from each samples (up to 96 samples) were pooled and 1ug of them was ligated with the illumina adaptors using the NEBNext Ultra II DNA Library Prep Kit (NEB). Illumina sequence (NEBNext Multiplex Oligos for Illumina; NEB) were added to the adaptor- ligated samples by the PCR. Clean up and size selection of the PCR product was done using SPRIselect (Beckman Coulter) and the quality of the library was confirmed by 2100 Bioanalyzer with the High Sensitivity DNA Kit (Agilent).

value: 4-cell embryo


title: PKI_BCC_3

description: Library name: Sample 20


title: PKI_BCC_2

description: Library name: Sample 19


title: T47D, Hypoxia, WT, Flag, replicate 3


title: T47D, Hypoxia, WT, Flag, replicate 2


title: siRif1_4Cell_002


title: Handling_45min_CRS1_v5

description: Library name: CRS1_v5


title: siRif1_4Cell_001


title: PKI_BCC_1

description: Library name: Sample 18


title: PKI_Con_3

description: Library name: Sample 17


title: Handling_5h30min_CRS1_v48

description: Library name: CRS1_v48


title: T47D, Hypoxia, WT, Flag, replicate 1


title: siCont_8Cell_008

value: 8-cell embryo

value: siControl


title: PKI_Con_2

description: Library name: Sample 16


title: OsmoStress-A375-Recovery-R2

city: Knoxville

first: Rachel

middle: Patton

last: McCord

state: TN

address: 309 Mossman Bldg. 1311 Cumberland Ave

department: BCMB

institute: University of Tennessee

description: Arima-HiC+ Kit (Mammalian Cell Lines A160134v01)

data_processing:
Sequenced reads were mapped to the hg19 or dm6 genomes using bowtie2
Mapping, filtering, iterative correction, and binning were performed using the Hi-C pro pipeline available at: https://github.com/nservant/HiC-Pro
Before mapping, Drosophila fastq files were trimmed to only the first 25 bases using trimmomatic CROP:25.  Longer reads often passed into the other ligated pair and therefore trimming increased mappability.
Assembly: hg19, dm6
Supplementary files format and content: Each .mcool file (see https://cooler.readthedocs.io/ for filetype information) contains the iteratively corrected contacts binned at multiple resolutions.  For human, resolutions include 10 kb, 20 kb, 40 kb, 100 kb, 250 kb, 1 Mb, and 2.5 Mb.  For Drosophila, resolutions include 1 kb, 2kb, 5 kb, 10 kb, 20 kb, 40 kb, 100 kb, 250 kb, 1 Mb, and 2.5 Mb for the replicates combined files, with 1 kb omitted for individual replicate files.  "RC" indicates replicates combined, where the mapped valid pairs for biological replicates 1 and 2 were pooled into the final processed contact matrices.  These .mcool files can be used for analysis with cooltools or loaded into HiGlass. See https://cooltools.readthedocs.io/ and https://github.com/higlass/higlass-docker

source_name: Melanoma (A375)

growth_protocol: S2 Cells were maintained in Schneider’s Drosophila Media (1X) (Gibco) supplemented with 10% fetal bovine serum to form complete Schneider’s Drosophila Media at 25°C.   A375 cells were cultured in Dulbecco’s Modified Eagle Medium (DMEM, Corning), supplemented with 10% fetal bovine serum, 1% Penicillin-Streptomycin, and 1% L-Glutamine, at 37°C in a 5% CO2 atmosphere.

extract_protocol:
For both Drosophila S2 and human A375 cells, Hi-C was performed using the Arima Hi-C (Arima Genomics) kit, following the manufacturer’s protocol A160134 v01.  The only exception is for A375 replicate 1 conditions, the Hi-C protocol from Golloshi et al., 2018 was used instead of Arima.
Library amplification was performed using the NEBNext Ultra II kit (NEB;E7645S).

treatment_protocol: 15 million S2 cells were used for each of the two replicates for each condition. Prior to the Hi-C assay, the S2 cells were pretreated with just the complete Schneider’s media and 250mM NaCl prepared in complete Schneider’s media as control and stress respectively for 1 hour. The recovery cells underwent the same stress treatment for 1 hour before a 1  hour recovery in the complete Schneider’s media. After these treatments, the cells were strained passing them through a 40µm strainer to remove clumps. We then fixed the cells with 2% formaldehyde at RT for 10 minutes. The crosslinking was quenched with 125mM glycine. Following fixation and quenching, nuclei were isolated using a 5ml cold lysis buffer  . The isolated nuclei were then snap frozen in liquid nitrogen and stored at -80°C for later Hi-C analysis.  The human A375 malignant melanoma cells were purchased from ATCC (ATCC® CRL-1619™). The cells were grown in DMEM enriched with 10% FBS, 1% Pen-strep, and 1% L-glutamine, and were sub-cultured to at a density of 80%. For salt stress experiments, A375 cells were introduced into media supplemented with 250mM NaCl for one hour, for stress samples, or subjected to 250mM NaCl for one hour followed by reintroduced to conditioned DMEM for an additional hour, for recovery samples.

value: Melanoma (A375)

tag: replicate

value: biological replicate 2

value: Return to standard media, 1 hr after Stress


title: PKI_Con_1

description: Library name: Sample 15


title: Handling_1h30min_CRS1_v47

description: Library name: CRS1_v47


title: OsmoStress-A375-Control-R2

value: Standard media


title: siCont_8Cell_007

value: (C57BL/6J xCBA) x DBA/2J


title: siRif1_4Cell_003


title: T47D, Hypoxia, WT, Flag, replicate 4

value: Hypoxia


title: Gnas-eKO_BCC_4

description: Library name: Sample 14

value: B


title: siCont_8Cell_006


title: Handling_3h_CRS1_v46

description: Library name: CRS1_v46

value: Ventral hippocampus

value: female

value: Handling


title: Handling_0min_CRS1_v6

description: Library name: CRS1_v6


title: Handling_24h_CRS1_v7

description: Library name: CRS1_v7


title: Handling_24h_CRS1_v44

description: Library name: CRS1_v44


title: OsmoStress-A375-250mMNaCl-R2

value: 250 mM NaCl, 1 hr


title: Handling_0min_CRS1_v45

description: Library name: CRS1_v45


title: OVCAR5_ALDHplus_CD133plus_PBS_scRNA

city: Chicago

first: Elizabeth

middle: Thomas

last: Bartom

state: IL

address: 303 E Superior Ave, SQBRC 7-406

department: Biochemistry and Molecular Genetics

institute: NORTHWESTERN UNIVERSITY AT CHICAGO

data_processing:
FASTQ files were aligned to GRCh38 using 10X Genomics Cellranger version 7.1.0 on a computing cluster.
A Seurat object was created for each condition with the minimum number of cells set to 3 and the minimum number of features set to 200.
The Seurat objects were filtered to remove cells with less than 20,000 and more than 100,000 mRNA reads.
Cells with 15% or more mitochondrial DNA expression were removed.
The gene expression was log normalized with a scale factor of 10,000.
A VST method was used to find variable features.
Variable features were used to scale each Seurat object.
PCA analysis was done on the scaled Seurat objects using the variable features.
Dimensions 1-20 from the PCA data were used for a three-dimensional t-SNE analysis.
Assembly: GRCh38
Supplementary files format and content: RDS files exported from the R Seurat objects.

source_name: Ovary

growth_protocol: OVCAR5 cells were cultured in the regular medium described in the manuscript. ALDH+/- cells were FACS sorted.

extract_protocol:
Sequencing libraries were created using a Chromium Next GEM Single Cell 3ʹ Kit v3.1 (10X Genomics, Cat. PN-1000269) targeting 10,000 cells per sample according to manufacturer’s instructions and pooled in equimolar quantities.
Pre-made scRNA-seq libraries were sequenced by NovaSeq S2 PE50 Sequencer.

treatment_protocol: ALDH+/- cells were FACS sorted from OVCAR5 cells treated with PBS or cisplatin (1mM, 24h), and further processed for single-cell sequencing libraries preparation.

value: Ovary

value: PBS


title: siCont_8Cell_004

city: Munich

first: Tamas

last: Schauer

address: Feodor-Lynen-Straße 21

institute: Helmholtz Zentrum München


title: siCont_8Cell_005


title: Gnas-eKO_BCC_3

description: Library name: Sample 13

value: skin

value: Tail keratinocytes


title: Handling_45min_CRS1_v43

description: Library name: CRS1_v43

value: male


title: Gnas-eKO_BCC_2

description: Library name: Sample 12


title: OVCAR5_ALDHplus_CD133plus_Cisplatin_scRNA

value: Cisplatin


title: siCont_8Cell_003

value: 8-cell embryo

value: siControl


title: Gnas-eKO_BCC_1

description: Library name: Sample 11


title: OVCAR5_ALDHminus_CD133minus_PBS_scRNA


title: Handling_1h30min_CRS1_v42

description: Library name: CRS1_v42


title: siCont_8Cell_002


title: OVCAR5_ALDHminus_CD133minus_Cisplatin_scRNA


title: Handling_5h30min_CRS1_v41

description: Library name: CRS1_v41


title: siCont_8Cell_001


title: Gnas-eKO_Con_2

description: Library name: Sample 9


title: SC3

first: Alsiel

last: Tang

address: Zhang zhidong road

department: Urology

institute: Renmin hospital of Wuhan

data_processing:
After the sequencing data were down-loaded, the data were analysed using the bioinformatics analysis process provided by the BMKCloud platform BMKCloud (www.biocloud.net). After filtering the offline data to obtain Clean Data, sequence comparison with the specified reference genome, and obtaining Mapped Data, library quality assessment, structure level analysis, differential expression analysis, gene function annotation and function enrichment are carried out. In addition, BMKCloud (www.biocloud.net) allows in-depth data mining analysis and a series of personalised interactive transcriptome operations, such as gene search mapping, unique and shared gene analysis, protein interaction network construction, gene set enrichment analysis (GSEA), differential gene co-expression analysis and gene co-expression network construction (WGCNA). network construction (WGCNA), etc.
Assembly: NC_000019.10 Chromosome 19 Reference GRCh38.p14 Primary Assembly
Supplementary files format and content: All_gene_fpkm

growth_protocol: T24 cells were purchased from Pricella, China (CL-0227), cultured in McCoy's 5A medium (PM150710; Pricella, China), and were cultured in a humidified environment containing 5% CO2.

extract_protocol:
Total RNA extraction by trizol method
(1) Eukaryotic mRNA was enriched with magnetic beads with Oligo (dT); (2) Add Fragmentation Buffer to interrupt the mRNA randomly; (3) Synthesis of the first cDNA strand and double strand using mRNA as template and cDNA purification; (4) The purified double-stranded cDNA was then subjected to end repair, addition of A-tail and ligation of sequencing junctions, followed by fragment size selection with AMPure XP beads; (5) Finally, the cDNA library was enriched by PCR.


title: siCont_4Cell_008

value: 4-cell embryo


title: Gnas-eKO_Con_1

description: Library name: Sample 8


title: Handling_1h30min_CRS1_v4

description: Library name: CRS1_v4


title: SC2


title: SmoM2_BCC_4

description: Library name: Sample 7

value: A


title: siCont_4Cell_007

value: (C57BL/6J xCBA) x DBA/2J


title: Handling_0min_CRS1_v38

description: Library name: CRS1_v38


title: SC1


title: siCont_4Cell_006


title: siCont_4Cell_005


title: SmoM2_BCC_3

description: Library name: Sample 6


title: SmoM2_BCC_2

description: Library name: Sample 5


title: Handling_24h_CRS1_v39

description: Library name: CRS1_v39


title: NC3

value: empty-vector-lentivirus transfection


title: Handling_1h30min_CRS1_v36

description: Library name: CRS1_v36


title: NC2


title: siCont_4Cell_004


title: Gnas-eKO_Con_3

description: Library name: Sample 10

value: B


title: SmoM2_BCC_1

description: Library name: Sample 4


title: NC1


title: Handling_3h_CRS1_v37

description: Library name: CRS1_v37

value: Ventral hippocampus


title: SmoM2_Con_3

description: Library name: Sample 3


title: Handling_3h_CRS1_v35

description: Library name: CRS1_v35

value: female


title: T47D, 1%1,6HD, Hypoxia, RNA, replicate 3

value: Breast

value: Tumor cell


title: Handling_45min_CRS1_v40

description: Library name: CRS1_v40

value: Handling


title: SmoM2_Con_2

description: Library name: Sample 2


title: siCont_4Cell_002


title: siCont_4Cell_001


title: Handling_45min_CRS1_v34

description: Library name: CRS1_v34


title: SmoM2_Con_1

description: Library name: Sample 1


title: siRif1_8C_12

data_processing:
Sequencing reads were aligned to the mouse genome (GRCm38, primary assembly) using STAR aligner (version 2.7.6a) with the annotation (GRCm38.101) and ERCC92 (Thermofisher).
Reads were counted per gene with the same STAR run by setting quantMode GeneCounts.
Assembly: GRCm38
Supplementary files format and content: tab-delimited text with read counts per gene

growth_protocol: Zygotes were collected from the oviduct and cumulus cells were removed upon brief incubation in M2 media containing hyaluronidase. Zygotes were placed in drops of KSOM and cultured at 37 ºC with 5% CO2 until they reached 4-cell and 8-cell stage.

extract_protocol:
Emrbyos were washed with PBS, placed in tubes with 1× Clontech lysis buffer (Z5013N) containing ERCC RNA Spike-In Mix (Invitrogen) and flash-frozen in liquid nitrogen.
Library preparation was carried out using the SMART-seq2 protocol.

treatment_protocol: 20 μM siControl (Dharmacon, D-001210-01) or 20 μM siRif1 (Dharmacon, D-040028-01) were injected into zygotes at 17-18 hours post-hCG injection and embryos were cultured until 63 and 70 hours post-hCG injection, respectively, at which point 4-cell and 8-cell embryos, respectively were collected.

value: (C57BL/6J xCBA) x DBA/41J

value: siRNA for Rif1 injected


title: T47D, 1%1,6HD, Hypoxia, RNA, replicate 1


title: Handling_1h30min_CRS1_v33

description: Library name: CRS1_v33


title: Control_3

description: Library name: Sample 6

data_processing:
Basecalling RTA 4.12.2, Illumina instrument run time analysis software
Demultiplexing, Bcl2fastq v2.20
Filtering (Adaptor and quality), Cutadapt 1.18
Alignment, STAR 2.7.0f
Counts were calculated in PartekFlow v12. Differential expression analysis against control mice was performed with Partek Flow GSA algorithm
Assembly: mm10
Supplementary files format and content: "Gene_counts.txt" contains the raw gene counts without normalization
Supplementary files format and content: "Normalized_counts.txt" contains TMM normalized counts

extract_protocol:
RNA was isolated and processed using RNeasy Plus Mini Kit (Qiagen) according to manufacturer’s instructions. Cells were lysed using the Precellys lysing kit (Bertin Instruments).
Illumina® Stranded mRNA  Prep

treatment_protocol: Keratinocytes were isolated from mice at 4 months of age. Tail skin was removed from mice, cleaned using 10% iodine in PBS and washed with sterile PBS several times. Each tail was cut into pieces and then incubated overnight at 4°C in 2.5 parts of 0.25% trypsin (Gibco 15050-057) and 1 part of 5U/mL dispase (Stem Cell Technologies 07913). The next day, the epidermis was scraped from the dermis and minced in 0.25% trypsin with EDTA (Gibco 25200056). Trypsin was neutralized in DMEM with 10% FBS and cells were strained in a 100μm cell strainer followed by a 40μm cell strainer. After centrifugation at 500G for 8 minutes cells were lysed in RLT Lysis buffer from the RNeasy Plus Mini Kit.

value: skin

value: Tail keratinocytes


title: T47D, 0.5%1,6HD, Hypoxia, RNA, replicate 3


title: Gpr161eko_3

description: Library name: Sample 5

value: K14cre+/ Gpr161Flox-Homozygous


title: Handling_0min_CRS1_v31

description: Library name: CRS1_v31


title: siCont_4Cell_003


title: siRif1_8C_10

value: 8-cell embryo

value: (C57BL/6J xCBA) x DBA/39J


title: T47D, 0.5%1,6HD, Hypoxia, RNA, replicate 2


title: Handling_24h_CRS1_v32

description: Library name: CRS1_v32

value: male


title: Handling_5h30min_CRS1_v30

description: Library name: CRS1_v30


title: T47D, Ctrl, Hypoxia, RNA, replicate 3

value: Ctrl


title: T47D, 0.5%1,6HD, Hypoxia, RNA, replicate 1


title: siRif1_8C_9

value: (C57BL/6J xCBA) x DBA/38J


title: siRif1_8C_11

value: (C57BL/6J xCBA) x DBA/40J


title: Gpr161eko_2

description: Library name: Sample 4


title: Handling_3h_CRS1_v3

description: Library name: CRS1_v3


title: Control_2

description: Library name: Sample 3


title: siRif1_8C_8

value: (C57BL/6J xCBA) x DBA/37J


title: siRif1_8C_7

value: (C57BL/6J xCBA) x DBA/36J


title: T47D, 1%1,6HD, Hypoxia, RNA, replicate 2


title: Handling_24h_CRS1_v29

description: Library name: CRS1_v29

value: Ventral hippocampus

value: female


title: Gpr161eko_1

description: Library name: Sample 1


title: T47D, Ctrl, Hypoxia, RNA, replicate 2

value: Breast

value: Tumor cell


title: T47D, Ctrl, Hypoxia, RNA, replicate 1


title: siRif1_8C_6

value: (C57BL/6J xCBA) x DBA/35J


title: Handling_0min_CRS1_v28

description: Library name: CRS1_v28

value: Handling


title: K4me3 ALDH plus rep2

description: K4me3.ALDH_Plus_cells in duplicates

data_processing:
The quality of libraries was checked by High Sensitivity DNA Assay (Agilent Technologies) and sequenced on Illumina HiSeq 4000 sequencer. Raw sequencing data generated from Illumina HiSeq was converted into fastq files which were run through the NF-Core/cutandrun pipeline v3.1 (https://doi.org/10.5281/zenodo.5653535). In short, raw paired-end 50bp sequencing reads were checked with FastQC (v0.11.9), trimmed with TrimGalore (v0.6.6), and mapped to human genome build GRCh38 using Bowtie2 (v.2.4.4) with standard settings. Peaks were called using MACS2 (v2.2.7.1) callpeak with cut-off FDR (q-value) at 0.05.  UCSC Genome Browser was used to visualize locus-specific signals and deeptools (v3.5.1) was used for genome-wide visualization and clustering.
Cell line identity was validated for all samples as OVCAR5 using NGSCheckmate.
Bigwig formatted track files were generated using deeptools v3.5.1 bamCoverage, from the Bowtie2-aligned bam files described above, normalized to counts per million reads (CPM).
Assembly: hg38
Supplementary files format and content: Bigwig track files
Library strategy: CUT&Tag

extract_protocol:
The CUT&Tag sequencing was performed with the CUT&Tag-IT Assay Kit (Active motif, 53160) by following the manufacturer’s protocol.
105 OVCAR5 ALDH+ CSCs and OVCAR5 ALDH- non-CSCs were FACS sorted and incubated with Concanavalin A beads for binding. Cells were then incubated with a primary antibody targeting H3K27me3 (Active motif, 39155), H3K4me3 (Abcam, ab8580), and H3K27ac (Active Motif, #39034) overnight at 4°C. Samples were then incubated with secondary antibody, followed by CUT&Tag-IT Assembled pA-Tn5 Transposomes. After tagmentation at 37°C for 1 hour, DNA was purified and cleaned up by SPRI beads. DNA was then amplified with a combination of i7 and i5 Indexed primers for library preparation.

treatment_protocol: No treatment on the ALDH+/- cells processed for the Cut and Tag

value: Ovary


title: Handling_5h30min_CRS1_v27

description: Library name: CRS1_v27


title: siRif1_8C_5

value: (C57BL/6J xCBA) x DBA/34J

value: siRNA for Rif1 injected


title: K4me3 ALDH plus rep1

description: K4me3.ALDH_Plus_cells in duplicates


title: T47D, shZHX2, Hypoxia, RNA, replicate 2

value: Hypoxia


title: Handling_3h_CRS1_v26

description: Library name: CRS1_v26


title: Control_1

description: Library name: Sample 2

value: skin

value: Tail keratinocytes


title: Handling_45min_CRS1_v25

description: Library name: CRS1_v25


title: T47D, shZHX2, Hypoxia, RNA, replicate 1


title: T47D, shCtrl, Hypoxia, RNA, replicate 3

value: shCtrl


title: K4me3 ALDH minus rep1

description: K4me3.ALDH_minus_cells in duplicates


title: siRif1_8C_2

value: 8-cell embryo

value: (C57BL/6J xCBA) x DBA/31J


title: siRif1_8C_4

value: (C57BL/6J xCBA) x DBA/33J


title: siRif1_8C_3

value: (C57BL/6J xCBA) x DBA/32J


title: K4me3 ALDH minus rep2

description: K4me3.ALDH_minus_cells in duplicates


title: K27me3 ALDH plus rep2

description: K27me3_ALDH_Plus_cells in duplicates


title: Handling_1h30min_CRS1_v23

description: Library name: CRS1_v23

value: Ventral hippocampus

value: male


title: K27me3 ALDH plus rep1

description: K27me3_ALDH_Plus_cells in duplicates


title: Handling_0min_CRS1_v24

description: Library name: CRS1_v24

value: female


title: siRif1_8C_1

value: (C57BL/6J xCBA) x DBA/30J


title: T47D, shCtrl, Hypoxia, RNA, replicate 1

value: Breast

value: Tumor cell


title: Handling_45min_CRS1_v22

description: Library name: CRS1_v22

value: Handling


title: Handling_3h_CRS1_v21

description: Library name: CRS1_v21


title: K27me3 ALDH minus rep2

description: K27me3.ALDH_minus_cells in duplicates

value: Ovary


title: siCon_8C_8

value: (C57BL/6J xCBA) x DBA/29J

value: siRNA for control injected


title: T47D, shCtrl, Normoxia, RNA, replicate 3

value: Normoxia


title: K27me3 ALDH minus rep1

description: K27me3.ALDH_minus_cells in duplicates


title: siCon_8C_7

value: (C57BL/6J xCBA) x DBA/28J


title: T47D, shZHX2, Hypoxia, RNA, replicate 3

value: Hypoxia


title: T47D, shCtrl, Normoxia, RNA, replicate 2

value: shCtrl


title: K27ac ALDH plus rep2

description: K27ac.ALDH_Plus_cells in duplicates


title: siCon_8C_6

value: 8-cell embryo

value: (C57BL/6J xCBA) x DBA/27J


title: T47D, shCtrl, Normoxia, RNA, replicate 1


title: Handling_5h30min_CRS1_v2

description: Library name: CRS1_v2


title: T47D, Hypoxia, ZHX2 ChIP-seq input, replicate 2

data_processing:
raw fastq data were initially processed to remove adaptor sequences using Cutadapt with parameters [-u 10 -u -15 -U 10 -U -15 -m 30]. The cleaned reads were aligned to the human reference genome (GRCh38, Ensemble release 100) using bowtie2 with default settings. Peak identification was performed using MACS2 with input data as controls. Replicates of ChIP-seq data were pooled for downstream analysis.
Assembly: hg38
Supplementary files format and content: bigWig, Peak


title: siCon_8C_5

value: (C57BL/6J xCBA) x DBA/26J


title: K27ac ALDH plus rep1

description: K27ac.ALDH_Plus_cells in duplicates


title: T47D, shCtrl, Hypoxia, RNA, replicate 2


title: siCon_8C_4

value: (C57BL/6J xCBA) x DBA/25J


title: K27ac ALDH minus rep2

description: K27ac.ALDH_minus_cells in duplicates


title: T47D, Hypoxia, ZHX2 ChIP-seq input, replicate 1


title: K27ac ALDH minus rep1

description: K27ac.ALDH_minus_cells in duplicates


title: Handling_5h30min_CRS1_v19

description: Library name: CRS1_v19

value: Ventral hippocampus

value: male


title: siCon_8C_3

value: (C57BL/6J xCBA) x DBA/24J


title: T47D, Hypoxia, ZHX2, replicate 2

value: Breast


title: Handling_45min_CRS1_v17

description: Library name: CRS1_v17


title: Handling_24h_CRS1_v16

description: Library name: CRS1_v16

value: female


title: Handling_3h_CRS1_v18

description: Library name: CRS1_v18

value: Handling


title: RUX+3

city: Tianjin

first: Rong

last: Fu

address: xinxing street

institute: Tianjin Medical University General Hospital

description: Library name: JZ24233289

data_processing:
The library was sequenced using next-generation high-throughput double-end sequencing, with 150 bp paired-end reads (Pair end 150 bp, PE150).
Assembly: hg38
Supplementary files format and content: The analysis included an assessment of the sequencing data quality, a comparison with reference sequences, and a differential gene function analysis.

extract_protocol:
Total RNA was extracted from the samples, the integrity of the extracted RNA was determined using agarose gel electrophoresis, and RNA concentration was determined using NanoDrop.
Oligo-dT magnetic beads were used to isolate mRNA from total RNA, and the captured mRNA was fragmented. The first and second strands of cDNA were synthesised using RT, and end repair was performed with the addition of an A base at the 3' end. Subsequently, the ligation product was purified, and PCR amplification was performed. The sequencing library was purified using magnetic beads. The library concentration was detected using a Qubit instrument, while the fragment length was determined using an Agilent fragment analyser.

value: human mononuclear

value: Lukotinib


title: siCon_8C_2

value: (C57BL/6J xCBA) x DBA/23J

value: siRNA for control injected


title: siCon_8C_1

value: (C57BL/6J xCBA) x DBA/22J


title: T47D, Hypoxia, ZHX2, replicate 1

value: Tumor cell

value: Hypoxia


title: siRif1_4C_13

value: 4-cell embryo

value: (C57BL/6J xCBA) x DBA/21J

value: siRNA for Rif1 injected


title: T47D, Hypoxia, input, replicate 2


title: RUX+1

description: Library name: JZ24233287


title: RUX+2

description: Library name: JZ24233288


title: Handling_5h30min_CRS1_v20

description: Library name: CRS1_v20


title: Handling_1h30min_CRS1_v14

description: Library name: CRS1_v14


title: Handling_24h_CRS1_v15

description: Library name: CRS1_v15


title: T47D, Hypoxia, input, replicate 1


title: siRif1_4C_12

value: (C57BL/6J xCBA) x DBA/20J


title: RUX-3

description: Library name: JZ24233286


title: T47D, Hypoxia, CTCF, replicate 2


title: T47D, Hypoxia, CTCF, replicate 1


title: Handling_0min_CRS1_v13

description: Library name: CRS1_v13

value: Ventral hippocampus


title: RUX-2

description: Library name: JZ24233285


title: Handling_24h_CRS1_v12

description: Library name: CRS1_v12

value: male


title: siRif1_4C_11

value: (C57BL/6J xCBA) x DBA/19J


title: siRif1_4C_10

value: (C57BL/6J xCBA) x DBA/18J


title: Handling_0min_CRS1_v11

description: Library name: CRS1_v11

value: female


title: RUX-1

description: Library name: JZ24233284


title: siRif1_4C_9

value: (C57BL/6J xCBA) x DBA/17J


title: Long reads polyA RNA from control OSCs for piRNA knockdown

city: Vienna

first: Dominik

last: Handler

address: Dr. Bohr-Gasse 3

country: Austria

institute: IMBA-Institute of Molecular Biotechnology of Austrian Academy of Sciences

description: Library name: OSCs_siGFP

data_processing:
Basecalling was conducted with Dorado v0.8+98ff765, with polyA-tail detection enabled (read-names contain the polyA-tail length detected by Dorado)
Reads with a detected polyA tail were aligned using minimap2 to the TE consensus sequences using options "--secondary=no -x splice"
3'ends of aligned reads were quantified and aggregated into single-nucleotide resolution histogram tables
Assembly: TE consensus sequences (in-house curated list of TE sequences)
Supplementary files format and content: Curated TE-consensus file used for the TE quantification analysis
Supplementary files format and content: Histogram tables show 3' end counts of minimap2 read alignments where only the very last aligned nucleotide was considered

organism: Drosophila melanogaster

source_name: OSCs

growth_protocol:
Ovaries: 25˚C, 12h dark/light, ovaries dissected into PBS on ice, snap frozen
OSCs: OSC culture according to Niki et al., PNAS, 2006

extract_protocol:
RNA was extracted with TRIzol
Poly(A) enrichment with magnetic Dynabeads Oligo(dT) beads followed by ONT RNA002 Direct RNA Library Prep Kit (SQK-002) including reverse-transcription step

value: OSCs

value: Somatic follicle cells

value: siGFP


title: Handling_3h_CRS1_v10

description: Library name: CRS1_v10

value: Handling


title: siRif1_4C_8

value: (C57BL/6J xCBA) x DBA/16J


title: T47D, Normoxia, ZHX2 ChIP-seq input, replicate 2

value: Breast

value: Tumor cell

value: Normoxia


title: Long reads polyA RNA from piRNA knockdown OSCs

description: Library name: OSCs_siPIWI

value: siPIWI


title: Long reads polyA RNA from somatic piRNA knockdown ovaries

description: Library name: ovaries_tjG4_vretGD

value: Ovary


title: siRif1_4C_7

value: 4-cell embryo

value: (C57BL/6J xCBA) x DBA/15J

value: siRNA for Rif1 injected


title: T47D, Normoxia, ZHX2 ChIP-seq input, replicate 1


title: siRif1_4C_6

value: (C57BL/6J xCBA) x DBA/14J


title: HPSC,rep4,adult,hic-seq,3m

city: Guangzhou

first: Feifei

last: Li

state: Guangdong

address: Guangzhou Higher Education Mega Center, Panyu District

institute: South China University of Technology

data_processing:
HiC-Pro (v.3.1.0) was used for the processing of Hi-C data. Only uniquely mapped read pairs with mapping quality no less than 10 were saved for further analysis, and dangling end reads, self circled reads, religated reads were all trimmed out. Non-duplicated reads were used to generate Hi-C contact matrices at the binning resolution of 10kb, 50kb and 100 kb. To validate the reproducibility of data, we calculated the GenomeDisco score between two libraries. Contact heatmaps were generated with matrices at different resolutions by fanc (v.0.9.25). The p(s)-curves were calculated from genome distances of 20 kb to 50 Mb separated into 500 bins logarithmically.We applied the Von Neumann Entropy (VNE) approach to quantify the disorder of chromatin structure for 100-kb resolution intra-chromosomal matrices. Hi-C matrix (M) was converted to correlation matrix C using corr (log2[M]).
Compartments were called d by analyzing the first eigenvector of the KR normalized contact maps at 100 kb resolution. The compartments with higher gene density were assigned as type A, while the compartments with lower gene density were assigned as type B. Compartment strength was calculated using AB / AA + BB. Saddle plots were calculated as previously described. Hi-C matrix bins were sorted according to the PC1 values. Sorted frequencies were aggregated into 50 groups and averaged to obtain a compartmentalization saddle plot. Number of ATAC-seq peaks overlapped with compartments were analyzed by BEDtools with at least 1bp shared.
TADs and TAD boundaries were identified at 50 kb resolution as described. Shared TADs between different samples were defined as overlapping area larger than 75% for both samples. We calculated the standard deviations of the insulation score of each TAD boundary across three-cell stages and sorted boundaries by standard deviations. Then the top 1000 variable TAD boundaries were selected based on the ranking order. Clustering of boundaries was carried out using Pheatmap package in R.
Loops and interactions were detected with HiCCUPS in Juicer Tools at 10 kb resolution. Enhancer or promoter involved loops were those with at least one anchor overlapped with enhancer regions (distal H3K27ac ChIP-seq peaks) or promoter regions (TSS ± 3 kb). Enhancer–promoter (E–P), promoter–promoter (P–P), and enhancer–enhancer (E–E) interactions were also identifed. Shared loops were defined as loops with both anchors not shift more than one bin. Aggregate peak analysis was processed with ‘apa’ in Juicer Tools, which generated aggregate heatmaps and average contact signals.
Assembly: GRCz10
Supplementary files format and content: ValidPairs.txt

organism: Danio rerio

source_name: hematopoietic stem cell

extract_protocol:
Cells sorted by FACS were fixed with freshly made 1% formaldehyde solution at room temperature for 10 min. 1.25M glycine solution was added to a final concentration of 0.2 M for quenching the reaction. Cells were lysed in ice-cold Hi-C lysis buffer (10 mM Tris-HCl pH 8.0, 10 mM NaCl, 0.2% Igepal CA630, 1x protease inhibitor cocktail) for 15 min. Pelleted nuclei were washed once with 1x NEBuffer 2 and incubated in 0.5% sodium dodecyl sulfate (SDS) at 62°C for 5 min. After incubating, water and Triton X-100 were added to quench the SDS. MboI restriction enzyme (NEB, R0147M) was added and chromatin was digested at 37°C for 5 hr.
Cells were fixed with 1% formaldehyde and lysed in ice-cold Hi-C lysis buffer (10 mM Tris-HCl pH 8.0, 10 mM NaCl, 0.2% Igepal CA630, 1x protease inhibitor cocktail) for 15 min. Pelleted nuclei were incubated in 0.5% sodium dodecyl sulfate at 62°C for 5 min. MboI restriction enzyme was added and chromatin was digested at 37°C for 5 hr. Biotin-14-dATP was used to mark the DNA ends followed by proximity ligation in intact nuclei. After crosslink reversal, DNA was sheared to a length of about 300 bp with Covaris M220. Biotin-labeled fragments were pulled down using Dynabeads MyOne Streptavidin C1 beads. The Hi-C libraries were amplified for 11-15 cycles with Q5 master mix following the operation manual. DNA was then purified and sequenced using NovaSeq platform.

value: hematopoietic stem cell

value: flow cytometry