description:
lab: Christine Disteche, UW
award: 1U54DK107979-01
4DN accession: 4DNEXK2CP3J1, 4DNEXU9FJ24U
description: 4DNEXK2CP3J1 - sci-Hi-C on a differentiation time course of F121-6 cells - this experiment is undifferentiated day 0 cells and to obtain reads specific for these cells the label F121_d0 from the barcode file(s) 4DNFI8WQR5EV should be used in parsing the associated FASTQs
4DNEXU9FJ24U - sci-Hi-C on a differentiation time course of F123 cells - this experiment is undifferentiated day 0 cells and to obtain reads specific for these cells the label F123_d0 from the barcode file(s) 4DNFI8WQR5EV should be used in parsing the associated FASTQs
submitted_by: Giancarlo Bonora
ligation_time: 240
digestion_time: 960
tagging_method: Biotin-dT
experiment_type: sci-Hi-C
ligation_volume: 0.3
digestion_enzyme: DpnII
contributing_labs: William Noble, UW, Zhijun Duan, UW, Jay Ashok Shendure, UW
crosslinking_time: 10
biosample_quantity: 10000000 cells
crosslinking_method: 3.5% Formaldehyde
fragment_size_range: 350-800
ligation_temperature: 22
average_fragment_size: 296
digestion_temperature: 37
crosslinking_temperature: 22
url: https://data.4dnucleome.org/experiments-hi-c/4DNEXK2CP3J1/ https://data.4dnucleome.org/experiments-hi-c/4DNEXU9FJ24U/
This record includes combined data from multiple BioSamples: SAMN21435439, SAMN21435432

data_processing:
See the file "TREE.sci-Hi-C.txt" for an overview of the folders and files described herein.

Sci-Hi-C libraries were processed using a publicly available pipeline (Ramani V. et al. Massively multiplex single-cell Hi-C. Nat Methods. 2017;14:263–6), which was adapted to process allelically segregated reads. Reads were aligned to an N-masked C57BL6/J reference genome (mm10) where every SNP locus (129 or cast for the F123, F121, and ES_Tsix-stop cell lines; B6 or spret for the Patski cell line) was substituted with an N to reduce mapping bias. The pipeline resulted in lists of contact pairs for all cells with at least 1,000 uniquely mapped contact pairs, a cis:trans ratio ≥1 and ≥95% of reads mapping to either the mouse or human genome (see manuscript Additional file 1: Table S1).

Contact matrices for the mouse genome were generated from the valid pairs by summing counts within bins of a specified size (e.g. 500kb). To obtain allelic information, each valid contact pair was segregated to its parental allele of origin if either end of the read pair contained at least one SNP particular to one of the parental strains. SNPs were based on Sanger data for mouse strain 129 and mouse species M. spretus and M. castaneus, compared to the mm10 B6 reference assembly. Read pairs containing no SNPs or containing SNPs belonging to both parental strains could not be unambiguously assigned to a single allele and were discarded.

Contact decay profiles (CDPs)
-----------------------------
Contact decay profiles (CDPs) for each cell were generated by summing the intrachromosomal contact counts with respect to contact distance within exponentially increasing contact distance ranges, as described in the manuscript (Additional file 1: Fig. S2A). Specifically, bin boundaries corresponded to the series of distances 2x to 2(x+1) for x within the range [10; 27.750] incrementing by a step size of 0.125. For each cell, counts within the 143 bins were scale normalized to account for coverage differences between cells.

Matrices of non-allelic CDPs were generated for each cell type and time point, with each column being a cell and each row a distance range. These matrices are contained within the folder "non-allelic_contact_decay_profiles" with matrices of CDPs for both genome-wide CDPs (e.g. "EBdiff_F121_d0.logbinContactDecay.mm10.txt.gz" and autosome-only CDPs ("EBdiff_F121_d0.autosomes.logbinContactDecay.mm10.txt.gz).

Matrices of allelic CDPs were generated for each chromosome, as well as genome-wide, for each cell type and time point, with each column being a cell and each row a distance range. These matrices are contained within the folder "allelic_contact_decay_profiles" with subfolders for each chromosome (e.g. "allelic_contact_decay_profiles/allelicContactDecayData.chr1/EBdiff_F121_d0.alt.chr1.logbinContactDecay.mm10.txt.gz") and genome-wide allelic CDPs ("allelic_contact_decay_profiles/allelicContactDecayData.genome/EBdiff_F121_d0.alt.logbinContactDecay.mm10.txt.gz").

The allelic CDPs for each chromosome were concatenated together for allelic trajectory analysis and topic modeling. Only cells with a total contact count at least 50 along both chr1 and chrX were included. The resulting CDP count matrices are saved to the folder "allelic_catenated_contact_decay_profiles" with one file per chromosome (e.g. "allelicContactDecayRates.catenatedAllelicCDPs.F121.chr1.tsv.gz").

Cell cycle analysis

-------------------
For cell cycle analysis, the cells were grouped into four clusters by k-means clustering using the Spearman correlation distance between the non-allelic CDPs aggregated across all autosomes within the 50kb to 8Mb range for each cell. The four clusters correspond to cells in different stages of the cell cycle progressing from mitosis into different stages of interphase. The cell cycle cluster groups of each cell are stored in the folder "autosomal_non-allelic_cell_cycle_cluster_ids" with one file for each cell type and time point "20191105_sciHiC_allSamples_Nmasked.EBdiff_F121_d0.countThresh1000.autosomalCDPs.50kb-8Mb.prop.kclust.disteuclidean.kCenters4.tsv." The files simply contain cell IDs and cluster IDs, e.g.
"mES_EBdiff_D0_rep1-AACGGTCG.AATCAGAG": 3
"mES_EBdiff_D0_rep1-AACGGTCG.ACTCTACG": 2
"mES_EBdiff_D0_rep1-AACGGTCG.ACTGCTAC": 3
...

Long-range to mid-range difference (LMD)
----------------------------------------

To determine which chrX homolog had acquired a 3D structure characteristic of the Xi in cells such as F121 cells, where XCI is only partially skewed during differentiation, the difference between the total long-range (6.5Mb – 87Mb) and mid-range (85kb – 1.1Mb) contact counts was assessed for each homolog of each cell, referred to hereafter as the long-range to mid-range difference (LMD). The difference between the resulting allelic LMDs for each homolog was calculated for each chromosome of every cell with sufficient coverage. A large LMD difference between the rebinned CDPs of chrX homologs A and B, say, is indicative of the fact that homolog A has assumed the Xi 3D structure. A threshold value (𝛿Xi) was chosen based on a 10% FPR using the distribution of LMD differences between the rebinned allelic CDPs of the chr1 homologs, which would be expected to show little difference in their LMDs. Cells with an absolute LMD difference between the rebinned allelic CDPs of the chrX homologs greater than 𝛿Xi were deemed to have an chrX homolog that had assumed the Xi 3D structure and the homolog with the higher LMD was classified as the Xi. The Xi status of each cell of each cell type and time point is saved in "LMD_XCI_cells_countthresh50" folder. For example, "F121_d11.altXCIcells.tsv" contains the cell IDs of d11 F121 cells that have an inactive castaneus chromosome, "F121_d11.refXCIcells.tsv" contains the cell IDs of d11 F121 cells that have an inactive 129 chromosome, and "F121_d11.nonXCIcells.tsv" contains the cell IDs of d11 F121 cells where XCI status could be confidently assigned to either X chromosome.

***************
file name: 4DNFI8WQR5EV.txt
genome_assembly: GRCm38
description: Bar codes (B1) used for selection of specific reads in the following Disteche Lab sci-HiC experiments with experiment selection tag in parens: 4DNEXK2CP3J1 (F121_d0), 4DNEXU9FJ24U (F123_d0)
file_type: barcodes
file_format: txt

source_name: Multiple biosources: F121-6-CASTx129, F123-CASTx129

value: Day 0 F121-6 or F123 cells from an embryoid body differentiaton time course experiment C

value: stem cell

value: stem cells


title: H9_D6_Veh-3

status: Public on Oct 21 2021

type: SRA

city: New Haven

first: Fabio

middle: R.

last: Santori

state: CT

address: Yale University Immunobiology Department TAC BLDG RM S640, 300 Cedar Street

department: Immunobiology

country: USA

institute: Yale University

description: WT H9 Cardiomyocytes vehicle treated day 6 rep2

library_source: transcriptomic

data_processing:
Demultiplexing and base calling was performed using Illumina's CASAVA 1.8.2 software suite.
Untrimmed FASTA files were mapped with Salmon (version 0.8.2) using GENECODE version 38 (GRCh38.p12) reference transcriptome.
DeSeq2 package was used to determine differential expression between samples
Data was processed on the Galaxy server (https://usegalaxy.org/).
Genome_build: Gencode.v29
Supplementary_files_format_and_content: Tab delimited matrix tables with Ensembl ID, Length, Effective length, TPM and Number of reads for every transcript in each sample
Supplementary_files_format_and_content: Tab delimited matrix table with TPM values for every gene and every sample
Supplementary_files_format_and_content: Tab delimited transcript to gene conversion table

molecule: polyA RNA

organism: Homo sapiens

source_name: Cardiomyocyte

growth_protocol: Cardiomyocyte differentiation was performed as described in (Burridge et al., 2014; Lian et al., 2013). Single cell suspensions of human ESC were prepared and plated for 24 hours onto Matrigel-coated 12-well tissue culture plates. Differentiation was initiated by culturing ESCs in RPMI-1640 medium supplemented with Insulin-free B-27 and CHIR99021 inhibitor for 48 hours followed by 24-hour culture in Insulin-free RPMI/B27 medium without inhibitor. 72 hours after addition of CHIR99021, cells were switched into the Insulin-free RPMI/B27 supplemented with IWP2 inhibitor. The media was replaced for the Insulin-free RPMI/B27 medium without inhibitor at day 5. On day 7 of differentiation media was replaced for fresh Insulin-containing RPMI/B27 medium and changed every two days.

extract_protocol:
Total RNA was isolated using Trizol Reagent, treated with DNAse I to remove genomic DNA, precipitated, washed with 70% ethanol and dissolved in water.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: for myriocin treated samples: myriocin was added at day 1 of differentiation process, for vehicle, 1-deoxysphingosine, D-erythro-sphingosine and doxycycline plus conditions, the tretament was started at day 3 of differentiation process

tag: cell type

value: ES-derived cardiomyocytes

tag: cell line

value: H9 human embryonic stem cells NIHhESC-10-0062

tag: genotype

value: WT

tag: treatmant

value: Vehicle


title: 4DNEX1BY7H2C (F123_d7), 4DNEXCDN76F9 (TsixStop_d7), 4DNEXJ33QCZU (TsixStop_d0), 4DNEXMYV77X1 (F121_d7)

city: Boston

last: DCIC

state: MA

address: 10 Shattuck St

institute: 4D Nucleome - Data Coordination and Integration Center

description:
lab: Christine Disteche, UW
award: 1U54DK107979-01
4DN accession: 4DNEX1BY7H2C, 4DNEXCDN76F9, 4DNEXJ33QCZU, 4DNEXMYV77X1
description: 4DNEX1BY7H2C - sci-Hi-C on a differentiation time course of F123 cells - this experiment is day 7 EB cells and to obtain reads specific for these cells the label F123_d7 from the barcode file(s) 4DNFIZXLPFWV should be used in parsing the associated FASTQs
4DNEXCDN76F9 - sci-Hi-C on a differentiation time course of ES_Tsix-stop cells - this experiment is day 7 EB cells and to obtain reads specific for these cells the label TsixStop_d7 from the barcode file(s) 4DNFIZXLPFWV should be used in parsing the associated FASTQs
4DNEXJ33QCZU - sci-Hi-C on a differentiation time course of ES_Tsix-stop cells - this experiment is undifferentiated day 0 cells and to obtain reads specific for these cells the label TsixStop_d0 from the barcode file(s) 4DNFIZXLPFWV should be used in parsing the associated FASTQs
4DNEXMYV77X1 - sci-Hi-C on a differentiation time course of F121-6 cells - this experiment is day 7 EB cells and to obtain reads specific for these cells the label F121_d7 from the barcode file(s) 4DNFIZXLPFWV should be used in parsing the associated FASTQs
submitted_by: Giancarlo Bonora
ligation_time: 240
digestion_time: 960
tagging_method: Biotin-dT
experiment_type: sci-Hi-C
ligation_volume: 0.3
digestion_enzyme: DpnII
contributing_labs: William Noble, UW, Zhijun Duan, UW, Jay Ashok Shendure, UW
crosslinking_time: 10
biosample_quantity: 10000000 cells
crosslinking_method: 3.5% Formaldehyde
fragment_size_range: 350-800
ligation_temperature: 22
average_fragment_size: 296
digestion_temperature: 37
crosslinking_temperature: 22
url: https://data.4dnucleome.org/experiments-hi-c/4DNEX1BY7H2C/ https://data.4dnucleome.org/experiments-hi-c/4DNEXCDN76F9/ https://data.4dnucleome.org/experiments-hi-c/4DNEXJ33QCZU/ https://data.4dnucleome.org/experiments-hi-c/4DNEXMYV77X1/
This record includes combined data from multiple BioSamples: SAMN21435442, SAMN21435440, SAMN21435435, SAMN21435459

library_source: genomic

data_processing:
See the file "TREE.sci-Hi-C.txt" for an overview of the folders and files described herein.

Sci-Hi-C libraries were processed using a publicly available pipeline (Ramani V. et al. Massively multiplex single-cell Hi-C. Nat Methods. 2017;14:263–6), which was adapted to process allelically segregated reads. Reads were aligned to an N-masked C57BL6/J reference genome (mm10) where every SNP locus (129 or cast for the F123, F121, and ES_Tsix-stop cell lines; B6 or spret for the Patski cell line) was substituted with an N to reduce mapping bias. The pipeline resulted in lists of contact pairs for all cells with at least 1,000 uniquely mapped contact pairs, a cis:trans ratio ≥1 and ≥95% of reads mapping to either the mouse or human genome (see manuscript Additional file 1: Table S1).

Contact matrices for the mouse genome were generated from the valid pairs by summing counts within bins of a specified size (e.g. 500kb). To obtain allelic information, each valid contact pair was segregated to its parental allele of origin if either end of the read pair contained at least one SNP particular to one of the parental strains. SNPs were based on Sanger data for mouse strain 129 and mouse species M. spretus and M. castaneus, compared to the mm10 B6 reference assembly. Read pairs containing no SNPs or containing SNPs belonging to both parental strains could not be unambiguously assigned to a single allele and were discarded.

Contact decay profiles (CDPs)
-----------------------------
Contact decay profiles (CDPs) for each cell were generated by summing the intrachromosomal contact counts with respect to contact distance within exponentially increasing contact distance ranges, as described in the manuscript (Additional file 1: Fig. S2A). Specifically, bin boundaries corresponded to the series of distances 2x to 2(x+1) for x within the range [10; 27.750] incrementing by a step size of 0.125. For each cell, counts within the 143 bins were scale normalized to account for coverage differences between cells.

Matrices of non-allelic CDPs were generated for each cell type and time point, with each column being a cell and each row a distance range. These matrices are contained within the folder "non-allelic_contact_decay_profiles" with matrices of CDPs for both genome-wide CDPs (e.g. "EBdiff_F121_d0.logbinContactDecay.mm10.txt.gz" and autosome-only CDPs ("EBdiff_F121_d0.autosomes.logbinContactDecay.mm10.txt.gz).

Matrices of allelic CDPs were generated for each chromosome, as well as genome-wide, for each cell type and time point, with each column being a cell and each row a distance range. These matrices are contained within the folder "allelic_contact_decay_profiles" with subfolders for each chromosome (e.g. "allelic_contact_decay_profiles/allelicContactDecayData.chr1/EBdiff_F121_d0.alt.chr1.logbinContactDecay.mm10.txt.gz") and genome-wide allelic CDPs ("allelic_contact_decay_profiles/allelicContactDecayData.genome/EBdiff_F121_d0.alt.logbinContactDecay.mm10.txt.gz").

The allelic CDPs for each chromosome were concatenated together for allelic trajectory analysis and topic modeling. Only cells with a total contact count at least 50 along both chr1 and chrX were included. The resulting CDP count matrices are saved to the folder "allelic_catenated_contact_decay_profiles" with one file per chromosome (e.g. "allelicContactDecayRates.catenatedAllelicCDPs.F121.chr1.tsv.gz").

Cell cycle analysis

-------------------
For cell cycle analysis, the cells were grouped into four clusters by k-means clustering using the Spearman correlation distance between the non-allelic CDPs aggregated across all autosomes within the 50kb to 8Mb range for each cell. The four clusters correspond to cells in different stages of the cell cycle progressing from mitosis into different stages of interphase. The cell cycle cluster groups of each cell are stored in the folder "autosomal_non-allelic_cell_cycle_cluster_ids" with one file for each cell type and time point "20191105_sciHiC_allSamples_Nmasked.EBdiff_F121_d0.countThresh1000.autosomalCDPs.50kb-8Mb.prop.kclust.disteuclidean.kCenters4.tsv." The files simply contain cell IDs and cluster IDs, e.g.
"mES_EBdiff_D0_rep1-AACGGTCG.AATCAGAG": 3
"mES_EBdiff_D0_rep1-AACGGTCG.ACTCTACG": 2
"mES_EBdiff_D0_rep1-AACGGTCG.ACTGCTAC": 3
...

Long-range to mid-range difference (LMD)
----------------------------------------

To determine which chrX homolog had acquired a 3D structure characteristic of the Xi in cells such as F121 cells, where XCI is only partially skewed during differentiation, the difference between the total long-range (6.5Mb – 87Mb) and mid-range (85kb – 1.1Mb) contact counts was assessed for each homolog of each cell, referred to hereafter as the long-range to mid-range difference (LMD). The difference between the resulting allelic LMDs for each homolog was calculated for each chromosome of every cell with sufficient coverage. A large LMD difference between the rebinned CDPs of chrX homologs A and B, say, is indicative of the fact that homolog A has assumed the Xi 3D structure. A threshold value (𝛿Xi) was chosen based on a 10% FPR using the distribution of LMD differences between the rebinned allelic CDPs of the chr1 homologs, which would be expected to show little difference in their LMDs. Cells with an absolute LMD difference between the rebinned allelic CDPs of the chrX homologs greater than 𝛿Xi were deemed to have an chrX homolog that had assumed the Xi 3D structure and the homolog with the higher LMD was classified as the Xi. The Xi status of each cell of each cell type and time point is saved in "LMD_XCI_cells_countthresh50" folder. For example, "F121_d11.altXCIcells.tsv" contains the cell IDs of d11 F121 cells that have an inactive castaneus chromosome, "F121_d11.refXCIcells.tsv" contains the cell IDs of d11 F121 cells that have an inactive 129 chromosome, and "F121_d11.nonXCIcells.tsv" contains the cell IDs of d11 F121 cells where XCI status could be confidently assigned to either X chromosome.

***************
file name: 4DNFIZXLPFWV.txt
genome_assembly: GRCm38
description: Bar codes (B2) used for selection of specific reads in the following Disteche Lab sci-HiC experiments with experiment selection tag in parens: 4DNEXMYV77X1 (F121_d7), 4DNEX1BY7H2C (F123_d7), 4DNEXJ33QCZU (TsixStop_d0), 4DNEXCDN76F9 (TsixStop_d7)
file_type: barcodes
file_format: txt

molecule: genomic DNA

organism: Mus musculus

source_name: Multiple biosources: undifferentiated ES_Tsix-stop cells, or F123-CASTx129, ES_Tsix-stop, F121-6-CASTx129 cells differentiated to embryoid body

extract_protocol:
url: https://www.ncbi.nlm.nih.gov/pubmed/31536770
description: This is the updated protocol for single-cell combinatorial indexed Hi-C (sci-Hi-C) from Ramani et al. 2020.

value: 129/Sv X Cast

tag: Sex

value: pooled male and female

tag: description

value: Day 7 F123, day 7 ES_Tsix-stop, day 0 ES_Tsix-stop, or day 7 F121-6 cells from an embryoid body differentiaton time course experiment C

value: stem cell or embryoid body

value: stem cells or in vitro differentiated cells

tag: url


title: W2 ATAC-seq rep2

city: Norfolk

first: Sanjeeva

middle: Reddy

last: Dodlapati

state: VA

address: E&CS, odu

department: Computer Science

institute: old dominion university

data_processing:
RNA-seq reads that passed filters were trimmed to remove low-quality reads and adaptors by TrimGalore-0.6.
The quality of reads after filtering was assessed by fastQC, followed by alignment to the mouse genome (MM10) by STAR (2.5.3a) with default parameters.
Individual mapped reads were adjusted to provide TPM (transcripts per million) values with mouse genome as the reference.
Differential gene expression analysis was done using DESeq2 17 and OneStopRNAseq.
ATAC-seq reads of all samples underwent adapter removal using TrimGalore-0.6, followed by quality assessment using FastQC. Reads were then aligned to the mouse reference genome MM10 using Bowtie 2.3 with the following options: – very-sensitive -X 2000 – no-mixed – no- discordant. Only unique alignments within each sample were retained in subsequent analysis. Macs2 was used to call peaks with following options: --nolambda --nomodel.
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: narrowPeak
Supplementary_files_format_and_content: count.gene.csv

source_name: Heart

growth_protocol: In vivo

extract_protocol:
Heart tissue samples were minced and digested in DMEM containing 0.75U/ml Collagenase D (Roche 11088866001), 1.0U/ml Dispase II (Roche 10165859001), and 1 mM CaCl2 at 37oC for 40 min. The slurry was then passed through a 100-μm cell strainer and then a 40-μm cell strainer. Cells were collected by centrifugation at 350 × g for 10 min. The cell pellet was then resuspended in PBS. Tcf21 lineage-traced eGFP+ cardiac fibroblasts were sorted on FACSaria II (BD Biosciences). Gates were made based on WT eGFP- control. Sorted eGFP+ cardiac fibroblasts were used for RNA-seq and ATAC-seq analyses.
RNA was extracted from 10,000 FACS-sorted Tcf21 lineage-traced fibroblasts using the miRNeasy Micro Kit (217084) from Qiagen. cDNA libraries were constructed using the NEBNext single cell/low input RNA library prep kit for Illumina (E6420. Tagmentated DNA was purified using MinElute Reaction Cleanup Kit (Qiagen).
FACS-sorted Tcf21 lineage-traced fibroblasts were lysed to isolated the nuclei. Isolated nuclei were then incubated with the Tn5 transposase (TDE1, Illumina) and tagmentation buffer at 37°C for 30 minutes with shaking on a thermomixer at 500 g. Tagmentated DNA was purified using MinElute Reaction Cleanup Kit (Qiagen). PCR was performed to amplify the ATAC-seq libraries using Illumina TruSeq primers and multiplex by indexes primers. After the PCR reaction, libraries were purified with the 1.1X AMPure beads (Beckman). The concentration of the sequencing libraries was determined by using Qubit dsDNA HS Assay Kit.

treatment_protocol: To induce the activity of the MerCreMer, mice were treated with tamoxifen (Sigma T5648) dissolved in corn oil through intraperitoneal (IP) injections at a dosage of 75 mg/kg body weight/day for 5 days.

value: Cardiac fibroblasts

tag: condition

value: Myocardial infarction

tag: time point


title: DKO_D6_Veh-2

description: DKO H9 Cardiomyocytes vehicle treated day 6 rep2


title: DKO_D6_Myr-3

description: DKO H9 Cardiomyocytes myriocin treated day 6 rep2

value: myriocin treated


title: H9_D6_Veh-1

description: WT H9 Cardiomyocytes vehicle treated day 6 rep1


title: DKO_D9_Veh-2

description: DKO H9 Cardiomyocytes vehicle treated day 9 rep2


title: DKO_D9_Deoxy-1

description: DKO H9 Cardiomyocytes 1-deoxysphingosine treated day 9 rep1


title: DKO_D6_Myr-1

description: DKO H9 Cardiomyocytes myriocin treated day 6 rep1


title: DKO_D9_Veh-1

description: DKO H9 Cardiomyocytes vehicle treated day 9 rep1


title: H9_D6_Myr-2

description: WT H9 Cardiomyocytes myriocin treated day 6 rep2


title: W2 ATAC-seq rep1


title: Pedi-I-294: MISC 10

city: Los Angeles

first: Rebecca

middle: Amelia

last: Porritt

state: CA

address: 8700 Beverly Blvd

department: Pediatrics

institute: Cedars Sinai

data_processing:
Raw sequencing data was demultiplexed and converted to fastq format by using bcl2fastq v2.20
Raw reads from fastq files were aligned to genome GRCh37-lite using STAR. Output were BAM files sorted by coordinates and tables with reads per gene. In RStudio, all tables for all samples were consolidated to one. Rlog normalization was performed using DEseq2.
Genome_build: GRCh37
Supplementary_files_format_and_content: Matrix table with counts

molecule: total RNA

source_name: Whole blood

extract_protocol:
RNA was extracted with the PAXgene Blood RNA kit
RNA libraries were prepared for sequencing using SMARTer Stranded Total RNA-Seq Kit v3 – Pico Input Mammalian kit

tag: disease state

value: Multisystem Inflammatory Syndrome in Children (MISC)

tag: tissue

value: Whole blood


title: H9_D6_Myr-1

description: WT H9 Cardiomyocytes myriocin treated day 6 rep1


title: DKO_D6_Veh-1

description: DKO H9 Cardiomyocytes vehicle treated day 6 rep1


title: Pedi-I-328: MISC 12


title: Pedi-I-282: MISC 8


title: 4DNEXLCFXRUP (F123_d20), 4DNEXOA4DNR8 (TsixStop_d20), 4DNEXTJOSWTW (F121_d20)

description:
lab: Christine Disteche, UW
award: 1U54DK107979-01
4DN accession: 4DNEXLCFXRUP, 4DNEXOA4DNR8, 4DNEXTJOSWTW
description: 4DNEXLCFXRUP - sci-Hi-C on a differentiation time course of F123 cells - this experiment is day 20 EB cells and to obtain reads specific for these cells the label F123_d20 from the barcode file(s) 4DNFIHGN8HST should be used in parsing the associated FASTQs
4DNEXOA4DNR8 - sci-Hi-C on a differentiation time course of ES_Tsix-stop cells - this experiment is day 20 EB cells and to obtain reads specific for these cells the label TsixStop_d20 from the barcode file(s) 4DNFIHGN8HST should be used in parsing the associated FASTQs
4DNEXTJOSWTW - sci-Hi-C on a differentiation time course of F121-6 cells - this experiment is day 20 EB cells and to obtain reads specific for these cells the label F121_d20 from the barcode file(s) 4DNFIHGN8HST should be used in parsing the associated FASTQs
submitted_by: Giancarlo Bonora
ligation_time: 240
digestion_time: 960
tagging_method: Biotin-dT
experiment_type: sci-Hi-C
ligation_volume: 0.3
digestion_enzyme: DpnII
contributing_labs: William Noble, UW, Zhijun Duan, UW, Jay Ashok Shendure, UW
crosslinking_time: 10
biosample_quantity: 10000000 cells
crosslinking_method: 3.5% Formaldehyde
fragment_size_range: 350-800
ligation_temperature: 22
average_fragment_size: 296
digestion_temperature: 37
crosslinking_temperature: 22
url: https://data.4dnucleome.org/experiments-hi-c/4DNEXLCFXRUP/ https://data.4dnucleome.org/experiments-hi-c/4DNEXOA4DNR8/ https://data.4dnucleome.org/experiments-hi-c/4DNEXTJOSWTW/
This record includes combined data from multiple BioSamples: SAMN21435456, SAMN21435453, SAMN21435452

data_processing:
See the file "TREE.sci-Hi-C.txt" for an overview of the folders and files described herein.

Sci-Hi-C libraries were processed using a publicly available pipeline (Ramani V. et al. Massively multiplex single-cell Hi-C. Nat Methods. 2017;14:263–6), which was adapted to process allelically segregated reads. Reads were aligned to an N-masked C57BL6/J reference genome (mm10) where every SNP locus (129 or cast for the F123, F121, and ES_Tsix-stop cell lines; B6 or spret for the Patski cell line) was substituted with an N to reduce mapping bias. The pipeline resulted in lists of contact pairs for all cells with at least 1,000 uniquely mapped contact pairs, a cis:trans ratio ≥1 and ≥95% of reads mapping to either the mouse or human genome (see manuscript Additional file 1: Table S1).

Contact matrices for the mouse genome were generated from the valid pairs by summing counts within bins of a specified size (e.g. 500kb). To obtain allelic information, each valid contact pair was segregated to its parental allele of origin if either end of the read pair contained at least one SNP particular to one of the parental strains. SNPs were based on Sanger data for mouse strain 129 and mouse species M. spretus and M. castaneus, compared to the mm10 B6 reference assembly. Read pairs containing no SNPs or containing SNPs belonging to both parental strains could not be unambiguously assigned to a single allele and were discarded.

Contact decay profiles (CDPs)
-----------------------------
Contact decay profiles (CDPs) for each cell were generated by summing the intrachromosomal contact counts with respect to contact distance within exponentially increasing contact distance ranges, as described in the manuscript (Additional file 1: Fig. S2A). Specifically, bin boundaries corresponded to the series of distances 2x to 2(x+1) for x within the range [10; 27.750] incrementing by a step size of 0.125. For each cell, counts within the 143 bins were scale normalized to account for coverage differences between cells.

Matrices of non-allelic CDPs were generated for each cell type and time point, with each column being a cell and each row a distance range. These matrices are contained within the folder "non-allelic_contact_decay_profiles" with matrices of CDPs for both genome-wide CDPs (e.g. "EBdiff_F121_d0.logbinContactDecay.mm10.txt.gz" and autosome-only CDPs ("EBdiff_F121_d0.autosomes.logbinContactDecay.mm10.txt.gz).

Matrices of allelic CDPs were generated for each chromosome, as well as genome-wide, for each cell type and time point, with each column being a cell and each row a distance range. These matrices are contained within the folder "allelic_contact_decay_profiles" with subfolders for each chromosome (e.g. "allelic_contact_decay_profiles/allelicContactDecayData.chr1/EBdiff_F121_d0.alt.chr1.logbinContactDecay.mm10.txt.gz") and genome-wide allelic CDPs ("allelic_contact_decay_profiles/allelicContactDecayData.genome/EBdiff_F121_d0.alt.logbinContactDecay.mm10.txt.gz").

The allelic CDPs for each chromosome were concatenated together for allelic trajectory analysis and topic modeling. Only cells with a total contact count at least 50 along both chr1 and chrX were included. The resulting CDP count matrices are saved to the folder "allelic_catenated_contact_decay_profiles" with one file per chromosome (e.g. "allelicContactDecayRates.catenatedAllelicCDPs.F121.chr1.tsv.gz").

Cell cycle analysis

-------------------
For cell cycle analysis, the cells were grouped into four clusters by k-means clustering using the Spearman correlation distance between the non-allelic CDPs aggregated across all autosomes within the 50kb to 8Mb range for each cell. The four clusters correspond to cells in different stages of the cell cycle progressing from mitosis into different stages of interphase. The cell cycle cluster groups of each cell are stored in the folder "autosomal_non-allelic_cell_cycle_cluster_ids" with one file for each cell type and time point "20191105_sciHiC_allSamples_Nmasked.EBdiff_F121_d0.countThresh1000.autosomalCDPs.50kb-8Mb.prop.kclust.disteuclidean.kCenters4.tsv." The files simply contain cell IDs and cluster IDs, e.g.
"mES_EBdiff_D0_rep1-AACGGTCG.AATCAGAG": 3
"mES_EBdiff_D0_rep1-AACGGTCG.ACTCTACG": 2
"mES_EBdiff_D0_rep1-AACGGTCG.ACTGCTAC": 3
...

Long-range to mid-range difference (LMD)
----------------------------------------

To determine which chrX homolog had acquired a 3D structure characteristic of the Xi in cells such as F121 cells, where XCI is only partially skewed during differentiation, the difference between the total long-range (6.5Mb – 87Mb) and mid-range (85kb – 1.1Mb) contact counts was assessed for each homolog of each cell, referred to hereafter as the long-range to mid-range difference (LMD). The difference between the resulting allelic LMDs for each homolog was calculated for each chromosome of every cell with sufficient coverage. A large LMD difference between the rebinned CDPs of chrX homologs A and B, say, is indicative of the fact that homolog A has assumed the Xi 3D structure. A threshold value (𝛿Xi) was chosen based on a 10% FPR using the distribution of LMD differences between the rebinned allelic CDPs of the chr1 homologs, which would be expected to show little difference in their LMDs. Cells with an absolute LMD difference between the rebinned allelic CDPs of the chrX homologs greater than 𝛿Xi were deemed to have an chrX homolog that had assumed the Xi 3D structure and the homolog with the higher LMD was classified as the Xi. The Xi status of each cell of each cell type and time point is saved in "LMD_XCI_cells_countthresh50" folder. For example, "F121_d11.altXCIcells.tsv" contains the cell IDs of d11 F121 cells that have an inactive castaneus chromosome, "F121_d11.refXCIcells.tsv" contains the cell IDs of d11 F121 cells that have an inactive 129 chromosome, and "F121_d11.nonXCIcells.tsv" contains the cell IDs of d11 F121 cells where XCI status could be confidently assigned to either X chromosome.

***************
file name: 4DNFIHGN8HST.txt
genome_assembly: GRCm38
description: Bar codes (B3) used for selection of specific reads in the following Disteche Lab sci-HiC experiments with experiment selection tag in parens: 4DNEXTJOSWTW (F121_d20), 4DNEXLCFXRUP (F123_d20), 4DNEXOA4DNR8 (TsixStop_d20)
file_type: barcodes
file_format: txt

source_name: Multiple biosources: F123-CASTx129, ES_Tsix-stop, or F121-6-CASTx129 cells differentiated to embryoid body

value: Day 20 F123, ES_Tsix-stop or F121-6 cells from an embryoid body differentiaton time course experiment C

value: embryoid body

value: in vitro differentiated cells


title: D3 ATAC-seq rep1


title: D7 ATAC-seq rep1


title: D3 ATAC-seq rep2


title: Pedi-I-279: MISC 7


title: Pedi-I-287: MISC 9


title: D7 ATAC-seq rep2


title: W4 ATAC-seq rep2


title: W4 ATAC-seq rep1


title: Pedi-I-255: MISC 4


title: Pedi-I-276: MISC 6


title: Pedi-I-243: MISC 3


title: Uninj ATAC-seq rep2

value: Uninjured


title: Pedi-I-206: MISC 1


title: Uninj ATAC-seq rep1


title: Pedi-I-325: MISC 11


title: Pedi-R-257: Febrile control 13

value: Febrile control


title: shRNA CDK8.1830  Senexin B replicate 3

city: Vienna

first: Veronika

last: Sexl

address: Veterinaerplatz 1

department: Pharmacology / Toxikology

country: Austria

institute: University of Veterinary Medicine Vienna

description: expression profile of shCDK8-2 transduced and Senexin B treated E0771 triple negative breast cancer cell line, replicate 3

data_processing:
Alignment to genome version GRCm38 using STAR
Adapter trimming and removing of low quality bases was performed using Trimmomatic
Counting of reads was done using featureCounts
Genome_build: GRCm38/mm10
Supplementary_files_format_and_content: raw count file (tab delimited)

source_name: E0771 – Triple negative breast cancer cell line

growth_protocol: Cells were cultured in DMEM incl. 10% FCS,  100 U/ml penicillin, 100 µg/ml streptomycin, 50µM β-mercaptoethanol and 0.02M HEPES.

extract_protocol:
QIAGEN RNeasy extraction kit
RNA-seq: NEBNext Multiplex Oligos for Illumina (Dual Index Primers Set 1), 50 bp single-end

treatment_protocol: E0771 cells were incubated 48 hours with 1 µM Senexin B or DMSO as a control.

value: knockdown CDK8

tag: agent

value: Senexin B


title: Pedi-R-256: Febrile control 12


title: T_A_MDSC

city: Hefei

first: tingting

last: Yin

address: Daoxiang Village

country: China

institute: University of Science and Technology of China

data_processing:
Illunima Casava 1.8 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence,then mapped to mm9 whole genome using STAR 2.5.1b with parameters --genomeDir --readFilesIn  --outFileNamePrefix  --alignEndsType EndToEnd
Fragments per kilobase of exon model per million reads mapped (FPKM) were calculated from the number of reads that mapped to each particular gene sequence taking into account the gene length (one expects more reads to be produced from longer genes) and the sequencing depth (one expects more reads to be produced from the sample that has been sequenced to a greater depth)
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include raw counts, and tab-delimited text files include FPKM values for all Samples

source_name: Alisertib treated tumor bed

growth_protocol: BM-neu were derived from WT bone marrow; TA and TC MDSCs were derived from tumor

extract_protocol:
MDSCs from the tumors of Alisertib-treated or untreated mice and normal neutrophils from bone marrow of WT BALB/c mice were isolated by a FACSAria Cell Sorter.Purity of isolated MDSCs and neutrophils were greater than 90%. Total RNA were extracted using Trizol Reagent
RNA-Seq libraries were prepared using NEBNext Ultra RNA Library Prep Kit for Illumina (NEB, USA) following the manufacturer’s protocols.

tag: strain

value: BALB/c

tag: age

value: 6-8 week

value: female

value: Alisertib treated tumor bed

value: myeloid-derived suppressor cells (MDSCs)


title: Pedi-R-217: Febrile control 11


title: 334: Skin 14 days post injury

city: Bonn

first: Joachim

last: Schultze

state: NRW

address: Carl-Troll-Strasse 31

department: Genomics and Immunoregulation

country: Germany

institute: LIMES (Life and Medical Sciences Center Genomics and Immunoregulation)

description: Raw data was unavailable at the time of submission because the raw read files had been deleted

data_processing:
base calling and de-multipexing using CASAVA version 1.8
Alignment with HiSat2 version 2.1.0 and SAMtools version 1.4 using the default parameters
Quantification with Partek Genomics Suite V6.6
reads mapped to each transcript against the RefSeq mm10 annotation download on October 2015
Normalization using DeSeq2
Genome_build: mm10
Supplementary_files_format_and_content: comma separated files include DeSeq2 rlog counts for each Sample.

source_name: Skin wound tissue

growth_protocol: cell isolation protocol: Single-cell suspensions of wound tissue were prepared by a combination of enzymatic digestion (Liberase Blendzyme, Roche Applied Science) and mechanical disruption (Medimachine System, BD Biosciences) as previously described. Cells were passed through 70 µm and 40 µm cell strainer, and washed with PBS/1% BSA/2 mM EDTA. Fc receptors were blocked with mouse SeroBlock FcR (CD16/CD32; eBioscience) and cells were stained with FITC-conjugated anti-CD45 (eBioscience), APC-conjugated anti-CD11b (Miltenyi Biotec), and PE conjugated anti-F4/80 (Bio-Rad Laboratories), and allophycocyanin-conjugated anti-CD115 (eBioscience) in PBS/1% BSA/2 mM EDTA. Dead cells were excluded using 7 amino-actinomycin D (7-AAD) (BD Biosciences). Cells were sorted using a FACSAria III cell sorting system (BD), equipped with FACSDiva software (BD).

extract_protocol:
RNA was harvested using Trizol reagent. Total RNA was extracted according to the manufactures’ protocol and the precipitated RNA was solved in RNAse free water
Total RNA was converted into libraries of double stranded cDNA molecules as a template for high throughput sequencing following the manufacturer’s recommendations using the Illumina TruSeq RNA Sample Preparation Kit v2
cDNA libraries were quantified using KAPA Library Quantification Kits (Kapa Biosystems). After cluster generation on a cBot, a 2 × 100 bp paired-end run was performed on a HiSeq1500.

treatment_protocol: No treatment, after sorting cells were directly processed for RNAseq

tag: genetic background

value: C57BL/6J wild-type

value: 14 days post injury

tag: sorted cells


title: shRNA CDK8.1830  Senexin B replicate 2

description: expression profile of shCDK8-2 transduced and Senexin B treated E0771 triple negative breast cancer cell line, replicate 2


title: shRNA CDK8.1830  Senexin B replicate 1

description: expression profile of shCDK8-2 transduced and Senexin B treated E0771 triple negative breast cancer cell line, replicate 1


title: BM_Neu

source_name: Bone marrow neutrophils

value: Bone marrow

value: neutrophils


title: shRNA CDK8.1593  Senexin B replicate 3

description: expression profile of shCDK8-1 transduced and Senexin B treated E0771 triple negative breast cancer cell line, replicate 3


title: Pedi-R-117: Febrile control 10

value: Whole blood


title: Pedi-I-274: MISC 5

value: Multisystem Inflammatory Syndrome in Children (MISC)


title: 332: Skin 14 days post injury


title: 333: Skin 14 days post injury


title: miRNA-seq_Control 3

city: Zhengzhou

first: Shuheng

last: Yang

state: Henan

address: Zhengzhou, No. 7 Kangfuqian Street, Erqi

institute: Third Affiliated Hospital of Zhengzhou University

data_processing:
Basecalls performed using CASAVA version 1.8
The raw reads were pre-processed with fastx (fastx_toolkit-0.0.13.2) to remove splice sequences and low quality sequences (including fuzzy base N, sequences with base mass less than 10 and sequences less than 18nt in length) and to perform length distribution statistics.
CLC genomics_workbench 5.5 commercial software was used to compare the pre-processed sequences with the latest Sanger miRBase database
Differential expression were analysed  using DEGseq function package in R program version 2.10.0
For the analysis of variance, the TPM (Transcripts permillion, formula: number of single miRNA reads × 106/total number of reads) was used as normalized data.
Genome_build: miRBase database
Supplementary_files_format_and_content: tab-delimited text files include normalized Tpm values and counts for each Sample

source_name: placenta

extract_protocol:
mirVana RNA Isolation Kit (Cat #. AM1561, Austin TX, US)
miRNA libraries were prepared for sequencing using standard Illumina protocols

value: placenta


title: miRNA-seq_Control 2


title: Pedi-R-064: Febrile control 8


title: shRNA CDK8.1593  Senexin B replicate 1

description: expression profile of shCDK8-1 transduced and Senexin B treated E0771 triple negative breast cancer cell line, replicate 1


title: miRNA-seq_Control 1


title: Pedi-I-239: MISC 2


title: 331: Skin 14 days post injury


title: Pedi-R-050: Febrile control 7


title: T_C_MDSC

source_name: Control treated tumor bed

value: Control treated tumor bed


title: non-targeting shRNA Renilla  Senexin B replicate 3

description: expression profile of shRenilla transduced and Senexin B treated E0771 triple negative breast cancer cell line, replicate 3

value: knockdown Renilla


title: miRNA-seq_IVF-ET 3


title: Pedi-R-046: Febrile control 6

value: Febrile control


title: 330: Skin 14 days post injury


title: non-targeting shRNA Renilla  Senexin B replicate 2

description: expression profile of shRenilla transduced and Senexin B treated E0771 triple negative breast cancer cell line, replicate 2


title: 329: Skin 4 days post injury

value: 4 days post injury


title: miRNA-seq_IVF-ET 2


title: 328: Skin 4 days post injury


title: Pedi-R-024: Febrile control 4


title: Pedi-R-032: Febrile control 5


title: non-targeting shRNA Renilla  Senexin B replicate 1

description: expression profile of shRenilla transduced and Senexin B treated E0771 triple negative breast cancer cell line, replicate 1

value: Senexin B


title: shRNA CDK8.1830  DMSO replicate 3

description: expression profile of shCDK8-2 transduced and DMSO treated E0771 triple negative breast cancer cell line, replicate 3

value: knockdown CDK8

value: DMSO


title: miRNA-seq_IVF-ET 1


title: 327: Skin 4 days post injury


title: shRNA CDK8.1830  DMSO replicate 2

description: expression profile of shCDK8-2 transduced and DMSO treated E0771 triple negative breast cancer cell line, replicate 2


title: Pedi-R-067: Febrile control 9


title: Pedi-R-017: Febrile control 3


title: shRNA CDK8.1593  Senexin B replicate 2

description: expression profile of shCDK8-1 transduced and Senexin B treated E0771 triple negative breast cancer cell line, replicate 2


title: Pedi-R-015: Febrile control 2


title: Pedi-R-014: Febrile control 1


title: shRNA CDK8.1593  DMSO replicate 3

description: expression profile of shCDK8-1 transduced and DMSO treated E0771 triple negative breast cancer cell line, replicate 3


title: RNA-seq_Control 1

data_processing:
Basecalls performed using CASAVA version 1.8
Apply Seqtk filtering to Raw Reads from sequencing
Genome mapping of pre-processed reads using TopHat's (version:2.0.9) spliced mapping algorithm
Transformation of reads into FPKM (Fragments Per Kilobase of exon model per Million mapped reads) for gene expression normalization. Genetic quantification of tophat mapping results using cufflinks (version:2.2.1)
The cuffdiff was applied to perform between-sample differential genetic analysis, and the p-value was corrected for multiple hypothesis testing by controlling the False Discovery Rate (FDR) to determine the threshold for the p-value, the corrected p-value, and the differential expression multiplier was calculated from the FPKM value.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include normalized FPKM values and raw fragment counts for each Sample

extract_protocol:
mirVana RNA Isolation Kit (Cat #. AM1561, Austin TX, US)
RNA libraries were prepared for sequencing using standard Illumina protocols


title: GFP_targeted_Mouse_Liver_FACS

city: Pittsburgh

first: Leah

last: Byrne

state: PA

address: 3501 Fifth Avenue

department: Ophthalmology

institute: University of Pittsburgh

description:
10x targeted enrichment against GFP
GFP_targeted_cell_by_aav_mouse_L-F_liver_facs_results.csv
aav_barcode_key_mouse.txt

data_processing:
Sequencing data was demultiplexed into sample-level fastq files using Cell Ranger mkfastq (v3 10X Genomics).
Alignment and cell demultiplexing were run using STARsolo(14) (v2.7) with default parameters, creating raw count matrices.
The performance of AAV variants was analyzed based on quantification of AAV variant-mediated GFP-barcode mRNA expression. For non-human primates, AAV-barcodes were analyzed from (1) the original scRNA-seq data and (2) PCR amplification of GFP from the 10x single cell prepped sample library. Mouse samples were analyzed using AAV- barcodes from (1) the original scRNA-seq data and (2) targeted gene enrichment against GFP and other marker genes. Targeted gene enrichment samples from the mouse were downsampled to a similar number of reads as the non-human primate GFP PCR-amplified non-human primate samples. AAV-barcodes were identified using Salmon (v0.9.1) transcript quantification. Only reads with 1 hit to an AAV- barcode were kept. Using these reads, AAV variants were identified based on the AAV- barcode. 10x barcodes in the reads from the PCR amplification analysis were corrected according to the 10x Cell Ranger count algorithm to mitigate any errors that may have been introduced by multiple rounds of PCR. As each UMI (unique molecular identifier) represents a single mRNA molecule captured, only one AAV- barcode should exist for each UMI. Rarely, multiple AAV- barcodes were found per UMI – possibly due to sequencing/PCR-introduced errors – in which case the AAV variant with the highest number of counts for that UMI was kept.
Genome_build: Cynomolgus macaque samples were aligned to the Macaca_fascicularis_5.0/macFas5 reference obtained from UCSC and marmoset samples were aligned to ASM275486v1 obtained from Ensembl. Mouse samples were aligned to the GRCm38 reference GCA_000001635.5 from NCBI.
Supplementary_files_format_and_content: Matrix tables with raw gene expression counts for every cell; Cell-by-GFP tables with raw GFP-barcode expression counts

source_name: Mouse liver

extract_protocol:
The NHP retinas were dissected and regions of interest were isolated (macula, superior and inferior periphery). For cynomolgus macaque, superior and inferior periphery were pooled. Retinal tissue was placed in Hibernate solution (Hibernate A -Ca Solution, BrainBits LLC), and cells were then dissociated using Macs Miltenyi Biotec Neural Tissue Dissociation Kit for postnatal neurons (130-094-802) according to manufacturer’s recommendations. Dissected retina pieces were incubated with agitation at 37 °C and further mechanically dissociated. The dissociated neural retina was filtered using a 70 µm MACS Smart Strainer (Miltenyi Biotec) to ensure single-cell suspension. Cells were resuspended in 0.1% BSA in D-PBS and processed immediately for scRNA-seq. Brain, heart, and liver of mice were freshly dissected, and cells were dissociated using Macs Miltenyi Adult Brain Tissue Dissociation Kit (130-107-677), Multi Tissue Dissociation Kit 2 (130-110-203) and Liver Dissociation Kit (130-105-807) according to manufacturer’s recommendations. The cells were resuspended in 0.1% BSA in D-PBS and processed immediately for scRNA-seq. Following dissociation using Macs Miltenyi Tissue Dissociation Kits specific for retina, brain, heart and liver, a Miltenyi MACS Tyto sorter was used to enrich for GFP-positive cells. Cells were resuspended 0.1% BSA in D-PBS and processed immediately for scRNA-seq.
Marmoset and cynomolgus macaque samples were prepared for single cell analysis using a 10x Chromium Single Cell 3’ v3 kit. Briefly, single cells from retina samples were captured using 10X Chromium system (10X Genomics), the cells were partitioned into Gel beads-in-emulsion (GEMS), mRNAs were reverse transcribed and cDNAs with 10X Genomics Barcodes were created with unique molecular identifiers (UMIs) for different transcripts. Purified cDNA was PCR amplified and further purified with SPRIselect reagent (Beckman Coulter, B23318). Final libraries were generated after fragmentation, end repair, A-tailing, adaptor ligation, and sample index PCR steps according to 10x Single Cell 3’ workflow. An additional targeted sequencing analysis was run on these 10x-prepped cDNA samples, using PCR amplification with Q5 High Fidelity DNA Polymerase to target the GFP sequence and its associated AAV barcode. Samples from mouse tissues and cultured 293AAV (Cell Biolabs) cells were prepared for single cell analysis using a 10X Chromium Single Cell 3’ v3.1 kit. The resulting libraries were pooled, and an additional targeted gene enrichment protocol was performed using 10X Chromium Targeted Gene Expression kit.

treatment_protocol: Marmosets, cynomolgus macaques and rhesus macaques between 3-10 years and retinas were injected intravitreally with AAV libraries. Monkeys used for K912-scCAG-GFP fluorophore expression received daily oral doses of cyclosporine at a dose of 6 mg/kg for the duration of the study. Marmosets received oral daily doses of meloxicam (0.2 mg/kg) for one week after injection. C57BL/6J mice from Jackson Laboratories were used for mouse experiments. 50 uL of pooled AAV vector library was delivered by systemic injections via facial vein injection to P0 mice, which were anesthetized on ice. Tissues were collected 3 weeks after injection.

value: Liver

tag: sorting strategy

value: FACS-sorted


title: shRNA CDK8.1830  DMSO replicate 1

description: expression profile of shCDK8-2 transduced and DMSO treated E0771 triple negative breast cancer cell line, replicate 1


title: RNA-seq_Control 3


title: RNA-seq_IVF-ET 3


title: TIME, TNFa

city: Palo Alto

last: Richards

address: 1000 Welch Rd

institute: Stanford University

data_processing:
Base calling was performed with Illumina software.
Adapter sequences were trimmed and reads were aligned using Salmon v1.2.0 .
Transcript annotation was performed with tximeta v1.6.2.
Differentially expressed genes were identified using DESeq2 v1.28.1.
Genome_build: GRCh38.p13
Supplementary_files_format_and_content: TPMs

source_name: Endothelial cell line

growth_protocol: Cells were grown under standard conditions with supportive media and supplemental amino acids and growth factors.

extract_protocol:
Cells were harvested 24h after treatment and flash frozen on ice. RNA was harvested using QIAGEN RNEasy kit,  with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols
cDNA libraries derived from RNA samples were sequenced on Illumina NovaSeq 6000 platform, then BCL files were converted to FASTQ files using bcl2fastq software

treatment_protocol: Cells were either untreated or treated for 24h with IFNg, TNFa, or IFNg+TNFa. Cytokine concentrations were 10 ng/ml.

value: TIME

tag: cell type

value: Endothelial

value: TNFa 10 ng/ml - 24h


title: RNA-seq_Control 2


title: TIME, IFNg + TNFa

tag: cell line

value: IFNg 10 ng/ml + TNFa 10 ng/ml - 24h


title: shRNA CDK8.1593  DMSO replicate 2

description: expression profile of shCDK8-1 transduced and DMSO treated E0771 triple negative breast cancer cell line, replicate 2

tag: genotype


title: shRNA CDK8.1593  DMSO replicate 1

description: expression profile of shCDK8-1 transduced and DMSO treated E0771 triple negative breast cancer cell line, replicate 1


title: GFP_targeted_Mouse_Heart

description:
10x targeted enrichment against GFP
GFP_targeted_cell_by_aav_mouse_H_heart_results.csv
aav_barcode_key_mouse.txt

source_name: Mouse heart

value: Heart

value: unsorted


title: RNA-seq_IVF-ET 2


title: RNA-seq_IVF-ET 1


title: TIME, IFNg

value: IFNg 10 ng/ml - 24h


title: non-targeting shRNA Renilla  DMSO replicate 3

description: expression profile of shRenilla transduced and DMSO treated E0771 triple negative breast cancer cell line, replicate 3


title: non-targeting shRNA Renilla  DMSO replicate 2

description: expression profile of shRenilla transduced and DMSO treated E0771 triple negative breast cancer cell line, replicate 2


title: GFP_targeted_Mouse_Brain_FACS

description:
10x targeted enrichment against GFP
GFP_targeted_cell_by_aav_mouse_B-F_brain_facs_results.csv
aav_barcode_key_mouse.txt

source_name: Mouse brain cortex/hippocampus

value: Brain


title: TIME, Untreated

value: Untreated


title: SpeciesMix_eGFP_Known_Phage

city: New York

first: Caleb

last: Lareau

state: New York

address: 417 E 68th St, Zuckerman - ZRC 1132

institute: Memorial Sloan Kettering

description: Mix of human and mouse cell lines

data_processing:
Fastqs were generated using CellRanger-ATAC mkfastq v1.1.0
Sequencing reads were aligned using CellRanger-ATAC count for the hg38 and mm10 reference genomes
For Phage libraries, phage tag abundances were quantified per barcode using a custom unix script.
Genome_build: hg38 / mm10
Supplementary_files_format_and_content: Per-barcode count abundance for phage library including the ATAC singlecell QC metrics; accessible chromatin fragments per atac library

organism:
Homo sapiens
Mus musculus

source_name: Cell line

growth_protocol: DMEM, 10%FBS, Pen/Strep

extract_protocol:
NP40 lysis, see method sections for full details
Custom 10x Genomics scATAC-seq

treatment_protocol: Transfection using 4µg EGFP-GPI-encoding plasmid for HEK293T

tag: cell mixture

tag: ab treatment

value: Known GFP


title: GFP_targeted_Mouse_Liver

description:
10x targeted enrichment against GFP
GFP_targeted_cell_by_aav_mouse_L_liver_results.csv
aav_barcode_key_mouse.txt


title: SpeciesMix_eGFP_Known_ATAC

description: Mix of human and mouse cell lines


title: non-targeting shRNA Renilla  DMSO replicate 1

description: expression profile of shRenilla transduced and DMSO treated E0771 triple negative breast cancer cell line, replicate 1

value: knockdown Renilla


title: GFP_targeted_Mouse_Heart_FACS

description:
10x targeted enrichment against GFP
GFP_targeted_cell_by_aav_mouse_H-F_heart_facs_results.csv
aav_barcode_key_mouse.txt


title: WT_hCAST_288

first: Riki

last: Kawaguchi

address: 760 Westwood Plaza, Room 37-420

department: Department of Psychiatry and Neurology Department of Psychiatry

institute: University of California, Los Angeles

data_processing:
The generated reads were mapped to the mouse genome GRCm38 with aligner STAR with default parameter settings
Raw counts were obtained with HTSeq using refSeq gene model (mm10) as reference.  Only uniquely mapped reads were used for the subsequent analyses.
Genome_build: Genome version Mouse GRCm38
Supplementary_files_format_and_content: Counts and FPKM values for each sample

source_name: hCAST

extract_protocol:
Total RNA extracted using RNeasy Mini Kit, RNA integrity assessed using Agilent Bioanalyzer 2100
TruSeq with Ribo-Zero, NuGEN Ovation

value: FVB/NJ


title: iHUVEC, IFNg + TNFa

value: iHUVEC


title: 326: Skin 4 days post injury

description: Raw data was unavailable at the time of submission because the raw read files had been deleted

value: C57BL/6J wild-type

value: 4 days post injury


title: CS29-DIV-150-SampleA (2 slices)

city: Cambridge

first: Lea

middle: Marion Denise

last: Wenger

address: Robinson Way

department: Clinical Neurosciences

country: United Kingdom

institute: University of Cambridge

data_processing:
Samples were pooled together and sequenced on an Illumina HiSeq4000 RTA platform, and then converted to the standard fastq format by bcl2fastq. The "Cellranger count" code was run in CellRanger 3.1 using the GRCh38 human reference genome.
CellRanger detected 85% fraction reads on average per cell and 1,600 to 2,100 median genes per cell. Low quality ends were disregarded during the mapping process. Only reads that were uniquely mapped to the transcriptome were used for UMI counting in CellRanger.
Two samples, one from each control line (WT and EpiC), showed low level ambient RNA contamination and counts were re-run using the ‘force cells’ function. Cells of aberrant identity were further removed from one of the samples.
Data was processed in Seurat and filtered based on a minimum of three cells expressing each gene. Only those cells were included in the analysis that expressed 200-5,000 genes and in which the proportion of mitochondrial genes were below 25% out of all genes.
The data was normalised through Log normalisation using Seurat's NormalizeData function (scale factor of 10,000). For certain analyses, cells expressing a high proportion genes involved in glycolysis or cells with unresolved identity based on the transcriptomic signature were discarded.
Genome_build: GRCh38
Supplementary_files_format_and_content: CSV file containing the gene names as rows and the cell names as columns

source_name: induced pluripotent stem-cell-derived cerebral organoid

growth_protocol:
Induced pluripotent stem cell-derived cerebral organoids were generated and grown as slice cultures as described in Szebenyi et al., 2021.
Organoids were supplemented with serum-free slice culture medium (SFSCM): Neurobasal (Invitrogen, cat. #21103049), 1:50 (v/v) B27+A (Invitrogen, cat. #17504044), 0.5% (w/v) glucose, 1X (v/v) Glutamax supplemented with Antibiotic-Antimycotic (ThermoFisher, cat. #15240062). The cultures were maintained in SFSCM at 37 °C and 5% CO2 with daily media changes.

extract_protocol:
Dissociation of the slices was achieved by Accumax (Sigma, A7089) using the gentleMACS Octo Dissociator. The cell suspension was run through a 70μm strainer prior to processing through the 10X Genomics platform. scRNA-seq libraries were prepared for sequencing using the 10X Genomics Chromium Single Cell 3’ Library & Gel Bead Kit (10X Genomics, 120237) workflow.
The cell suspension was loaded onto a 10X Genomics Chromium Single Cell 3’ Chip with the appropriate amount of Mastermix. RNA extraction was performed following the same 10X Genomics Chromium workflow (Next GEM sequencing v3.0 for batch 1 and 3.1 for batch 2).
The reverse transcriptase reaction and subsequent amplification was carried out in a C1000 Touch Thermal Cycler (Biorad), with the cDNA being amplified for 12 cycles. Before sequencing, libraries were quality tested using the 2100 Bioanalyzer Instrument (Agilent) and their concentration was measured by qPCR.

tag: embryonic stem cell line

value: organoid

value: 150 days


title: CS29-DIV-150-SampleB (2 slices)


title: GFP_targeted_Mouse_Brain_1

description:
10x targeted enrichment against GFP
GFP_targeted_cell_by_aav_mouse_B1_brain_results.csv
aav_barcode_key_mouse.txt


title: Mouse_Liver_FACS

description:
mouse_barcodes.tsv
mouse_genes.tsv
aav_barcode_key_mouse.txt

value: Liver

value: FACS-sorted


title: ISO29-DIV-150-SampleB (2 slices)


title: WT_hCAST_282


title: Mouse_Liver


title: ISO29-DIV-150-SampleA (2 slices)


title: iHUVEC, IFNg

value: Endothelial


title: CS30-DIV-150-SampleB (2 slices)


title: THP-1, TNFa

source_name: AML cell line

value: AML

value: TNFa 10 ng/ml - 24h


title: WT_286

source_name: WT

value: WT


title: THP-1, IFNg + TNFa

value: IFNg 10 ng/ml + TNFa 10 ng/ml - 24h


title: WT_283


title: GFP_targeted_Mouse_Brain_2

description:
10x targeted enrichment against GFP
GFP_targeted_cell_by_aav_mouse_B2_brain_results.csv
aav_barcode_key_mouse.txt

value: Brain

value: unsorted


title: CS30-DIV-150-SampleA (2 slices)


title: Mouse_Heart

value: Heart


title: Mouse_Brain_FACS


title: Mouse_Brain_2


title: iHUVEC, TNFa


title: iHUVEC, Untreated

value: Untreated


title: WT_296

value: FVB/NJ


title: WT_hCAST_287


title: rTG_2782

source_name: rIAPP

value: rTG


title: NOMO-1, IFNg + TNFa


title: EpiC-DIV-150-SampleA (2 slices)


title: rTG_2781


title: NOMO-1, IFNg

value: IFNg 10 ng/ml - 24h


title: NOMO-1, TNFa


title: WTS42b-DIV-150-SampleB (2 slices)


title: WTS42b-DIV-150-SampleA (2 slices)


title: Mouse_Brain_1


title: hTG_hCAST_616


title: THP-1, Untreated


title: NGS192

city: Strasbourg

first: Thalia

last: Salinas-Giegé

address: 12 rue du général Zimmer

country: France

institute: CNRS

data_processing:
Adapter trimming with Trim-galore v 0.6.5
Mapping with Bowtie2 v2.4.1 with options : --end-to-end --very-sensitive -N 0 -L 22
BigWig file conversion with BamCoverage version 3.5.0 with CPM option
Genome_build: EU306622

organism: Chlamydomonas reinhardtii

source_name: RNA extracted from purified mitochondrial ribosome

extract_protocol:
Mitoribosome purification was conducted as previously (Waltz et al., 2019, 2020). The RNA  was prepared  using TRI Reagent® (Molecular Research Center) according to the manufacturer’s instructions.
The RNA was not fragmented but enzymatically treated with Antarctic Phosphatase and T4 Polynucleotide Kinase. We used the Truseq Stranded Total RNA with Ribozero Plant, reference guide #10000000404499v00 October 2017 for the NGS192-total library preparation and the NEBNext multiplex small RNA Library set for Illumina reference E7580 for the NGS192-small library preparation.

value: CC-4351 strain


title: rTG_2780


title: THP-1, IFNg


title: hTG_hCAST_597


title: p204

source_name: Total RNA extracted from mitochondria

extract_protocol:
Mitochondria purification was performed as in (Salinas et al. 2012) by digitonin treatment followed by a discontinuous Percoll gradient. The total RNA from mitochondria was prepared the RNA using TRI Reagent® (Molecular Research Center) according to the manufacturer’s instructions.
The RNA was first chemically fragmented (4 min) and then enzymatically treated with Antarctic Phosphatase (NEB#M0289S) and T4 Polynucleotide Kinase (NEB#M0201S). Library preparation was done according to the TruSeq Small RNA Sample Preparation Guide #15004197 Rev. F February 2014.

treatment_protocol: RNA extracted from purified mitochondria


title: EpiC-DIV-150-SampleB (2 slices)

value: organoid


title: hTG_617

source_name: hIAPP

value: hTG


title: HYR__789b3f__20200723_by_50um

city: Leuven

first: Stein

last: Aerts

state: Vlaams-Brabant

address: O&N4 Herestraat 49 PO Box 602

country: Belgium

institute: KU Leuven

data_processing:
For HyDrop-ATAC samples (prefix HYA): Barcode reads (read 2) were trimmed to exclude the intersub-barcode PCR adapters MAWK
For HyDrop-ATAC samples (prefix HYA): Barcode reads (read 2) were trimmed using trimgalore (trim_galore -j 2 -o . $R1 $R2 --paired --gzip), corrected to a whitelist allowing 1 mismatch (custom seq script inVSN pipeline version 41df185308 [develop_atac]), and appended to the fastq sequence identifier of the paired-end ATAC-seq reads (read 1 and read 3)
For HyDrop-ATAC samples (prefix HYA): Cell barcodes were written to the bam as a CB SAM tag using SAMtools and AWK (custom VSN pipeline version 41df185308 [develop_atac] script) (samtools view -h HYA__combined__20210323_cortex_phu_dv_etssb_1-5_S5.bwa.out.possorted.bam| mawk '/^@/ {print;next} {N=split($1,n,"_"); NN=split(n[1],nbc,"-"); ucorr_bc=""; corr_bc=""; if(NN==1){ # BioRad data with format {corrected_bc}_qname; corr_bc="
For HyDrop-ATAC samples (prefix HYA): Reads were mapped to reference genomes using bwa-mem and duplicate-marked using samtools markdup by the VSN pipeline version 41df185308 [develop_atac] (bwa mem -t 8 genome.fa $R1.fq.gz $R2.fq.gz | samtools fixmate -@ 6 -m -u -O bam - - | samtools sort -@ 6 -u -O bam - | samtools markdup -@ 6 -f markdup.log - bwa.out.possorted.bam).
For HyDrop-ATAC samples (prefix HYA): Fragments files were generated using Sinto (sinto fragments -b $bam -m 30 --barcodetag CB --use_chrom "(?i)^chr" --min_distance 10 --max_distance 5000 --chunksize 5000000 -p 2 -f $fragments.bed)
For HyDrop-ATAC samples (prefix HYA): Per-cluster differentially accessible region were generated using pycistopic '0.1.dev214+gc72ef83.d20210522' (markers_dict = find_diff_features(cistopic_obj, imputed_acc_obj, variable='cell_type_finetuned', var_features=variable_regions, contrasts=None, adjpval_thr=0.05, log2fc_thr=np.log2(1.5), n_cpu=12)) and written to BED format using a custom python script.
For HyDrop-ATAC samples (prefix HYA): Per-cluster coverage bigwigs were generated using pycistopic '0.1.dev214+gc72ef83.d20210522' (bw_paths, bed_paths = export_pseudobulk(input_data = cistopic '0.1.dev214+gc72ef83.d20210522'_obj.cell_data, variable = 'cell_type_finetuned', chromsizes = chromsizes, bed_path = bed_path, bigwig_path = bw_path, path_to_fragments = fragments_dict, n_cpu = nclusters, normalize_bigwig = True, remove_duplicates = True))
For HyDrop-ATAC samples (prefix HYA): Aggregate genome coverage bigwigs were generated using DeepTools 3.5.0 (bamCoverage -b ${file} -o ${file%.bam}.RPGCnormalized.bw -bs 1 -p 4 --normalizeUsing RPGC  --effectiveGenomeSize 2913022398)
For HyDrop-RNA samples (prefix HYR): Barcode reads (read 2) were trimmed to exclude the intersub-barcode PCR adapters MAWK
For HyDrop-RNA samples (prefix HYR): Reads were mapped  to reference genomes and expression matrices were generated using STAR version: 2.7.8a_2021-04-27 in STARsolo mode (STAR --runThreadN 6 --runMode alignReads --outSAMtype BAM SortedByCoordinate --sysShell /bin/bash --genomeDir "${star_reference_dir}" --readFilesIn "${fastq_R1_filename}" "${fastq_R2_filename}" --readFilesCommand 'gzip -c -d' --soloCBwhitelist "${whitelist_part1_filename}" "${whitelist_part2_filename}" "${whitelist_part3_filename}" --soloType CB_UMI_Complex --soloCBposition 0_0_0_9 0_20_0_29 0_40_0_49 --soloUMIposition 0_50_0_57 --sjdbGTFfile $sjdbgtf --soloCellFilter CellRanger2.2 2000 0.99 10 --soloCBmatchWLtype 1MM --outFilterMultimapNmax 1 --outSAMattributes NH HI AS nM CB UB CR CY UR UY --outFileNamePrefix ${bam_filename%bam} --outReadsUnmapped Fastx --quantMode GeneCounts --bamRemoveDuplicatesType UniqueIdentical --soloFeatures Gene GeneFull Velocyto)
For HyDrop-RNA samples (prefix HYR): For the optimisation samples (HYR__1ec4a0__20200929_Exo_S1 HYR__3ac717__20201006_non-exo_S2 HYR__70afb2__20201006_TSO-LNA_S3 HYR__c6c4b7__20201016_gtp_S4 HYR__d0a5b4__20201023_klenow_S5 HYR__f0eb5a__20201023_bst_S6), FASTQs were downsampled to match the reads per cell depth of the lowest sample and re-mapped using the same STAR parameters to generate the DOWNSAMPLED expression matrices.
Genome_build: For human samples: hg38, for mouse samples: mm10, for hybrid samples: GRCh38_GRCm10 hybrid genome, for fly samples: dm6
Supplementary_files_format_and_content: For HyDrop-ATAC samples (prefix HYA): standard tab-separated fragments files, tar archive with per-cluster differentially accessible region bed files, tar archive with per-cluster genome coverage bigwig
Supplementary_files_format_and_content: For HyDrop-RNA samples (prefix HYR): STARsolo gene expression matrix in MEX format

molecule: cytoplasmic RNA

source_name: 50:50 mixture of human MM087 cells and mouse melanoma cells

growth_protocol: MM087 mouse melanoma cells were cultured in F-10 Nutrient mix supplemented with 10% FBS and 1% penicillin/streptomycin and passaged once per week. Mouse melanoma cells were cultured in DMEM supplemented with 10% FBS and 1% penicillin/streptomycin and passaged once per week.

extract_protocol:
Cells were washed in PBS and dissociated into single cell suspensions using 1.5 mL of 0.05% Trypsin. The single-cell suspension was centrifuged at 500 rcf for 5 min at 4°C and the resulting pellet was resuspended in PBS. This PBS wash was repeated once more. For a recovery of 2000 cells, 3795 cells were resuspended in 85 μL of RT mix (1x Maxima RT Buffer, 0.9 mM dNTPs, 25 mM DTT, 1.3 mM GTP, 15 % Optiprep, 1.3 U/μL RNAse inhibitor, 15 U/μL Maxima hRT, 12.5 uM TSO, 4.4% PEG-8000). RT mix was co-encapsulated with 35 μL of freshly thawed HyDrop-RNA beads in RAN oil on the Onyx microfluidics platform. The resulting emulsion was collected in aliquots of 50 μL total volume and thermocycled according to the RT program (42 °C for 90 min., 11 cycles of [50 °C for 2 min., 42 °C for 2 min.], 85 °C for 5 min., followed by a final hold on 4 °C). 125 μL of recovery agent (20% PFO in HFE), 55 μL of GITC Buffer (5 M GITC, 25 mM EDTA, 50 mM Tris-HCl pH 7.4) and 5 μL of 1 M DTT was added to each separate aliquot of 50 μL thermocycled emulsion and incubated on ice for 5 minutes. 99 μL of Ampure XP beads was added to the aqueous phase and incubated for 10 minutes. Ampure beads were pelleted on a Nd magnet and washed twice with 80% EtOH. Elution was performed in 50 μL of EB-DTT-Tween (10 mM DTT, 0.1% Tween-20 in EB). Exonuclease treatment was performed by adding 3 μL of 10x NEBuffer 3.1, 3 μL of ExoI, and 4 μL of dH2O to 30 μL of eluted library. The ExoI reaction mix was incubated at 37 °C for 5 min., 80 °C for 1 min. followed by a final hold at 4 °C. 2 μL of 1 M DTT was added and a 0.8X Ampure XP purification was performed according to manufacturer’s recommendations. cDNA was eluted in 40.5 μL of EB-DTT (10 mM DTT in EB) and added to ISPCR mix (40 μL library, 50 μL 2x KAPA HiFi, 10 μL 10 uM TSO-P primer). PCR cycling was performed according to the ISPCR program (95 °C for 3 min., 13 cycles of [98 °C for 20s, 63 °C for 20s, 72 °C for 3 min.], 72 °C for 5 min. followed by a final hold at 4 °C. 2 μL of 1M DTT was added and a 0.6x Ampure XP purification was performed according to manufacturer’s recommendations. cDNA was eluted in 28.5 μL of EB-DTT.
Final sequencing library was prepared according to the following customised NEB Ultra II FS protocol. 80 ng of amplified cDNA was fragmented in Ultra II fragmentation mix (26 μL of amplified cDNA, 7 μL of NEBNext Ultra II FS Reaction Buffer, 2 μL of NEBNext Ultra II FS Enzyme Mix) on the following thermocycling program: 37 °C for 10 min., 65 °C for 30 min. and a final hold at 4 °C. 15 μL of EB was added and a 0.8X Ampure purification was performed according to manufacturer’s recommendation and eluted in 35 μL . Fragmented library was adapter-ligated in NEBNext Ultra II adapter ligation mix (35 μL of fragmented library, 30 μL of NEBNext Ultra II Ligation Master Mix, 1 μL of NEBNext Ligation Enhancer, 2.5 μL of NEBNext Adapter for Illumina) at 20 °C for 15 min., with 4 °C final hold. 28.5 μL of EB was added and a 0.8X Ampure purification was performed according to manufacturer’s recommendation and eluted in 30 μL . Eluted library was amplified in PCR master mix (50 μL 2x KAPA HiFi, 10 μL 10 uM Hy-i7 primer, 10 μL 10 uM Hy-i5 primer, 30 μL eluted library) in the following thermocycling program: 95 °C for 3 min., 13 cycles of [98 °C for 20 s, 64 °C for 30 s, 72 °C for 30 s], 72 °C for 5 min. and a final hold at 4 °C. Sequencing-ready library was purified using a 0.8X Ampure purification and eluted in 30 μL of EB.

value: Human:breast cancer cell line/mouse:melanoma cell line


title: NOMO-1, Untreated


title: CpG proBs recipients [Sample 6]

type: RNA

city: PARIS

first: VIVIANE

last: AGBOGAN

state: Île-de-France

address: 160 RUE DE VAUGIRARD

institute: INEM

description:
SAMPLE 6
Treated group

data_processing:
Analysis was performed with Qlucore software (Lund, Sweden).
For the normalization it uses the geometrical mean of six housekeeping genes: PPIA, TBP, B2M, RPLPO, TFRC, GUSB.
Target gene signals normalized to housekeeping genes; 2^-deltaCt, where deltaCt = (Ct_Target − Ct_HKG)]
The threshold for the selection of differentially expressed genes was an expression fold-change ≥1.4, with fold change 2^ΔΔCt, where ΔΔCt = -[ΔCt GVHD control group -ΔCt CpG-proBs groupl].
Fold-Change.txt reports difference between GVHD control group and CpG-proBs recipient mice.

label: SYBRGreen

source_name: mouse skin sample

label_protocol: Production of cDNA from 1ng of total extracted RNA was performed using random primers (Invitrogen) and reverse transcriptase superscript II (Life Technologies). qRT-PCR array for measuring the expression of 84 genes of interest (and 6 house-keeping genes), targeting cytokines and fibrosis related genes, was performed on a custom-made plate (Anygenes) with SYBRGreen, using a qTower2 thermal cycler (Analytic Jena).

extract_protocol: Skin samples (2cm2) were collected from the back of mice with cGVHD, either controls or CpG-proB recipients, frozen in liquid nitrogen and stored at -80°C. Frozen tissues were then placed in Qiagen lysis buffer and dissociated using GentleMACS dissociator. RNA was extracted with RNeasy Plus Universal mini-Kit.

treatment_protocol: Balb/c mice were irradiated and reconstituted with 5 x 10^6 of T- and B-cell depleted bone marrow cells and 1 x 10^6 splenocytes from C57BL/6 mice. One group received following the allogeneic graft, 7.5 x 10^5 CpG-proBs.

tag: mouse

value: Female Balb/c mouse irradiated and grafted with bone marrow and splenocytes from C57BL/6 mouse

tag: group

value: CpG proBs recipient

value: Skin


title: Kasumi-1, IFNg + TNFa

value: AML

tag: condition


title: HYR__3f9a39__20210904_by_6um

value: Human:melanoma cell line/mouse:melanoma cell line


title: Kasumi-1, IFNg


title: Kasumi-1, TNFa

value: TNFa 10 ng/ml - 24h


title: hTG_598


title: CpG proBs recipients [Sample 4]

description:
SAMPLE 4
Treated group


title: NF2 KO CD31+ tumor EC

city: Daejeon

first: Myung Jin

country: South Korea

institute: Institute for Basic Science

description: NF2 KO CD31+ tumor EC

data_processing:
Cell Ranger (v3.0.0) was used to process single cell 3' RNA-seq ouput. First, cell ranger mkfastq demultiplexed illumina BCLs into fastq files.
Then, using cell ranger count, reads were aligned to mm10 mouse reference genome.
Aligned reads were then read by Seurat (v3.1.1) and cell-gene raw expression matrices were made. Then, low quality cells (expressing less than 500 genes), potential dead cells (>10% mitochondrial gene percentage) and contaminating CD31- cells were removed. Also, genes that are only expressed in less than 3 cells were discarded.
Expression matrices were made after quality control. Matrices were log normalized and variables such as number of UMIs and mitochondrial gene percentage were regressed out and scaled with Seurat to produce processed data files.
Identification of differentially expressed genes and dimensionality reductions were performed by Seurat.
Genome_build: mm10
Supplementary_files_format_and_content: Cell-gene expression matrix of log normalized UMI counts for PBS and STING injected tumor ECs

source_name: tumor EC

extract_protocol:
FACS sorted tumor endothelial cells were processed on the 10X chromium system following the manufacturer's protocols.
Using 10x single cell RNA sequencing 3' NEXT GEM v3.1 reagent Kit (10X genomics), cDNA libraries were constructed

value: Tumor endothelial cells

value: Adult


title: Control CD31+ tumor EC

description: Control CD31+ tumor EC


title: CpG proBs recipients [Sample 5]

description:
SAMPLE 5
Treated group


title: GVHD control [Sample 3]

description:
SAMPLE 3
Control group

value: GVHD control


title: Kasumi-1, Untreated

value: Untreated


title: hTG_hCAST_594

value: FVB/NJ


title: hTG_596


title: GVHD control [Sample 2]

description:
SAMPLE 2
Control group


title: GVHD control [Sample 1]

description:
SAMPLE 1
Control group


title: NRF3KD-HCT116-p53KO

status: Public on Oct 20 2021

city: Kyotanabe

first: Tsuyoshi

last: Waku

address: 1-3 Tatara Miyakodani

country: Japan

institute: Doshisha University

description: Gene expression data from HCT116-p53KO cells transfected with NRF3 siRNA

hyb_protocol: Following fragmentation, 2 ug of cDNA were hybridized for 17 hr at 45C on GeneChip Human Gene 1.0ST array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the GeneArray Scanner 3000-7G.

data_processing: The data were analyzed with Expression console  (Build 1.4.1.46) using Affymetrix default analysis settings and RMA scaling as normalization method.

label: biotin

source_name: HCT116-p53KO cells cells transfected with NRF3 siRNA

label_protocol: Biotinated cRNA were prepared according to the standard Affymetrix protocol from 100 ng total RNA (Ambion WT expression kit and Gene Chip WT Terminal Labeling and Hybridization Kit Manual, Affymetrix).

growth_protocol: HCT116 and HCT116-p53KO cells were cultured in DMEM supplemented with 10% FBS, 40 μg/ml streptomycin, and 40 units/ml penicillin. H1299 cells were cultured in RPMI-1640 supplemented with 10% FBS, 40 μg/ml streptomycin, and 40 units/ml penicillin.

extract_protocol: ISOGEN II extraction of total RNA was performed according to the manufacturer's instructions.

treatment_protocol: HCT116 or HCT116-p53KO cells were transciently transfected with siRNA, and total RNA of the cells were extracted at 48 hr after transfection. H1299 cells were transfected with plasmid DNA and then selected with G-418. Total RNA of stable cell lines  were extracted.

value: Human cell line derived from colon cancer

value: NRF3 siRNA


title: NRF3-H1299

description: Gene expression data from H1299 cells transfected with NRF3 expression plasmid

value: Human cell line derived from non-small cell lung carcinoma

value: NRF3 expression


title: NRF3KD-HCT116

description: Gene expression data from HCT116 cells transfected with NRF3 siRNA


title: GFP-H1299

description: Gene expression data from H1299 cells transfected with GFP expression plasmid

value: GFP expression


title: SK-N-MC plus MS-275

city: Berlin

first: Guenther

middle: HS

last: Richter

address: Augustenburger Platz 1

department: Department of Pediatrics, Division of Oncology and Hematology

institute: Charité - Universitätsmedizin Berlin

description: Gene expression data of adherent Ewing sarcoma cell line cultured in tissue culture plates and treated for 27 hrs as described in overall design

hyb_protocol: cRNA was hybridized to Affymetrix Human Gene 1.0 ST arrays

scan_protocol: Affymetrix GCS 3000 Genechip system, scanner GC30007G, software expression console, version 1.6

data_processing: RMA normalization.

source_name: Ewing sarcoma cell line SK-N-MC + 0.5 µM MS-275

label_protocol: Total RNA (200 ng) was amplified and labeled using Affymetrix GeneChip Whole Transcript Sense Target Labeling Kit

growth_protocol: Cell lines were grown in plastic tissue culture platesin a humidified incubator at 37°C in 5% CO2 atmosphere in RPMI 1640 media containing 10% heat-inactivated fetal bovine serum, 1% glutamine, 100 U/ml penicillin, 100 µg/mL streptomysin and 200 mg/dl D-glucose .

extract_protocol: RNA was isolated using the RNeasy RNA isolation kit according to the manufacturer´s instructions

treatment_protocol: Ewing sarcoma cell lines CHLA-10 or SK-N-MC were treated either with A-395, FK228, MS-275 or acombination of  A-395+ FK228 or A395+MS-275 or solvent control for 27 hrs at 37 °C, 5% CO2 respectively.

tag: soft tissue

value: Ewing sarcoma, 14 year old female


title: Control-HCT116-p53KO

description: Gene expression data from HCT116-p53KO cells transfected with control siRNA

value: Control siRNA


title: SK-N-MC plus A-395

source_name: Ewing sarcoma cell line SK-N-MC + 50 µM A395


title: CHLA-10 plus A-395/FK228

source_name: Ewing sarcoma cell line CHLA-10 + 50 µM A-395/0.5 nM FK228


title: SK-N-MC-HDAC2 ko, clone 21

description: Gene expression data of adherent Ewing sarcoma cell line cultured in tissue culture plates as described in overall design

source_name: Ewing sarcoma cell line SK-N-MC knock out of HDAC2 with sgHDAC2 #6a, clone 21

treatment_protocol: Ewing sarcoma cell lines CHLA-10, EW7 or SK-N-MC were lentiviraly infected with Cas9 expression plasmids and subsequently with sgRNAs specific for HDAC1 or HDAC2, respectively.  Stable clones were generated from these infectants and cultivated at 37 °C, 5% CO2 respectively.


title: CHLA-10 plus control

source_name: Ewing sarcoma cell line CHLA-10 + solvent control


title: SK-N-MC plus A-395/MS-275

source_name: Ewing sarcoma cell line SK-N-MC + 50 µM A-395/0.5 µM MS-275


title: SK-N-MC plus FK228

source_name: Ewing sarcoma cell line SK-N-MC + 0.5 nM FK228


title: SK-N-MC plus control

source_name: Ewing sarcoma cell line SK-N-MC + solvent control


title: CHLA-10 plus FK228

source_name: Ewing sarcoma cell line CHLA-10 + 0.5 nM FK228


title: CHLA-10 plus A-395

source_name: Ewing sarcoma cell line CHLA-10 + 50 µM A395


title: CHLA-10 plus MS-275

source_name: Ewing sarcoma cell line CHLA-10 + 0.5 µM MS-275


title: SK-N-MC-HDAC2 ko, clone 6

source_name: Ewing sarcoma cell line SK-N-MC knock out of HDAC2 with sgHDAC2 #6a, clone 6


title: SK-N-MC-Cas9, replicate 2

source_name: Ewing sarcoma cell line SK-N-MC expressing Cas9, replicate


title: SK-N-MC-HDAC2 ko, clone 4

source_name: Ewing sarcoma cell line SK-N-MC knock out of HDAC2 with sgHDAC2 #6a, clone 4


title: SK-N-MC-Cas9

source_name: Ewing sarcoma cell line SK-N-MC expressing Cas9


title: SK-N-MC-HDAC1 ko, clone 2

source_name: Ewing sarcoma cell line SK-N-MC knock out of HDAC1 with sgHDAC1 #3a, clone 2


title: SK-N-MC-HDAC2 ko, clone 5

source_name: Ewing sarcoma cell line SK-N-MC knock out of HDAC2 with sgHDAC2 #6a, clone 5


title: EW7-HDAC2 ko, clone 17

source_name: Ewing sarcoma cell line EW7 knock out of HDAC2 with sgHDAC2 #6a, clone 17

value: Ewing sarcoma, 20 year old female


title: SK-N-MC plus A-395/FK228

source_name: Ewing sarcoma cell line SK-N-MC + 50 µM A-395/0.5 nM FK228


title: Control-HCT116

description: Gene expression data from HCT116 cells transfected with control siRNA


title: SK-N-MC-HDAC1 ko, clone 15

source_name: Ewing sarcoma cell line SK-N-MC knock out of HDAC1 with sgHDAC1 #3a, clone 15


title: SK-N-MC-Cas9, replicate 1


title: CHLA-10 plus A-395/MS-275

source_name: Ewing sarcoma cell line CHLA-10 + 50 µM A-395/0.5 µM MS-275


title: SK-N-MC-HDAC1 ko, clone 21

source_name: Ewing sarcoma cell line SK-N-MC knock out of HDAC1 with sgHDAC1 #3a, clone 21


title: Mouse_Heart_FACS

source_name: Mouse heart

tag: tissue

value: Heart

value: FACS-sorted


title: CHLA-10-HDAC2 ko, clone 4

source_name: Ewing sarcoma cell line CHLA-10 knock out of HDAC2 with sgHDAC2 #6a, clone 4


title: CHLA-10-HDAC2 ko, clone 18

source_name: Ewing sarcoma cell line CHLA-10 knock out of HDAC2 with sgHDAC2 #6a, clone 18


title: SK-N-MC + MS-275/Vincristine

description: Gene expression data of adherent Ewing sarcoma cell line cultured in tissue culture plates and treated for 17 hrs as described in overall design

source_name: Ewing sarcoma cell line SK-N-MC + 0.5 µM MS-275/1 nM Vincristine

treatment_protocol: Ewing sarcoma cell lines A673, CHLA-10, EW7 or SK-N-MC were treated either with FK228, MS-275, PCI-34051, TSA, or solvent control for 17 hrs at 37 °C, 5% CO2 respectively. Cell lines EW7 and SK-N-MC in addition were treated either with Doxorubicin, Vincristin or a combination of Doxorubicin or Vincristine with FK228, MS275 0r PCI-34051, respectively.

value: SK-N-MC


title: CHLA-10-Cas9, replicate

source_name: Ewing sarcoma cell line CHLA-10 expressing Cas9, replicate


title: CHLA-10-HDAC1 ko, clone17

source_name: Ewing sarcoma cell line CHLA-10 knock out of HDAC1 with sgHDAC1 #3a, clone 17


title: EW7-HDAC2 ko, clone 9

source_name: Ewing sarcoma cell line EW7 knock out of HDAC2 with sgHDAC2 #6a, clone 9


title: CHLA-10-HDAC2 ko, clone 38

source_name: Ewing sarcoma cell line CHLA-10 knock out of HDAC2 with sgHDAC2 #6a, clone 38


title: EW7-Cas9

source_name: Ewing sarcoma cell line EW7 expressing Cas9


title: EW7-Cas9, replicate

source_name: Ewing sarcoma cell line EW7 expressing Cas9, replicate


title: SK-N-MC + MS-275/Doxorubicin

source_name: Ewing sarcoma cell line SK-N-MC + 0.5 µM MS-275/50 nM Doxorubicin


title: EW7-HDAC1 ko, clone 1

source_name: Ewing sarcoma cell line EW7 knock out of HDAC1 with sgHDAC1 #3a, clone 1


title: EW7-HDAC1 ko, clone 36

source_name: Ewing sarcoma cell line EW7 knock out of HDAC1 with sgHDAC1 #3a, clone 36


title: SK-N-MC + FK228/Vincristine

source_name: Ewing sarcoma cell line SK-N-MC + 0.5 nM FK228/1 nM Vincristine


title: EW7 + PCI-34051/Vincristine

source_name: Ewing sarcoma cell line EW7 + 20 µM PCI-34051/1 nM Vincristine


title: EW7 + PCI-34051/Doxorubicin

source_name: Ewing sarcoma cell line EW7 + 20 µM PCI-34051/50 nM Doxorubicin


title: SK-N-MC + Doxorubicin

source_name: Ewing sarcoma cell line SK-N-MC + 80 nM Doxorubicin


title: EW7 + FK228/Doxorubicin

source_name: Ewing sarcoma cell line EW7 + 0.5 nM FK228/50 nM Doxorubicin


title: SK-N-MC + Vincristine

source_name: Ewing sarcoma cell line SK-N-MC + 2 nM Vincristine


title: SK-N-MC + FK228/Doxorubicin

source_name: Ewing sarcoma cell line SK-N-MC + 0.5 nM FK228/50 nM Doxorubicin


title: SK-N-MC + PCI-34051/Vincristine

source_name: Ewing sarcoma cell line SK-N-MC + 20 µM PCI-34051/1 nM Vincristine


title: EW7 + MS-275/Vincristine

source_name: Ewing sarcoma cell line EW7 + 0.5 µM MS-275/1 nM Vincristine


title: CHLA-10-Cas9

source_name: Ewing sarcoma cell line CHLA-10 expressing Cas9


title: SK-N-MC + control

source_name: Ewing sarcoma cell line SK-N-MC + solvent control


title: EW7 + FK228/Vincristine

source_name: Ewing sarcoma cell line EW7 + 0.5 nM FK228/1 nM Vincristine


title: EW7 + Doxorubicin

source_name: Ewing sarcoma cell line EW7 + 80 nM Doxorubicin


title: SK-N-MC + PCI-34051/Doxorubicin

source_name: Ewing sarcoma cell line SK-N-MC + 20 µM PCI-34051/50 nM Doxorubicin


title: EW7 + MS-275/Doxorubicin

source_name: Ewing sarcoma cell line EW7 + 0.5 µM MS-275/50 nM Doxorubicin


title: EW7-HDAC2 ko, clone 11

source_name: Ewing sarcoma cell line EW7 knock out of HDAC2 with sgHDAC2 #6a, clone 11


title: EW7 + Vincristine

source_name: Ewing sarcoma cell line EW7 + 2 nM Vincristine


title: EW7 + TSA

source_name: Ewing sarcoma cell line EW7 + 400 nM TSA


title: CHLA-10 + PCI-34051

source_name: Ewing sarcoma cell line CHLA-10 + 50 µM PCI-34051


title: EW7 + control

source_name: Ewing sarcoma cell line EW7 + solvent control


title: SK-N-MC + FK228

source_name: Ewing sarcoma cell line SK-N-MC + 4 nM FK228


title: CHLA-10 + TSA

source_name: Ewing sarcoma cell line CHLA-10 + 400 nM TSA


title: SK-N-MC + TSA

source_name: Ewing sarcoma cell line SK-N-MC + 400 nM TSA


title: SK-N-MC + PCI-34051

source_name: Ewing sarcoma cell line SK-N-MC + 50 µM PCI-34051


title: SK-N-MC + MS-275

source_name: Ewing sarcoma cell line SK-N-MC + 3 µM MS-275


title: EW7 + MS-275

source_name: Ewing sarcoma cell line EW7 + 3 µM MS-275


title: EW7 + control 1


title: EW7 + FK228

source_name: Ewing sarcoma cell line EW7 + 4 nM FK228


title: SK-N-MC + control 1

source_name: Ewing sarcoma cell line SK-N-MC + solvent control


title: SK-N-MC + control 2

source_name: Ewing sarcoma cell line SK-N-MC + solvent control, replicate


title: EW7 + PCI-34051

source_name: Ewing sarcoma cell line EW7 + 50 µM PCI-34051


title: A673 + PCI-34051

source_name: Ewing sarcoma cell line A673 + 50 µM PCI-34051


title: EW7 + control 2


title: SmallRNA.mouse.testis.wt.8weeks.unox.rep2

city: Rochester

first: Xin

last: Li

state: NY

address: 601 Elmwood Ave

department: Biochemistry and Biophysics

institute: University of Rochester

description: Small RNAseq

data_processing:
Analyses were performed using piPipes v1.4. All data from the small RNA sequencing, ribosome profiling (Ribo-seq), RNA sequencing, and degradome sequencing were analyzed using the latest mouse genome release mm10 (GCA_000001635.7), and chicken genome release galGal6 (GCA_000002315.5). Generally, one mismatch is allowed for genome mapping.
For small RNA sequencing, libraries were normalized to the sum of total miRNA reads. Uniquely mapping reads >23 nt were selected for further piRNA analysis. To ensure precision of the mapping, a piRNA is counted only when the 5´-end of the piRNA maps to the transcript.
For RNA-seq reads, the tpm (transcripts per million) values were quantified using the Salmon software.
For Ribo-seq analysis, uniquely mapping reads between 26 nt and 32 nt were selected for further analysis.
Genome_build: Mouse: mm10 (GCA_000001635.7), Chicken: galGal6 (GCA_000002315.5)
Supplementary_files_format_and_content: For Small RNAseq, processed data files are unique genome alignment results in BED2 format (https://github.com/bowhan/piPipes/wiki/smallRNA-seq). For Ribo-seq, results are unique genome alignment bed13 files, with an additional sequence column after a regular bed12 format. For Degradome, unique mapping reads are in bed12 format. RNAseq quantification results are .sf files output by Salmon software.

source_name: testis

growth_protocol: Mice were maintained and used according to guidelines for animal care of the NIH and the University Committee on Animal Resources at the University of Rochester. White Leghorn testes of the Cornell Special C strain from one-year old roosters were used according to guidelines for animal care of the NIH and the University Committee on Animal Resources at the University of Rochester.

extract_protocol:
Total RNAs were extracted using mirVana miRNA Isolation Kit (ThermoFisher, AM1560), and rRNAs were depleted from total RNAs with complementary DNA oligomers (IDT) and RNaseH (Invitrogen, Waltham, MA, USA)
1, Strand-specific RNA-seq: libraries were constructed following the TruSeq RNA sample preparation protocol. 2, Ribo-seq: Testes samples were lysed, RNase T1 & A treated and loaded on sucrose gradients, and 80S monosomes were recovered for library constrution. The 3'-adapter is TGGAATTCTCGGGTGCCAAGG. 3, Degradome: The RNAs were first oxidized at room temperature for 30 minutes with sodium periodate (Sigma, St. Louis, MO, USA) to block the 3´-ends from ligation, and were then size-selected to isolate RNA ≥ 200 nt (DNA Clean & Concentrator™-5, Zymo Research). 5´ adaptors were attached using T4 RNA ligase (Ambion) at 20°C for 3 hours. The ligated products were subjected to rRNA depletion with complementary DNA oligomers (IDT) and RNaseH (invitrogen). The rRNA depleted ligation products were reverse transcribed using a degenerate primer (5´-GCACCCGAGAATTCCANNNNNNNNC-3´). cDNA was amplified by PCR using KAPA HIFI Hotstart polymerase (Kapa Biosystems, Wilmington, MA, USA), and 250–350 nt dsDNA was isolated on 8% native PAGE gels. 4, Small RNAseq: Small RNA libraries were constructed and sequenced using oxidation to enrich for piRNAs by virtue of their 2´-O-methyl-modified 3´ termini. The oxidation procedure selects against in vitro-digested products with a 3´ phosphate. A 25-mer RNA with 2´-O-methyl-modified 3´ termini (5´-UUACAUAAGAUAUGAACGGAGCCCmG -3´) was used as a spike-in control. The 3'-adapter is TGGAATTCTCGGGTGCCAAGG.

treatment_protocol: The mice were anesthetized with Ketamine/Xylazine mixture (Ketamine 100 mg/kg; Xylazine 25 mg/kg) via intraperitoneal injection. After complete anesthesia, testes were exteriorized with a longitudinal incision around 1 cm at the center of abdomen. The tunica albuginea was penetrated using a sharp 26 G needle (BD, Franklin Lakes, NJ, USA, 30511) 1 mm from the vascular pedicle, and the needle was withdrawn to generate path for introducing a blunt end Hamilton needle (Hamilton, Reno, NV, USA, 7786-02). PBS containing 0.02% Fast Green FCF (Thermo Fisher Scientific, Waltham, MA, USA) with 4EGI was slowly injected using a Hamilton microsyringe (1705RN) into one testis, and vehicle control without drug was injected into the other testis. The needle was held in place for 30 seconds before removal to prevent back flow of the solution. Successful completion of injection was indicated by testis filled with green solution. The testes were returned to the abdominal cavity after injection. The incisions were sutured. At the end point, the mice were euthanized by cervical dislocation, and the testes were collected. For immunoprecipitations, anti-CBP80 rabbit antibody (Bethyl laboratories, A301-794A) or anti-eIF4E rabbit antibody (Bethyl laboratories, A301-153A) were used.

value: whole testis

value: wt

tag: treatment

tag: molecule subtype

value: small RNA


title: SmallRNA.mouse.testis.wt.8weeks.ox.rep3

description: Small RNAseq

tag: strain

tag: age

value: Oxidation


title: SmallRNA.mouse.testis.wt.8weeks.unox.rep1

description: Small RNAseq

value: Untreated


title: SmallRNA.mouse.testis.wt.8weeks.unox.rep3

description: Small RNAseq


title: A673 + control 1

source_name: Ewing sarcoma cell line A673 + solvent control


title: A673 + MS-275

source_name: Ewing sarcoma cell lineA673 + 3 µM MS-275


title: A673 + TSA

source_name: Ewing sarcoma cell line A673 + 400 nM TSA


title: CHLA-10 + MS-275

source_name: Ewing sarcoma cell line CHLA-10 + 3 µM MS-275


title: CHLA-10 + control 2

source_name: Ewing sarcoma cell line CHLA-10 + solvent control, replicate


title: CHLA-10 + FK228

source_name: Ewing sarcoma cell line CHLA-10 + 4 nM FK228


title: CHLA-10 + control 1

source_name: Ewing sarcoma cell line CHLA-10 + solvent control


title: A673 + control 2

source_name: Ewing sarcoma cell lineA673 + solvent control, replicate


title: A673 + FK228

source_name: Ewing sarcoma cell lineA673 + 4 nM FK228


title: SmallRNA.mouse.testis.wt.8weeks.ox.rep2

description: Small RNAseq


title: RNAseq.mouse.testis.wt.OkacidAcid.adult.rep1

description: RNAseq

value: adult

value: OkacidAcid

value: rRNA depleted RNA


title: RNAseq.mouse.testis.wt.pUPF1IP.adult.rep1

description: RNAseq

value: RIP

tag: rip antibody

value: anti-pUPF1 from Lynne Maquat's lab, Ser1127


title: RNAseq.mouse.testis.wt.Eif4EIP.adult.rep1

description: RNAseq

value: anti-eIF4E rabbit antibody (Bethyl laboratories, A301-153A)


title: S95

city: Changsha

first: Touming

last: Liu

address: NO.348, western road of xianjia lake

department: Institute of Bast Fiber Crops

institute: Chinese Academy of Agricultural Sciences

data_processing:
After filtering the low-quality reads, the clean reads were aligned with the garlic genome (GenBank accession: GCA_014155895.2) using hisat2 software (version: 2.2.1.0)
gene expression level was quantified by estimating fragments per kilobase per million reads (FPKM)
To identify genes with an expressed association with bulb traits, Pearson’s correlation analysis was performed between four bulb traits and FPKM values of each gene in 84 accessions, and a significant correlation was assumed at P < 0.01.
Genome_build: GCA_014155895.2
Supplementary_files_format_and_content: the excel file contain the gene name and FPKM value,

organism: Allium sativum

source_name: Chalingzipisuan

growth_protocol: All these 84 accessions were grown in the experimental farm of Shandong Research Center of garlic Engineering, JinXiang, Shandong, in Oct., 2019. In April., 2020, three enlarging-growth bulbs of each accessions were collected and stored at －80 °C.

extract_protocol:
Total RNAs of each sample were extracted using an E.Z.N.A. Plant RNA Kit (OMEGA Bio-Tek, Norcross, GA, USA) according to the protocol of manufacturer.
these RNAs were individually used for performing the construction of cDNA libraries, with a fragment length of 300 bp (± 150 bp), using a NEBNext UltraTM RNA Library Prep Kit for Illumina (New England BioLabs, Ipswich, MA, USA) according to the manufacturer’s instructions.

value: bulb

tag: developmental stage

value: enlarging growth of bulb

tag: country/collection site

value: Ukraine


title: S97

value: Guizhou, China


title: RNAseq.mouse.testis.wt.20.5dpp.rep1

description: RNAseq


title: SmallRNA.mouse.testis.wt.8weeks.ox.rep1

description: Small RNAseq


title: S92

value: Greece


title: RNAseq.mouse.testis.wt.UPF1IP.adult.rep1

description: RNAseq

value: anti-UPF1 from Lynne Maquat's lab (P0357, 1-416ab)


title: S93

value: Thailand


title: RNAseq.mouse.testis.Mov10l1CKOTg.CBP80IP.adult.rep1

description: RNAseq

value: whole testis

value: anti-CBP80 rabbit antibody (Bethyl laboratories, A301-794A)


title: S89

value: Taiwan, China


title: RNAseq.mouse.testis.Mov10l1CKOTg.Eif4EIP.adult.rep1

description: RNAseq


title: Riboseq.mouse.testis.Neurog3-cre.Ribotag.HAIP_Unligated.adult.rep1

description: Ribo-seq

data_processing:
Library strategy: Ribo-seq
Analyses were performed using piPipes v1.4. All data from the small RNA sequencing, ribosome profiling (Ribo-seq), RNA sequencing, and degradome sequencing were analyzed using the latest mouse genome release mm10 (GCA_000001635.7), and chicken genome release galGal6 (GCA_000002315.5). Generally, one mismatch is allowed for genome mapping.
For small RNA sequencing, libraries were normalized to the sum of total miRNA reads. Uniquely mapping reads >23 nt were selected for further piRNA analysis. To ensure precision of the mapping, a piRNA is counted only when the 5´-end of the piRNA maps to the transcript.
For RNA-seq reads, the tpm (transcripts per million) values were quantified using the Salmon software.
For Ribo-seq analysis, uniquely mapping reads between 26 nt and 32 nt were selected for further analysis.
Genome_build: Mouse: mm10 (GCA_000001635.7), Chicken: galGal6 (GCA_000002315.5)
Supplementary_files_format_and_content: For Small RNAseq, processed data files are unique genome alignment results in BED2 format (https://github.com/bowhan/piPipes/wiki/smallRNA-seq). For Ribo-seq, results are unique genome alignment bed13 files, with an additional sequence column after a regular bed12 format. For Degradome, unique mapping reads are in bed12 format. RNAseq quantification results are .sf files output by Salmon software.

value: Ribosome footprints

value: anti-HA mouse antibody (Covance; MMS-101P)


title: S9

value: Shandong, China


title: S85

value: China


title: S81

value: Xinjiang, China


title: S88

value: Russia