title: iPCR_P14_NC_Downstream_lib

city: Amsterdam

first: Bas

last: van Steensel

address: Plesmanlaan 121

country: Netherlands

institute: The Netherlands Cancer Institute (NKI)

description:
iPCR sequences matching insert and barcodes Negative controls Downstream Sublibrary
ActivitiesAndBoostIndices_Downstream.tsv

data_processing:
Basecalling and filtering were performed using standard software of the Illumina HiSeq 2500 or MiSeq
For cDNA and pDNA samples, the barcode sequence was extracted from the read (using a custom python scripts) and counted.
For iPCR samples the insert sequence was aligned to a custom genome (using bowtie2) containing only the target sequences extracted from the mm10 genome, and the barcode was extracted from the ead using a custom python script.
Barcodes were clustered using Starcode (version 1.1) {Zorita, 2015, 25638815} to remove errors from barcode sequencing.
barcodes present in multiple libraries or matched with multiple element combinations were removed from the data
Per unique singlet or combination an activity value was calculated as the ratio of the mean readcount in the RNA samples and the mean readcount in the pDNA library samples across all barcodes assigned to the singlet or combination.
Genome_build: mm10
Supplementary_files_format_and_content: The processed data files are tables in TSV format containig the identity and orientation of the fragments of each combination, their genomic coordinates, the activity of the single elements and the activity of the combination. For the Boost indices tables the Boost index was calculated as a log2 ratio of the activity of the combination over the median activity of all the combinations of the Promoter involved in the combination.

source_name: mouse embryonic stem cells

growth_protocol: in E14TG2a mouse embryonic stem cells (mESC) (ATCC CRL-1821) cultured in 2i+LIFulturing media. 2i+LIF was made according to the 4DN nucleome protocol for culturing mESCs (https://data.4dnucleome.org/protocols/cb03c0c6-4ba6-4bbe-9210-c430ee4fdb2c/).

extract_protocol:
For iPCR samples: the combination of barcode and element(s) was excised from the plasmid by digestion with I-ceuI; this fragment was circularised; remaining linear fragments were destroyed; and circular fragments were linearised again with I-sceI. These linear fragments were amplified by PCR with sequencing adaptors. The final product was sequenced on an Illumina MiSeq platform using 150 bp paired-end reads. This process was done separately for each of the libraries. For mor details see van Arensbergen et a., 2017 (PMID: 28024146). For pDNA samples: For each library 1 µg of plasmid was digested with I-sceI in order to linearise the plasmid. Then, barcodes were amplified by PCR from 50 ng of material using the same primers and reaction conditions as in the amplification of cDNA in the Upstream assay, but only 9 cycles of amplification were used (1 min 96 °C, 9×(15 s 96 °C, 15 s 60 °C, 15 s 72 °C)). For each library, two technical replicates were carried out by using different index primers for each replicate. Samples were sequenced on an Illumina 2500 HiSeq platform with 65bp single end reads. For cDNA samples: RNA was extracted and processed for sequencing as described {van Arensbergen, 2017, 28024146} with a few modifications. Cells were harvested 24 h after transfection, resuspended in Trisure (#BIO-38032; Bioline) and frozen at -80 °C until further processing. From the Trisure suspension, the aqueous phase containing the RNA was extracted and loaded into RNA extraction columns (#K0732, Thermo Scientific). Total RNA was divided into 10 µl reactions containing 5 μg of RNA and was treated for 30 mins with 10 units of DNAse I (#04716728001; Roche). Then DNAse I was inactivated by addition of 1 ul of 1 μl of 25 mM EDTA and incubation at 70°C for 10 min. For the Upstream Assay the cDNA was produced and amplified by PCR as described {van Arensbergen, 2017, 28024146}. Per biological replicate 8 to 10 reactions were carried  in parallel in order to cover enough barcode complexity of the library. For the Downstream Assay the RNA was extracted and processed the same way until cDNA production. Here, cDNA was produced using a specific primer. Then cDNA was amplified in 2 steps (nested PCRs) in order to make the reaction strand-specific. The first PCR reaction run for 10 cycles (1 min 96 °C, 10×(15 s 96 °C, 15 s 60 °C, 15 s 72 °C)) using primers (index variants of) 285JvA (containing the S2, index and p7 adaptor) and 305JvA. Each 20 μl RT reaction was amplified in a 100-μl PCR reaction with MyTaq Red mix. The second PCR reaction was performed using 10ul of the product of the previous reaction in 100 μl reactions  (1 min 96 °C, 8×(15 s 96 °C, 15 s 60 °C, 15 s 72 °C)) using the same index variant primer and primer 437JvA (containing the S1, and p5 adaptor). For both Upstream and Downstream assays, the resulting PCR products were sequenced on an Illumina 2500 HiSeq platform with 65bp single end reads.
PCR

treatment_protocol: Cells were transiently transfected using Amaxa nucleofector II, program A-30, and Mouse Embryonic Stem Cell NucleofectorTM Kit (#VPH-1001, Lonza). Negative controls, Klf2 and Nanog loci Upstream Assay libraries were mixed and transfected together, Tfcp2l1 Upstream Assay libraries were transfected in separate experiments. All the Downstream assay sub-libraries were transfected as a mix. Three independent biological replicates were done for each library mix. For each biological replicate 16 million cells were transfected (4 million cells with 4 µg plasmid per cuvette).

value: mESC


title: iPCR_P22_NC_Downstream_lib

status: Public on Oct 21 2021

type: SRA

library_source: genomic

molecule: genomic DNA

organism: Mus musculus

tag: cell type

tag: cell line


title: iPCR_P16_NC_Downstream_lib


title: iPCR_P1_NC_Downstream_lib


title: PBMC_ASAP_Phage_compare_C_PDT

city: New York

first: Caleb

last: Lareau

state: New York

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

country: USA

institute: Memorial Sloan Kettering

data_processing:
Fastqs were generated using CellRanger-ATAC mkfastq v1.1.0
Sequencing reads were aligned using CellRanger-ATAC count for the hg38 reference genome
For Phage libraries, phage tag abundances were quantified per barcode using a custom unix script.
For ASAP libraries, tag abundances were quantified per barcode using a custom unix script
Genome_build: hg38
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

source_name: Peripherial Blood Mononucler Cells

growth_protocol: Cryopreserved cells were thawed in DMEM with 10% FBS and washed in media

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

value: Peripherial Blood Mononucler Cells

tag: antigen capture

value: Phage nanobodies:anti-CD4, anti-CD8, anti-CD16, anti-CEACAM4


title: Intracellular_GFP_Phage

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
Supplementary_files_format_and_content: Per-barcode count abundance for phage library including the ATAC singlecell QC metrics; accessible chromatin fragments per atac library

source_name: HEK293T cells

growth_protocol: DMEM, 10%FBS, Pen/Strep

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

tag: nb treatment

value: anti-EGFP phage nanobody


title: PBMC_ASAP_Phage_compare_C_ATAC


title: iPCR_P21_Downstream_lib

description:
iPCR sequences matching insert and barcodes cCRE Downstream Sublibrary
ActivitiesAndBoostIndices_Downstream.tsv


title: PBMC_ASAP_Phage_compare_B_ADT

value: TBNK - Biolegend TotalSeqA


title: Oxy_rep1

city: Moscow

first: Stepan

last: Nersisyan

address: Vavilova str 7

department: Faculty of Biology and Biotechnology

country: Russia

institute: HSE University

library_source: transcriptomic

data_processing:
The FASTQ file quality was assessed with FastQC v0.11.9 (Babraham Bioinformatics, Cambridge, United Kingdom). After adapter trimming with cutadapt v2.10 (Martin, 2011) reads were mapped on the reference human genome (GENCODE GRCh38.p13) with STAR v2.7.5b (Dobin et al., 2013). The count matrix was generated with GENCODE genome annotation (release 34) (Frankish et al., 2019).
Genome_build: GENCODE GRCh38.p13
Supplementary_files_format_and_content: Read counts matrix

molecule: total RNA

growth_protocol: Caco-2 cells were received from the Russian Vertebrate Cell Culture Collection (Institute of Cytology, Russian Academy of Sciences, St. Petersburg, Russia). The cells were incubated in Gibco minimal essential medium with L-glutamine, 20% Gibco FBS One Shot, and 1% Gibco Pen Strep (Thermo Fisher Scientific, USA). The cells were seeded in the 6-well culture plates (TPP Techno Plastic Products AG, Germany) at a seeding density of 0.3 x 106 cells per well.

extract_protocol:
Cells were lysed in 700 μL of QIAzol Lysis Reagent (Qiagen, Hilden, Germany) with subsequent RNA extraction with miRNeasy Mini Kit (Qiagen) according to the manufacturer protocol, including on-column treatment with RNase-Free DNase Set (Qiagen). RNA was extracted in 30 μL of RNase-free water. RNA concentration was measured with NanoDrop 2000 Spectrophotometer (Thermo Fisher Scientific). A260/A280 and A260/A230 ratios were more than 2.0, and RNA Integrity Number (RIN) according to 2100 Bioanalyzer with Agilent RNA 6000 Pico Kit (Agilent Technologies, Santa Clara, CA, USA) was not less than 9.7 for all RNA samples.
Libraries for mRNA sequencing were prepared with TruSeq Stranded mRNA Library Prep (Illumina, San Diego, CA, United States). Library quality check was provided with Agilent High Sensitivity DNA Kit (Agilent Technologies). Sequencing with NextSeq 550 (Illumina) generated single-end 75-nucleotide reads.

treatment_protocol: The cell culture medium of undifferentiated Caco-2 was replaced with either medium with 300 μM CoCl2, medium with 5 μM oxyquinoline derivative (OD) 4896-3212 (ChemDiv Research Institute, Khimki, Russia), or fresh medium. OD stock solution was diluted in DMSO at 10 mM, so 0.5% DMSO was also added to CoCl2 and control medium, and cells were incubated 24 h before lysis for RNA and protein extraction.

tag: treatment

value: oxyquinoline


title: iPCR_P18_Downstream_lib


title: PBMC_ASAP_Phage_compare_B_PDT


title: PBMC_ASAP_Phage_compare_A_ATAC


title: iPCR_P17_NC_Downstream_lib


title: PBMC_293T_Mix_Phage

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

source_name: Peripherial Blood Mononucler Cells and HEK293T cell line

growth_protocol: Cryopreserved cells were thawed in DMEM with 10% FBS and washed in media. 293Ts were grown in DMEM + 10% FBS and 1x PenStrep

treatment_protocol: Transfection using 4µg EGFP-GPI-encoding plasmid or 4µg SARS-CoV-2 spike protein encoding plasmid for HEK293T

tag: cell mixing ratio

value: PBMCs and 293Ts at 2.5:1, 293Ts expressing either SARS-CoV-2 spike protein or EGFP

value: Phage nanobodies:anti-EGFP (2 different Nbs), anti-SARS-CoV-2 spike protein (7 different Nbs), anti-CD4, anti-CD16, anti-CD8


title: iPCR_NoP_NC_Downstream_lib


title: iPCR_P21_NC_Downstream_lib


title: iPCR_P16_Downstream_lib


title: Intracellular_GFP_ATAC


title: iPCR_P19_NC_Downstream_lib


title: iPCR_P14_Downstream_lib


title: PBMC_293T_Mix_ATAC


title: iPCR_P18_NC_Downstream_lib


title: iPCR_Tfcp2l1_Comb_Upstream_lib_Reseq

description:
iPCR sequences matching insert and barcodes of Tfcp2l1 locus Upstream Combinatorial library resequenced
Activities_allcombinations_Upstream.tsv
BoostIndices_cCRE-P_Upstream.tsv


title: iPCR_Nanog_Singlet_Upstream_lib

description:
iPCR sequences matching insert and barcodes of Nanog locus Upstream singlet library
Activities_allcombinations_Upstream.tsv
BoostIndices_cCRE-P_Upstream.tsv


title: iPCR_Klf2_Comb_Upstream_lib

description:
iPCR sequences matching insert and barcodes of Klf2 locus Upstream combinatorial library
Activities_allcombinations_Upstream.tsv
BoostIndices_cCRE-P_Upstream.tsv


title: iPCR_Nanog_Comb_Upstream_lib

description:
iPCR sequences matching insert and barcodes of Nanog locus Upstream combinatorial library
Activities_allcombinations_Upstream.tsv
BoostIndices_cCRE-P_Upstream.tsv


title: iPCR_P22_Downstream_lib


title: iPCR_Klf2_Singlet_Upstream_lib

description:
iPCR sequences matching insert and barcodes of Klf2 locus Upstream singlet library
Activities_allcombinations_Upstream.tsv
BoostIndices_cCRE-P_Upstream.tsv


title: iPCR_P13_NC_Downstream_lib


title: iPCR_P17_Downstream_lib


title: iPCR_P9_NC_Downstream_lib


title: iPCR_P19_Downstream_lib


title: iPCR_P13_Downstream_lib


title: iPCR_P1_Downstream_lib


title: iPCR_NC_Singlet_Upstream_lib

description:
iPCR sequences matching insert and barcodes of Negative controls and Klf2 locus promoters Upstream singlet library
Activities_allcombinations_Upstream.tsv
BoostIndices_cCRE-P_Upstream.tsv


title: iPCR_Tfcp2l1_Singlet_Upstream_lib

description:
iPCR sequences matching insert and barcodes of Tfcp2l1 locus singlet Upstreamlibrary
Activities_allcombinations_Upstream.tsv
BoostIndices_cCRE-P_Upstream.tsv


title: iPCR_P9_Downstream_lib


title: iPCR_NoP_Downstream_lib


title: WT_Tcra_rep1_control_for_Trav151KO

city: Durham

first: Danielle

last: Dauphars

state: NC

address: 207 Research Drive

department: Immunology

institute: Duke University

data_processing:
Illumina MiSeq software: base calling and demultiplexing.
Sequences were aligned and clones assembled using MiXCR (version 3.0.7) software with a modified strain 129 reference library from IMGT sequence information. Unique clones were identified with ‘-OassemblingFeatures=[CDR2+FR3+CDR3]’.
MiXCR exportClones was used to make human-readable format.
Supplementary_files_format_and_content: .txt files with sequences, gene segment identities, and counts of unique Tcra clones.
Genome_build: Custom strain 129 V-alpha, V-delta, and J-alpha reference library (the sequences used are from IMGT: http://www.imgt.org/IMGTrepertoire/LocusGenes/)
Supplementary_files_format_and_content: .txt files with sequences, gene segment identities, and counts of unique Tcra clones.

source_name: pre-selection DP thymocytes

growth_protocol:
Thymocytes were harvested from 4-5 week-old mice.
Thymocytes were harvested from 4-5 week-old mice.

extract_protocol:
Trizol (Life Technologies) was used to extract total RNA from sorted DP thymocytes.
Template-switch RACE was used to ligate adapaters to the 5' ends and amplify Tcra transcripts. Illumia adapters were added to the 5' template-switch oligo and the antisense Trac-specific primer.

treatment_protocol: Cells were subjected to FACS. Sorting was performed on either the Astrios (Beckman Coulter), MoFlo XDP (Beckman Coulter), or FACSDiVa (Becton Dickinson). All samples are CD3e(-) DP thymocytes.

tag: strain

value: C57BL/6J with strain 129 TcrdCreER at Tcra-Tcrd loci. Also contains Rosa26ZsG/ZsG and Id3f/f alleles.

tag: genotype

value: Homozygous TcrdCreER. Rosa26ZsG/+. Id3f/f. Untreated.

tag: tissue

value: thymus

value: pre-selection DP thymocytes


title: Trav15d1KO_rep1

value: C57BL/6J with strain 129 TcrdCreER with a deletion of Trav15d-1-dv6d-1 at both Tcra-Tcrd loci. Also contains Rosa26ZsG/ZsG and Id3f/f alleles.

value: Homozygous TcrdCreER with Trav15d-1-dv6d-1 KO. Rosa26ZsG/+. Id3f/f. Untreated.


title: Trav15d1KO_rep2


title: Trav151KO_rep1

value: C57BL/6J with strain 129 TcrdCreER with a deletion of Trav15-1-dv6-1 at both Tcra-Tcrd loci. Also contains Rosa26ZsG/ZsG and Id3f/f alleles.

value: Homozygous TcrdCreER with Trav15-1-dv6-1 KO. Rosa26ZsG/+. Id3f/f. Untreated.


title: Trav151KO_rep2


title: WT_Tcra_rep2_control_for_Trav151KO


title: iPCR_Tfcp2l1_Comb_Upstream_lib

description:
iPCR sequences matching insert and barcodes of Tfcp2l1 locus Upstream combinatorial library
Activities_allcombinations_Upstream.tsv
BoostIndices_cCRE-P_Upstream.tsv


title: 12h_DJD_rep1

growth_protocol:
4-5 week old mice were injected i.p. with 1 mg Tamoxifen 12 hours prior to sacrifice. Thymocytes were harvested.
Thymocytes were harvested from 4-5 week-old mice.

value: mixed 129/C57BL/6J with strain 129 Tcra-Tcrd loci- TcrdCreER-CaM at one allele and DJD at one allele. Also contains Rosa26ZsG/+ allele.

value: Heterozygous Tcra-Tcrd alleles:DJD+/- TcrdCreER-CaM+/-. Rosa26ZsG/+. Tamoxifen-treated.

value: ZsGreen+ pre-selection DP thymocytes


title: iPCR_NC_Comb_Upstream_lib

description:
iPCR sequences matching insert and barcodes of Negative controls and Klf2 locus promoters Upstream combinatorial library
Activities_allcombinations_Upstream.tsv
BoostIndices_cCRE-P_Upstream.tsv

value: mESC


title: Rumen_AD_2

city: Hangzhou

first: Jiajin

last: Wu

state: Zhejiang

address: Yuhangtang road

country: China

institute: Zhejiang University

data_processing:
Sequences from NovaSeq 6000 system were  de-multiplexed and aligned using CellRanger version 3.1.0, available from 10x Genomics with default parameters.
Genome_build: Bos_taurus ensemblV99
Supplementary_files_format_and_content: Tab-delimited text files include barcodes, gene and count matrix for each Sample

organism: Bos taurus

source_name: Rumen

extract_protocol:
The rumen tissues isolated from dairy cows were stripped of the outer muscle layers, and then minced into 10×0.5mm2 pieces on ice with scissors. The tissues were incubated in a 37℃ water bath with 20 mM EDTA for 30 min, and then were rinsed with DPBS and chopped into 1 mm pieces. Tissue pieces were transferred to a 15 mL centrifuge tube, and re-suspended with 0.25% Trypsin-EDTA (Gibco). After incubated in a 37℃ water bath for 5 min, the centrifuge tube containing tissues was inserted into ice for 2min, and pre-chilled HBSS was added to stop the digestion. After centrifuged at 300 × g for 2 min at 4℃, the supernatant was discarded, and samples were washed twice with cold HBSS and then re-suspended with dissociation enzymes(1.5mg/ml collagenase I, 1.5ml/ml collagenase IV,1.5mg/ml dispase, 100U/ml hyaluronidase, and 50U/ml DNase I) for 30 min at 37℃.
The single-cell RNA-seq library preparation was performed using the Chromium Single Cell 3' Reagent Kits v3.

tag: breed

value: Holstein dairy cows

value: rumen

tag: developmental stage

value: adult


title: DJD_Tcra_rep1

value: mixed 129/C57BL/6J with strain 129 Tcra-Tcrd loci with D and J delta deletion (DJD).

value: Homozygous DJD


title: WT_Tcra_rep2_control_for_Trav15d1KO

value: C57BL/6J with strain 129 TcrdCreER at Tcra-Tcrd loci. Also contains Rosa26ZsG/ZsG and Id3f/f alleles.


title: WT_Tcra_rep1_control_for_DJD

value: mixed 129/C57BL/6J with strain 129 Tcra-Tcrd loci.

value: Homozygous WT


title: WT_Tcra_rep1_control_for_Trav15d1KO

value: Homozygous TcrdCreER. Rosa26ZsG/+. Id3f/f. Untreated.

value: thymus

value: pre-selection DP thymocytes


title: 12h_DJD_rep2


title: 12h_WT_Tcra_rep2_control_for_DJD

value: mixed 129/C57BL/6J with strain 129 TcrdCreER-CaM/+ at Tcra-Tcrd loci. Also contains Rosa26ZsG/ZsG and Id3f/f alleles.

value: Heterozygous Tcra-Tcrd alleles:WT+/- TcrdCreER-CaM+/-. Rosa26ZsG/+. Tamoxifen-treated.


title: WT_Tcra_rep2_control_for_DJD


title: 12h_WT_Tcra_rep1_control_for_DJD


title: med23si-rep2

city: Shanghai

first: Gang

last: Wang

address: 2005 Songhu Rd

department: School of life sciences

institute: Fudan university

data_processing:
The RNA-Seq FASTQ raw data were trimmed to remove low-quality reads and adapters using Trimmomatic.
The trimmed reads were aligned to the mouse reference genome UCSC GRCh37/hg19 with HISAT2.
Gene and transcript quantification was performed using Cutdiff.
The results of the mapping of the RNA-seq reads, transcript assembly and abundance estimation were reported as fragments per kilobase of exon per million fragments mapped (FPKM).
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample

source_name: Human Umbilical Vein Endothelial Cells

extract_protocol:
Total RNA was isolated with TRIzol from Med23 knockdown HUVECs (n = 3) or control cells (n = 3).
cDNA sequencing libraries were prepared with an NEBNext® Ultra™ RNA Library Prep Kit for Illumina.

treatment_protocol: Stable Med23 knock-down HUVEC cell line was established using retrovirus.

value: Vein Endothelial

value: HUVEC


title: med23si-rep3


title: ctrl-rep3

value: control


title: ctrl-rep2


title: med23si-rep1


title: H1_CXCR4_plus_Rep1

city: Guangzhou

first: Zhijun

last: Ren

address: 74 Zhongshan Rd.2

institute: Sun Yat-sen University

data_processing:
Basecalls performed using CASAVA version 1.4
adapter removed by cutadapt
The frequency of each sgRNA was measured using MAGeCK tools.
Genome_build: NOT PROVIDED
Supplementary_files_format_and_content: count_normalized.txt

growth_protocol: A549 (ATCC® CCL-185™) cells were cultured in high glucose Dulbecco’s Modified Eagle’s Medium (Hyclone, SH30022.01), supplemented with 10% fetal bovine serum (FBS, Hyclone, SH30406.05) and 2 mM GlutaMAX (Gibco, 35050061) at 37 °C with 5% CO2. H1 hESCs (obtained from the WiCell Research Institute) and the TRME hESCs cell line39 were grown in Matrigel (BD, 354277)-coated 6-well plates in E8 medium (Stem Cells Technology, 05940) at 37 °C with 5% CO2. Both cells were authenticated and tested for the absence of mycoplasma contamination using Myco-Blue Mycoplasma Detector (Vazyme).

extract_protocol:
Genomic DNA (gDNA) was extracted using the FastPure Cell/Tissue DNA Isolation Mini Kit (Vazyme, DC102) and DNA concentration was measured by Qubit using the Qubit™ dsDNA HS Assay Kit (Invitrogen).
To generate sgRNA amplicons, we used a single-step PCR protocol which was adopted from the protocol published by Julia Joung et al 41. All the gDNA harvested from the screen was used for PCR amplification in 50 µl PCR reactions. Each reaction consisted of 2.5 µg gDNA plus water, 25 μL NEBNext Ultra II Q5 PCR Master Mix, 1.25 μL 10μM stagger forward primer, and 1.25 μL 10μM barcoded reverse primer. PCR reactions were cycling as follow: initial denature 3min at 98℃; followed by 30s denature at 98℃, 10s anneal at 63℃, 25s extension at 72℃, for 23 cycles; and final extension for 2min at 72℃. PCR products were size-selected using VAHTS DNA Clean Beads (Vazyme) according to the manufacturer’s instructions and sequenced on a HiSeq2000 sequencer (Illumina).

tag: treatment/time point


title: H1_Day0


title: H1_CXCR4_plus_Rpe2


title: H1_CXCR4_minus_Rep2


title: A549-D30_Rep1


title: A549-D20_Rep1


title: A549-D30_Rep2


title: DJD_Tcra_rep2


title: A549-D20_Rep2


title: A549-D10_Rep1


title: A549-D10_Rep2


title: ctrl-rep1


title: ETP3

first: Marissa

last: Rashkovan

state: NY

address: 1130 Saint Nicholas Avenue

institute: Columbia University

data_processing:
Reads were trimmed of contaminating adapter sequences using Trimmomatic (v.0.39) and aligned to the GRCh37 (hg19) build human genome using Bowtie2 (v 2.3.4.1)
Mapped reads were processed with Samtools (v. 1.7) and bigwigs were generated and analyzed with deepTools (v. 3.3.1)
Genome_build: hg19

source_name: bone marrow

extract_protocol:
Transposed DNA fragments were amplified by PCR
Libraries were prepared for sequencing using NEBNext High-Fidelity 2 PCR Master Mix (NEB M0541) and custom primer indexes to generate ATAC-seq libraries

value: bone marrow


title: ETP1


title: ETP2


title: CUTLL3_Vehicle

data_processing:
Reads were trimmed of contaminating adapter sequences using Trimmomatic (v.0.39) and aligned to the GRCh37 (hg19) build human genome using Bowtie2 (v 2.3.4.1)
Mapped reads were processed with Samtools (v. 1.7) and bigwigs were generated and analyzed with deepTools (v. 3.3.1)
Genome_build: hg19
Supplementary_files_format_and_content: bigWig

extract_protocol:
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody.
Libraries were prepared for sequencing using standard Illumina protocols

tag: agent

value: Vehicle

tag: chip antibody

value: H3K27 acetylation (Abcam ab4729)


title: CUTLL3_Vehicle [ATAC-seq]


title: H1_CXCR4_minus_Rep1


title: CUTLL3_Vehicle_2

data_processing:
We aligned RNA-seq raw reads to the human genome GRCh37 (hg19) using HiSat2 (v. 4.8.2)
Count matrices were generated using HTseq (v.0.12.4) using Gencode assembly (v.33)
We performed differential gene expression analysis in R (v. 3.6.3) using the Bioconductor package DESeq2
Genome_build: hg19
Supplementary_files_format_and_content: FPKM

extract_protocol:
We extracted RNA using the RNeasy Mini Kit (Qiagen 74104).
RNA libraries were prepared for sequencing using standard Illumina protocols


title: CUTLL3_Pitavastatin_2

value: Pitavastatin


title: A549-D0


title: H1_CXCR4_plus_Rpe3


title: CUTLL3_Vehicle_1


title: CUTLL3_Vehicle_3


title: CUTLL3_Pitavastatin [ATAC-seq]


title: CUTLL3_Pitavastatin_1


title: CUTLL3_1

data_processing:
We aligned RNA-seq raw reads to the human genome GRCh37 (hg19) using HiSat2 (v. 4.8.2)
Count matrices were generated using HTseq (v.0.12.4) using Gencode assembly (v.33)
We performed differential gene expression analysis in R (v. 3.6.3) using the Bioconductor package DESeq2
Genome_build: hg19
Supplementary_files_format_and_content: normalizedTPM


title: Control for exosomes replicate 2

status: Public on Oct 22 2021

type: RNA

city: Boston

first: Naser

last: Jafari

state: MA

address: 72 East Concord

department: Hem Onc

institute: Boston University

description: Control

data_processing: Ct values were generated by ABI 7500 Fast System Software

label: SYBR Green

source_name: MCF7 cells

growth_protocol: MCF7 cells were cultured in DMEM including 10% FBS and 1% antibiotics for an over night

extract_protocol: RNA isolated using Qiagen RNA purification protocol and reagents

treatment_protocol: MCF7 Cancer cells were treated with ND or T2D adipocytes exosomes for 5 days

value: breast cancer

value: Control


title: CUTLL1_2


title: CUTLL3_Pitavastatin


title: CUTLL3_3


title: Het_3

city: Aachen

first: Steffen

last: Koschmieder

state: Nordrhein-Westfalen

address: Pauwelsstraße 30

department: Department of Hematology, Oncology, Hemostaseology, and Stem Cell Transplantation

country: Germany

institute: RWTH Aachen

description: bulk RNA-seq of human iPS cell-derived megakaryocytes

data_processing:
We use nf-core/rnaseq pipeline for analysis of RNA sequencing data.
Reads were aligned to hg38.
Transcript abundance were quantified by Salmon.
Differential expression analysis was performed by limma.
Genome_build: hg38
Supplementary_files_format_and_content: abundance measurements: comma-delimited text file estimated gene counts for each sample

source_name: iPS cell-derived hematopoietic stem and progenitor cells

growth_protocol: Feeder-free iPS cell culture was maintained on matrigel coated 6-well plates and routinely passaged with 1 ml accutase or 0.5 mM EDTA (Thermo Fisher Scientific). To enhance single cell survival, 10 µM ROCK inhibitor Y‑27632 was added to the maintenance culture medium StemMACs iPS Brew XF for 24 h after seeding. iPS cell medium was changed daily.Human iPS cells were differentiated into HSPCs and MKs adapted from the differentiation protocol by Liu et. al (Liu et al., 2015). Briefly, iPS cells were seeded into U-bottom-shaped 96 well plates with a density of 3,000 cells/well in cytokine supplemented serum-free medium (SFM). To allow spheroid formation, plates were spun at 380 g for 5 min. From day 2 to day 8, cells were cultured in SFM with 10 ng/ml VEGF (Miltenyi Biotec), 10 ng/ml BMP4 (Miltenyi Biotec), 10 ng/ml bFGF (Peprotech, Hamburg, Germany) and SCF (0.5 % supernatant of SCF secreting CHO KLS cells). From day 8 onwards, BMP4 and VEGF were removed from the medium. On day 11, 20 ng/ml TPO (Miltenyi Biotec) was added to the medium. On day 14, cells were harvested and filtered through a 100 µm filter to separate the EBs from the suspension cells.  CD61+ cells were separated by magnetic activated cell sorting.

extract_protocol:
RNA was extracted using RNeasy Kit from Qiagen following the manufactor's protocol
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: not applicable

value: iPS cell-derived CD61+ megakaryocyte

value: heterozygous CALRins5 frameshift


title: CUTLL1_1


title: CUTLL3_2


title: CUTLL3_Pitavastatin_3


title: Hom_3

value: homozygous CALRins5 frameshift


title: WT_3

value: CRISPR/Cas9 engineered WT CALR


title: Het_2


title: Hom_2


title: WT_1


title: Het_1


title: cells treated for 24 hrs with iP300w rep3

city: Minneapolis

first: Micah

last: Gearhart

state: MN

address: 6-160 Jackson Hall, 321 Church St.

department: Genetics, Cell Biology and Development

institute: University of Minnesota

data_processing:
Paired-end Illumina sequencing reads were trimmed with TrimGalore (0.6.0).
Transcript abundance was quantified using the human Gencode annotations (v34) using Salmon (v 1.2.1) with the GC-bias correction option.
Counts were imported into R (4.0.2) using tximeta (v 1.6.3). Differentially expressed genes were identified with DESeq2 (v1.28.1).
Genome_build: GRCh38
Supplementary_files_format_and_content: NA

molecule: polyA RNA

source_name: CIC-DUX4 sarcoma cell line NCC-CDS-X9

growth_protocol: NCC-CDS-X1 cell line was cultured in RPMI (Hyclone) with 10% FBS (PeakSerum Ps-FB3, lot 293Q16).

extract_protocol:
RNA was extracted using an RNA extraction kit (Zymo Research).
RNAseq library preparation was done with 500 ng total RNA using Swift Rapid RNA Library Kit (Swift Bioscience).

treatment_protocol: Cells were untreated or treated for 4 and 24 hours with iP300w (0.3 µM).

value: 0.3 uM iP300w for 24hrs


title: cells treated for 24 hrs with iP300w rep2

source_name: CIC-DUX4 sarcoma cell line NCC-CDS-X8


title: Hom_1


title: WT_2


title: cells treated for 4 hrs with iP300w rep3

source_name: CIC-DUX4 sarcoma cell line NCC-CDS-X6

value: 0.3 uM iP300w for 4hrs


title: cells treated for 24 hrs with iP300w rep1

source_name: CIC-DUX4 sarcoma cell line NCC-CDS-X7


title: cells treated for 4 hrs with iP300w rep1

source_name: CIC-DUX4 sarcoma cell line NCC-CDS-X4


title: Untreated  cells rep3

source_name: CIC-DUX4 sarcoma cell line NCC-CDS-X3

value: no treatment


title: cells treated for 4 hrs with iP300w rep2

source_name: CIC-DUX4 sarcoma cell line NCC-CDS-X5


title: Untreated  cells rep2

source_name: CIC-DUX4 sarcoma cell line NCC-CDS-X2


title: Untreated  cells rep1

source_name: CIC-DUX4 sarcoma cell line NCC-CDS-X1


title: involved.6.2

city: Ann Arbor

first: Bioinformatics

last: Core

state: MI

address: BRCF Bioinformatics Core, 2800 Plymouth Rd

institute: University of Michigan

description: mouse bones grossly involved by tumor

data_processing:
The Tuxedo Suite of software was used for alignment, differential expression analysis, and post-analysis diagnostics.
Reads were aligned to the reference genome  using TopHat (version 2.0.13) and Bowtie2 (version 2.2.1.), with default parameter settings for alignment,  except: “--b2-very-sensitive” was set.
Cufflinks/CuffDiff (version 2.1.1) for expression quantitation, normalization, and differential expression analysis.
For normalization of expression values,  “--multi-read-correct” was used to adjust expression calculations for reads that map in more than one locus, as well as “--compatible-hits-norm” and “--upper-quartile–norm”.
Genome_build: UCSC hg19
Genome_build: UCSC mm10
Supplementary_files_format_and_content: tab-delimited text - raw reads quantified by Cufflinks

organism:
Homo sapiens
Mus musculus

source_name: Du145 prostate cancer cell line grown in mouse

growth_protocol: cardiac left ventricular injection

extract_protocol:
Qiagen Rneasy micro kit
Clontech SMART-seq V4 Ultra Low kit
poly-A / mRNA

value: mouse bones grossly involved by tumor


title: not.involved.6.2

description: mouse bones not involved by tumor

value: mouse bones not involved by tumor


title: PBMC_Channel1_Phage

source_name: Peripherial Blood Mononucler Cells

value: Peripherial Blood Mononucler Cells

value: CD16, CD4, CD8


title: CD8_Human_T-cell_Hashing_ATAC

tag: donor #

value: 4 distinct

value: CD8 T-cells

tag: ab treatment


title: PBMC_Channel2_ATAC


title: CD8_Human_T-cell_Hashing_Phage

value: CD8 with hash barcode


title: not.involved.3.2

description: mouse bones not involved by tumor


title: PBMC_Channel2_Phage


title: nTg_9_mo_Sample_214-16-Tg9

city: Providence

first: Bess

last: Frost

state: RI

address: 185 Meeting St

institute: Center for Alzheimer’s Disease Research, Brown University

description:
Total RNA - rRNA depeletion
R547.214.16.Tg9_S11_L001

data_processing:
Sequenced reads were trimmed with trimmomatic and alligned to the mouse mm10 genome using STAR. Counts were then generated with TEtranscripts.
Genome_build: mm10
Supplementary_files_format_and_content: Matrix table with Deseq2 normalized transposon expression counts for every sample.

source_name: hippocampus

extract_protocol:
Qiagen RNeasy Mini kit
Illumina Truseq 76 bp paired-end stranded reads

value: Total Brain Lysate

tag: age

value: 9 months


title: nTg_9mo_Sample_213-15-Tg9

description:
Total RNA - rRNA depeletion
R547.213.15.Tg9_S8_L001


title: nTg_9mo_Sample_207-9-Tg9

description:
Total RNA - rRNA depeletion
R547.207.9.Tg9_S12_L001


title: Tg4510_9mo_Sample_208-10-Tg9

description:
Total RNA - rRNA depeletion
R547.208.10.Tg9_S13_L001

value: non-transgenic


title: tumor sample 27

city: Milan

first: Giulia

middle: Maria

last: Scotti

state: Milan

address: Viale Rita Levi Montalcini, 1

department: National Facility for Data Handling and Analysis

country: Italy

institute: Fondazione Human Technopole

data_processing:
Low quality reads and Illumina adapters were trimmed using Trimmomatic (version 0.36)
Retained reads were mapped to the reference mouse genome, GRCm38, using STAR (version 2.5.3a)
Uniquely mapped reads were assigned to the corresponding genes using the featureCounts function in the Rsubread R package. Only reads mapped to exons were considered in the counting procedure. Genomic features were annotated according to Gencode basic annotations, version M13
Genome_build: UCSC mm10
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: Medulloblastoma tissue from a Ptch1+/-p53-/- (abbreviated to ‘heterozygous/null’, HN) mouse

extract_protocol:
Total RNA was extracted using the RNeasy Mini Kit from Qiagen.
Libraries were PCR amplified and sequenced on an Illumina NextSeq 500 System with QuantSeq 3'mRNA-Seq Library Prep kit (Lexogen), generating single-end 75 base-pair reads.

value: Medulloblastoma


title: Tg4510_9mo_Sample_211-13-Tg9

description:
Total RNA - rRNA depeletion
R547.211.13.Tg9_S4_L001


title: tumor sample 31


title: tumor sample 30


title: Tg4510_9mo_Sample_203-5-Tg9

description:
Total RNA - rRNA depeletion
R547.203.5.Tg9_S85_L008


title: PBMC_Channel1_ATAC

tag: cell type


title: Bone marrow – JP – rep3

city: Genoa

first: Paolo

last: Uva

address: Via Gerolamo Gaslini, 5

institute: IRCCS Istituto Giannina Gaslini

data_processing:
Base calling was performed using Illumina RTA v2.11.3.0
Sequenced reads were trimmed for adaptor sequence and low  quality sequences using TrimGalore v0.6.2
Transcript abundance was computed with Kallisto v0.43.0
Genome_build: mm10
Supplementary_files_format_and_content: Transcript abundance estimated with Kallisto

source_name: Bone marrow

extract_protocol:
Total RNA was extracted with Direct-zol RNA Microprep kit (Zymo Research)
Libraries for Poly(A) mRNA sequencing were constructed using the SMART-Seq v4 Ultra Low Input RNA kit (Takara Clontech) according to manufacturer's instruction

treatment_protocol: JAK2-cKI, JP and WT control mice were treated with 10mg/Kg of polyinosinic-polycytidylic acid (pIpC) (High Molecular Weight, InvivoGen)

value: Bone marrow derived LKS (Lineage-/cKit+/Sca1+) cells

value: Bone marrow

tag: condition

value: JP


title: tumor sample 34

source_name: Medulloblastoma tissue from a Ptch1+/-p53+/+ (abbreviated to ‘heterozygous/wildtype’, HW) mouse


title: Tg4510_9mo_Sample_205-7-Tg9

description:
Total RNA - rRNA depeletion
R547.205.7.Tg9_S7_L001


title: nTg_9mo_Sample_206-8-Tg9

description:
Total RNA - rRNA depeletion
R547.206.8.Tg9_S10_L001


title: tumor sample 26


title: nTg_9mo_Sample_202-4-Tg9

description:
Total RNA - rRNA depeletion
R547.202.4.Tg9_S86_L008


title: involved.3.2

description: mouse bones grossly involved by tumor


title: tumor sample 33


title: Tg4510_9mo_Sample_199-1-Tg9

description:
Total RNA - rRNA depeletion
R547.199.1.Tg9_S89_L008


title: MCF7 cells, KO#2 (clone with HSF1 knockout)_estrogen_1h

city: Bergen

first: Tomasz

last: Stokowy

address: Nygardsgaten 5

department: IT Division

country: Norway

institute: University of Bergen

description: MCF7 KO#2 (clone with HSF1 knockout) - estrogen treated for 1h (10nM)

data_processing:
Quality control of reads was performed with FastQC software
Reads were mapped to the human genome (hg19) with Bowtie2 version 2.2.9
Peak detection was carried with the MACS program (detected peaks are given in bed files)
ERalpha target sites were annotated to genomic regions using HOMER software (annotated binding sites are given in text file)
Peak intersections and their genomic coordinates were found using Bedtools software
The significance of differences between two analyzed samples was estimated using MACS software; the FDR=0.05 level was selected as the significance threshold.
Genome_build: hg19
Supplementary_files_format_and_content: bed - detected peaks, can be open in text editors/Excel; txt - annotated binding sites, can be opened in text editors/Excel.

source_name: MCF7 cells

growth_protocol: The wild-type MCF7 cells were purchased from ATCC (HTB-22) and used as a primary model. Cells were grown in DMEM/F12 medium supplemented with 10% fetal bovine serum and antibiotic-antimycotic cocktail (penicillin, streptomycin, amphotericin) at 37 °C in a humidified 5% CO2 atmosphere.

extract_protocol:
At the appointed experimental points culture medium was removed and fixation was performed using 1% formaldehyde in PBS for 12 min at RT with rotating. Formaldehyde fixation was quenched by glycine (125 mM final concentration) and then nuclei were isolated using buffers and protocol from iDeal ChIP-seq Kit for Transcription Factors (Diagenode). Chromatin of nuclei re-suspended in 200 µl was sheared using Bioruptor® PLUS combined with the Bioruptor® Water cooler & Single Cycle Valve (at HIGH power setting) with 20 cycles of 30 sec shearing followed by 30 sec of standby; chromatin fragments with approximate length 100-600 bp were obtained. Chromatin immunoprecipitation was carried out using the iDeal ChIP-seq Kit for Transcription Factors (Diagenode) with 30μg of chromatin and 4µl/sample of anti-ERalpha mouse monoclonal antibody (Diagenode, C15100066) or without antibody (mock-IP), according to the manufacturer protocol.
Immunoprecipitated DNA fragments from four biological ChIP replicates was pooled. ChIP samples and input DNA (mixed input DNA of all modified cell lines and treatments) were sequenced using the HiSeq 1500 system with TruSeq workflow (Illumina)

treatment_protocol: Cells were seeded on 10cm2 culture plates. Next day the medium was replaced into phenol-free DMEM/F12 medium supplemented with 5% dextran-activated charcoal-stripped FBS and 48 hours later cells 17β-estradiol was added to final concentration of 10nM for indicated time (30minutes and 1h).

tag: cell line

tag: tumor

value: adenocarcinoma

tag: Sex

value: female

value: 69 years

value: breast

value: KO#2 (clone with HSF1 knockout)

value: Eralpha monoclonal antibody (Diagenode, C15100066)


title: Bone marrow – JAK2 – rep3


title: MCF7 cells, KO#2 (clone with HSF1 knockout)_control

description: MCF7 KO#2 (clone with HSF1 knockout) - untreated control

tag: treatment

value: control


title: MCF7 cells, KO#2 (clone with HSF1 knockout)_estrogen_30min

description: MCF7 KO#2 (clone with HSF1 knockout) - estrogen treated for 30 minutes (10nM)


title: tumor sample 32


title: Tg4510_6mo_Sample_198-18-Tg6

description:
Total RNA - rRNA depeletion
R547.198.18.Tg6_S90_L008

value: 6 months


title: Tg4510_6mo_Sample_197-17-Tg6

description:
Total RNA - rRNA depeletion
R547.197.17.Tg6_S91_L008


title: Bone marrow – JP – rep4

tag: strain


title: MCF7 cells, MIX (pooled control clones)_estrogen_1h

description: MCF7 MIX (pooled control clones) - estrogen treated for 1h (10nM)

tag: genotype

value: MIX (pooled control clones)


title: MCF7 cells, WT_estrogen_1h

description: MCF7 wild type - estrogen treated for 1h (10nM)

tag: tissue

value: WT


title: nTg_9mo_Sample_204-6-Tg9

description:
Total RNA - rRNA depeletion
R547.204.6.Tg9_S84_L008

value: Total Brain Lysate


title: Bone marrow – JAK2 – rep2


title: nTg_6mo_Sample_195-15-Tg6

description:
Total RNA - rRNA depeletion
R547.195.15.Tg6_S93_L008


title: MCF7 cells, MIX (pooled control clones)_estrogen_30min

description: MCF7 MIX (pooled control clones) - estrogen treated for 30 minutes (10nM)


title: Bone marrow – JP – rep2


title: MCF7 cells, WT_estrogen_30min

description: MCF7 wild type - estrogen treated for 30 minutes (10nM)


title: Bone marrow – JAK2 – rep1


title: MCF7 cells, WT_control

description: MCF7 wild type - untreated control


title: MCF7 cells, MIX (pooled control clones)_control

description: MCF7 MIX (pooled control clones) - untreated control


title: Bone marrow – JP – rep1


title: nTg_6mo_Sample_193-13-Tg6

description:
Total RNA - rRNA depeletion
R547.193.13.Tg6_S73_L007


title: Tg4510_6mo_Sample_196-16-Tg6

description:
Total RNA - rRNA depeletion
R547.196.16.Tg6_S92_L008


title: Bone marrow – WT – rep2

value: Wild type


title: Sample 35: maternal protein restriction RNAseq

city: Botucatu

first: Bruno

middle: Evaristo de Almeida

last: Fantinatti

state: São Paulo

address: Prof Antonio Celso Wagner Zanin

department: Morphology

country: Brazil

institute: Unesp

data_processing:
Illumina data were recovered and adaptors were removed by using Trimmomatic.
Read quality filtering was carried out by using Trimmomatic.
Reads were aligned against Rattus novergicus genome by using Hisat2.
Read-counts were extracted ba using featureCounts
Differential expression analysis were carried out by using R and DESeq2
Genome_build: Rattus novergicus genome build GCF_000001895.5_Rnor_6.0
Supplementary_files_format_and_content: raw.counts and normalized.counts both contains raw data and normalized counts

organism: Rattus norvegicus

source_name: Skeletal muscle

extract_protocol:
Skeletal muscle were removed, flash frozen on liquid nitrogen, and RNA was harvested using Trizol reagent.
Illumina TruSeq RNA Sample Prep Kit (Cat # FC-122-1001) was used with 1 ug of total RNA for construction of sequencing libraries.

value: Skeletal muscle

value: post natal day 540

value: maternal protein restriction


title: Tg4510_6mo_Sample_191-11-Tg6

description:
Total RNA - rRNA depeletion
R547.191.11.Tg6_S75_L007

value: non-transgenic


title: MCF7 cells, Input

description: input sample (mix of all modified cell lines and treatments)

value: mix of all modified cell lines


title: Sample 23: control RNAseq


title: Bone marrow – WT – rep4

value: Bone marrow derived LKS (Lineage-/cKit+/Sca1+) cells

value: Bone marrow


title: nTg_6mo_Sample_184-4-Tg6

description:
Total RNA - rRNA depeletion
R547.184.4.Tg6_S82_L007


title: Sample 33: maternal protein restriction RNAseq


title: Sample 12: maternal protein restriction RNAseq


title: Bone marrow – WT – rep3


title: A1

city: Chiyoda-ku

first: Shogo

last: Okazaki

state: Tokyo

address: 1-8-13 Kanda-Surugadai

department: School of Dentistry

country: Japan

institute: Nihon University

description: Gene expression data

data_processing:
Spatial transcriptomics raw sequencing data was processed using the Space Ranger v1.2.2 (10x Genomics) with the GRCm38 genome assembly as reference and transcript counts quantified for each annotated gene within every spot.
Using Space Ranger’s count, reads were aligned to the mm10 mouse reference genome, and transcript counts quantified for each annotated gene within every spot. The resulting UMI count matrices (genes × spots) were then provided as input to Seurat suite (version 3.2.0).
Genome_build: GRCm38 (mm10)
Supplementary_files_format_and_content: Genes by barcode counts matrices in HDF5 binary data format, PNG of all replicate images (tissue_hires_image.png), JSON file containing scaling factors that converts pixel positions (scalefactors_json.json), and text file containing spot barcode position information (tissue_positions_list.csv).

source_name: gastric tumor

growth_protocol: Fresh frozen dissected mouse gastric tumor.

extract_protocol:
For Visium, the section was cut at 10 µm thickness and mounted onto Visium slide capture areas. Sequencing libraries were prepared following the manufacturer’s protocol. After tissue staining, bright-field images were taken as described in the Spatial Transcriptomics procedure. Tissue permeabilization was performed for 12 minutes, as established in the TO assay. The Visium Spatial Gene Expression Slide & Reagent kit (10X Genomics) was used to generate sequencing libraries for Visium samples.
Visium spatial gene expression libraries were prepared for sequencing using 10x Genomics protocols. Enzymatic fragmentation and size selection are used to optimize the cDNA amplicon size. P5, P7, i7 and i5 sample indexes, and TruSeq Read 2 (read 2 primer sequence) are added via End Repair, A-tailing, Adaptor Ligation, and PCR. The final libraries contain the P5 and P7 primers used in Illumina amplification.

value: GAN-KP tumor


title: nTg_6mo_Sample_192-12-Tg6

description:
Total RNA - rRNA depeletion
R547.192.12.Tg6_S74_L007


title: Sample 32: maternal protein restriction RNAseq


title: Sample 3: control RNAseq


title: cDNA_BR3_Downstream

city: Amsterdam

first: Bas

last: van Steensel

address: Plesmanlaan 121

institute: The Netherlands Cancer Institute (NKI)

description:
Quantification of barcodes in cDNA
ActivitiesAndBoostIndices_Downstream.tsv

data_processing:
Basecalling and filtering were performed using standard software of the Illumina HiSeq 2500 or MiSeq
For cDNA and pDNA samples, the barcode sequence was extracted from the read (using a custom python scripts) and counted.
For iPCR samples the insert sequence was aligned to a custom genome (using bowtie2) containing only the target sequences extracted from the mm10 genome, and the barcode was extracted from the ead using a custom python script.
Barcodes were clustered using Starcode (version 1.1) {Zorita, 2015, 25638815} to remove errors from barcode sequencing.
barcodes present in multiple libraries or matched with multiple element combinations were removed from the data
Per unique singlet or combination an activity value was calculated as the ratio of the mean readcount in the RNA samples and the mean readcount in the pDNA library samples across all barcodes assigned to the singlet or combination.
Genome_build: mm10
Supplementary_files_format_and_content: The processed data files are tables in TSV format containig the identity and orientation of the fragments of each combination, their genomic coordinates, the activity of the single elements and the activity of the combination. For the Boost indices tables the Boost index was calculated as a log2 ratio of the activity of the combination over the median activity of all the combinations of the Promoter involved in the combination.

source_name: mouse embryonic stem cells

extract_protocol:
For iPCR samples: the combination of barcode and element(s) was excised from the plasmid by digestion with I-ceuI; this fragment was circularised; remaining linear fragments were destroyed; and circular fragments were linearised again with I-sceI. These linear fragments were amplified by PCR with sequencing adaptors. The final product was sequenced on an Illumina MiSeq platform using 150 bp paired-end reads. This process was done separately for each of the libraries. For mor details see van Arensbergen et a., 2017 (PMID: 28024146). For pDNA samples: For each library 1 µg of plasmid was digested with I-sceI in order to linearise the plasmid. Then, barcodes were amplified by PCR from 50 ng of material using the same primers and reaction conditions as in the amplification of cDNA in the Upstream assay, but only 9 cycles of amplification were used (1 min 96 °C, 9×(15 s 96 °C, 15 s 60 °C, 15 s 72 °C)). For each library, two technical replicates were carried out by using different index primers for each replicate. Samples were sequenced on an Illumina 2500 HiSeq platform with 65bp single end reads. For cDNA samples: RNA was extracted and processed for sequencing as described {van Arensbergen, 2017, 28024146} with a few modifications. Cells were harvested 24 h after transfection, resuspended in Trisure (#BIO-38032; Bioline) and frozen at -80 °C until further processing. From the Trisure suspension, the aqueous phase containing the RNA was extracted and loaded into RNA extraction columns (#K0732, Thermo Scientific). Total RNA was divided into 10 µl reactions containing 5 μg of RNA and was treated for 30 mins with 10 units of DNAse I (#04716728001; Roche). Then DNAse I was inactivated by addition of 1 ul of 1 μl of 25 mM EDTA and incubation at 70°C for 10 min. For the Upstream Assay the cDNA was produced and amplified by PCR as described {van Arensbergen, 2017, 28024146}. Per biological replicate 8 to 10 reactions were carried  in parallel in order to cover enough barcode complexity of the library. For the Downstream Assay the RNA was extracted and processed the same way until cDNA production. Here, cDNA was produced using a specific primer. Then cDNA was amplified in 2 steps (nested PCRs) in order to make the reaction strand-specific. The first PCR reaction run for 10 cycles (1 min 96 °C, 10×(15 s 96 °C, 15 s 60 °C, 15 s 72 °C)) using primers (index variants of) 285JvA (containing the S2, index and p7 adaptor) and 305JvA. Each 20 μl RT reaction was amplified in a 100-μl PCR reaction with MyTaq Red mix. The second PCR reaction was performed using 10ul of the product of the previous reaction in 100 μl reactions  (1 min 96 °C, 8×(15 s 96 °C, 15 s 60 °C, 15 s 72 °C)) using the same index variant primer and primer 437JvA (containing the S1, and p5 adaptor). For both Upstream and Downstream assays, the resulting PCR products were sequenced on an Illumina 2500 HiSeq platform with 65bp single end reads.
PCR

value: mESC


title: Tg4510_6mo_Sample_189-9-Tg6

description:
Total RNA - rRNA depeletion
R547.189.9.Tg6_S77_L007


title: Patient 26 NPH 0026

city: Obu

first: Yuya

last: Asanomi

state: Aichi

address: 7-430 Morioka-cho

institute: National Center for Geriatrics and Gerontology

hyb_protocol: Hybridized for 16 h at 32 ºC with rotary shaker (250 rpm). Hybridization buffer and washing protocol was attached in the 3D-Gene® miRNA oligo chip kit.

scan_protocol: 3D-Gene® Scanner (Toray Industries, Inc.) was used for scanning. Images were quantified using Extraction version 2.0.0.6 (Toray Industries, Inc.)

data_processing: Mean and standard deviation (SD) were calculated using a set of pre-selected negative control signals (background signals) that the top and bottom 5% of which were removed. Signal values greater than mean + 2SD of the background signals were replaced using log2(signal – mean) and labeled effective signals. The remaining signal values were replaced by the minimum of the effective signals – 0.1. Undetected signal values were replaced by the average signal of each miRNA signals. To normalize the signals across different microarrays, a set of pre-selected internal control miRNAs (miR-149-3p, miR-2861 and miR-4463), which had been stably detected in more than 500 serum samples, was used. Each miRNA signal value was standardized with the ratio of the average signal of the three internal control miRNA signals30.

source_name: serum

label_protocol: miRNA was labeled using 3D-Gene® miRNA Labeling kit in accordance with the manufacturer's instructions.

extract_protocol: Total RNA was extracted each from 300uL serum samples using 3D-Gene® RNA extraction reagent from liquid sample kit (Toray Industries, Inc.).

value: serum

tag: diagnosis

value: NPH

value: female


title: Sample 28: control RNAseq

value: control


title: nTg_6mo_Sample_181-1-Tg6

description:
Total RNA - rRNA depeletion
R547.181.1.Tg6_S62_L006

value: 6 months


title: cDNA_BR2_Downstream


title: Sample 13: maternal protein restriction RNAseq


title: Sample 15: maternal protein restriction RNAseq


title: Sample 9: control RNAseq


title: Sample 29: control RNAseq


title: nTg_6mo_Sample_183-3-Tg6

description:
Total RNA - rRNA depeletion
R547.183.3.Tg6_S83_L007


title: Sample 8: control RNAseq


title: Bone marrow – WT – rep1


title: Y_OE_2

first: Pengyu

address: 555 Zu Chong Zhi Road , Zhang Jiang Hi-Tech Park, Pudong

institute: Shanghai Institute of Materia Medica

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to Homo sapiens whole genome using hisat v2.1.0 with default parameter
The expression level of each transcript was calculated according to the (TPM) method. RSEM v1.3.1 was used to quantify gene abundances
Differential gene expression analysis was done using R package DESeq2 v1.24.0
Genome_build: Human NCBI genome build 38
Supplementary_files_format_and_content: tab-delimited text files include TPM values for each Sample

source_name: cell line

extract_protocol:
Total RNA was extracted from BxPC-3 cells using TRIzol® Reagent according the manufacturer’s instructions (Invitrogen) and genomic DNA was removed using DNase I (TaKara). Then RNA quality was determined by 2100 Bioanalyser (Agilent) and quantified using the ND-2000 (NanoDrop Technologies).
RNA-seq transcriptome librariy was prepared following TruSeqTM RNA sample preparation Kit from Illumina (San Diego, CA) using 1μg of total RNA. Shortly, messenger RNA was isolated according to polyA selection method by oligo(dT) beads and then fragmented by fragmentation buffer firstly. Secondly double-stranded cDNA was synthesized using a SuperScript double-stranded cDNA synthesis kit (Invitrogen, CA) with random hexamer primers (Illumina). Then the synthesized cDNA was subjected to end-repair, phosphorylation and ‘A’ base addition according to Illumina’s library construction protocol. Libraries were size selected for cDNA target fragments of 300 bp on 2% Low Range Ultra Agarose followed by PCR amplified using Phusion DNA polymerase (NEB) for 15 PCR cycles. After quantified by TBS380, paired-end RNA-seq sequencing library was sequenced with the Illumina NovaSeq 6000 sequencer (2 × 150bp read length)

treatment_protocol: DMSO, 20 μM ZG111, sterile water, 1.0 μg/mL Dox

value: pancreatic tumor

value: BxPC-3 cell line

value: 1.0 microg/mL Dox


title: Y_OE_1


title: Tg4510_6mo_Sample_186-6-Tg6

description:
Total RNA - rRNA depeletion
R547.186.6.Tg6_S80_L007

value: Total Brain Lysate


title: cDNA_BR1_Downstream


title: Y_OE_3


title: Y_0_2

value: Sterile water


title: Y_0_1


title: Y_0_3


title: Tg4510_3mo_Sample_179-17-Tg3

description:
Total RNA - rRNA depeletion
R547.179.17.Tg3_S64_L006

value: 3 months


title: nTg_3mo_Sample_180-18-Tg3

description:
Total RNA - rRNA depeletion
R547.180.18.Tg3_S63_L006

value: non-transgenic


title: pDNA_BR1_Downstream

description:
Quantification of barcodes on plasmid library mix for input normalisation
ActivitiesAndBoostIndices_Downstream.tsv


title: BX_111_3

value: 20 microM ZG111


title: Tg4510_3mo_Sample_178-16-Tg3

description:
Total RNA - rRNA depeletion
R547.178.16.Tg3_S65_L006


title: pDNA_BR2_Downstream


title: BX_111_1


title: BX_111_2


title: BX_DM_3

value: DMSO


title: BX_DM_2


title: cDNA_BR3_Tfcp2l1_Upstream

description:
Quantification of barcodes in cDNA
Activities_allcombinations_Upstream.tsv
BoostIndices_cCRE-P_Upstream.tsv


title: cDNA_BR1_Tfcp2l1_Upstream


title: cDNA_BR2_Tfcp2l1_Upstream


title: nTg_3mo_Sample_176-14-Tg3

description:
Total RNA - rRNA depeletion
R547.176.14.Tg3_S67_L006


title: BX_DM_1


title: pDNA_BR2_Tfcp2l1_Upstream

description:
Quantification of barcodes on plasmid library mix for input normalisation
Activities_allcombinations_Upstream.tsv
BoostIndices_cCRE-P_Upstream.tsv


title: H9_HSAN_D7_noDox-2

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

institute: Yale University

description: Cardiomyocytes WT H9_rtTA inducible HSAN1 Knockin no doxycycline day 7 rep2

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

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

value: ES-derived cardiomyocytes

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

value: WT AAVS1-KI SPTLC1 C133W (HSAN1)/ rtTA

tag: treatmant

value: Doxycycline minus


title: Tg4510_3mo_Sample_175-13-Tg3

description:
Total RNA - rRNA depeletion
R547.175.13.Tg3_S68_L006


title: H9_HSAN_D7_Dox-1

description: Cardiomyocytes WT H9_rtTA inducible HSAN1 Knockin treated with doxycycline day 7 rep1

value: Doxycycline plus


title: H9_ESC-1

description: WT H9 ESC day 0 rep1

value: WT

value: untreated


title: H9_HSAN_D7_Dox-2

description: Cardiomyocytes WT H9_rtTA inducible HSAN1 Knockin treated with doxycycline day 7 rep2


title: H9_HSAN_D7_noDox-1

description: Cardiomyocytes WT H9_rtTA inducible HSAN1 Knockin no doxycycline day 7 rep1


title: nTg_3mo_Sample_172-10-Tg3

description:
Total RNA - rRNA depeletion
R547.172.10.Tg3_S71_L006


title: nTg_3mo_Sample_173-11-Tg3

description:
Total RNA - rRNA depeletion
R547.173.11.Tg3_S70_L006


title: Tg4510_3mo_Sample_174-12-Tg3

description:
Total RNA - rRNA depeletion
R547.174.12.Tg3_S69_L006


title: H9_D19_Veh-3

description: WT H9 Cardiomyocytes vehicle treated day 19 rep2

value: Vehicle


title: pDNA_BR1_Tfcp2l1_Upstream

value: mESC


title: nTg_3mo_Sample_177-15-Tg3

description:
Total RNA - rRNA depeletion
R547.177.15.Tg3_S66_L006


title: Tg4510_3mo_Sample_170-8-Tg3

description:
Total RNA - rRNA depeletion
R547.170.8.Tg3_S49_L005


title: cDNA_BR3_Klf2_Nanog_NC_Upstream


title: cDNA_BR2_Klf2_Nanog_NC_Upstream


title: cDNA_BR1_Klf2_Nanog_NC_Upstream


title: H9_D19_Veh-2

description: WT H9 Cardiomyocytes vehicle treated day 19 rep1


title: DKO_ESC-2

description: DKO H9 ESC day 0 rep2


title: H9_D19_Myr-1

description: WT H9 Cardiomyocytes myriocin treated day 19 rep1

value: myriocin treated


title: H9_D19_Myr-3

description: WT H9 Cardiomyocytes myriocin treated day 19 rep2


title: H9_ESC-2

description: WT H9 ESC day 0 rep2


title: DKO_D19_Veh-2

description: DKO H9 Cardiomyocytes vehicle treated day 19 rep2


title: DKO_ESC-1

description: DKO H9 ESC day 0 rep1


title: nTg_3mo_Sample_167-5-Tg3

description:
Total RNA - rRNA depeletion
R547.167.5.Tg3_S3_L001


title: DKO_D19_Veh-1

description: DKO H9 Cardiomyocytes vehicle treated day 19 rep1


title: DKO_D19_Myr-3

description: DKO H9 Cardiomyocytes myriocin treated day 19 rep2


title: pDNA_BR1_Klf2_Nanog_NC_Upstream

description:
Quantification of barcodes on plasmid library mix for input normalisation
ActivitiesAndBoostIndices_Downstream.tsv


title: pDNA_BR2_Klf2_Nanog_NC_Upstream


title: Tg4510_3mo_Sample_166-4-Tg3

description:
Total RNA - rRNA depeletion
R547.166.4.Tg3_S39_L004


title: H9_HSAN_D9_Dox-2

description: Cardiomyocytes WT H9_rtTA inducible HSAN1 Knockin treated with doxycycline day 9 rep2


title: DKO_D19_Myr-1

description: DKO H9 Cardiomyocytes myriocin treated day 19 rep1


title: DKO_HSAN_D9_Dox-1

description: Cardiomyocytes DKO H9_rtTA inducible HSAN1 Knockin treated with doxycycline day 9 rep1

value: DKO AAVS1-KI SPTLC1 C133W (HSAN1)/ rtTA


title: DKO_HSAN_D9_Dox-2

description: Cardiomyocytes DKO H9_rtTA inducible HSAN1 Knockin treated with doxycycline day 9 rep2


title: DKO_HSAN_D9_noDox-2

description: Cardiomyocytes DKO H9_rtTA inducible HSAN1 Knockin no doxycycline day 9 rep2


title: W2 RNA-seq rep2

city: Norfolk

first: Sanjeeva

middle: Reddy

last: Dodlapati

state: VA

address: E&CS, odu

department: Computer Science

institute: old dominion university

description:
B31
count.gene.csv

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

value: Myocardial infarction

tag: time point


title: D7 RNA-seq rep2

description:
C26
count.gene.csv


title: rheb BAD KO

city: guangzhou

first: zhipeng

last: zou

state: guangdong

address: tonghe road

department: Cell Biology

institute: southern medical university

data_processing:
Total RNA quantity and purity were analyzed using a Bioanalyzer 2100 and an RNA 6000 Nano LabChip kit (Agilent), with RNA integrity values of >7.0.
The final cDNA library were created in accordance with the protocol for the TruSeq RNA Sample Preparation v.2
Before assembly, low-quality reads were removed using Trimmomatic software.
Sequencing reads were aligned to the reference genome using the HISAT2 package.
The mapped reads of each sample were assembled and counted using the featureCounts package and a matrix of read counts was generated.
Genome_build: mm10
Supplementary_files_format_and_content: read counts matrix

source_name: brown adipose tissue

growth_protocol: Mice lacking Rheb in the brown adipocyte lineage were generated by mating RhebFL/FL mice with UCP1-Cre mice.

extract_protocol:
Total RNA was extracted with Trizol.
Following purification, the mRNA was fragmented into small pieces using divalent cations under elevated temperature. Then the cleaved RNA fragments were reverse-transcribed to create the final cDNA library in accordance with the protocol for the TruSeq RNA Sample Preparation v.2 (cat. no. RS-122-2001, RS-122-2002) (Illumina)

value: littermates with rheb knockout in brown adipocytes

value: male


title: H9_HSAN_D9_Dox-1

description: Cardiomyocytes WT H9_rtTA inducible HSAN1 Knockin treated with doxycycline day 9 rep1


title: W4 RNA-seq rep1

description:
C24
count.gene.csv


title: W4 RNA-seq rep2

description:
C25
count.gene.csv


title: D7 RNA-seq rep1

description:
C20
count.gene.csv


title: control

value: control littermates


title: H9_HSAN_D9_noDox-2

description: Cardiomyocytes WT H9_rtTA inducible HSAN1 Knockin no doxycycline day 9 rep2


title: control1

source_name: BMSCs

value: control


title: H9_HSAN_D9_noDox-1

description: Cardiomyocytes WT H9_rtTA inducible HSAN1 Knockin no doxycycline day 9 rep1

value: ES-derived cardiomyocytes


title: D3 RNA-seq rep2

description:
C18
count.gene.csv


title: H9_D9_Veh-2

description: WT H9 Cardiomyocytes vehicle treated day 9 rep2

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


title: 4DNEXB7EWKCM (TsixStop_d0), 4DNEXJAHCEIN (TsixStop_d11), 4DNEXLZWN9VH (TsixStop_d7), 4DNEXV3C383J (TsixStop_d3)

last: DCIC

address: 10 Shattuck St

institute: 4D Nucleome - Data Coordination and Integration Center

description:
lab: Christine Disteche, UW
award: 1U54DK107979-01
4DN accession: 4DNEXB7EWKCM, 4DNEXJAHCEIN, 4DNEXLZWN9VH, 4DNEXV3C383J
description: 4DNEXB7EWKCM - 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) 4DNFI2G4RTJP should be used in parsing the associated FASTQs
4DNEXJAHCEIN - sci-Hi-C on a differentiation time course of ES_Tsix-stop cells - this experiment is day 11 EB cells and to obtain reads specific for these cells the label TsixStop_d11 from the barcode file(s) 4DNFI2G4RTJP should be used in parsing the associated FASTQs
4DNEXLZWN9VH - 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) 4DNFI2G4RTJP should be used in parsing the associated FASTQs
4DNEXV3C383J - sci-Hi-C on a differentiation time course of ES_Tsix-stop cells - this experiment is day 3 EB cells and to obtain reads specific for these cells the label TsixStop_d3 from the barcode file(s) 4DNFI2G4RTJP 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/4DNEXB7EWKCM/ https://data.4dnucleome.org/experiments-hi-c/4DNEXJAHCEIN/ https://data.4dnucleome.org/experiments-hi-c/4DNEXLZWN9VH/ https://data.4dnucleome.org/experiments-hi-c/4DNEXV3C383J/
This record includes combined data from multiple BioSamples: SAMN21435451, SAMN21435447, SAMN21435444, SAMN21435428

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: 4DNFI2G4RTJP.txt
genome_assembly: GRCm38
description: Bar codes (A2) used for selection of specific reads in the following Disteche Lab sci-HiC experiments with experiment selection tag in parens: 4DNEXB7EWKCM (TsixStop_d0), 4DNEXV3C383J (TsixStop_d3), 4DNEXLZWN9VH (TsixStop_d7), 4DNEXJAHCEIN (TsixStop_d11)
file_type: barcodes
file_format: txt

source_name: Multiple biosources: undifferentiated ES_Tsix-stop, or ES_Tsix-stop 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: F1 2-1 mESC line

value: 129/Sv X Cast

value: female

tag: description

value: Day 0, 3, 7, or 11 ES_Tsix-stop cells from an embryoid body differentiaton time course experiment A

value: stem cell or embryoid body

value: stem cells or in vitro differentiated cells

tag: url


title: rhebCKO2

value: rheb knockout in brown adipocytes


title: DKO_D9_Sph-2

description: DKO H9 Cardiomyocytes D-erythro-sphingosine treated day 9 rep2

value: D-erythro-sphingosine


title: W2 RNA-seq rep1

description:
C22
count.gene.csv


title: rhebCKO1


title: DKO_HSAN_D9_noDox-1

description: Cardiomyocytes DKO H9_rtTA inducible HSAN1 Knockin no doxycycline day 9 rep1

value: DKO AAVS1-KI SPTLC1 C133W (HSAN1)/ rtTA

value: Doxycycline minus


title: control2


title: H9_D9_Sph-1

description: WT H9 Cardiomyocytes D-erythro-sphingosine treated day 9 rep1

value: WT


description:
lab: Christine Disteche, UW
award: 1U54DK107979-01
4DN accession: 4DNEXEE1N4JI, 4DNEXMNAHJPG, 4DNEXJNGKL32, 4DNEXXNEYDTM, 4DNEXPLD13JA, 4DNEXTLVDZQP
description: 4DNEXEE1N4JI - 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) 4DNFIFQWKVUQ, 4DNFIF8IX3B6 should be used in parsing the associated FASTQs
4DNEXMNAHJPG - sci-Hi-C on a differentiation time course of F121-6 cells - this experiment is undifferentiated day 0 cells rep 2 and to obtain reads specific for these cells the label F121_d0 from the barcode file(s) 4DNFIFQWKVUQ, 4DNFIF8IX3B6 should be used in parsing the associated FASTQs
4DNEXJNGKL32 - sci-Hi-C on a differentiation time course of ES_Tsix-stop cells - this experiment is differentiated NPCs rep 2 and to obtain reads specific for these cells the label TsixStop_NPC_P7-2 from the barcode file(s) 4DNFIF8IX3B6, 4DNFI22IEKS3 should be used in parsing the associated FASTQs
4DNEXXNEYDTM - sci-Hi-C on a differentiation time course of ES_Tsix-stop cells - this experiment is differentiated NPCs rep 1 and to obtain reads specific for these cells the label TsixStop_NPC_P7-1 from the barcode file(s) 4DNFIF8IX3B6, 4DNFI22IEKS3 should be used in parsing the associated FASTQs
4DNEXPLD13JA - sci-Hi-C on a differentiation time course of F121-6 cells - this experiment is differentiated NPCs and to obtain reads specific for these cells the label F121_NPC from the barcode file(s) 4DNFIFQWKVUQ, 4DNFI22IEKS3 should be used in parsing the associated FASTQs
4DNEXTLVDZQP - sci-Hi-C on a differentiation time course of F123 cells - this experiment is differentiated NPCs and to obtain reads specific for these cells the label 123_NPC from the barcode file(s) 4DNFIFQWKVUQ, 4DNFI22IEKS3 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/4DNEXEE1N4JI/ https://data.4dnucleome.org/experiments-hi-c/4DNEXMNAHJPG/ https://data.4dnucleome.org/experiments-hi-c/4DNEXJNGKL32/ https://data.4dnucleome.org/experiments-hi-c/4DNEXXNEYDTM/ https://data.4dnucleome.org/experiments-hi-c/4DNEXPLD13JA/ https://data.4dnucleome.org/experiments-hi-c/4DNEXTLVDZQP/
This record includes combined data from multiple BioSamples: SAMN21435436, SAMN21435427, SAMN21435458, SAMN21435457, SAMN21435430, SAMN21435446

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: 4DNFIFQWKVUQ.txt
genome_assembly: GRCm38
description: Bar codes (A3) used for selection of specific reads in the following Disteche Lab sci-HiC experiments with experiment selection tag in parens: 4DNEXMNAHJPG (F121_d0), 4DNEXEE1N4JI (F123_d0), 4DNEXPLD13JA (F121_NPC), 4DNEXTLVDZQP (F123_NPC)
file_type: barcodes
file_format: txt
***************
file name: 4DNFIF8IX3B6.txt
genome_assembly: GRCm38
description: Bar codes (A4) used for selection of specific reads in the following Disteche Lab sci-HiC experiments with experiment selection tag in parens: 4DNEXMNAHJPG (F121_d0), 4DNEXEE1N4JI (F123_d0), 4DNEXXNEYDTM (TsixStop_NPC_P7-1), 4DNEXJNGKL32 (TsixStop_NPC_P7-2)
file_type: barcodes
file_format: txt
***************
file name: 4DNFI22IEKS3.txt
genome_assembly: GRCm38
description: Bar codes (A5) used for selection of specific reads in the following Disteche Lab sci-HiC experiments with experiment selection tag in parens: 4DNEXXNEYDTM (TsixStop_NPC_P7-1), 4DNEXJNGKL32 (TsixStop_NPC_P7-2), 4DNEXPLD13JA (F121_NPC), 4DNEXTLVDZQP (F123_NPC)
file_type: barcodes
file_format: txt

source_name: F123-CASTx129, F121-6-CASTx129, ES_Tsix-stop differentiated to neuronal stem cell, F121-6-CASTx129 differentiated to neuronal stem cell, F123-CASTx129 differentiated to neuronal stem cell

value: pooled male and female

value: Day 0 F123 or F121-6 cells from an embryoid body differentiaton time course experiment B, or Neural precursor cells clonally derived from day 11 ES_Tsix-stop, F121-6, or F123 cells from an embryoid body differentiaton time course experiment A

value: stem cell, neuronal stem cell


title: H9_D9_Deoxy-1

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


title: H9_D9_Veh-1

description: WT H9 Cardiomyocytes vehicle treated day 9 rep1

value: Vehicle


title: Uninj RNA-seq rep2

description:
C16
count.gene.csv

value: Cardiac fibroblasts

value: Uninjured


title: H9_D9_Deoxy-2

description: WT H9 Cardiomyocytes 1-deoxysphingosine treated day 9 rep2

value: ES-derived cardiomyocytes

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


title: D3 RNA-seq rep1

description:
C17
count.gene.csv

value: Myocardial infarction


title: DKO_D9_Deoxy-2

description: DKO H9 Cardiomyocytes 1-deoxysphingosine treated day 9 rep2


title: DKO_D9_Sph-1

description: DKO H9 Cardiomyocytes D-erythro-sphingosine treated day 9 rep1


title: H9_D9_Sph-2

description: WT H9 Cardiomyocytes D-erythro-sphingosine treated day 9 rep2


title: Uninj RNA-seq rep1

description:
C15
count.gene.csv


title: 4DNEXMN3ZJ4X (d0), 4DNEXRMWXOKT (d3), 4DNEXVG7LXZE (d11), 4DNEXWHKWMSY (d7)

description:
lab: Christine Disteche, UW
award: 1U54DK107979-01
4DN accession: 4DNEXMN3ZJ4X, 4DNEXRMWXOKT, 4DNEXVG7LXZE, 4DNEXWHKWMSY
description: 4DNEXMN3ZJ4X - sci-Hi-C on a differentiation time course of F121-6 cells - this experiment is undifferentiated day 0 cells rep 1 and to obtain reads specific for these cells the label d0 from the barcode file(s) 4DNFI15SLK95 should be used in parsing the associated FASTQs
4DNEXRMWXOKT - sci-Hi-C on a differentiation time course of F121-6 cells - this experiment is day 3 EB cells and to obtain reads specific for these cells the label d3 from the barcode file(s) 4DNFI15SLK95 should be used in parsing the associated FASTQs
4DNEXVG7LXZE - sci-Hi-C on a differentiation time course of F121-6 cells - this experiment is day 11 EB cells and to obtain reads specific for these cells the label d11 from the barcode file(s) 4DNFI15SLK95 should be used in parsing the associated FASTQs
4DNEXWHKWMSY - 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 d7 from the barcode file(s) 4DNFI15SLK95 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/4DNEXMN3ZJ4X/ https://data.4dnucleome.org/experiments-hi-c/4DNEXRMWXOKT/ https://data.4dnucleome.org/experiments-hi-c/4DNEXVG7LXZE/ https://data.4dnucleome.org/experiments-hi-c/4DNEXWHKWMSY/
This record includes combined data from multiple BioSamples: SAMN21435438, SAMN21435445, SAMN21435441, SAMN21435449

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: 4DNFI15SLK95.txt
genome_assembly: GRCm38
description: Bar codes (A1) used for selection of specific reads in the following Disteche Lab sci-HiC experiments with experiment selection tag in parens: 4DNEXMN3ZJ4X (d0), 4DNEXRMWXOKT (d3), 4DNEXWHKWMSY (d7), 4DNEXVG7LXZE (d11)
file_type: barcodes
file_format: txt

source_name: Multiple biosources: undifferentiated F121-6-CASTx129, or F121-6-CASTx129 differentiated to embryoid body

value: 129/Sv X Cast

value: female

value: Day 0, 3, 7, or 11 F121-6 cells from an embryoid body differentiaton time course experiment A