title: Degradome.mouse.testis.Mov10l1CKOControl.adult.rep1

description: Degradome

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

value: adult

value: RNA degradation products


title: EW7-HDAC1 ko, clone 3

status: Public on Oct 20 2021

type: RNA

city: Berlin

first: Guenther

middle: HS

last: Richter

address: Augustenburger Platz 1

department: Department of Pediatrics, Division of Oncology and Hematology

country: Germany

institute: Charité - Universitätsmedizin Berlin

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

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

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

data_processing: RMA normalization.

label: biotin

molecule: total RNA

organism: Homo sapiens

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

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

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

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

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

tag: soft tissue

value: Ewing sarcoma, 20 year old female


title: Degradome.mouse.testis.Mov10l1CKOTg.adult.rep1

type: SRA

city: Rochester

first: Xin

last: Li

state: NY

address: 601 Elmwood Ave

department: Biochemistry and Biophysics

country: USA

institute: University of Rochester

description: Degradome

library_source: transcriptomic

organism: Mus musculus

source_name: testis

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

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

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

tag: tissue

value: whole testis

tag: strain

tag: genotype

tag: age

tag: treatment

tag: molecule subtype


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

description: Ribo-seq

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

molecule: polyA RNA

value: Ribosome footprints

tag: rip antibody

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


title: S82

city: Changsha

first: Touming

last: Liu

address: NO.348, western road of xianjia lake

department: Institute of Bast Fiber Crops

country: China

institute: Chinese Academy of Agricultural Sciences

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

organism: Allium sativum

source_name: Chalingzipisuan

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

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

value: bulb

tag: developmental stage

value: enlarging growth of bulb

tag: country/collection site

value: Japan


title: Degradome.mouse.testis.wt.Ribozero.adult.rep1

description: Degradome

value: wt

value: Ribozero


title: Snubar-mouse1

city: Houston

first: Anil

middle: K

last: Sood

state: TX

address: 6767 Bertner Ave

department: genetics

institute: MDACC

description:
Snubar-mouse1_ATAC and Snubar-mouse1_BC
SnubarATAC-mouse-drug-treatment-1-scATAC and sample_barcode
For ATAC pair-end read: R1: READ1, R2: CELL BARCODE, R3: READ2. For BC pair-end read: R1: Sample barcode+ UMI, R2: CELL BARCODE
SnubarATAC single cell ATAC-seq and barcode library

library_source: genomic

data_processing:
Basecalls performed using CASAVA version 1.8.1
cellranger atac V1.2.0 mkfastq
cellranger atac V1.2.0 count and cellranger-arc-1.0.0 count
Mixing experiment data was aligned to the combined reference genomes of human (hg19 reference) and mouse (mm10 reference). All other experimental data was aligned to human hg19 or mouse mm10 genome.
UMI counts and peak count are summarized
Genome_build: hg19 and mm10
Supplementary_files_format_and_content: tab-delimited text files include UMI and Peak values for each Sample

molecule: genomic DNA

growth_protocol: The A20 and K562 cell lines were purchased from the American Type Culture Collection and cultured based on ATCC guidelines. The MDA-MB-231 and MDA-MB-436  cell lines were obtained from the MD Anderson Characterized Cell Line Core Facility and were cultured in Dulbecco’s Modified Eagle’s Medium-high glucose medium supplemented with 10% FBS  and 1X penicillin-streptomycin. Mice were purchased from the Jackson Laboratory and housed in the Research Animal Support Facility at MD Anderson Cancer Center.

extract_protocol:
Cell nuclei for Snubar-ATAC were isolated according to Nuclei Isolation for Single Cell ATAC Sequencing Protocol (CG000169 Rev D, 10X Genomics) or Nuclei Isolation from Mouse Brain Tissue for Single Cell ATAC Sequencing Protocol (CG000212 Rev B, 10X Genomics). Nuclei used for SNubar-ARC were isolated according to Nuclei Isolation for Single Cell Multiome ATAC + Gene Expression Sequencing Protocol (10X Genomics, CG000365 Rev A).
Single cell capture, barcoding and library preparation was performed by following the 10X Genomics protocols (CG000168 Rev A for Chromium Single Cell ATAC Reagent Kits,  CG000209 Rev D for Chromium Next GEM Single Cell ATAC Library Kit v1.1, or CG000338 Rev A for Chromium Next GEM Single Cell Multiome ATAC + Gene Expression)
single cell ATAC-seq, single cell RNA&ATAC co-assay, and barcode libraries

treatment_protocol: 28 mice were treated under 7 different conditions (4 mice in each group): 1) Control; 2) Chemotherapy + 2 Gy Radiotherapy; 3) 4 Gy Radiotherapy; 4) Chemotherapy + 2 Gy Radiotherapy + Talazoparib; 5) Chemotherapy + 2 Gy Radiotherapy + PD-L1 Blockade; 6) 4Gy Radiotherapy + PD-L1 Blockade; 7) 4Gy Radiotherapy + Talazoparib + PD-L1 Blockade.

value: syngeneic lung tumors derived from LKR13 lung cancer cell line


title: S60

value: Gansu, China


title: S59

value: Shandong, China


title: S64

value: Shanxi, China


title: S54


title: A965

city: Valbonne - Sophia-Antipolis

first: Kevin

last: Lebrigand

address: 660 route des lucioles

country: France

institute: IPMC/CNRS

data_processing:
Library strategy: exome-seq
Raw data were first filtered using an in house quality control
Paired-end clean reads are aligned to the reference genome (UCSC mm9) using Burrows–Wheeler Aligner (BWA) software. If a read or reads pair is mapped to multiple positions, BWA will choose the most likely placement. While if two or more most-likely placements are present, BWA will choose any one randomly. Aligned reads were realigned to the genome. Genome Analysis Toolkit (GATK)34 was used to ignore those duplicates resulted from PCR amplification with Picard-tool. We utilized the Indelrealigner and RealignerTargetCreator in GATK do realignment around the indels according to GATK best practice. Furthermore, we performed base quality score recalibration with GATK to avoid system bias. After realignment to genome, we identified and filtered variants (SNP, INDELs) using GATK HaplotypeCaller and variantFiltration to guarantee meaningful analysis. Variants obtained from previous steps were compared based on the dbSNP35 and 1000 Genomes database36 and annotates with ANNOVAR
Genome_build: mm9
Supplementary_files_format_and_content: Variant call files of Single Nucleotide Polymorphisms (SNPs) and Indels

source_name: Spleen

extract_protocol:
For whole exome sequencing genomic DNA was extracted from CD4+ T cells, isolated from plck-GAPDH tumors by negative microbead selection (see above), using the Nucleospin Tissue Kit (Macherey Nagel, #740901)
Paired-end DNA library was prepared according to the manufacturer’s instructions (Agilent). The adapter-modified gDNA fragments were enriched by six cycles of PCR. Whole exome capture was carried out using Agilent’s SureSelect All Exon V5 Kit. Finally, 50 Mb of DNA sequences of 33,4378 exons from 20,965 genes were captured. After DNA quality evaluation, pooled samples were sequenced on Illunima Hiseq 2000

value: Spleen

tag: cell type

value: CD4+  splenoctyes

tag: genotype/variation

value: plkcGAPDH transgenic mice

tag: concentration sample (ng/nl)

tag: rin number


title: Snubar-mouse2

description:
Snubar-mouse2_ATAC and Snubar-mouse2_BC
SnubarATAC-mouse-drug-treatment-2-scATAC and sample_barcode
For ATAC pair-end read: R1: READ1, R2: CELL BARCODE, R3: READ2. For BC pair-end read: R1: Sample barcode+ UMI, R2: CELL BARCODE
SnubarATAC single cell ATAC-seq and barcode library


title: S56


title: S61


title: KO-LPS

city: Hangzhou

first: Lulu

last: Zhang

address: Yuhangtang Road 866

institute: Zhejiang Province Key Laboratory of Anti-Cancer Drug Research

description: KO_LPSVSWT_LPS_Gene_differential_expression

data_processing:
Illumina Casava software used for basecalling.
Sequenced reads were trimmed for adaptor sequence.
Reads mapped to mm10 whole genome by Tophat with default options
Fragment Per Kilobase of exon per Megabase of library size (FPKM) were calculated using Cufflinks with default options. Outputs from Cufflinks are provided as supplementary files as a tab-delimited text file.
Genome_build: mm10
Supplementary_files_format_and_content: format:fpkm_traking ; Contain the estimated expression values produced by Cufflinks.

source_name: Bone marrow

growth_protocol: BMDCs from Ctrl and DC conditional Optn ko mice was cultured in RPMI-1640 medium (Gibco) supplemented with 10% FBS (Gibco) , recombinant mouse GM-CSF (10 ng/ml, Peprotech), and IL-4 (1 ng/ml, Peprotech). After 4 days, non-adherent cells were gently removed and the remaining loosely adherent clusters were used on day 6 as immature DCs.

extract_protocol:
Total RNA was extracted using Trizol regent (Invitrogen, CA, USA)
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: BMDCs were treated with LPS (50 ng/ml, Sigma-Aldrich) for 8h.

value: DC conditional Optn ko

value: 8 weeks


title: A690


title: WT-LPS

value: Ctrl


title: S5

value: Tianjin, China


title: A508


title: S7

value: Guizhou, China


title: A331


title: A249


title: S78

value: bulb

value: Henan, China


title: S41

value: enlarging growth of bulb

value: Xinjiang, China


title: A547


title: S39


title: S33

value: Heilongjiang, China


title: S31


title: S29


title: 96_1_JRX567: HT29_ORF_IFIH1_96_1

city: Montréal

first: John

middle: D

last: Rioux

state: QC

address: 5000 Bélanger St.

department: Research Center

country: Canada

institute: Montreal Heart Institute

hyb_protocol: The labeled cRNA was  normalized to 1050 ng and hybridized on HumanHT-12. Hyb Chambers were incubated in Illumina Hybridization Oven for 16 hours at 58C at rocking speed of 5 according to Illumina’s Whole-Genome Gene Expression Direct Hybridization Assay Guide. Beadchips were washed according to Illumina's protocol

scan_protocol: Illumina iScan Reader

data_processing:
Beadarray v2.20.1 and illuminaHuman4.db v1.24.0 packages (R Bioconductor v3.0) were used to load and annotate (readBeadSummary and add FeatureData) the fluorescence intensity data into R-3.2.0. After normalization of the array data (normaliseIllumina, method=”neqc”), data was converted and handled using Limma package v3.26.9 (Bioconductor v3.0).
Probes annotated as “Bad” or “No match” were removed. Manual quality control of each array was performed. Quality control was performed within each batch of arrays. Duplicated probes were combined.
Batch effects were then corrected using ComBat for known batches and sva v3.18.0 for unknown systematic artefacts. Given the chips were performed in five batches, each with at least two processing date, the dates from each batch were combined first before merging the batches.
To reduce impact of residual noise or batch effects on very low expression values, the fluorescence intensity values were truncated at 2^3.5, and translated down by the same amount. Repeated samples were removed. Data provided includes only samples included in the final dataset.

label: Biotin

source_name: HT-29 IFIH1 transduction, UniqueID 96_1

label_protocol: Biotin-labeled cRNA corresponding to poly A RNA using Illumina® TotalPrep RNA Amplification Kit, according to manufacturer’s instructions (Life Technologies)

growth_protocol: The colorectal adenocarcinoma cell line HT-29 (ATCC HTB-38) was maintained at confluence between 20% and 80% at all times in McCoy’s 5A (Wisent, 317-010CL) 10% FBS. All experiments described herein were performed in cell at passages below 25.

extract_protocol:
The RNeasy Plus Mini kit (#74036, Qiagen Inc Canada) according to manufacturer’s protocol.
The RNA samples were quantified, and quality controlled using an Agilent RNA 6000 Nano kit (Agilent, Cat No./ID 5067-1511) on 2100 Bioanalyzer system.
Number (RIN) below 8 were discarded; RIN values were routinely in the range of 9.2-10

treatment_protocol:
ORFs for IBD gene candidates were cloned into a GATEWAY® compatible polycistronic lentiviral expression vector, pLVX-EF1a-IRES-PURO/eGFP expressing an enhanced green fluorescent protein (eGFP) and puromycin N-acetyl-transferase fusion protein.
Proliferative HT-29 cells at 50% confluency in 12 well plate (Corning) were transduced in triplicate with the different ORFs (multiplicity of infection) MOI of 40-100 with 8µg/ml of polybrene (Sigma, Cat: H-9268).
Twenty-four hours post-transduction, media was changed and 3ug/ml puromycin (Millipore Sigma) was added.
The appearance and confluence of the cultures were recorded daily, and cells were grown for an average of 8 days (with a range of 5-27 days) to select successfully transduced cells and reach confluence before RNA extraction.
Transduction of the whole set of IBD gene candidate ORFs was performed in batches of about 15 ORFs, each done in triplicate, and including an empty vector control.

tag: orf

tag: uniqueid

tag: arraybatch

tag: transductiondate

tag: subset


title: S30

tag: tissue

value: Hebei, China


title: 94_1_JRX565: HT29_ORF_IFIH1_94_1

source_name: HT-29 IFIH1 transduction, UniqueID 94_1


title: S259


title: S261


title: S258


title: 2232_JRX640: HT29_ORF_SMAD3 170V_2232

source_name: HT-29 SMAD3 170V transduction, UniqueID 2232

value: SMAD3 170V


title: S46

value: ShandongChina


title: S254

value: Gansu, China


title: S249


title: S257

value: Canada


title: S269

value: Sichuan, China


title: S25


title: 2233_JRX641: HT29_ORF_SMAD3 170V_2233

source_name: HT-29 SMAD3 170V transduction, UniqueID 2233


title: S248


title: 2231_JRX639: HT29_ORF_SMAD3 170V_2231

source_name: HT-29 SMAD3 170V transduction, UniqueID 2231


title: 2195_JRX610: HT29_ORF_IFIH1 SP1_2195

source_name: HT-29 IFIH1 SP1 transduction, UniqueID 2195

value: IFIH1 SP1


title: 2198_JRX613: HT29_ORF_IFIH1 SP2_2198

source_name: HT-29 IFIH1 SP2 transduction, UniqueID 2198

value: IFIH1 SP2


title: 2192_JRX607: HT29_ORF_IFIH1 923V_2192

source_name: HT-29 IFIH1 923V transduction, UniqueID 2192

value: IFIH1 923V


title: 2197_JRX612: HT29_ORF_IFIH1 SP1_2197

source_name: HT-29 IFIH1 SP1 transduction, UniqueID 2197


title: 2196_JRX611: HT29_ORF_IFIH1 SP1_2196

source_name: HT-29 IFIH1 SP1 transduction, UniqueID 2196


title: S38


title: 2199_JRX614: HT29_ORF_IFIH1 SP2_2199

source_name: HT-29 IFIH1 SP2 transduction, UniqueID 2199


title: 2200_JRX615: HT29_ORF_IFIH1 SP2_2200

source_name: HT-29 IFIH1 SP2 transduction, UniqueID 2200


title: 2193_JRX608: HT29_ORF_IFIH1 923V_2193

source_name: HT-29 IFIH1 923V transduction, UniqueID 2193


title: S246

value: Xizang, China


title: S241

value: Shandong, China


title: S240

value: Jiangsu, China


title: S232

value: bulb

value: Israel


title: S243

value: enlarging growth of bulb


title: 2165_JRX589: HT29_ORF_SMAD3 170V_2165

source_name: HT-29 SMAD3 170V transduction, UniqueID 2165


title: 2194_JRX609: HT29_ORF_IFIH1 923V_2194

source_name: HT-29 IFIH1 923V transduction, UniqueID 2194


title: 2166_JRX590: HT29_ORF_SMAD3 170V_2166

source_name: HT-29 SMAD3 170V transduction, UniqueID 2166


title: S230

source_name: Chalingzipisuan

value: Greece


title: S2

value: Australia


title: S220


title: S22

value: Hebei, China


title: S215

value: Shanxi, China


title: S212


title: S236

value: Yunan, China


title: 2155_JRX573: HT29_ORF_IFIH1 SP1_2155

source_name: HT-29 IFIH1 SP1 transduction, UniqueID 2155


title: S210

value: Jilin, China


title: 2154_JRX572: HT29_ORF_IFIH1 SP1_2154

source_name: HT-29 IFIH1 SP1 transduction, UniqueID 2154


title: 2158_JRX576: HT29_ORF_IFIH1 SP2_2158

source_name: HT-29 IFIH1 SP2 transduction, UniqueID 2158


title: 2156_JRX574: HT29_ORF_IFIH1 SP2_2156

source_name: HT-29 IFIH1 SP2 transduction, UniqueID 2156


title: S213

value: Qinghai, China


title: 2167_JRX591: HT29_ORF_SMAD3 170V_2167

source_name: HT-29 SMAD3 170V transduction, UniqueID 2167

value: SMAD3 170V


title: S201


title: S198

value: China


title: S21


title: 2157_JRX575: HT29_ORF_IFIH1 SP2_2157

source_name: HT-29 IFIH1 SP2 transduction, UniqueID 2157

value: IFIH1 SP2


title: 209_1_JRX587: HT29_ORF_SMAD3_209_1

source_name: HT-29 SMAD3 transduction, UniqueID 209_1


title: 2151_JRX569: HT29_ORF_IFIH1 923V_2151

source_name: HT-29 IFIH1 923V transduction, UniqueID 2151

value: IFIH1 923V


title: 2150_JRX568: HT29_ORF_IFIH1 923V_2150

source_name: HT-29 IFIH1 923V transduction, UniqueID 2150


title: S196

value: Hubei, China


title: 2152_JRX570: HT29_ORF_IFIH1 923V_2152

source_name: HT-29 IFIH1 923V transduction, UniqueID 2152


title: 2230_JRX638: HT29_ORF_SMAD3_2230

source_name: HT-29 SMAD3 transduction, UniqueID 2230


title: 210_1_JRX588: HT29_ORF_SMAD3_210_1

source_name: HT-29 SMAD3 transduction, UniqueID 210_1


title: S190


title: 208_1_JRX586: HT29_ORF_SMAD3_208_1

source_name: HT-29 SMAD3 transduction, UniqueID 208_1


title: 2153_JRX571: HT29_ORF_IFIH1 SP1_2153

source_name: HT-29 IFIH1 SP1 transduction, UniqueID 2153

value: IFIH1 SP1


title: S209


title: S202

value: Shandong, China


title: 2178_JRX600: HT29_ORF_DUSP16_2178

source_name: HT-29 DUSP16 transduction, UniqueID 2178


title: S19

value: bulb

value: Sichuan, China


title: 2191_JRX606: HT29_ORF_IFIH1_2191

source_name: HT-29 IFIH1 transduction, UniqueID 2191


title: S182

source_name: Chalingzipisuan

value: enlarging growth of bulb

value: Eygpt


title: S18


title: S172

value: Canada


title: S158


title: S15

value: Hunan, China


title: 2219_JRX628: HT29_ORF_RNF186_2219

source_name: HT-29 RNF186 transduction, UniqueID 2219


title: S191


title: 2229_JRX637: HT29_ORF_SMAD3_2229

source_name: HT-29 SMAD3 transduction, UniqueID 2229


title: S197


title: 2120_2_JRX536: HT29_ORF_ATG16L1_2120_2

source_name: HT-29 ATG16L1 transduction, UniqueID 2120_2


title: S136


title: S133

value: Henan, China


title: S203

value: Amrica


title: 151_2_JRX559: HT29_ORF_OTUD3_151_2

source_name: HT-29 OTUD3 transduction, UniqueID 151_2


title: 152_2_JRX526: HT29_ORF_OTUD3_152_2

source_name: HT-29 OTUD3 transduction, UniqueID 152_2


title: 2221_JRX630: HT29_ORF_RNF186_2221

source_name: HT-29 RNF186 transduction, UniqueID 2221


title: 2228_JRX636: HT29_ORF_SMAD3_2228

source_name: HT-29 SMAD3 transduction, UniqueID 2228


title: 2240_JRX647: HT29_ORF_ZFP90_2240

source_name: HT-29 ZFP90 transduction, UniqueID 2240


title: 251_2_JRX529: HT29_ORF_ZFP36L1_251_2

source_name: HT-29 ZFP36L1 transduction, UniqueID 251_2


title: 2179_JRX601: HT29_ORF_DUSP16_2179

source_name: HT-29 DUSP16 transduction, UniqueID 2179


title: 2239_JRX646: HT29_ORF_Empty_2239

source_name: HT-29 Empty transduction, UniqueID 2239

value: Empty


title: 2237_JRX644: HT29_ORF_Empty_2237

source_name: HT-29 Empty transduction, UniqueID 2237


title: 2220_JRX629: HT29_ORF_RNF186_2220

source_name: HT-29 RNF186 transduction, UniqueID 2220


title: S129

value: Yunan, China


title: 2189_JRX604: HT29_ORF_IFIH1_2189

source_name: HT-29 IFIH1 transduction, UniqueID 2189


title: 2226_JRX635: HT29_ORF_SBNO2_2226

source_name: HT-29 SBNO2 transduction, UniqueID 2226


title: 2238_JRX645: HT29_ORF_Empty_2238

source_name: HT-29 Empty transduction, UniqueID 2238


title: S144

source_name: Chalingzipisuan


title: 2234_JRX642: HT29_ORF_TSPAN14_2234

source_name: HT-29 TSPAN14 transduction, UniqueID 2234


title: S148


title: 113_JRX453: HT29_ORF_LACC1_113

source_name: HT-29 LACC1 transduction, UniqueID 113


title: S14


title: S117

value: Xinjiang, China


title: S111

value: Shanxi, China


title: 2216_JRX626: HT29_ORF_PPM1G_2216

source_name: HT-29 PPM1G transduction, UniqueID 2216


title: 2241_JRX648: HT29_ORF_ZFP90_2241

source_name: HT-29 ZFP90 transduction, UniqueID 2241


title: 2213_JRX624: HT29_ORF_POP7_2213

source_name: HT-29 POP7 transduction, UniqueID 2213


title: S110


title: S130


title: S131

value: China


title: Naive CD4 T cell rep2

city: CLAYTON

first: Aidil

last: Zaini

state: VICTORIA

address: LEVEL 3, BUILDING 77, MONASH UNIVERSITY

department: BIOCHEMISTRY AND MOLECULAR BIOLOGY

country: Australia

institute: MONASH UNIVERSITY

data_processing:
data was processed using the nfcore/atacseq pipeline version 1.2.1 (doi: 10.5281/zenodo.2634132), using the GRCm38 reference, calling narrow peaks.
Data visualization and exploration were performed on Degust (Powell, 2015) web tool.
Genome_build: GRCm38
Supplementary_files_format_and_content: wig files were generated using MACS2
Supplementary_files_format_and_content: Count tables for merged peaks across all replicates separately
Supplementary_files_format_and_content: peak annotation was performed using HOMER

source_name: mesenteric lymph node

extract_protocol:
DNA from FACS-sorted cells was extracted using Illumina Nextera DNA Library Kit (FC121-1030) as per manufacturers’ standard protocol.
DNA libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: Mice were infected with either low dose/LD/30 or high dose/HD/200 parasitic eggs and culled 21 days after infection, and mesentric lymph nodes were extracted. Tfh cells (CD4+ CD44hi FOXP3- Ly6C- CD162- PD-1+ CXCR5+) at d21 pi and naive Th cells (CD4+ FOXP3- CD44low CD62Lhigh ) from uninfected mice were FACS-sorted and purified for DNA extraction and purification.

tag: strain

value: FIR mice

value: mesenteric lymph node

tag: post infection

value: not infected


title: Naive CD4 T cell rep1


title: S139

value: Turkey


title: 2212_JRX623: HT29_ORF_PNKD_2212

source_name: HT-29 PNKD transduction, UniqueID 2212

value: PNKD


title: 2209_JRX621: HT29_ORF_MAGI3_2209

source_name: HT-29 MAGI3 transduction, UniqueID 2209


title: 2211_JRX622: HT29_ORF_PNKD_2211

source_name: HT-29 PNKD transduction, UniqueID 2211


title: 2208_JRX620: HT29_ORF_MAGI3_2208

source_name: HT-29 MAGI3 transduction, UniqueID 2208


title: 2225_JRX634: HT29_ORF_SBNO2_2225

source_name: HT-29 SBNO2 transduction, UniqueID 2225


title: S125

value: bulb

value: Guangxi, China


title: 112_JRX452: HT29_ORF_LACC1_112

source_name: HT-29 LACC1 transduction, UniqueID 112


title: S119

value: enlarging growth of bulb

value: Shandong, China


title: S123


title: S122

value: Hebei, China


title: 2236_JRX643: HT29_ORF_TSPAN14_2236

source_name: HT-29 TSPAN14 transduction, UniqueID 2236


title: 2218_JRX627: HT29_ORF_PPM1G_2218

source_name: HT-29 PPM1G transduction, UniqueID 2218


title: 2201_JRX616: HT29_ORF_JAK2_2201

source_name: HT-29 JAK2 transduction, UniqueID 2201


title: 2205_JRX619: HT29_ORF_JAZF1_2205

source_name: HT-29 JAZF1 transduction, UniqueID 2205


title: High dose Tfh cell rep2

value: 21 days


title: 2185_JRX603: HT29_ORF_GPR35_2185

source_name: HT-29 GPR35 transduction, UniqueID 2185


title: Neutro_liver_KO_3

city: Braunschweig

first: Andreas

last: Jeron

state: Nierdersachsen

address: Inhoffenstraße 7

department: Viral Immunology

institute: Helmholtz Center for Infection Research

hyb_protocol: Sample hybridisation was performed according to Affymtrix Clariom S protocol instructions

scan_protocol: Microarray scanning was performed according to Affymtrix Clariom S protocol instructions

data_processing:
Raw data were analyzed with TAC software (Thermo Fisher) using SST-RMA algorithm.
Clariom_S_Mouse.r1.pgf
Clariom_S_Mouse.r1.mps

source_name: KO, liver, neutrophils

label_protocol: Sample labeling was performed according to Affymtrix Clariom S protocol instructions

extract_protocol: Total RNA was isolated with RNeasy Mini-Kit (Qiagen) followed by DNAse treatment

tag: genotype

value: ADAP-/- knockout

value: neutrophils

tag: organ

value: liver


title: S114

source_name: Chalingzipisuan


title: S116

value: Xiangjiang, China


title: Low dose Tfh cell rep2


title: Neutro_liver_KO_1


title: 2215_JRX625: HT29_ORF_POP7_2215

source_name: HT-29 POP7 transduction, UniqueID 2215


title: Neutro_liver_WT_1

source_name: WT, liver, neutrophils

value: wild type


title: 2173_JRX596: HT29_ORF_ADO_2173

source_name: HT-29 ADO transduction, UniqueID 2173

value: ADO


title: Low dose Tfh cell rep1

source_name: mesenteric lymph node

value: FIR mice


title: 2170_JRX594: HT29_ORF_Empty_2170

source_name: HT-29 Empty transduction, UniqueID 2170

value: Empty


title: 2183_JRX602: HT29_ORF_GPR35_2183

source_name: HT-29 GPR35 transduction, UniqueID 2183


title: 2168_JRX592: HT29_ORF_Empty_2168

source_name: HT-29 Empty transduction, UniqueID 2168


title: 2177_JRX599: HT29_ORF_DUSP16_2177

source_name: HT-29 DUSP16 transduction, UniqueID 2177


title: Neutro_spleen_WT_3

source_name: WT, spleen, neutrophils

value: spleen


title: Neutro_spleen_KO_2

source_name: KO, spleen, neutrophils


title: High dose Tfh cell rep1

value: mesenteric lymph node


title: Neutro_spleen_WT_2


title: Neutro_spleen_KO_3


title: 55_2_JRX558: HT29_ORF_ETS2_55_2

source_name: HT-29 ETS2 transduction, UniqueID 55_2


title: 444_JRX532: HT29_ORF_SYT11_444

source_name: HT-29 SYT11 transduction, UniqueID 444


title: 2203_JRX617: HT29_ORF_JAK2_2203

source_name: HT-29 JAK2 transduction, UniqueID 2203


title: 2204_JRX618: HT29_ORF_JAZF1_2204

source_name: HT-29 JAZF1 transduction, UniqueID 2204


title: 2190_JRX605: HT29_ORF_IFIH1_2190

source_name: HT-29 IFIH1 transduction, UniqueID 2190


title: 2175_JRX598: HT29_ORF_CISD1_2175

source_name: HT-29 CISD1 transduction, UniqueID 2175


title: 443_JRX561: HT29_ORF_SYT11_443

source_name: HT-29 SYT11 transduction, UniqueID 443


title: Neutro_liver_WT_2


title: 2174_JRX597: HT29_ORF_CISD1_2174

source_name: HT-29 CISD1 transduction, UniqueID 2174


title: 53_2_JRX523: HT29_ORF_ERRFI1_53_2

source_name: HT-29 ERRFI1 transduction, UniqueID 53_2


title: 57_2_JRX525: HT29_ORF_ETS2_57_2

source_name: HT-29 ETS2 transduction, UniqueID 57_2


title: iMono_liver_WT_2

source_name: WT, liver, iMono

value: inflammatory monocytes


title: Neutro_spleen_KO_1


title: Neutro_liver_KO_2

source_name: KO, liver, neutrophils


title: 2169_JRX593: HT29_ORF_Empty_2169

source_name: HT-29 Empty transduction, UniqueID 2169


title: iMono_liver_WT_3


title: 2148_JRX551: HT29_ORF_Empty_2148

source_name: HT-29 Empty transduction, UniqueID 2148


title: 324_JRX560: HT29_ORF_STAT3_324

source_name: HT-29 STAT3 transduction, UniqueID 324


title: 2172_JRX595: HT29_ORF_ADO_2172

source_name: HT-29 ADO transduction, UniqueID 2172


title: 323_JRX531: HT29_ORF_STAT3_323

source_name: HT-29 STAT3 transduction, UniqueID 323


title: 2145_JRX548: HT29_ORF_ZBTB40_2145

source_name: HT-29 ZBTB40 transduction, UniqueID 2145


title: 250_2_JRX528: HT29_ORF_ZFP36L1_250_2

source_name: HT-29 ZFP36L1 transduction, UniqueID 250_2


title: Neutro_spleen_WT_1

source_name: WT, spleen, neutrophils


title: iMono_liver_KO_3

source_name: KO, liver, iMono


title: iMono_liver_KO_1


title: iMono_spleen_KO_1

source_name: KO, spleen, iMono


title: 213_JRX553: HT29_ORF_SMAD7_213

source_name: HT-29 SMAD7 transduction, UniqueID 213


title: 2147_JRX550: HT29_ORF_Empty_2147

source_name: HT-29 Empty transduction, UniqueID 2147


title: iMono_liver_KO_2


title: 394_JRX556: HT29_ORF_RASGRP1_394

source_name: HT-29 RASGRP1 transduction, UniqueID 394


title: iMono_spleen_WT_2

source_name: WT, spleen, iMono


title: Meroclone, biological rep 6

city: Amman

first: Deema

middle: Adnan

last: Ali

address: queen Rania street

department: cell therapy center

country: Jordan

institute: The University of Jordan

description: Gene expression data from foreskin derived transient amplifying cells

hyb_protocol: Following fragmentation and labeling, 5.2 ug of ss-DNA were hybridized for 16 hr at 45C on Human Transcriptome Analysis 2 (HTA 2) chips. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned with Affymetrix® GeneChip Scanner 3000.

data_processing: The data were analyzed with Affymetrix® Transcriptome Analysis Console (TAC®) Software V4.

source_name: transient amplifying cells from foreskin

label_protocol: The fragmented cDNA was biotin labelled by terminal deoxynucleotidyl transferase (TdT) using the DNA Labeling Reagent ( Manual target preperation for GeneChip whole trascript expression array, 2013, Affymetrix).

growth_protocol: Cells were cultured (2.5 × 104/cm2) onto a feeder layer of lethally irradiated 3T3-J2 cells (Rheinwald & Green, 1975) in keratinocytes medium: DMEM and Ham's F12 media (2:1 mixture) containing 10% FCS , adenine (0.18 mM), insulin (5 μg/ml), cholera toxin (0.1 nM), triiodothyronine (2 nM), hydrocortisone (0.4 μg/ml), glutamine (4 mM), and penicillin-streptomycin (50 IU/ml). Epidermal growth factor (10 ng/ml) was added starting at day3.

extract_protocol: RNA was extracted using the mixed Trizol- Qiagen® RNeasy Mini kit (Qiagen, USA) , according to the manufacturer's instructions.

treatment_protocol: Keratinocytes colonies (Holoclones, meroclones, paraclones) were cultured in 25 cm2 tisuue culure flasks. At 80-90% confluence, the cells were washed with PBS and lysed using Trizol® reagent (Ambion, ThermoFisher scientific, USA)

value: foreskin


title: Paraclone, Biological rep 6

description: Gene expression data from foreskin derived Differentiated cells

source_name: Differentiated cells from foreskin

value: Differentiated cells from foreskin


title: iMono_spleen_KO_2


title: iMono_spleen_WT_1


title: 2112_2_JRX563: HT29_ORF_IKZF1_2112_2

source_name: HT-29 IKZF1 transduction, UniqueID 2112_2


title: 2136_JRX545: HT29_ORF_NOD2_2136

source_name: HT-29 NOD2 transduction, UniqueID 2136


title: 2111_2_JRX534: HT29_ORF_IKZF1_2111_2

source_name: HT-29 IKZF1 transduction, UniqueID 2111_2


title: iMono_spleen_WT_3


title: 2128_JRX564: HT29_ORF_CDKAL1_2128

source_name: HT-29 CDKAL1 transduction, UniqueID 2128


title: 2126_JRX538: HT29_ORF_CDKAL1_2126

source_name: HT-29 CDKAL1 transduction, UniqueID 2126


title: 2135_JRX544: HT29_ORF_NOD2_2135

source_name: HT-29 NOD2 transduction, UniqueID 2135


title: 2121_2_JRX537: HT29_ORF_ATG16L1_2121_2

source_name: HT-29 ATG16L1 transduction, UniqueID 2121_2


title: 2144_JRX562: HT29_ORF_ZBTB40_2144

source_name: HT-29 ZBTB40 transduction, UniqueID 2144


title: Meroclone, biological rep 5

value: transient amplifying cells from foreskin


title: Holoclone, biological rep 6

description: Gene expression data from foreskin derived epidermal stem cells

source_name: skin stem cells from foreskin

value: skin stem cells from foreskin


title: 210_JRX552: HT29_ORF_SMAD3_210

source_name: HT-29 SMAD3 transduction, UniqueID 210


title: Paraclone, Biological rep 5


title: 2083_JRX557: HT29_ORF_NFKB1_2083

source_name: HT-29 NFKB1 transduction, UniqueID 2083


title: Holoclone, biological rep 5


title: Holoclone, biological rep 4


title: iMono_spleen_KO_3

source_name: KO, spleen, iMono


title: Paraclone, Biological rep 4


title: Holoclone, biological rep 3


title: Meroclone, biological rep 4


title: Meroclone, biological rep 2


title: iMono_liver_WT_1

source_name: WT, liver, iMono


title: 97_JRX464: HT29_ORF_IPMK_97

source_name: HT-29 IPMK transduction, UniqueID 97

value: IPMK


title: 497_JRX468: HT29_ORF_SLC2A4RG_497

source_name: HT-29 SLC2A4RG transduction, UniqueID 497


title: 495_JRX511: HT29_ORF_SLAIN2_495

source_name: HT-29 SLAIN2 transduction, UniqueID 495


title: 98_JRX465: HT29_ORF_IPMK_98

source_name: HT-29 IPMK transduction, UniqueID 98


title: VISp_L6a

city: Seattle

first: Hongkui

last: Zeng

state: WA

address: 615 Westlake Ave N

institute: Allen Institute for Brain Science

description:
processed data file:
metadata_ssv4.csv
expression_matrix_ssv4.hdf5
umap.2d.ssv4.csv

data_processing:
For Smart-seq v4 libraries, 50-base pair paired-end reads were aligned to GRCm38 (mm10) using a RefSeq annotation gff file retrieved from NCBI on 01/18/2016 (https://www.ncbi.nlm.nih.gov/genome/annotation_euk/all/). Sequence alignment was performed using STAR v2.5.3 (Dobin et al., 2013) in twopassMode. PCR duplicates were masked and removed using STAR option “bamRemoveDuplicates”. Only uniquely aligned reads were used for gene quantification. Gene counts were computed using the R GenomicAlignments package (Lawrence et al., 2013) sumarizeOverlaps function using “IntersectionNotEmpty”.
10xv2 libraries were sequenced on Illumina NovaSeq6000 and sequencing reads were aligned to the mouse pre-mRNA reference transcriptome (mm10) using the 10x Genomics CellRanger pipeline (version 3.0.0) with default parameters.
For Smart-seq v4, cells with fewer than 2,000 detected genes (count > 0) and less than 30% of reads mapped to the transcriptome were removed. Doublets were removed by first classifying cells into broad classes of excitatory, inhibitory, and non-neuronal based on known markers. For each class, we selected highly specific genes that are only present in this class against all other classes, and computed the eigengene (the first principle component based on the given gene set). Eigengenes for all classes were normalized in the range of 0 and 1, and we removed any cells that scored > 0.2 in more than one class
For 10xv2 libraries, cells that had < 1,500 detected genes (with UMI count > 0) were filtered out for downstream processing in each 10x run. Doublets were identified using a modified version of the DoubletFinder algorithm (McGinnis et al., 2019) and removed when doublet score > 0.3. Doublets were further removed by first classifying cells into broad cell classes (neuronal versus non-neuronal) based on the co-expression of any pair of broad class marker genes.
Genome_build: mm10
Supplementary_files_format_and_content: hdf5

source_name: VISp

growth_protocol: All procedures were carried out in accordance with Institutional Animal Care and Use Committee protocols at the Allen Institute for Brain Science. Animals were provided food and water ad libitum and were maintained on a regular 14/10-h day/night cycle at no more than five adult animals per cage. Animals were maintained on the C57BL/6J background, and newly received or generated transgenic lines were backcrossed to C57BL/6J. Experimental animals were heterozygous for the recombinase transgenes and the reporter transgenes. Standard tamoxifen treatment for CreER lines included a single dose of tamoxifen (40 μl of 50 mg ml−1) dissolved in corn oil and administered via oral gavage at postnatal day (P)10–14. Cux2-CreERT2;Ai140 mice received tamoxifen treatment at P35 ± 5 for five consecutive days. We excluded any animals with anophthalmia or microphthalmia.

extract_protocol:
We isolated single cells by adapting previously described procedures (Tasic et al., 2018). The brain was dissected, submerged in ACSF, embedded in 2% agarose, and sliced into 250-μm (SMART-Seq) or 350-μm (10x Genomics) coronal sections on a compresstome (Precisionary Instruments). Block-face images were captured during slicing. Regions of interest (ROIs) were then microdissected from the slices and dissociated into single cells with 1 mg/ml pronase (SMART-Seq before 28 June 2018, Sigma P6911-1G) and processed as previously described (Tasic et al., 2018). For all 10xv2 samples and for SSv4 samples after 28 June 2018, we improved our protocol with the following changes. Tissue pieces were digested with 30 U/ml papain (Worthington PAP2) in ACSF for 30 minutes at 30°C. Due to the short incubation period in a dry oven, we set the oven temperature to 35°C to compensate for the indirect heat exchange, with a target solution temperature of 30°C. Enzymatic digestion was quenched by exchanging the papain solution three times with quenching buffer (ACSF with 1% FBS and 0.2% BSA). Samples were incubated on ice for 5 minutes before trituration. The tissue pieces in the quenching buffer were triturated through a fire-polished pipette with 600-µm diameter opening approximately 20 times. The single cell suspension was passed through a 70-µm filter into a 15-ml conical tube with 500 ul of high BSA buffer (ACSF with 1% FBS and 1% BSA) at the bottom to help cushion the cells during centrifugation at 100 x g in a swinging bucket centrifuge for 10 minutes. The supernatant was discarded, and the cell pellet was resuspended in the quenching buffer. All cells were collected by fluorescence-activated cell sorting (FACS, BD Aria II) using a 130-μm nozzle. For SSv4, single cells were sorted into individual wells of 8-well PCR strips containing lysis buffer from the SMART-Seq v4 kit with RNase inhibitor (0.17 U/μl), immediately frozen on dry ice, and stored at −80°C. For 10x Genomics, 30,000 cells were sorted within 10 minutes into a tube containing 500 µl of quenching buffer. The resuspended cells were stored at 4°C until all samples were collected, usually within 30 minutes. Samples from the same ROI were pooled, cell concentration quantified, and immediately loaded onto the 10x Genomics Chromium controller.
For SSv4 processing, we used the SMART-Seq v4 Ultra Low Input RNA Kit for Sequencing (Takara Cat# 634894) to reverse transcribe poly(A) RNA and amplify full-length cDNA. We performed reverse transcription and cDNA amplification for 18 PCR cycles (neurons) or 21 PCR cycles (non-neuronal cells) in 8-well strips, in sets of 12–24 strips at a time. All samples proceeded through Nextera XT DNA Library Preparation (Illumina Cat# FC-131-1096) using Nextera XT Index Kit V2 (Illumina Cat# FC-131-2001) and custom index sets (Integrated DNA Technologies). Custom index sets were validated to confirm the same performance as Nextera Index sets before being used on experimental samples. Nextera XT DNA Library prep was performed according to manufacturer’s instructions, with a modification to reduce the volumes of all reagents and cDNA input to 0.4x or 0.5x of the original protocol. Details are available in ‘Documentation’ on the Allen Institute data portal at: http://celltypes.brain-map.org.   For 10xv2 processing, we used Chromium Single Cell 3’ Reagent Kit v2 (10x Genomics Cat# 120237). We followed the manufacturer’s instructions for cell capture, barcoding, reverse transcription, cDNA amplification, and library construction. We targeted sequencing depth of 60,000 reads per cell.

tag: sample type

value: VISp


title: 498_JRX469: HT29_ORF_SLC2A4RG_498

source_name: HT-29 SLC2A4RG transduction, UniqueID 498


title: Paraclone, Biological rep 3

source_name: Differentiated cells from foreskin


title: Paraclone, Biological rep 2


title: Meroclone, biological rep 3

source_name: transient amplifying cells from foreskin


title: PAR_POST_PRE

source_name: PAR-POST-PRE

value: PAR-POST-PRE


title: 52_JRX418: HT29_ORF_ERRFI1_52

source_name: HT-29 ERRFI1 transduction, UniqueID 52


title: Holoclone, biological rep 2


title: SUB_ProS

source_name: SUB-ProS

value: SUB-ProS


title: 450_JRX499: HT29_ORF_HDAC7_450

source_name: HT-29 HDAC7 transduction, UniqueID 450


title: Paraclone, Biological rep 1


title: ENTm

source_name: ENTm

value: ENTm


title: 469_JRX509: HT29_ORF_ZGPAT_469

source_name: HT-29 ZGPAT transduction, UniqueID 469

value: ZGPAT


title: 46_JRX462: HT29_ORF_DLD_46

source_name: HT-29 DLD transduction, UniqueID 46

value: DLD


title: 468_JRX508: HT29_ORF_ZGPAT_468

source_name: HT-29 ZGPAT transduction, UniqueID 468


title: AI_posterior

source_name: AI

value: AI


title: 494_JRX510: HT29_ORF_SLAIN2_494

source_name: HT-29 SLAIN2 transduction, UniqueID 494


title: ENTl

source_name: ENTl

value: ENTl


title: 405_JRX497: HT29_ORF_SLC9A3_405

source_name: HT-29 SLC9A3 transduction, UniqueID 405


title: 53_JRX419: HT29_ORF_ERRFI1_53

source_name: HT-29 ERRFI1 transduction, UniqueID 53


title: Holoclone, biological rep 1

source_name: skin stem cells from foreskin


title: AI_anterior


title: Meroclone, biological rep 1


title: PL_ILA_Anterior

source_name: PL-ILA

value: PL-ILA


title: PL_ILA_Posterior


title: 449_JRX498: HT29_ORF_HDAC7_449

source_name: HT-29 HDAC7 transduction, UniqueID 449


title: PTLp_L1-L2-3-L4-L5-L6

source_name: PTLp

value: PTLp


title: RSP

source_name: RSP

value: RSP


title: 404_JRX496: HT29_ORF_SLC9A3_404

source_name: HT-29 SLC9A3 transduction, UniqueID 404


title: 402_JRX495: HT29_ORF_SLC2A13_402

source_name: HT-29 SLC2A13 transduction, UniqueID 402


title: TEa_PERI_ECT

source_name: TEa-PERI-ECT

value: TEa-PERI-ECT


title: AI


title: PL_ILA


title: CnT-nonBS_H3K27me3_250K

city: RTP

first: ruifang

last: li

state: NC

address: 111 T.W. Alexander Drive

institute: NIEHS

data_processing:
Library strategy: CUT&Tag
Filtering and mapping:  Raw reads were filtered to exclude pairs with average base quality <20.  Adapters removed by Cutadapt v1.12 with parameters "-a CTGTCTCTTATACAC -A CTGTCTCTTATACAC -O 5 -q 0 -m 20 -p", then reads were filtered to exclude fragments with length <30bp.  Filtered, trimmed read pairs were mapped against  mm10  via Bismark v0.23.0 with "-X 2000" using Bowtie2 v2.3.0 as the underlying mapper. Duplicate mapped fragments were removed by the Bismark v0.23.0 deduplicate_bismark tool with parameter "-p".
Peak calls:  HOMER v4.10.3 was used for peak calls with the makeTagDirectory function (parameters "-format sam -read1 -keepAll -fragLength 200") followed by the findPeaks function (parameters "-size 500 -minDist 1000 -L 0 -region" for H3K4me1 and  "-size 1000 -minDist 2500 -L 0 -region" for H3K9me3 and H3K27me3). Peaks overlapping mm10 blacklist regions were discarded. Unified peak sets were defined as the union of peak calls (per mark) via BEDtools v2.29.2 merge.
Signal tracks: Coverage tracks for genome browser views were generated by converting paired-end hits to a single fragment by BEDtools v2.29.2 bamtobed with the "-bedpe" option, BEDtools v2.29.2 genomecov to generate bedGraph format, then UCSC utility bedGraphToBigWig to convert to bigWig format.
Collecting methylation counts:  The Bismark v0.23.0 bismark_methylation_extractor tool was run with parameters "-p --ignore_r2 9 --comprehensive --mbias_off --bedGraph --cytosine_report".
Percent methylation tracks: For visualization purposes, the methylated and unmethylated cytosine counts from both strands (in the CpG context output from Bismark v0.23.0 bismark_methylation_extractor) were collapsed to calculate percent methylation per genomic CpG. Files were converted from variableStep WIG format to bigWig format by UCSC utility wigToBigWig.
Genome_build: mm10
Supplementary_files_format_and_content: percent methylation per CpG in bigWig format, coverage in bigWig format, peaks in BED format,  matrix of methylated and total cytosine base counts per CpG in tab-delimited text format

source_name: E14 mouse embryonic stem cells

growth_protocol: Mouse E14 embryonic stem cells (129/Ola background) were maintained in Glasgow Minimum Essential Medium (GMEM, Sigma) containing 15% fetal bovine serum, supplemented with 1× Pen-Strep (Gibco), 2 mM Glutamax (Gibco), 50 µM β-mercaptoethanol (Gibco), 0.1 mM nonessential amino acids (Gibco), 1 mM sodium pyruvate (Gibco), and Leukemia Inhibitory Factor (LIF, 1000U/ml, Millipore).

extract_protocol:
CUT&Tag was performed according to previously published protocol (Kaya-Okur et al., 2019) with slight modification, namely using pA-Tn5 transposome assembled with methylated adapter instead. Briefly, harvested cells were washed and then bound to concanavalin A-coated magnetic beads. The cells were permeabilized and incubated with target-specific primary antibody and then with secondary antibody, followed by incubation with pA-Tn5 transposome and tagmentation at target-binding sites. The tagmented DNA was extracted with Qiagen MinElute PCR Purification Kit.
In CUT&Tag-BS, the purified CUT&Tag-DNA was subsequently subjected to tagmentation-based bisulfite sequencing library preparation, which includes an oligonucleotide replacement and gap repair step to ensure that each DNA strand is covalently attached to methylated adapters on both ends, followed by bisulfite conversion and PCR amplification to generate sequencing library. While for non-bisulfite-treated CUT&Tag control, the bisulfite conversion step was removed in library preparation.

tag: cell line

value: E14 mouse embryonic stem cells

tag: chip antibody

value: anti-H3K27me3 (CST #9733S)

tag: cell count


title: SSs_GU

source_name: SSs

value: SSs


title: CnT-BS_H3K27me3_100K

data_processing:
Library strategy: CUT&Tag-BS
Filtering and mapping:  Raw reads were filtered to exclude pairs with average base quality <20.  Adapters removed by Cutadapt v1.12 with parameters "-a CTGTCTCTTATACAC -A CTGTCTCTTATACAC -O 5 -q 0 -m 20 -p", then reads were filtered to exclude fragments with length <30bp.  Filtered, trimmed read pairs were mapped against  mm10  via Bismark v0.23.0 with "-X 2000" using Bowtie2 v2.3.0 as the underlying mapper. Duplicate mapped fragments were removed by the Bismark v0.23.0 deduplicate_bismark tool with parameter "-p".
Peak calls:  HOMER v4.10.3 was used for peak calls with the makeTagDirectory function (parameters "-format sam -read1 -keepAll -fragLength 200") followed by the findPeaks function (parameters "-size 500 -minDist 1000 -L 0 -region" for H3K4me1 and  "-size 1000 -minDist 2500 -L 0 -region" for H3K9me3 and H3K27me3). Peaks overlapping mm10 blacklist regions were discarded. Unified peak sets were defined as the union of peak calls (per mark) via BEDtools v2.29.2 merge.
Signal tracks: Coverage tracks for genome browser views were generated by converting paired-end hits to a single fragment by BEDtools v2.29.2 bamtobed with the "-bedpe" option, BEDtools v2.29.2 genomecov to generate bedGraph format, then UCSC utility bedGraphToBigWig to convert to bigWig format.
Collecting methylation counts:  The Bismark v0.23.0 bismark_methylation_extractor tool was run with parameters "-p --ignore_r2 9 --comprehensive --mbias_off --bedGraph --cytosine_report".
Percent methylation tracks: For visualization purposes, the methylated and unmethylated cytosine counts from both strands (in the CpG context output from Bismark v0.23.0 bismark_methylation_extractor) were collapsed to calculate percent methylation per genomic CpG. Files were converted from variableStep WIG format to bigWig format by UCSC utility wigToBigWig.
Genome_build: mm10
Supplementary_files_format_and_content: percent methylation per CpG in bigWig format, coverage in bigWig format, peaks in BED format,  matrix of methylated and total cytosine base counts per CpG in tab-delimited text format


title: HIP_Posterior

source_name: HIP

value: HIP


title: SSs_GU_VISC


title: CnT-BS_H3K27me3_250K


title: CnT-BS_H3K27me3_20K


title: ORB

source_name: ORB

value: ORB


title: 389_JRX490: HT29_ORF_PTGER4_389

source_name: HT-29 PTGER4 transduction, UniqueID 389


title: HIP_Mid_Posterior


title: CnT-BS_H3K27me3_4K


title: 26_JRX417: HT29_ORF_CHP1_26

source_name: HT-29 CHP1 transduction, UniqueID 26


title: 47_JRX463: HT29_ORF_DLD_47

source_name: HT-29 DLD transduction, UniqueID 47


title: 302_JRX427: HT29_ORF_ERAP2_302

source_name: HT-29 ERAP2 transduction, UniqueID 302


title: 242_JRX467: HT29_ORF_UBQLN4_242

source_name: HT-29 UBQLN4 transduction, UniqueID 242


title: 301_JRX426: HT29_ORF_ERAP2_301

source_name: HT-29 ERAP2 transduction, UniqueID 301


title: 398_JRX492: HT29_ORF_SLC22A4_398

source_name: HT-29 SLC22A4 transduction, UniqueID 398


title: 257_JRX425: HT29_ORF_ZFP91_257

source_name: HT-29 ZFP91 transduction, UniqueID 257


title: 390_JRX491: HT29_ORF_PTGER4_390

source_name: HT-29 PTGER4 transduction, UniqueID 390


title: 399_JRX493: HT29_ORF_SLC22A4_399

source_name: HT-29 SLC22A4 transduction, UniqueID 399


title: 25_JRX416: HT29_ORF_CHP1_25

source_name: HT-29 CHP1 transduction, UniqueID 25


title: 256_JRX424: HT29_ORF_ZFP91_256

source_name: HT-29 ZFP91 transduction, UniqueID 256


title: 230_JRX489: HT29_ORF_TMEM258_230

source_name: HT-29 TMEM258 transduction, UniqueID 230


title: 401_JRX494: HT29_ORF_SLC2A13_401

source_name: HT-29 SLC2A13 transduction, UniqueID 401


title: HIP_Anterior


title: HIP_Mid_Anterior


title: CD8 387

city: Pozzilli

first: Daniela

last: Carnevale

address: Via dell'Elettronica

country: Italy

institute: IRCCS Neuromed and "Sapienza" University of Rome

data_processing:
Illumina software used for basecalling.
STAR 2.7.5c was used to map reads on reference genome
FeatureCounts 2.0 was used to produce the quantification of read transcripts
DESeq2 package of Bioconductor was used to perform the differential expression analysis
Genome_build: Gencode (release M27 (GRCm39))
Supplementary_files_format_and_content: Normalized raw counts

source_name: Splenic CD8

extract_protocol:
Total RNA was obtained from either CD4+ or CD8+ FACS-sorted cells by disrupting samples in Trizol. Following phenol chloroform extraction, RNA integrity was quantified on a Nanodrop Spectrophotometer and samples with A260/280 > 1.8 utilized for RNA sequencing.
Indexed libraries were prepared from 500 ng/ea purified RNA with the TruSeq Stranded mRNA Sample Prep Kit (Illumina) according to the manufacturer’s instructions

treatment_protocol: Mice were treated with Angiotensin-2 delivered by subcutaneous osmotic mini-pumps

value: Spleen

tag: treatment

value: Angiotensin-II


title: 2121_JRX457: HT29_ORF_ATG16L1_2121

source_name: HT-29 ATG16L1 transduction, UniqueID 2121


title: CD8 395


title: ACA_L6b

source_name: ACA

value: ACA


title: CD8 389


title: 229_JRX488: HT29_ORF_TMEM258_229

source_name: HT-29 TMEM258 transduction, UniqueID 229


title: 2124_JRX458: HT29_ORF_IRF5_2124

source_name: HT-29 IRF5 transduction, UniqueID 2124


title: CD4 395

source_name: Splenic CD4


title: 2125_JRX459: HT29_ORF_IRF5_2125

source_name: HT-29 IRF5 transduction, UniqueID 2125


title: CD4 393


title: CD4 385


title: GU_VISC_AIp_L1-L2-3-L4-L5-L6

source_name: GU

value: GU


title: CnT-nonBS-H3K9me3

source_name: E14 mouse embryonic stem cells

extract_protocol:
CUT&Tag was performed according to previously published protocol (Kaya-Okur et al., 2019) with slight modification, namely using pA-Tn5 transposome assembled with methylated adapter instead. Briefly, harvested cells were washed and then bound to concanavalin A-coated magnetic beads. The cells were permeabilized and incubated with target-specific primary antibody and then with secondary antibody, followed by incubation with pA-Tn5 transposome and tagmentation at target-binding sites. The tagmented DNA was extracted with Qiagen MinElute PCR Purification Kit.
In CUT&Tag-BS, the purified CUT&Tag-DNA was subsequently subjected to tagmentation-based bisulfite sequencing library preparation, which includes an oligonucleotide replacement and gap repair step to ensure that each DNA strand is covalently attached to methylated adapters on both ends, followed by bisulfite conversion and PCR amplification to generate sequencing library. While for non-bisulfite-treated CUT&Tag control, the bisulfite conversion step was removed in library preparation.
CUT&Tag, Bisulfite Sequencing

value: anti-H3K9me3 (abcam ab176916)


title: 2119_JRX455: HT29_ORF_IRF1_2119

source_name: HT-29 IRF1 transduction, UniqueID 2119


title: HIP_CAAnterior

source_name: HIP


title: 2115_JRX451: HT29_ORF_TYK2_2115

source_name: HT-29 TYK2 transduction, UniqueID 2115


title: 241_JRX466: HT29_ORF_UBQLN4_241

source_name: HT-29 UBQLN4 transduction, UniqueID 241


title: 2120_JRX456: HT29_ORF_ATG16L1_2120

source_name: HT-29 ATG16L1 transduction, UniqueID 2120


title: 2118_JRX454: HT29_ORF_IRF1_2118

source_name: HT-29 IRF1 transduction, UniqueID 2118


title: CnT-nonBS-H3K4me1

value: anti-H3K4me1 (CST #5326)


title: AUD_L1-L2-3-L4-L5-L6

source_name: AUD

value: AUD


title: 2109_JRX449: HT29_ORF_KPNA7_2109

source_name: HT-29 KPNA7 transduction, UniqueID 2109


title: HIP_CAMid_Anterior


title: 2100_JRX521: HT29_ORF_Empty_2100

source_name: HT-29 Empty transduction, UniqueID 2100

value: Empty


title: 2108_JRX448: HT29_ORF_KPNA7_2108

source_name: HT-29 KPNA7 transduction, UniqueID 2108


title: SSs_L1-L2-3-L4-L5-L6

source_name: SSs


title: HIP_CAMid_Posterior


title: 2114_JRX450: HT29_ORF_TYK2_2114

source_name: HT-29 TYK2 transduction, UniqueID 2114


title: 2099_JRX520: HT29_ORF_Empty_2099

source_name: HT-29 Empty transduction, UniqueID 2099


title: 2082_JRX487: HT29_ORF_NFKB1_2082

source_name: HT-29 NFKB1 transduction, UniqueID 2082


title: 2076_JRX485: HT29_ORF_MTMR3_2076

source_name: HT-29 MTMR3 transduction, UniqueID 2076


title: 2069_JRX442: HT29_ORF_YDJC_2069

source_name: HT-29 YDJC transduction, UniqueID 2069

value: YDJC


title: CnT-BS-H3K9me3.run2

source_name: E14 mouse embryonic stem cells


title: 2067_JRX441: HT29_ORF_RPL3_2067

source_name: HT-29 RPL3 transduction, UniqueID 2067


title: 2078_JRX446: HT29_ORF_FOXF1_2078

source_name: HT-29 FOXF1 transduction, UniqueID 2078


title: 2075_JRX484: HT29_ORF_MTMR3_2075

source_name: HT-29 MTMR3 transduction, UniqueID 2075


title: CnT-BS-H3K4me1.run2


title: 2079_JRX447: HT29_ORF_FOXF1_2079

source_name: HT-29 FOXF1 transduction, UniqueID 2079


title: 2081_JRX486: HT29_ORF_NFKB1_2081

source_name: HT-29 NFKB1 transduction, UniqueID 2081


title: 2070_JRX443: HT29_ORF_YDJC_2070

source_name: HT-29 YDJC transduction, UniqueID 2070


title: 2058_JRX501: HT29_ORF_IRGM_2058

source_name: HT-29 IRGM transduction, UniqueID 2058

value: IRGM


title: CnT-BS-H3K9me3.run1


title: Snubar-CoAssay_cell_line_BC

description:
SnubarATAC&RNA-Coassay-2cell line mixture (A20-K562)-sample_barcode
CELL BARCOE + UMI ,R2: SAMPLE BARCODE

data_processing:
Basecalls performed using CASAVA version 1.8.1
cellranger atac V1.2.0 mkfastq
cellranger atac V1.2.0 count and cellranger-arc-1.0.0 count
Mixing experiment data was aligned to the combined reference genomes of human (hg19 reference) and mouse (mm10 reference). All other experimental data was aligned to human hg19 or mouse mm10 genome.
UMI counts and peak count are summarized
Genome_build: hg19 and mm10
Supplementary_files_format_and_content: mtx

organism:
Homo sapiens
Mus musculus

extract_protocol:
Cell nuclei for Snubar-ATAC were isolated according to Nuclei Isolation for Single Cell ATAC Sequencing Protocol (CG000169 Rev D, 10X Genomics) or Nuclei Isolation from Mouse Brain Tissue for Single Cell ATAC Sequencing Protocol (CG000212 Rev B, 10X Genomics). Nuclei used for SNubar-ARC were isolated according to Nuclei Isolation for Single Cell Multiome ATAC + Gene Expression Sequencing Protocol (10X Genomics, CG000365 Rev A).
Single cell capture, barcoding and library preparation was performed by following the 10X Genomics protocols (CG000168 Rev A for Chromium Single Cell ATAC Reagent Kits,  CG000209 Rev D for Chromium Next GEM Single Cell ATAC Library Kit v1.1, or CG000338 Rev A for Chromium Next GEM Single Cell Multiome ATAC + Gene Expression)

value: A20 and K562


title: 2057_JRX500: HT29_ORF_IRGM_2057

source_name: HT-29 IRGM transduction, UniqueID 2057


title: 2039_JRX478: HT29_ORF_RSPO3_2039

source_name: HT-29 RSPO3 transduction, UniqueID 2039


title: 2066_JRX440: HT29_ORF_RPL3_2066

source_name: HT-29 RPL3 transduction, UniqueID 2066


title: HIP_CAPosterior

source_name: HIP


title: VIS_VISam_VISpm

source_name: VIS

value: VIS


title: CLA_anterior

source_name: CLA

value: CLA


title: CnT-BS-H3K4me1.run1

value: E14 mouse embryonic stem cells


title: 2043_JRX481: HT29_ORF_AIRE_2043

source_name: HT-29 AIRE transduction, UniqueID 2043

value: AIRE


title: RSPv

source_name: RSPv

value: RSPv


title: Snubar-NextGem

description:
Snubar-NextGem_ATAC and Snubar-NextGem_BC
SnubarATAC-NextGEM: 2 cell line mixture (A20-K562)-scATAC and sample_barcode
For ATAC pair-end read: R1: READ1, R2: CELL BARCODE, R3: READ2. For BC pair-end read: R1: Sample barcode+ UMI, R2: CELL BARCODE
SnubarATAC single cell ATAC-seq and barcode library

source_name: Snubar-NextGem

tag: cell lines


title: SnubarLowAK

description:
SnubarLowAK_ATAC and  SnubarLowAK_BC
SnubarATAC-lowAK: 2 cell line mixture (A20-K562)-scATAC and sample_barcode sample
For ATAC pair-end read: R1: READ1, R2: CELL BARCODE, R3: READ2. For BC pair-end read: R1: Sample barcode+ UMI, R2: CELL BARCODE
SnubarATAC single cell ATAC-seq and barcode library

source_name: SnubarLowAK


title: VIS_VISpl_VISpor


title: 2022_2_JRX461: HT29_ORF_MAP3K8_2022_2

source_name: HT-29 MAP3K8 transduction, UniqueID 2022_2


title: VIS_VISl_VISal_VISli


title: 6B2-pre bedrest muscle biopsy RNA-seq library

city: Richardson

first: Theodore

middle: John

last: Price

address: 800 W Campbell Rd

department: Behavioral and Brain Sciences

institute: The University of Texas at Dallas

description: total RNA (rRNA depleted)

data_processing:
Trimming and mapping (detailed in overall design)
Relative abunmdance quantification (detailed in overall design)
Genome_build: Ref transcriptome GENCODE v27, and reference genome GRCh38.p10
Supplementary_files_format_and_content: tpm_table.xlsx (Excel spreadsheet) contains Transcripts per Million based relative abundances for all non-mitochondrial coding genes across all samples

source_name: muscle biopsy obtained from the midbelly of the right (pre) and left (post) vastus lateralis muscle

extract_protocol:
Methods for muscle biopsy previously described (Krainski et al., 2014)
Stranded mRNA library preparation and sequencing were completed at the University of Texas at Dallas (UT Dallas), TX, USA. 76-bp, single-end sequencing of RNA-seq libraries was performed on the Illumina Hi-Seq sequencing platform. Library construction and sequencing were done based on manufacturers protocol (Illumina)

tag: subject id

tag: Sex

value: female

tag: subject age at sample biopsy

tag: sample regimen

value: pre-bedrest

tag: sample intervention

value: Not applicable (Pre-regimen)


title: SSp_L1-L2-3-L4-L5-L6

source_name: SSp

value: SSp


title: 2028_JRX435: HT29_ORF_GPR12_2028

source_name: HT-29 GPR12 transduction, UniqueID 2028

tag: orf

tag: uniqueid

tag: arraybatch

tag: transductiondate

tag: subset


title: 2042_JRX480: HT29_ORF_AIRE_2042

source_name: HT-29 AIRE transduction, UniqueID 2042


title: Snubar-CoAssay_cell_line_ATAC

description:
Snubar-CoAssay_ATAC
SnubarATAC&RNA-Coassay-2cell line mixture (A20-K562)-scATAC
For ATAC pair-end read: R1: READ1, R2: CELL BARCODE, R3: READ2
SnubarARC single cell ATAC-seq library

source_name: Snubar-CoAssay


title: 2013_JRX471: HT29_ORF_FOXD1_2013

source_name: HT-29 FOXD1 transduction, UniqueID 2013


title: 2010_JRX515: HT29_ORF_CARD9_2010

source_name: HT-29 CARD9 transduction, UniqueID 2010


title: 2027_JRX434: HT29_ORF_GPR12_2027

source_name: HT-29 GPR12 transduction, UniqueID 2027


title: 2040_JRX479: HT29_ORF_RSPO3_2040

source_name: HT-29 RSPO3 transduction, UniqueID 2040


title: ACA_L2-3-L5

source_name: ACA

value: ACA


title: 6B1-pre bedrest muscle biopsy RNA-seq library

description: total RNA (rRNA depleted)


title: Snubar-CoAssay_cell_line_RNA

description:
SnubarATAC&RNA-Coassay-2cell line mixture (A20-K562)-scRNA
FOR RNA,R1: CELL BARCODE + UMI, R2: RNA READS. For BC pair-end read: R1:


title: 6B2-post bedrest muscle biopsy RNA-seq library

description: total RNA (rRNA depleted)

value: post 5 week bedrest

value: Exercise


title: SSp_L6b


title: ACA_L6


title: 2012_JRX470: HT29_ORF_FOXD1_2012

source_name: HT-29 FOXD1 transduction, UniqueID 2012


title: 2025_JRX473: HT29_ORF_GIGYF1_2025

source_name: HT-29 GIGYF1 transduction, UniqueID 2025


title: 2007_JRX513: HT29_ORF_ATG5_2007

source_name: HT-29 ATG5 transduction, UniqueID 2007


title: ACA_L5


title: MOp_L6b

source_name: MOp

value: MOp


title: 2024_JRX472: HT29_ORF_GIGYF1_2024

source_name: HT-29 GIGYF1 transduction, UniqueID 2024


title: 2004_JRX433: HT29_ORF_USP25_2004

source_name: HT-29 USP25 transduction, UniqueID 2004


title: 2021_2_JRX460: HT29_ORF_MAP3K8_2021_2

source_name: HT-29 MAP3K8 transduction, UniqueID 2021_2


title: MOp_L1-L2-3-L5-L6


title: 6B1-post bedrest muscle biopsy RNA-seq library

description: total RNA (rRNA depleted)

source_name: muscle biopsy obtained from the midbelly of the right (pre) and left (post) vastus lateralis muscle


title: ACA_L2-3


title: 2000_JRX430: HT29_ORF_UBAC2_2000

source_name: HT-29 UBAC2 transduction, UniqueID 2000


title: 2001_JRX431: HT29_ORF_UBAC2_2001

source_name: HT-29 UBAC2 transduction, UniqueID 2001


title: 2009_JRX514: HT29_ORF_CARD9_2009

source_name: HT-29 CARD9 transduction, UniqueID 2009


title: 2006_JRX512: HT29_ORF_ATG5_2006

source_name: HT-29 ATG5 transduction, UniqueID 2006


title: 6A-pre bedrest muscle biopsy RNA-seq library

description: total RNA (rRNA depleted)


title: ALMp_L6b

source_name: ALM

value: ALM


title: 158_JRX423: HT29_ORF_PEX3_158

source_name: HT-29 PEX3 transduction, UniqueID 158


title: 2003_JRX432: HT29_ORF_USP25_2003

source_name: HT-29 USP25 transduction, UniqueID 2003


title: SSp_L1

source_name: SSp


title: 5B-pre bedrest muscle biopsy RNA-seq library

description: total RNA (rRNA depleted)

value: male


title: 157_JRX422: HT29_ORF_PEX3_157

source_name: HT-29 PEX3 transduction, UniqueID 157


title: 5B-post bedrest muscle biopsy RNA-seq library

description: total RNA (rRNA depleted)


title: 133_JRX420: HT29_ORF_NRBP1_133

source_name: HT-29 NRBP1 transduction, UniqueID 133


title: 8_JRX225: HT29_ORF_AAMP_8

source_name: HT-29 AAMP transduction, UniqueID 8

value: AAMP


title: MOp_L2-3-L5


title: 134_JRX421: HT29_ORF_NRBP1_134

source_name: HT-29 NRBP1 transduction, UniqueID 134


title: MOp_L1

source_name: MOp


title: 6A-post bedrest muscle biopsy RNA-seq library

description: total RNA (rRNA depleted)

value: Control


title: 5A-pre bedrest muscle biopsy RNA-seq library

description: total RNA (rRNA depleted)


title: SSp_L4-L5


title: 5A-post bedrest muscle biopsy RNA-seq library

description: total RNA (rRNA depleted)


title: 74_JRX243: HT29_ORF_GIPC2_74

source_name: HT-29 GIPC2 transduction, UniqueID 74


title: 4B-post bedrest muscle biopsy RNA-seq library

description: total RNA (rRNA depleted)


title: 4B-pre bedrest muscle biopsy RNA-seq library

description: total RNA (rRNA depleted)


title: SSp_L4


title: 73_JRX242: HT29_ORF_GIPC2_73

source_name: HT-29 GIPC2 transduction, UniqueID 73


title: 7_JRX224: HT29_ORF_AAMP_7

source_name: HT-29 AAMP transduction, UniqueID 7


title: VISp_L2

source_name: VISp

value: VISp


title: 75_JRX244: HT29_ORF_GIPC2_75

source_name: HT-29 GIPC2 transduction, UniqueID 75


title: 4A-post bedrest muscle biopsy RNA-seq library

description: total RNA (rRNA depleted)

source_name: muscle biopsy obtained from the midbelly of the right (pre) and left (post) vastus lateralis muscle


title: 489_JRX411: HT29_ORF_ACTN1_489

source_name: HT-29 ACTN1 transduction, UniqueID 489


title: 9_JRX226: HT29_ORF_AAMP_9

source_name: HT-29 AAMP transduction, UniqueID 9


title: 72_JRX241: HT29_ORF_FUT2_72

source_name: HT-29 FUT2 transduction, UniqueID 72


title: 71_JRX240: HT29_ORF_FUT2_71

source_name: HT-29 FUT2 transduction, UniqueID 71


title: 70_JRX239: HT29_ORF_FUT2_70

source_name: HT-29 FUT2 transduction, UniqueID 70


title: 3B-pre bedrest muscle biopsy RNA-seq library

description: total RNA (rRNA depleted)


title: 3B-post bedrest muscle biopsy RNA-seq library

description: total RNA (rRNA depleted)


title: 484_JRX409: HT29_ORF_H2AFY_484

source_name: HT-29 H2AFY transduction, UniqueID 484


title: 485_JRX380: HT29_ORF_SBNO2_485

source_name: HT-29 SBNO2 transduction, UniqueID 485


title: 488_JRX410: HT29_ORF_ACTN1_488

source_name: HT-29 ACTN1 transduction, UniqueID 488


title: 4A-pre bedrest muscle biopsy RNA-seq library

description: total RNA (rRNA depleted)


title: 487_JRX382: HT29_ORF_SBNO2_487

source_name: HT-29 SBNO2 transduction, UniqueID 487


title: 480_JRX378: HT29_ORF_NDFIP1_480

source_name: HT-29 NDFIP1 transduction, UniqueID 480


title: 479_JRX377: HT29_ORF_NDFIP1_479

source_name: HT-29 NDFIP1 transduction, UniqueID 479


title: 3A-pre bedrest muscle biopsy RNA-seq library

description: total RNA (rRNA depleted)


title: 477_JRX375: HT29_ORF_CFL1_477

source_name: HT-29 CFL1 transduction, UniqueID 477


title: 471_JRX405: HT29_ORF_GPBAR1_471

source_name: HT-29 GPBAR1 transduction, UniqueID 471


title: 472_JRX406: HT29_ORF_GPBAR1_472

source_name: HT-29 GPBAR1 transduction, UniqueID 472


title: 2B-post bedrest muscle biopsy RNA-seq library

description: total RNA (rRNA depleted)


title: 476_JRX374: HT29_ORF_CFL1_476

source_name: HT-29 CFL1 transduction, UniqueID 476


title: 2B-pre bedrest muscle biopsy RNA-seq library

description: total RNA (rRNA depleted)


title: 463_JRX370: HT29_ORF_ASXL1_463

source_name: HT-29 ASXL1 transduction, UniqueID 463


title: 462_JRX369: HT29_ORF_ASXL1_462

source_name: HT-29 ASXL1 transduction, UniqueID 462


title: ALM_L1-L2-3

source_name: ALM


title: 459_JRX366: HT29_ORF_PTPN1_459

source_name: HT-29 PTPN1 transduction, UniqueID 459


title: 458_JRX365: HT29_ORF_PTPN1_458

source_name: HT-29 PTPN1 transduction, UniqueID 458


title: 452_JRX362: HT29_ORF_HINT1_452

source_name: HT-29 HINT1 transduction, UniqueID 452


title: 457_JRX403: HT29_ORF_PPP5C_457

source_name: HT-29 PPP5C transduction, UniqueID 457


title: VISp_L2-3-L4

source_name: VISp


title: 453_JRX363: HT29_ORF_HINT1_453

source_name: HT-29 HINT1 transduction, UniqueID 453


title: 447_JRX360: HT29_ORF_FIBP_447

source_name: HT-29 FIBP transduction, UniqueID 447

value: FIBP


title: VISp_L4-L5


title: 2A-post bedrest muscle biopsy RNA-seq library

description: total RNA (rRNA depleted)

source_name: muscle biopsy obtained from the midbelly of the right (pre) and left (post) vastus lateralis muscle


title: VISp_L1-L2-3


title: 1B-pre bedrest muscle biopsy RNA-seq library

description: total RNA (rRNA depleted)


title: ALM_L5-L6


title: 42_JRX238: HT29_ORF_CUL2_42

source_name: HT-29 CUL2 transduction, UniqueID 42


title: 483_JRX408: HT29_ORF_H2AFY_483

source_name: HT-29 H2AFY transduction, UniqueID 483


title: VISp_L1-L2-3-L4-L5-L6


title: 426_JRX354: HT29_ORF_IRF8_426

source_name: HT-29 IRF8 transduction, UniqueID 426


title: 424_JRX352: HT29_ORF_ZMIZ1_424

source_name: HT-29 ZMIZ1 transduction, UniqueID 424


title: VISp_L1-L2-3-L4


title: 1A-pre bedrest muscle biopsy RNA-seq library

description: total RNA (rRNA depleted)


title: MOp_L2-3

source_name: MOp


title: 423_JRX351: HT29_ORF_ZMIZ1_423

source_name: HT-29 ZMIZ1 transduction, UniqueID 423


title: ALM_L1-L2-3-L5-L6


title: 41_JRX237: HT29_ORF_CUL2_41

source_name: HT-29 CUL2 transduction, UniqueID 41


title: 414_JRX348: HT29_ORF_TAGAP_414

source_name: HT-29 TAGAP transduction, UniqueID 414

value: TAGAP


title: 455_JRX401: HT29_ORF_PPP5C_455

source_name: HT-29 PPP5C transduction, UniqueID 455


title: 2A-pre bedrest muscle biopsy RNA-seq library

description: total RNA (rRNA depleted)


title: 3A-post bedrest muscle biopsy RNA-seq library

description: total RNA (rRNA depleted)


title: MOp_L6


title: Sample 52- 104675 GFP- cells, Single Ventral Organoid Day 70

city: Vienna

first: Sunanjay

last: Bajaj

address: Dr.-Bohr-Gasse 3

country: Austria

institute: Institute for Molecular Biotechnology of the Austrian Academy of Sciences

data_processing:
Adapter were clipped with trimgalore (v0.5.0)
Abudant sequences (Rrna, mitochondrion, phiX, adapter, polyA/C) were removed with bowtie2 (v2.3.4.1)
Cleaned reads were aligned against the genome (GRCh38) with STAR (v.6.0c)
Reads were counted towards their corresponding gene (ENSEMBL 94) with featureCounts (v1.6.2)
Differentially expressed genes were detected with DESeq2 (v1.18.1) and coverage tracks were created with deepTools (v3.0.2)
Genome_build: GRCh38
Supplementary_files_format_and_content: Txt, Files contain gene counts for each sample

source_name: Single Cerebral Organoid

growth_protocol: Cerebral organoid fusions (Fusions) were generated with a modified protocol, expanding upon previous organoid generation protocols from our lab (Lancaster et al., 2013, 2017). Please see methods of manuscript for details.

extract_protocol:
Organoid Fusions were manually dissected, single organoids were kept whole. Tissue was then dissociated using a gentleMACS dissociator (Miltenyi). GFP+ and GFP- cells were then obatiend via FACS.
Libraries were generated with the SmartSeq-2 protocol 2 (Illumina ). Libraries were pooled and sequenced on a HiSeq V4 flow cell (Illumina) with up to 4 billion single-end reads.
We sequenced all samples twice to improve the yield and then combined the samples using samtools (htslib.org). Raw files for both sequencing runs are included in this upload.

tag: stem cell type

value: H9 Feeder Free Human ESCs


title: VISp_L4-L5-L6

tag: sample type


title: SSp_L2-3

source_name: SSp


title: 1B-post bedrest muscle biopsy RNA-seq library

description: total RNA (rRNA depleted)


title: SSp_L6


title: MOp_L5


title: SSp_L5


title: Sample 48- 104671 GFP- cells, Single Ventral Organoid Day 90


title: Sample 51- 104674 GFP+ cells, Single Ventral Organoid Day 70


title: 413_JRX347: HT29_ORF_TAGAP_413

source_name: HT-29 TAGAP transduction, UniqueID 413


title: 35_JRX234: HT29_ORF_CPSF3L_35

source_name: HT-29 CPSF3L transduction, UniqueID 35


title: 374_JRX335: HT29_ORF_MMP24_374

source_name: HT-29 MMP24 transduction, UniqueID 374


title: 446_JRX359: HT29_ORF_FIBP_446

source_name: HT-29 FIBP transduction, UniqueID 446


title: 1A-post bedrest muscle biopsy RNA-seq library

description: total RNA (rRNA depleted)


title: 392_JRX341: HT29_ORF_RASGRP1_392

source_name: HT-29 RASGRP1 transduction, UniqueID 392


title: 393_JRX342: HT29_ORF_RASGRP1_393

source_name: HT-29 RASGRP1 transduction, UniqueID 393


title: Sample 47- 104670 GFP+ cells, Single Ventral Organoid Day 90


title: 378_JRX339: HT29_ORF_NKX2-3_378

source_name: HT-29 NKX2-3 transduction, UniqueID 378


title: VISp_L6b

source_name: VISp


title: Sample 50- 104673 GFP- cells, Single Ventral Organoid Day 90


title: 346_JRX326: HT29_ORF_LACC1_346

source_name: HT-29 LACC1 transduction, UniqueID 346


title: 36_JRX235: HT29_ORF_CPSF3L_36

source_name: HT-29 CPSF3L transduction, UniqueID 36


title: VISp_L5-L6


title: 344_JRX324: HT29_ORF_CLN3_344

source_name: HT-29 CLN3 transduction, UniqueID 344


title: Sample 49- 104672 GFP+ cells, Single Ventral Organoid Day 90


title: 40_JRX236: HT29_ORF_CUL2_40

source_name: HT-29 CUL2 transduction, UniqueID 40


title: 343_JRX323: HT29_ORF_CLN3_343

source_name: HT-29 CLN3 transduction, UniqueID 343


title: 425_JRX353: HT29_ORF_IRF8_425

source_name: HT-29 IRF8 transduction, UniqueID 425


title: 321_JRX319: HT29_ORF_SATB1_321

source_name: HT-29 SATB1 transduction, UniqueID 321


title: 375_JRX336: HT29_ORF_MMP24_375

source_name: HT-29 MMP24 transduction, UniqueID 375


title: Sample 43- 104666 GFP- cells, Single Dorsal Organoid Day 90

source_name: Single Cerebral Organoid


title: ALM_L1

source_name: ALM


title: ALM_L2-3


title: ALM_L5


title: ALM_L6


title: Sample 46- 104669 GFP- cells, Single Ventral Organoid Day 90


title: 347_JRX327: HT29_ORF_LACC1_347

source_name: HT-29 LACC1 transduction, UniqueID 347


title: Sample 42- 104665 GFP- cells, Single Dorsal Organoid Day 90


title: VISp_L4


title: Sample 44- 104667 GFP- cells, Single Dorsal Organoid Day 70


title: VISp_L2-3


title: Sample 45- 104668 GFP+ cells, Single Ventral Organoid Day 90


title: VISp_L6


title: VISp_L1


title: Sample 40- 104663 GFP- cells, Ventral Region Organoid Fusion Day 70

source_name: Cerebral Organoid Fusion


title: Sample 39- 104662 GFP+ cells, Ventral Region Organoid Fusion Day 70


title: Wildtype Femur

city: Buffalo

first: Jonathan

middle: E

last: Bard

state: New York

address: 701 Ellicott Street

department: Genomics and Bioinformatics Core

institute: University at Buffalo

description: Wildtype Femure Bonemarrow

data_processing:
Illumina RTA 2.2.68 Basecaller
Cellranger 3.0.1 mkoutput with Bcl2Fastq 2.20.0.422
Cellranger 3.0.1 Count against mm10 genome to produce count matrix
Seurat 4.0.1 used for marker gene analysis and visualization
Genome_build: mm10
Supplementary_files_format_and_content: CSV File containing UMI corrected read counts

source_name: Femur

extract_protocol:
Chromimum Single Cell 3' v2 (10x Genomics)
TruSeq Stranded RNA (illumina)

tag: strain

tag: tissue

value: Femur Bonemarrow

tag: developmental stage

value: 3 Month


title: 34_JRX233: HT29_ORF_CPSF3L_34

source_name: HT-29 CPSF3L transduction, UniqueID 34


title: 316_JRX314: HT29_ORF_LRRK2_316

source_name: HT-29 LRRK2 transduction, UniqueID 316


title: VISp_L5


title: Sample 41- 104664 GFP- cells, Single Dorsal Organoid Day 90


title: 311_JRX312: HT29_ORF_ITLN1_311

source_name: HT-29 ITLN1 transduction, UniqueID 311


title: 305_JRX309: HT29_ORF_GSDMB_305

source_name: HT-29 GSDMB transduction, UniqueID 305

value: GSDMB


title: 319_JRX317: HT29_ORF_SATB1_319

source_name: HT-29 SATB1 transduction, UniqueID 319


title: Wildtype Mandible

description: Wildtype Mandible Bonemarrow

source_name: Mandible

value: Mandible Bonemarrow


title: Sample 38- 104661 GFP- cells, Ventral Region Organoid Fusion Day 70


title: 377_JRX338: HT29_ORF_NKX2-3_377

source_name: HT-29 NKX2-3 transduction, UniqueID 377


title: 317_JRX315: HT29_ORF_LRRK2_317

source_name: HT-29 LRRK2 transduction, UniqueID 317


title: 310_JRX311: HT29_ORF_ITLN1_310

source_name: HT-29 ITLN1 transduction, UniqueID 310


title: 318_JRX316: HT29_ORF_LRRK2_318

source_name: HT-29 LRRK2 transduction, UniqueID 318


title: 290_JRX303: HT29_ORF_RNFT1_290

source_name: HT-29 RNFT1 transduction, UniqueID 290


title: 289_JRX302: HT29_ORF_RNFT1_289

source_name: HT-29 RNFT1 transduction, UniqueID 289


title: 287_JRX300: HT29_ORF_CEP72_287

source_name: HT-29 CEP72 transduction, UniqueID 287


title: 304_JRX308: HT29_ORF_GSDMB_304

source_name: HT-29 GSDMB transduction, UniqueID 304


title: Sample 37- 104660 GFP+ cells, Ventral Region Organoid Fusion Day 70


title: Trim28 haplo Liver CFP1 CUT&RUN rep3

city: Cambridge

middle: Richard

last: Costello

state: Cambridgeshire

address: Genetics Building Downing St.

department: Department of Genetics

country: United Kingdom

institute: Univerity of Cambridge

description: Reads were aligned to mm10

data_processing:
Library strategy: CUT&RUN
For  Cut and run processing:  Basecalling was performed using CASAVA version 1.4 Reads were trimmed using trimgalore with the --trim1 option for paired end aligments. Reads were aligned using Bowtie version 1.2.3 using the following parameters -m 1 -X 1000 -m 1 --best. Files were sorted using Samtools sort and were filtered for PCR duplicates using picardTools Mark Duplicates with the REMOVE_DUPLICATES=true option ; reads were further filtere to remove all reads mapping to blacklisted sites as identified using RSEG deadzones.  Pileups of fragments were generated using genomeCoverageBed from bedtools version2.29.0. with the -pc option. bigWigs were generated using ucsctools wigToBigWig
For minION processing:  nanopolish index was run on individual files. minimap2 version 2.11 was run to align reads to both the mm10 genome and human chromosone 21. Files were then sorted and filtered with the -F 4 option using samtools. Methylation calling was preformed using nanopolish call-methylation with the -t 8 option
Genome_build: both mm10 and chromosone 21 of hg38; Tc1 Liver minION-seq, aligned t0 mm9 mouse
Supplementary_files_format_and_content: bigWig of human chromosone 21 with Cfp1 ChIP signal or CpG methylation percentage

source_name: Liver

extract_protocol:
Cut and Run was performed using the Millipore Cfp1 monoclonal antibody (ABE211). Briefly, unfixed permeabilized cells are incubated with the Cfp1 antibody fused to A-Micrococcal Nuclease.
Isolated DNA was sequenced on an Illumina HiSeq 2500 System

tag: genotype

value: Trim28 haplo

value: FVB Trim28 +/D9


title: Trim28 haplo Liver CFP1 CUT&RUN rep2

description: Reads were aligned to mm10


title: Sample 36- 104659 GFP- cells, Ventral Region Organoid Fusion Day 70

source_name: Cerebral Organoid Fusion


title: Trim28 haplo Liver CFP1 CUT&RUN rep1

description: Reads were aligned to mm10


title: Sample 35- 104658 GFP+ cells, Ventral Region Organoid Fusion Day 70


title: Trim28 wild type Liver CFP1 CUT&RUN rep3

description: Reads were aligned to mm10

value: Trim28 wild type

value: FVB Trim28 +/+


title: 288_JRX301: HT29_ORF_CEP72_288

source_name: HT-29 CEP72 transduction, UniqueID 288


title: 291_JRX304: HT29_ORF_RNFT1_291

source_name: HT-29 RNFT1 transduction, UniqueID 291


title: 312_JRX313: HT29_ORF_ITLN1_312

source_name: HT-29 ITLN1 transduction, UniqueID 312


title: 238_JRX398: HT29_ORF_TTPAL_238

source_name: HT-29 TTPAL transduction, UniqueID 238

value: TTPAL


title: 237_JRX289: HT29_ORF_DENND1B_237

source_name: HT-29 DENND1B transduction, UniqueID 237


title: 236_JRX288: HT29_ORF_DENND1B_236

source_name: HT-29 DENND1B transduction, UniqueID 236


title: Sample 34- 104657 GFP- cells, Ventral Region Organoid Fusion Day 70


title: 239_JRX399: HT29_ORF_TTPAL_239

source_name: HT-29 TTPAL transduction, UniqueID 239


title: 2087_JRX389: HT29_ORF_Empty_2087

source_name: HT-29 Empty transduction, UniqueID 2087

value: Empty


title: Sample 33- 104656 GFP+ cells, Ventral Region Organoid Fusion Day 70


title: Trim28 wild type Liver CFP1 CUT&RUNrep2

description: Reads were aligned to mm10


title: 2088_JRX390: HT29_ORF_Empty_2088

source_name: HT-29 Empty transduction, UniqueID 2088


title: 286_JRX299: HT29_ORF_CEP72_286

source_name: HT-29 CEP72 transduction, UniqueID 286


title: 235_JRX287: HT29_ORF_DENND1B_235

source_name: HT-29 DENND1B transduction, UniqueID 235


title: Trim28 wild type Liver CFP1 CUT&RUN rep1

description: Reads were aligned to mm10


title: 2085_JRX387: HT29_ORF_RTEL1_2085

source_name: HT-29 RTEL1 transduction, UniqueID 2085


title: Sample 32- 104655 GFP- cells, Dorsal Region Organoid Fusion Day 70


title: Sample 30- 104653 GFP- cells, Dorsal Region Organoid Fusion Day 70


title: Trim28 haplo Liver H3K4me3 ChIP-seq rep1

description: Reads were aligned to mm10

data_processing:
For  Cut and run processing:  Basecalling was performed using CASAVA version 1.4 Reads were trimmed using trimgalore with the --trim1 option for paired end aligments. Reads were aligned using Bowtie version 1.2.3 using the following parameters -m 1 -X 1000 -m 1 --best. Files were sorted using Samtools sort and were filtered for PCR duplicates using picardTools Mark Duplicates with the REMOVE_DUPLICATES=true option ; reads were further filtere to remove all reads mapping to blacklisted sites as identified using RSEG deadzones.  Pileups of fragments were generated using genomeCoverageBed from bedtools version2.29.0. with the -pc option. bigWigs were generated using ucsctools wigToBigWig
For minION processing:  nanopolish index was run on individual files. minimap2 version 2.11 was run to align reads to both the mm10 genome and human chromosone 21. Files were then sorted and filtered with the -F 4 option using samtools. Methylation calling was preformed using nanopolish call-methylation with the -t 8 option
Genome_build: both mm10 and chromosone 21 of hg38; Tc1 Liver minION-seq, aligned t0 mm9 mouse
Supplementary_files_format_and_content: bigWig of human chromosone 21 with Cfp1 ChIP signal or CpG methylation percentage

extract_protocol:
Chromatin immunoprecipitation was performed with an H3K4me3 antibody (ab8580, Abcam)
Isolated DNA was sequenced on an Illumina HiSeq 2500 System

tag: antibody


title: 2030_JRX383: HT29_ORF_PITX1_2030

source_name: HT-29 PITX1 transduction, UniqueID 2030


title: 2086_JRX388: HT29_ORF_RTEL1_2086

source_name: HT-29 RTEL1 transduction, UniqueID 2086


title: 2031_JRX384: HT29_ORF_PITX1_2031

source_name: HT-29 PITX1 transduction, UniqueID 2031


title: Sample 31- 104654 GFP+ cells, Dorsal Region Organoid Fusion Day 70


title: Sample 28- 104651 GFP- cells, Dorsal Region Organoid Fusion Day 70


title: Trim28 wild type Liver H3K4me3 ChIP-seq rep3

description: Reads were aligned to mm10

source_name: Liver


title: Trim28 haplo Liver H3K4me3 ChIP-seq rep3

description: Reads were aligned to mm10


title: Sample 27- 104650 GFP+ cells, Dorsal Region Organoid Fusion Day 70

source_name: Cerebral Organoid Fusion


title: Trim28 wild type Liver H3K4me3 ChIP-seq rep2

description: Reads were aligned to mm10


title: 320_JRX318: HT29_ORF_SATB1_320

source_name: HT-29 SATB1 transduction, UniqueID 320


title: 202_JRX284: HT29_ORF_SLC26A3_202

source_name: HT-29 SLC26A3 transduction, UniqueID 202


title: 198_JRX280: HT29_ORF_SFMBT1_198

source_name: HT-29 SFMBT1 transduction, UniqueID 198


title: 199_JRX281: HT29_ORF_SLC22A5_199

source_name: HT-29 SLC22A5 transduction, UniqueID 199


title: Sample 29- 104652 GFP+ cells, Dorsal Region Organoid Fusion Day 70


title: Trim28 wild type Liver H3K4me3 ChIP-seq rep1

description: Reads were aligned to mm10


title: 191_JRX276: HT29_ORF_RXFP4_191

source_name: HT-29 RXFP4 transduction, UniqueID 191


title: 197_JRX279: HT29_ORF_SFMBT1_197

source_name: HT-29 SFMBT1 transduction, UniqueID 197


title: 201_JRX283: HT29_ORF_SLC22A5_201

source_name: HT-29 SLC22A5 transduction, UniqueID 201


title: Trim28 haplo Liver H3K4me3 ChIP-seq rep2

description: Reads were aligned to mm10


title: Sample 25- 104648 GFP+ cells, Dorsal Region Organoid Fusion Day 70


title: Sample 26- 104649 GFP- cells, Dorsal Region Organoid Fusion Day 70


title: 203_JRX285: HT29_ORF_SLC26A3_203

source_name: HT-29 SLC26A3 transduction, UniqueID 203


title: 196_JRX278: HT29_ORF_SFMBT1_196

source_name: HT-29 SFMBT1 transduction, UniqueID 196


title: Tc1 liver CFP1 CUT&RUN rep3

description: Reads were aligned to both the hg38 chromosone 21 and mm10 genomes. reported bigwig is mapped to hg38 chromosone 21

value: Tc1 wildtype

value: B6129S-Tc(HSA21)1TybEmcf/J mice purchased from JAX Laboratory


title: Sample 23- 104646 GFP+ cells, Ventral Region Organoid Fusion Day 70


title: Sample 21- 104644 GFP+ cells, Ventral Region Organoid Fusion Day 70


title: Sample 22- 104645 GFP- cells, Ventral Region Organoid Fusion Day 70


title: Sample 24- 104647 GFP- cells, Ventral Region Organoid Fusion Day 70


title: 170_JRX396: HT29_ORF_PSMG1_170

source_name: HT-29 PSMG1 transduction, UniqueID 170


title: Tc1 liver CFP1 CUT&RUN rep1


title: Sample 19- 104642 GFP+ cells, Ventral Region Organoid Fusion Day 70


title: Tc1 liver CFP1 CUT&RUN rep2


title: 200_JRX282: HT29_ORF_SLC22A5_200

source_name: HT-29 SLC22A5 transduction, UniqueID 200


title: Sample 20- 104643 GFP- cells, Ventral Region Organoid Fusion Day 70


title: 169_JRX395: HT29_ORF_PSMG1_169

source_name: HT-29 PSMG1 transduction, UniqueID 169


title: Primary kidney ECs 3

city: New York

first: José Gabriel

last: Barcia Durán

address: 1300 York Avenue, Room A-809

department: Medicine

institute: Weill Cornell Medicine

description: processed data file: genecounts_fig 1.txt

data_processing:
FastQC (v0.11.5) to check FASTQ quality.
Skewer (v0.2.2) for adapter trimming
Minion from Kraken tool (reaper-13-100) for adapter diagnosis
STAR (v2.7.6a) for alignment and gene count quantification using --quantMode GeneCounts
Genome_build: GRCm38
Supplementary_files_format_and_content: Gene count matrix with ensembl IDs as tab separated file.

source_name: Primary kidney ECs

extract_protocol:
Cells were isolated by fluorescence-activated cell sorting and subjected to TRIzol treatment for RNA extraction and sequencing.
RNA-seq libraries of polyadenylated RNA were prepared using the TruSeq RNA Library Prep Kit v2 (Illumina) or TruSeq Stranded mRNA Library Prep Kit (Illumina) according to the manufacturer’s instructions.

tag: strain/genotype

value: Kidney endothelium

tag: cell type

value: endothelial cells (ECs)


title: Sample 18- 104641 GFP- cells, Dorsal Region Organoid Fusion Day 70


title: Primary kidney ECs 2


title: Sample 17- 104640 GFP+ cells, Dorsal Region Organoid Fusion Day 70


title: Primary kidney ECs 1


title: Sample 16- 104639 GFP- cells, Dorsal Region Organoid Fusion Day 70


title: Sample 15- 104638 GFP+ cells, Dorsal Region Organoid Fusion Day 70


title: Primary heart ECs 2

source_name: Primary heart ECs

value: Heart endothelium


title: Primary heart ECs 3


title: Primary heart ECs 1


title: Sample 14- 104637 GFP- cells, Dorsal Region Organoid Fusion Day 70


title: Sample 13- 104636 GFP+ cells, Dorsal Region Organoid Fusion Day 70


title: Primary lung ECs 3

source_name: Primary lung ECs

value: Lung endothelium


title: 190_JRX275: HT29_ORF_RXFP4_190

source_name: HT-29 RXFP4 transduction, UniqueID 190


title: 105_JRX253: HT29_ORF_KIF21B_105

source_name: HT-29 KIF21B transduction, UniqueID 105


title: 162_JRX268: HT29_ORF_POFUT1_162

source_name: HT-29 POFUT1 transduction, UniqueID 162


title: 137_JRX261: HT29_ORF_RCL1_137

source_name: HT-29 RCL1 transduction, UniqueID 137


title: 192_JRX277: HT29_ORF_RXFP4_192

source_name: HT-29 RXFP4 transduction, UniqueID 192


title: 119_JRX255: HT29_ORF_LRRC32_119

source_name: HT-29 LRRC32 transduction, UniqueID 119


title: 161_JRX267: HT29_ORF_POFUT1_161

source_name: HT-29 POFUT1 transduction, UniqueID 161


title: 151_JRX263: HT29_ORF_OTUD3_151

source_name: HT-29 OTUD3 transduction, UniqueID 151


title: 160_JRX266: HT29_ORF_POFUT1_160

source_name: HT-29 POFUT1 transduction, UniqueID 160


title: 89_JRX158: HT29_ORF_HNF4A_89

source_name: HT-29 HNF4A transduction, UniqueID 89


title: 123_JRX259: HT29_ORF_AHRR_123

source_name: HT-29 AHRR transduction, UniqueID 123

value: AHRR


title: 136_JRX260: HT29_ORF_RCL1_136

source_name: HT-29 RCL1 transduction, UniqueID 136


title: 118_JRX254: HT29_ORF_LRRC32_118

source_name: HT-29 LRRC32 transduction, UniqueID 118


title: 103_JRX251: HT29_ORF_KIF21B_103

source_name: HT-29 KIF21B transduction, UniqueID 103


title: 95_JRX160: HT29_ORF_IFIH1_95

source_name: HT-29 IFIH1 transduction, UniqueID 95


title: 120_JRX256: HT29_ORF_LRRC32_120

source_name: HT-29 LRRC32 transduction, UniqueID 120


title: 187_JRX272: HT29_ORF_RPS6KA4_187

source_name: HT-29 RPS6KA4 transduction, UniqueID 187


title: 188_JRX273: HT29_ORF_RPS6KA4_188

source_name: HT-29 RPS6KA4 transduction, UniqueID 188


title: Sample 12- 104635 GFP- cells, Ventral Region Organoid Fusion Day 90

source_name: Cerebral Organoid Fusion

value: H9 Feeder Free Human ESCs


title: 104_JRX252: HT29_ORF_KIF21B_104

source_name: HT-29 KIF21B transduction, UniqueID 104


title: 90_JRX159: HT29_ORF_HNF4A_90

source_name: HT-29 HNF4A transduction, UniqueID 90


title: 122_JRX258: HT29_ORF_AHRR_122

source_name: HT-29 AHRR transduction, UniqueID 122


title: 152_JRX264: HT29_ORF_OTUD3_152

source_name: HT-29 OTUD3 transduction, UniqueID 152


title: 138_JRX262: HT29_ORF_RCL1_138

source_name: HT-29 RCL1 transduction, UniqueID 138


title: 121_JRX257: HT29_ORF_AHRR_121

source_name: HT-29 AHRR transduction, UniqueID 121


title: 117_JRX394: HT29_ORF_KSR1_117

source_name: HT-29 KSR1 transduction, UniqueID 117


title: 96_JRX161: HT29_ORF_IFIH1_96

source_name: HT-29 IFIH1 transduction, UniqueID 96


title: 153_JRX265: HT29_ORF_OTUD3_153

source_name: HT-29 OTUD3 transduction, UniqueID 153


title: Sample 11- 104634 GFP+ cells, Ventral Region Organoid Fusion Day 90


title: 81_JRX157: HT29_ORF_GNB2_81

source_name: HT-29 GNB2 transduction, UniqueID 81


title: Primary lung ECs 2

source_name: Primary lung ECs


title: Sample 10- 104633 GFP- cells, Ventral Region Organoid Fusion Day 90


title: 80_JRX156: HT29_ORF_GNB2_80

source_name: HT-29 GNB2 transduction, UniqueID 80


title: 77_JRX154: HT29_ORF_GNA12_77

source_name: HT-29 GNA12 transduction, UniqueID 77


title: Primary liver ECs 3

source_name: Primary liver ECs

value: Liver endothelium


title: Primary liver ECs 2


title: Sample 7- 104630 GFP+ cells, Ventral Region Organoid Fusion Day 90


title: Primary lung ECs 1


title: Sample 9- 104632 GFP+ cells, Ventral Region Organoid Fusion Day 90


title: 115_JRX392: HT29_ORF_KSR1_115

source_name: HT-29 KSR1 transduction, UniqueID 115


title: Sample 8- 104631 GFP- cells, Ventral Region Organoid Fusion Day 90


title: 2CLC-HiC-rep1

first: Li

last: Shen

state: Zhejiang Province

address: 866 Yuhangtang Road

institute: Life Sciences Institute, Zhejiang University

data_processing:
Paired-end raw reads of Hi-C libraries were trimmed to 50bp and then aligned, processed and iteratively corrected using HiCPro (version 2.11.1). Briefly, sequencing reads were first independently aligned to the mouse reference genome (mm9) using the bowtie2 end-to-end algorithm and ‘-very-sensitive’ option. To rescue the chimeric fragments spanning the ligation junction, the ligation site was detected and the 5’ fraction of the reads was aligned back to the reference genome. Unmapped reads, multiple mapped reads and singletons were then discarded. Pairs of aligned reads were then assigned to MboI restriction fragments. Read pairs from uncut DNA, self-circle ligation and PCR artefacts were filtered out and the valid read pairs involving two different restriction fragments were used to build the contact matrix. Valid read pairs were then binned at a specific resolution by dividing the genome into bins of equal size. The binned interaction matrices were then normalized using the iterative correction method to correct for biases such as GC content, mappability and effective fragment length in Hi-C data.
Genome_build: mm9
Supplementary_files_format_and_content: allValidPairs

source_name: Mouse embryonic stem cell

growth_protocol: mESCs were cultured routinely in LIF and serum medium.

extract_protocol: Hi-C libraries were prepared using sisHi-C developed by Du et al., Nature 2017 (PMID: 28703188).

treatment_protocol: mESCs containing a stably integrated transgene (MERVL::tdTomato) were cultured on 0.1% gelatin in DMEM containing 15% FBS, leukemia inhibiting factor (LIF), penicillin/streptomycin, L-glutamine, β-mercaptoethanol, and non-essential amino acids. After digestion with 0.05% trypsin, ESCs (non-2CLCs) and 2CLCs were sorted using the fluorescent reporters. The cells were then cross-linked for 10 min with 1% final concentration fresh formaldehyde at room temperature. The cross-linked cells were subsequently lysed in lysis buffer for sisHi-C.

tag: stain

value: 129/Ola, XY

tag: transgene


title: 2CLC-HiC-rep2


title: Primary liver ECs 1


title: Sample 5- 104628 GFP+ cells, Dorsal Region Organoid Fusion Day 90

source_name: Cerebral Organoid Fusion


title: Sample 4- 104627 GFP- cells, Dorsal Region Organoid Fusion Day 90


title: 66_JRX151: HT29_ORF_FOSL2_66

source_name: HT-29 FOSL2 transduction, UniqueID 66


title: Sample 6- 104629 GFP- cells, Dorsal Region Organoid Fusion Day 90


title: 63_JRX149: HT29_ORF_FOSL1_63

source_name: HT-29 FOSL1 transduction, UniqueID 63


title: ESC-HiC-rep2


title: 68_JRX152: HT29_ORF_FOXO1_68

source_name: HT-29 FOXO1 transduction, UniqueID 68


title: 78_JRX155: HT29_ORF_GNA12_78

source_name: HT-29 GNA12 transduction, UniqueID 78


title: ESC-HiC-rep1


title: 69_JRX153: HT29_ORF_FOXO1_69

source_name: HT-29 FOXO1 transduction, UniqueID 69


title: 62_JRX148: HT29_ORF_FOSL1_62

source_name: HT-29 FOSL1 transduction, UniqueID 62


title: 51_JRX143: HT29_ORF_DUSP16_51

source_name: HT-29 DUSP16 transduction, UniqueID 51


title: 39_JRX139: HT29_ORF_CTH_39

source_name: HT-29 CTH transduction, UniqueID 39

value: CTH