title: ss3_23_056s_O04_accepted_hits_sorted_deduplicated.bam

description:
Library name: Single cell sample 224
Smart-seq3

tag: group

tag: batch


title: hapo_newborn_cordblood_E0400

status: Public on Feb 16 2026

type: genomic

city: Chicago

first: Jami

middle: L

last: Josefson

state: Illinois

address: 225 E Chicago Avenue

country: USA

institute: Ann & Robert H. Lurie Children's Hospital of Chicago

description: Illumina Infinium MethylationEPIC BeadChip (850K chip)

hyb_protocol: Genome-wide methylation profiling was conducted with the Infinium MethylationEPIC BeadChip version 1.0 (Illumina, Inc., San Diego, California) array, which interrogates > 850,000 CpG sites at singlenucleotide resolution

scan_protocol: BeadChips were scanned with an Illumina iScan

data_processing:
minfi package in R environment (version 1.40.0)
processed value definition: M values transformed from beta (HAPO_GA_illumina_methylation.xlsx linked to the Series record)

label: Cy3, Cy5

molecule: genomic DNA

organism: Homo sapiens

source_name: newborn cordblood

label_protocol: Standard Illumina Protocol

extract_protocol: DNA was extracted from whole blood that was stored at -80 C and was quantified with the Qubit Fluorometer (Thermo Fisher Scientific, Waltham, Massachusetts)

tag: Sex

value: Female

tag: tissue

value: cord clood

tag: developmental stage

value: newborn

tag: cell type

value: whole blood cells


title: P7657_1132

type: SRA

city: Stockholm

first: Andreas

last: Liontos

state: Stockholm

address: Svante Arrheniusväg 20C

department: Molecular Biosciences-The Wenner Gren Institute

country: Sweden

institute: Stockholm University

description:
single cell library
Smart-Seq2

library_source: transcriptomic single cell

data_processing:
Sequencing was done with Illumina 2500 HiSeq Rapid mode using paired-end (2x125 bp) and single-end (1x50 bp). For downstream analysis, we used the one strand sequencing out of paired-end libraries and trimmed the reads to 50 bp
High quality transcriptomic libraries were obtained after filtering, for doublet cells included in our experiment as sequencing controls, for cells obtaining less than 40% uniquely mapped reads, for cells that had number of detected genes outside mean ± 2s.d range and for cells whose GFP  expression ratio was lower than the GFP ration determined in embryonic epithelial cells.
The following single cells were removed as known doublets in our analysis: "P7657_1067", "P7657_1189", "P2661_1003", "P4730_1029". The following single cells were removed because they had <40% uniquely mapped reads: "P2272_1042", "P2661_1042", "P3504_1071", "P3504_1082", "P4730_1040", "P7657_1022", "P7657_1024", "P7657_1025", "P7657_1032", "P7657_1070".
Assembly: Custom Mus Musculus (GRCm38) reference genome that contained GFP sequence and Ai14 cassette (RFP and WPRE sequences). The reference genome was created with the 10x Genomics "cell ranger mkref" and the mapping of the reads was done with the "cellranger count" function, using default settings.
Supplementary files format and content: raw count matrix and metadata files for the 464/478 single cells remaining after removal of doublet cells (4 cells removed) and removal of cells that failed uniquely map read filtering (10 cells removed) step.

molecule: total RNA

organism: Mus musculus

source_name: lung

extract_protocol:
For full-length (Smart-Seq2) library preparation (Picelli et al., 2014), the left lungs were used for enzymatic digestion and right lungs were treated as described above for histological analysis. Briefly, we cut the lungs in small pieces using a razor blade and digested with elastase (Worthington, LS002292) and DNase I 0.5 mg/ml (Sigma-Aldrich, DN25) in HBSS (Gibco, 14175), at 37oC for 1 hour with rotation. Equal volume of HBSS++ [HBSS (Gibco, 14175), supplemented with 2% 0.2µm filtered FCS (Gibco, 10500), 0.1 M HEPES (Sigma-Aldrich, H0887), antibiotics (Gibco, 15240096) and EGTA 2 mM] was added and the suspension was mixed gently. Then cells were centrifuged at 800g for 10 minutes at 4oC. Supernatant was removed with a serological pipette and cells were resuspended in HBSS++. Viability was tested using trypan blue (Sigma-Aldrich, T8154) (1:1 dilution) and presence of fluorescence positive cells was evaluated using a normal fluorescence microscope. Just before sorting, cells were passed through a 100 µm BD Filcon (BD Biosciences, 340610) in order to remove cell aggregates. For E16.5 lungs, after digestion, centrifuge and cell resuspension in HBSS++, cells were passed through a 100 µm BD Filcon (BD Biosciences, 340610) and counted. We resuspented the cells in the proper amount of HBSS++ in order to obtain 20x106 cells/ml cell concentration. 100 µl of cell suspension were stained with 0.5 µl of anti-EpCam-PE antibody (Biolegend, 118205) and 0.5 µl anti-CD45-APC antibody (Biolegend, 103112). Replicates of the above reactions were set in separate tubes; in order to prevent the formation of cell aggregates, which is typical when we centrifuge large amount of epithelial cells.
For cell-sorting, we used a BD FACSARIA III cell-sorter, using 100 µm nozzle, applying single-cell sorting purity setting. For E16.5 lungs, EpCampos CD45neg cells were sorted. Cells from all other stages were isolated according to GFP expression.
Cell sorting and single-cell library preparation were done according to Smart Seq2 protocol (Picelli et al., 2013; Picelli et al., 2014) with some modifications. Cells were sorted in 96-well plates (Piko PCR Plates 24-well, Thermo Scientific, SPL0240 and Plate Frame for 24-well PikoPCR Plates, Thermo Scientific, SFR0241).  Each well contained Triton-X100 (0.2%) (Sigma-Aldrich, T9284-100ML), ERCC RNA Spike-In Mix (1:400.000) (Life-Technologies, 4456740), Oligo-dT30 VN (1,25uM) AAGCAGTGGTATCAACGCAGAGTAC (30 x T) VN, dNTPs (2.5mM/each) (Thermo Scientific-Fermentas, R0192) and Rnase Inhibitor (1U/ul) (Clontech, 2313A) in 4 µl final volume. After sorting, strips were covered with Axygen PCR-tube caps (VWR, PCR-02-FCP-C), centrifuged and placed on dry ice until storage at -80oC for further use. For cell culture cells were sorted into HBSS++ buffer and kept on ice until they were placed in culture.
Smart Seq2 protocol is optimal for cell lines and/or large human cells (Picelli et al., 2014). Mouse primary pulmonary cells are smaller and they contain smaller amount of RNA, as a result high amount of primer concatamers were formed during cDNA library preparation, compromising its efficiency. Our optimized protocol contains 50% less Oligo-dT30 VN and cDNA synthesis was divided into two steps, the first was without TSO LNA and the second contained 1µM TSO LNA and additional 40 U of SuperScript II RT (Thermo-Fisher Scientific, 18064071). Reaction lasted 30 minutes at 42oC. Then enzyme was deactivated at 70oC for 15 minutes. For Pre-Amplification PCR, we used the KAPA HiFi Hotstart ReadyMix (2x) (KAPA Biosystems, KK2602) and the ISPCR-primer AAGCAGTGGTATCAACGCAGAGT. PCR included 21 cycles and the total volume increased to 50ul in order to reduce the concentration of the unused Oligo-dT30 VN and TSO-LNA primers.
Tagmentation and indexed library amplification were done with Nextera® XT DNA Library Preparation Kit (Illumina, FC-131-1096) and Nextera® XT Index Kit (96 indexes, 384 samples), (Illumina, FC-131-1002) according to the manufacturer protocol (with 2.5 x volume reduction in all reactions). The quantity of the used library for tagmentation was 50 pg of the 500-9000 bp fraction of the library, as indicated by its Bioanalyzer profile.

value: lung

tag: strain

value: Scgb1a1CREERT2; Rosa26R-fGFP

value: lung epithelial secretory cells

tag: genotype

value: WT

tag: individual

tag: sorting date

tag: isolation criteria

value: GFP^pos

tag: ercc spike-in_lot_no

tag: cdna library_preparation_date

tag: type of_sequencing

value: single-end 50bp

tag: lane

tag: plate well

tag: internal number

tag: n primer

tag: s primer


title: hapo_newborn_cordblood_E0184

tag: Sex

value: Male


title: hapo_newborn_cordblood_E0180

tag: tissue


title: ss3_23_056s_O03_accepted_hits_sorted_deduplicated.bam

city: Huddinge

first: Lars

last: Muhl

address: Blickagången 6

department: MedH

institute: Karolinska Institutet

description:
Library name: Single cell sample 223
Smart-seq3

data_processing:
Samples were de-multiplexed yielding single-cell fastq files that were quality-trimmed using Trim Galore and UMI were extracted using the UMI-tools package.
Reads were then mapped to the danio rerio reference genome GRCz11 using STAR and duplicates were removed using UMI-tools dedup based on identified UMI’s
Per cell and gene raw-count expression matrices were prepared using the featureCounts package
Counts data was processed and analyzed using Seurat and pagoda2 packages in R-software
Assembly: GRCz11
Supplementary files format and content: tab-deliminated txt file as expression matrix including non-normalized counts of all samples

molecule: polyA RNA

organism: Danio rerio

source_name: meninges

extract_protocol:
3 brains per group were dissected and put in a buffer containing 0.5% Trypsin, 1mM EDTA, and 10U DNaseI (Promega) for 10 min at 30°C and shaken at 600rpm every 3 minutes until the BLECs were detached from the brain. Brains were removed, and the cells were centrifuged at 2000 rpm for 5 min. The pellet was washed and resuspended in PBS containing 3 % FCS and then filtered through a 40 µm nylon cell strainer. Cells were FACS-sorted into 384-well plates containing lysis buffer.
RNA libraries were prepared using the Smart-Seq3 protocol at SICOF Huddinge, Sweden.

value: meninges

value: Neuronal/Glia

tag: group

value: control

tag: batch


title: hapo_newborn_cordblood_E0174

tag: developmental stage

tag: cell type


title: ss3_23_056s_O01_accepted_hits_sorted_deduplicated.bam

description:
Library name: Single cell sample 222
Smart-seq3


title: hapo_newborn_cordblood_E0150


title: P7657_1131

description:
single cell library
Smart-Seq2

tag: strain

tag: genotype

tag: individual


title: hapo_newborn_cordblood_E0593


title: hapo_newborn_cordblood_E0140


title: P7657_1130

description:
single cell library
Smart-Seq2

tag: sorting date

tag: isolation criteria

tag: ercc spike-in_lot_no


title: hapo_newborn_cordblood_E0137


title: ss3_23_056s_N23_accepted_hits_sorted_deduplicated.bam

description:
Library name: Single cell sample 221
Smart-seq3


title: hapo_newborn_cordblood_E0124


title: P7657_1129

description:
single cell library
Smart-Seq2

tag: cdna library_preparation_date

tag: type of_sequencing

tag: lane


title: hapo_newborn_cordblood_E0104


title: P7657_1139

description:
single cell library
Smart-Seq2

tag: plate well

tag: internal number

tag: n primer


title: hapo_newborn_cordblood_E0076

tag: Sex

tag: tissue


title: ss3_23_056s_N22_accepted_hits_sorted_deduplicated.bam

description:
Library name: Single cell sample 220
Smart-seq3

tag: group

tag: batch


title: hapo_newborn_cordblood_E0062

tag: developmental stage

tag: cell type


title: ss3_23_056s_N21_accepted_hits_sorted_deduplicated.bam

description:
Library name: Single cell sample 219
Smart-seq3

value: Immune


title: P7657_1128

description:
single cell library
Smart-Seq2

tag: strain

tag: genotype

tag: s primer


title: hapo_newborn_cordblood_E0057


title: P7657_1127

description:
single cell library
Smart-Seq2

tag: individual

tag: sorting date

tag: isolation criteria


title: hapo_newborn_cordblood_E0031


title: ss3_23_056s_N20_accepted_hits_sorted_deduplicated.bam

description:
Library name: Single cell sample 218
Smart-seq3

value: Fibroblast


title: P7657_1126

description:
single cell library
Smart-Seq2

tag: ercc spike-in_lot_no

tag: cdna library_preparation_date

tag: type of_sequencing


title: hapo_newborn_cordblood_E0026


title: ss3_23_056s_N19_accepted_hits_sorted_deduplicated.bam

description:
Library name: Single cell sample 217
Smart-seq3


title: hapo_newborn_cordblood_D0991


title: P7657_1125

description:
single cell library
Smart-Seq2

tag: lane

tag: plate well

tag: internal number


title: hapo_newborn_cordblood_D0984

tag: Sex

tag: tissue


title: hapo_newborn_cordblood_D0980


title: hapo_newborn_cordblood_D0971


title: ss3_23_056s_N17_accepted_hits_sorted_deduplicated.bam

description:
Library name: Single cell sample 215
Smart-seq3

value: Network

tag: group

tag: batch


title: hapo_newborn_cordblood_D0968

value: Female

tag: developmental stage

tag: cell type


title: P7657_1123

description:
single cell library
Smart-Seq2

tag: strain

tag: genotype

tag: n primer


title: hapo_newborn_cordblood_D0957

value: cord clood


title: ss3_23_056s_N16_accepted_hits_sorted_deduplicated.bam

description:
Library name: Single cell sample 214
Smart-seq3


title: hapo_newborn_cordblood_D0956

value: newborn


title: hapo_newborn_cordblood_D0946

value: whole blood cells


title: P7657_1122

description:
single cell library
Smart-Seq2

value: lung

tag: individual

tag: sorting date

tag: s primer


title: ss3_23_056s_N15_accepted_hits_sorted_deduplicated.bam

description:
Library name: Single cell sample 213
Smart-seq3


title: hapo_newborn_cordblood_D0943


title: P7657_1121

description:
single cell library
Smart-Seq2

value: Scgb1a1CREERT2; Rosa26R-fGFP

tag: isolation criteria

tag: ercc spike-in_lot_no

tag: cdna library_preparation_date


title: hapo_newborn_cordblood_D0939


title: ss3_23_056s_N14_accepted_hits_sorted_deduplicated.bam

description:
Library name: Single cell sample 212
Smart-seq3


title: hapo_newborn_cordblood_D0935


title: P7657_1120

description:
single cell library
Smart-Seq2

value: lung epithelial secretory cells

tag: type of_sequencing

tag: lane

tag: plate well


title: hapo_newborn_cordblood_D0934

tag: Sex

tag: tissue


title: ss3_23_056s_N12_accepted_hits_sorted_deduplicated.bam

description:
Library name: Single cell sample 211
Smart-seq3

value: BLEC

tag: group

tag: batch


title: hapo_newborn_cordblood_D0933

tag: developmental stage

tag: cell type


title: P7657_1119

description:
single cell library
Smart-Seq2

tag: strain

tag: genotype

value: WT

value: GFP^pos

tag: internal number


title: ss3_23_056s_N09_accepted_hits_sorted_deduplicated.bam

description:
Library name: Single cell sample 210
Smart-seq3


title: hapo_newborn_cordblood_D0932

value: Male


title: hapo_newborn_cordblood_D0919


title: P7657_1118

description:
single cell library
Smart-Seq2

tag: individual

tag: sorting date

value: single-end 50bp

tag: n primer


title: hapo_newborn_cordblood_D0910


title: ss3_23_056s_N05_accepted_hits_sorted_deduplicated.bam

description:
Library name: Single cell sample 209
Smart-seq3

value: meninges


title: P7657_1117

description:
single cell library
Smart-Seq2

tag: isolation criteria

tag: ercc spike-in_lot_no

tag: s primer


title: hapo_newborn_cordblood_D0907


title: ss3_23_056s_N04_accepted_hits_sorted_deduplicated.bam

description:
Library name: Single cell sample 208
Smart-seq3

value: Neuronal/Glia

value: control


title: hapo_newborn_cordblood_D0880


title: P7657_1116

description:
single cell library
Smart-Seq2

tag: cdna library_preparation_date

tag: type of_sequencing

tag: lane


title: hapo_newborn_cordblood_D0892

tag: Sex

tag: tissue


title: ss3_23_056s_N03_accepted_hits_sorted_deduplicated.bam

description:
Library name: Single cell sample 207
Smart-seq3

value: Immune

tag: group

tag: batch


title: P7657_1115

description:
single cell library
Smart-Seq2

tag: cell type

tag: developmental stage

tag: plate well


title: hapo_newborn_cordblood_D0875

description: Illumina Infinium MethylationEPIC BeadChip (850K chip)


title: ss3_23_056s_N01_accepted_hits_sorted_deduplicated.bam

description:
Library name: Single cell sample 206
Smart-seq3


title: P7657_1114

description:
single cell library
Smart-Seq2

tag: strain

tag: genotype

tag: internal number


title: P7657_1151

description:
single cell library
Smart-Seq2

tag: individual

tag: sorting date

tag: n primer


title: hapo_newborn_cordblood_D0873


title: ss3_23_056s_M24_accepted_hits_sorted_deduplicated.bam

description:
Library name: Single cell sample 205
Smart-seq3


title: hapo_newborn_cordblood_D0870


title: P7657_1113

description:
single cell library
Smart-Seq2

tag: isolation criteria

tag: ercc spike-in_lot_no

tag: s primer


title: hapo_newborn_cordblood_D0868


title: hapo_newborn_cordblood_D0867


title: ss3_23_056s_M23_accepted_hits_sorted_deduplicated.bam

description:
Library name: Single cell sample 204
Smart-seq3


title: hapo_newborn_cordblood_E0030


title: P7657_1112

description:
single cell library
Smart-Seq2

tag: cdna library_preparation_date

tag: type of_sequencing

tag: lane


title: hapo_newborn_cordblood_D0859

tag: Sex

tag: tissue


title: ss3_23_056s_M22_accepted_hits_sorted_deduplicated.bam

description:
Library name: Single cell sample 203
Smart-seq3

tag: cell type

tag: group

tag: batch


title: ss3_23_056s_N18_accepted_hits_sorted_deduplicated.bam

description:
Library name: Single cell sample 216
Smart-seq3

value: Fibroblast


title: hapo_newborn_cordblood_D0848

value: Female

tag: developmental stage


title: P7657_1111

description:
single cell library
Smart-Seq2

tag: strain

tag: genotype

tag: plate well


title: hapo_newborn_cordblood_D0846

value: cord clood


title: ss3_23_056s_M20_accepted_hits_sorted_deduplicated.bam

description:
Library name: Single cell sample 202
Smart-seq3


title: P7657_1124

description:
single cell library
Smart-Seq2

tag: individual

tag: sorting date

tag: internal number


title: hapo_newborn_cordblood_D0845

value: newborn


title: P7657_1110

description:
single cell library
Smart-Seq2

tag: isolation criteria

tag: ercc spike-in_lot_no

tag: n primer


title: hapo_newborn_cordblood_D0843

value: whole blood cells


title: ss3_23_056s_M19_accepted_hits_sorted_deduplicated.bam

description:
Library name: Single cell sample 201
Smart-seq3


title: hapo_newborn_cordblood_D0842


title: P7657_1109

description:
single cell library
Smart-Seq2

value: lung

tag: cdna library_preparation_date

tag: type of_sequencing

tag: s primer


title: hapo_newborn_cordblood_D0837

tag: Sex

tag: tissue


title: hapo_newborn_cordblood_D0835

tag: cell type


title: ss3_23_056s_M18_accepted_hits_sorted_deduplicated.bam

description:
Library name: Single cell sample 200
Smart-seq3

tag: group

tag: batch


title: P7657_1108

description:
single cell library
Smart-Seq2

tag: strain

value: Scgb1a1CREERT2; Rosa26R-fGFP

tag: developmental stage

tag: lane


title: hapo_newborn_cordblood_D0834


title: ss3_23_056s_M17_accepted_hits_sorted_deduplicated.bam

description:
Library name: Single cell sample 199
Smart-seq3


title: hapo_newborn_cordblood_D0830


title: hapo_newborn_cordblood_D0823


title: P7657_1107

description:
single cell library
Smart-Seq2

value: lung epithelial secretory cells

tag: genotype

tag: individual

tag: plate well


title: ss3_23_056s_M16_accepted_hits_sorted_deduplicated.bam

description:
Library name: Single cell sample 198
Smart-seq3

value: Network


title: hapo_newborn_cordblood_D0822


title: P7657_1106

description:
single cell library
Smart-Seq2

value: WT

tag: sorting date

tag: isolation criteria

tag: internal number


title: hapo_newborn_cordblood_D0818


title: hapo_newborn_cordblood_D0816


title: ss3_23_056s_M15_accepted_hits_sorted_deduplicated.bam

description:
Library name: Single cell sample 197
Smart-seq3


title: P7657_1105

description:
single cell library
Smart-Seq2

value: GFP^pos

tag: ercc spike-in_lot_no

tag: cdna library_preparation_date

tag: n primer


title: hapo_newborn_cordblood_D0812

tag: Sex

value: Male


title: ss3_23_056s_M14_accepted_hits_sorted_deduplicated.bam

description:
Library name: Single cell sample 196
Smart-seq3

tag: tissue


title: hapo_newborn_cordblood_D0811

tag: cell type


title: hapo_newborn_cordblood_D0809


title: ss3_23_056s_M12_accepted_hits_sorted_deduplicated.bam

description:
Library name: Single cell sample 195
Smart-seq3

value: BLEC

tag: group


title: hapo_newborn_cordblood_D0808


title: P7657_1103

description:
single cell library
Smart-Seq2

tag: type of_sequencing

value: single-end 50bp

tag: s primer


title: hapo_newborn_cordblood_D0803

tag: developmental stage


title: ss3_23_056s_M10_accepted_hits_sorted_deduplicated.bam

description:
Library name: Single cell sample 194
Smart-seq3

value: meninges

tag: batch


title: hapo_newborn_cordblood_D0788


title: P7657_1102

description:
single cell library
Smart-Seq2

tag: strain

tag: genotype

tag: lane


title: ss3_23_056s_M09_accepted_hits_sorted_deduplicated.bam

description:
Library name: Single cell sample 193
Smart-seq3

value: Neuronal/Glia

value: control


title: hapo_newborn_cordblood_D0787


title: hapo_newborn_cordblood_D0779


title: ss3_23_056s_M04_accepted_hits_sorted_deduplicated.bam

description:
Library name: Single cell sample 192
Smart-seq3


title: hapo_newborn_cordblood_D0771

description: Illumina Infinium MethylationEPIC BeadChip (850K chip)


title: P7657_1100

description:
single cell library
Smart-Seq2

tag: individual

tag: sorting date

tag: plate well


title: hapo_newborn_cordblood_D0767


title: ss3_23_056s_M03_accepted_hits_sorted_deduplicated.bam

description:
Library name: Single cell sample 191
Smart-seq3


title: hapo_newborn_cordblood_D0743


title: P7657_1099

description:
single cell library
Smart-Seq2

tag: isolation criteria

tag: ercc spike-in_lot_no

tag: internal number


title: hapo_newborn_cordblood_D0741

tag: Sex


title: P7657_1098

description:
single cell library
Smart-Seq2

tag: tissue

tag: cdna library_preparation_date

tag: n primer


title: hapo_newborn_cordblood_D0736

tag: cell type


title: ss3_23_056s_M01_accepted_hits_sorted_deduplicated.bam

description:
Library name: Single cell sample 189
Smart-seq3

tag: group


title: hapo_newborn_cordblood_D0725

tag: developmental stage


title: hapo_newborn_cordblood_D0719


title: P7657_1097

description:
single cell library
Smart-Seq2

tag: type of_sequencing

tag: s primer


title: hapo_newborn_cordblood_D0717


title: ss3_23_056s_L24_accepted_hits_sorted_deduplicated.bam

description:
Library name: Single cell sample 188
Smart-seq3

value: Immune

tag: batch


title: hapo_newborn_cordblood_D0716


title: P7657_1096

description:
single cell library
Smart-Seq2

tag: strain

tag: genotype

tag: lane


title: hapo_newborn_cordblood_D0710

value: Female


title: hapo_newborn_cordblood_D0707

value: cord clood


title: hapo_newborn_cordblood_D0911

value: newborn


title: P7657_1095

description:
single cell library
Smart-Seq2

tag: individual

tag: sorting date

tag: plate well


title: ss3_23_058s_O08_accepted_hits_sorted_deduplicated.bam

description:
Library name: Single cell sample 499
Smart-seq3

value: treated


title: ss3_23_056s_L23_accepted_hits_sorted_deduplicated.bam

description:
Library name: Single cell sample 187
Smart-seq3


title: hapo_newborn_cordblood_D0697

value: whole blood cells


title: ss3_23_056s_L22_accepted_hits_sorted_deduplicated.bam

description:
Library name: Single cell sample 186
Smart-seq3


title: P7657_1094

description:
single cell library
Smart-Seq2

value: lung

value: Scgb1a1CREERT2; Rosa26R-fGFP

tag: isolation criteria

tag: ercc spike-in_lot_no

tag: internal number


title: hapo_newborn_cordblood_D0670

tag: Sex

tag: tissue


title: hapo_newborn_cordblood_D0669

tag: cell type


title: ss3_23_056s_L21_accepted_hits_sorted_deduplicated.bam

description:
Library name: Single cell sample 185
Smart-seq3

tag: group


title: hapo_newborn_cordblood_D0706

tag: developmental stage


title: P7657_1093

description:
single cell library
Smart-Seq2

value: lung epithelial secretory cells

tag: cdna library_preparation_date

tag: type of_sequencing

tag: n primer


title: ss3_23_056s_L20_accepted_hits_sorted_deduplicated.bam

description:
Library name: Single cell sample 184
Smart-seq3

tag: batch


title: hapo_newborn_cordblood_D0668


title: hapo_newborn_cordblood_D0660


title: P7657_1092

description:
single cell library
Smart-Seq2

tag: strain

tag: genotype

value: WT

tag: s primer


title: ss3_23_056s_L19_accepted_hits_sorted_deduplicated.bam

description:
Library name: Single cell sample 183
Smart-seq3


title: hapo_newborn_cordblood_D0644


title: P7657_1091

description:
single cell library
Smart-Seq2

tag: individual

tag: sorting date

value: GFP^pos

tag: lane


title: hapo_newborn_cordblood_D0639

value: Male


title: ss3_23_056s_L16_accepted_hits_sorted_deduplicated.bam

description:
Library name: Single cell sample 182
Smart-seq3


title: hapo_newborn_cordblood_D0629


title: hapo_newborn_cordblood_D0621


title: P7657_1090

description:
single cell library
Smart-Seq2

tag: isolation criteria

tag: ercc spike-in_lot_no

tag: plate well


title: ss3_23_056s_L15_accepted_hits_sorted_deduplicated.bam

description:
Library name: Single cell sample 181
Smart-seq3

tag: tissue


title: hapo_newborn_cordblood_D0614

tag: Sex

tag: cell type


title: P7657_1089

description:
single cell library
Smart-Seq2

tag: developmental stage

tag: internal number


title: hapo_newborn_cordblood_D0613


title: ss3_23_056s_L14_accepted_hits_sorted_deduplicated.bam

description:
Library name: Single cell sample 180
Smart-seq3

value: Fibroblast

tag: group


title: hapo_newborn_cordblood_D0610


title: P7657_1088

description:
single cell library
Smart-Seq2

tag: cdna library_preparation_date

tag: type of_sequencing

value: single-end 50bp

tag: n primer


title: hapo_newborn_cordblood_D0603


title: ss3_23_056s_L13_accepted_hits_sorted_deduplicated.bam

description:
Library name: Single cell sample 179
Smart-seq3

value: meninges

value: BLEC

tag: batch


title: hapo_newborn_cordblood_D0601


title: P7657_1087

description:
single cell library
Smart-Seq2

tag: strain

tag: genotype

tag: s primer


title: hapo_newborn_cordblood_D0596


title: hapo_newborn_cordblood_D0593


title: ss3_23_056s_L08_accepted_hits_sorted_deduplicated.bam

description:
Library name: Single cell sample 178
Smart-seq3

value: Neuronal/Glia

value: control


title: P7657_1086

description:
single cell library
Smart-Seq2

tag: individual

tag: sorting date

tag: lane


title: ss3_23_056s_L07_accepted_hits_sorted_deduplicated.bam

description:
Library name: Single cell sample 177
Smart-seq3


title: hapo_newborn_cordblood_D0583


title: hapo_newborn_cordblood_D0587

value: Female


title: P7657_1104

description:
single cell library
Smart-Seq2

tag: isolation criteria

tag: ercc spike-in_lot_no

tag: plate well


title: P7657_1085

description:
single cell library
Smart-Seq2

tag: tissue

tag: cell type


title: hapo_newborn_cordblood_D0571

tag: Sex

value: cord clood

tag: developmental stage


title: ss3_23_056s_L04_accepted_hits_sorted_deduplicated.bam

description:
Library name: Single cell sample 176
Smart-seq3

tag: group


title: hapo_newborn_cordblood_D0549

description: Illumina Infinium MethylationEPIC BeadChip (850K chip)

value: newborn


title: ss3_23_058s_K20_accepted_hits_sorted_deduplicated.bam

description:
Library name: Single cell sample 440
Smart-seq3

value: Immune

value: treated


title: hapo_newborn_cordblood_D0543

value: whole blood cells


title: P7657_1084

description:
single cell library
Smart-Seq2

value: lung

value: Scgb1a1CREERT2; Rosa26R-fGFP

tag: cdna library_preparation_date

tag: type of_sequencing

tag: internal number


title: ss3_23_056s_L03_accepted_hits_sorted_deduplicated.bam

description:
Library name: Single cell sample 175
Smart-seq3

tag: batch


title: hapo_newborn_cordblood_D0534


title: P7657_1083

description:
single cell library
Smart-Seq2

tag: strain

value: lung epithelial secretory cells

tag: genotype

value: WT

tag: n primer


title: hapo_newborn_cordblood_D0531


title: ss3_23_056s_L02_accepted_hits_sorted_deduplicated.bam

description:
Library name: Single cell sample 174
Smart-seq3


title: hapo_newborn_cordblood_D0526


title: P7657_1082

description:
single cell library
Smart-Seq2

tag: individual

tag: sorting date

value: GFP^pos

tag: s primer


title: hapo_newborn_cordblood_D0516


title: ss3_23_056s_L01_accepted_hits_sorted_deduplicated.bam

description:
Library name: Single cell sample 173
Smart-seq3


title: hapo_newborn_cordblood_D0510

value: Male


title: P7657_1081

description:
single cell library
Smart-Seq2

tag: isolation criteria

tag: ercc spike-in_lot_no

value: single-end 50bp

tag: lane


title: hapo_newborn_cordblood_D0509

tag: tissue

tag: cell type


title: ss3_23_056s_K23_accepted_hits_sorted_deduplicated.bam

description:
Library name: Single cell sample 172
Smart-seq3

value: meninges

value: Fibroblast


title: hapo_newborn_cordblood_D0502

tag: Sex

tag: developmental stage


title: P7657_1080

description:
single cell library
Smart-Seq2

tag: cdna library_preparation_date

tag: plate well


title: hapo_newborn_cordblood_D0501


title: ss3_23_056s_K22_accepted_hits_sorted_deduplicated.bam

description:
Library name: Single cell sample 171
Smart-seq3

tag: group


title: hapo_newborn_cordblood_D0498


title: hapo_newborn_cordblood_D0469


title: ss3_23_056s_K18_accepted_hits_sorted_deduplicated.bam

description:
Library name: Single cell sample 170
Smart-seq3

tag: batch


title: hapo_newborn_cordblood_D0468


title: P7657_1079

description:
single cell library
Smart-Seq2

tag: strain

tag: type of_sequencing

tag: internal number


title: P7657_1078

description:
single cell library
Smart-Seq2

tag: genotype

tag: individual

tag: n primer


title: hapo_newborn_cordblood_D0446


title: ss3_23_056s_K17_accepted_hits_sorted_deduplicated.bam

description:
Library name: Single cell sample 169
Smart-seq3


title: hapo_newborn_cordblood_D0441


title: P7657_1077

description:
single cell library
Smart-Seq2

tag: sorting date

tag: isolation criteria

tag: s primer


title: hapo_newborn_cordblood_D0437

tag: tissue


title: ss3_23_056s_K16_accepted_hits_sorted_deduplicated.bam

description:
Library name: Single cell sample 168
Smart-seq3

tag: cell type

value: Network


title: hapo_newborn_cordblood_D0431

tag: Sex


title: P7657_1076

description:
single cell library
Smart-Seq2

tag: developmental stage

tag: ercc spike-in_lot_no

tag: lane


title: hapo_newborn_cordblood_D0424


title: ss3_23_056s_K15_accepted_hits_sorted_deduplicated.bam

description:
Library name: Single cell sample 167
Smart-seq3

tag: group

value: control


title: hapo_newborn_cordblood_D0422


title: P7657_1075

description:
single cell library
Smart-Seq2

tag: cdna library_preparation_date

tag: plate well


title: hapo_newborn_cordblood_D0407


title: ss3_23_056s_K14_accepted_hits_sorted_deduplicated.bam

description:
Library name: Single cell sample 166
Smart-seq3

tag: batch


title: hapo_newborn_cordblood_D0404

value: Female


title: hapo_newborn_cordblood_D0373

value: cord clood


title: ss3_23_056s_K13_accepted_hits_sorted_deduplicated.bam

description:
Library name: Single cell sample 165
Smart-seq3

value: BLEC


title: hapo_newborn_cordblood_D0352

value: newborn


title: P7657_1073

description:
single cell library
Smart-Seq2

tag: strain

tag: type of_sequencing

tag: internal number


title: hapo_newborn_cordblood_D0342


title: P7657_1072

description:
single cell library
Smart-Seq2

tag: genotype

tag: individual

tag: n primer


title: hapo_newborn_cordblood_D0327


title: hapo_newborn_cordblood_D0310


title: P7657_1071

description:
single cell library
Smart-Seq2

tag: sorting date

tag: isolation criteria

tag: s primer


title: hapo_newborn_cordblood_D0303

tag: Sex

tag: tissue

tag: cell type


title: ss3_23_056s_K07_accepted_hits_sorted_deduplicated.bam

description:
Library name: Single cell sample 162
Smart-seq3

value: Neuronal/Glia


title: ss3_23_056s_M02_accepted_hits_sorted_deduplicated.bam

description:
Library name: Single cell sample 190
Smart-seq3


title: P7657_1070

description:
single cell library
Smart-Seq2

tag: developmental stage

tag: ercc spike-in_lot_no

tag: lane


title: hapo_newborn_cordblood_D0292

value: whole blood cells


title: ss3_23_056s_K06_accepted_hits_sorted_deduplicated.bam

description:
Library name: Single cell sample 161
Smart-seq3

tag: group


title: hapo_newborn_cordblood_D0285


title: P7657_1069

description:
single cell library
Smart-Seq2

value: lung

tag: cdna library_preparation_date

tag: plate well


title: P7657_1074

description:
single cell library
Smart-Seq2

tag: strain

value: Scgb1a1CREERT2; Rosa26R-fGFP

tag: type of_sequencing


title: hapo_newborn_cordblood_D0346


title: hapo_newborn_cordblood_D0271


title: ss3_23_056s_K05_accepted_hits_sorted_deduplicated.bam

description:
Library name: Single cell sample 160
Smart-seq3

tag: batch


title: hapo_newborn_cordblood_D0253

description: Illumina Infinium MethylationEPIC BeadChip (850K chip)


title: P7657_1068

description:
single cell library
Smart-Seq2

value: lung epithelial secretory cells

tag: genotype

tag: individual

tag: internal number


title: hapo_newborn_cordblood_D0252


title: ss3_23_056s_K04_accepted_hits_sorted_deduplicated.bam

description:
Library name: Single cell sample 159
Smart-seq3


title: hapo_newborn_cordblood_D0250


title: P7657_1067

description:
single cell library
Smart-Seq2

value: WT

tag: sorting date

tag: isolation criteria

tag: n primer


title: ss3_23_056s_K03_accepted_hits_sorted_deduplicated.bam

description:
Library name: Single cell sample 158
Smart-seq3

tag: tissue


title: hapo_newborn_cordblood_D0238

tag: Sex

tag: cell type


title: hapo_newborn_cordblood_D0226

tag: developmental stage


title: ss3_23_056s_K01_accepted_hits_sorted_deduplicated.bam

description:
Library name: Single cell sample 157
Smart-seq3


title: hapo_newborn_cordblood_D0215


title: hapo_newborn_cordblood_G0658


title: hapo_newborn_cordblood_G0632


title: P7657_1065

description:
single cell library
Smart-Seq2

value: GFP^pos

tag: ercc spike-in_lot_no

tag: lane

tag: s primer


title: P7657_1066

description:
single cell library
Smart-Seq2

tag: cdna library_preparation_date

tag: plate well


title: hapo_newborn_cordblood_D0214


title: hapo_newborn_cordblood_D0219

value: Male


title: hapo_newborn_cordblood_G0523


title: hapo_newborn_cordblood_G0633


title: ss3_23_056s_J24_accepted_hits_sorted_deduplicated.bam

description:
Library name: Single cell sample 156
Smart-seq3

value: Immune

tag: group


title: hapo_newborn_cordblood_D0209


title: hapo_newborn_cordblood_D0188


title: ss3_23_056s_J22_accepted_hits_sorted_deduplicated.bam

description:
Library name: Single cell sample 155
Smart-seq3

value: meninges

tag: batch


title: hapo_newborn_cordblood_D0174


title: hapo_newborn_cordblood_D0178


title: P7657_1063

description:
single cell library
Smart-Seq2

tag: strain

tag: genotype

tag: type of_sequencing

value: single-end 50bp


title: hapo_newborn_cordblood_D0177


title: ss3_23_056s_J21_accepted_hits_sorted_deduplicated.bam

description:
Library name: Single cell sample 154
Smart-seq3


title: hapo_newborn_cordblood_D0173


title: ss3_23_056s_J20_accepted_hits_sorted_deduplicated.bam

description:
Library name: Single cell sample 153
Smart-seq3

value: Fibroblast


title: P7657_1061

description:
single cell library
Smart-Seq2

tag: individual

tag: sorting date

tag: internal number


title: P7657_1062

description:
single cell library
Smart-Seq2

tag: tissue

tag: isolation criteria

tag: n primer


title: hapo_newborn_cordblood_D0170

tag: Sex

tag: developmental stage

tag: cell type


title: hapo_newborn_cordblood_D0162


title: ss3_23_056s_J18_accepted_hits_sorted_deduplicated.bam

description:
Library name: Single cell sample 152
Smart-seq3

value: control


title: P7657_1064

description:
single cell library
Smart-Seq2

tag: ercc spike-in_lot_no

tag: lane

tag: s primer


title: hapo_newborn_cordblood_D0160

value: Female


title: P7657_1060

description:
single cell library
Smart-Seq2

tag: cdna library_preparation_date

tag: plate well


title: hapo_newborn_cordblood_D0149

value: cord clood


title: ss3_23_056s_J16_accepted_hits_sorted_deduplicated.bam

description:
Library name: Single cell sample 150
Smart-seq3

tag: group

tag: batch


title: P7657_1059

description:
single cell library
Smart-Seq2

tag: strain

tag: genotype

tag: type of_sequencing


title: hapo_newborn_cordblood_D0138


title: hapo_newborn_cordblood_D0126


title: ss3_23_056s_J17_accepted_hits_sorted_deduplicated.bam

description:
Library name: Single cell sample 151
Smart-seq3


title: P7657_1058

description:
single cell library
Smart-Seq2

tag: individual

tag: sorting date

tag: internal number


title: hapo_newborn_cordblood_D0117

tag: tissue


title: ss3_23_056s_J15_accepted_hits_sorted_deduplicated.bam

description:
Library name: Single cell sample 149
Smart-seq3


title: hapo_newborn_cordblood_D0111

tag: Sex


title: P7657_1057

description:
single cell library
Smart-Seq2

tag: developmental stage

tag: isolation criteria

tag: n primer


title: hapo_newborn_cordblood_D0109

tag: cell type


title: ss3_23_056s_J14_accepted_hits_sorted_deduplicated.bam

description:
Library name: Single cell sample 148
Smart-seq3


title: hapo_newborn_cordblood_D0103


title: P7657_1056

description:
single cell library
Smart-Seq2

tag: ercc spike-in_lot_no

tag: lane

tag: s primer


title: hapo_newborn_cordblood_D0080


title: ss3_23_056s_J06_accepted_hits_sorted_deduplicated.bam

description:
Library name: Single cell sample 146
Smart-seq3

tag: group


title: hapo_newborn_cordblood_D0098


title: ss3_23_056s_J10_accepted_hits_sorted_deduplicated.bam

description:
Library name: Single cell sample 147
Smart-seq3

tag: batch


title: hapo_newborn_cordblood_D0032


title: hapo_newborn_cordblood_B0943


title: P7657_1054

description:
single cell library
Smart-Seq2

tag: strain

tag: cdna library_preparation_date

tag: plate well


title: hapo_newborn_cordblood_B0933


title: ss3_23_056s_J05_accepted_hits_sorted_deduplicated.bam

description:
Library name: Single cell sample 145
Smart-seq3


title: hapo_newborn_cordblood_B0932


title: P7657_1053

description:
single cell library
Smart-Seq2

tag: genotype

tag: individual

tag: type of_sequencing


title: ss3_23_056s_J04_accepted_hits_sorted_deduplicated.bam

description:
Library name: Single cell sample 144
Smart-seq3

tag: tissue


title: hapo_newborn_cordblood_B0927

description: Illumina Infinium MethylationEPIC BeadChip (850K chip)

tag: Sex


title: P7657_1052

description:
single cell library
Smart-Seq2

tag: developmental stage

tag: sorting date

tag: internal number


title: P7657_1055

description:
single cell library
Smart-Seq2

tag: cell type

tag: isolation criteria

tag: n primer


title: hapo_newborn_cordblood_B0912


title: hapo_newborn_cordblood_B0911


title: ss3_23_056s_J03_accepted_hits_sorted_deduplicated.bam

description:
Library name: Single cell sample 143
Smart-seq3


title: P7657_1051

description:
single cell library
Smart-Seq2

tag: ercc spike-in_lot_no

tag: lane

tag: s primer


title: hapo_newborn_cordblood_B0908


title: ss3_23_056s_J02_accepted_hits_sorted_deduplicated.bam

description:
Library name: Single cell sample 142
Smart-seq3

tag: group

tag: batch


title: P7657_1050

description:
single cell library
Smart-Seq2

tag: strain

tag: cdna library_preparation_date

tag: plate well


title: hapo_newborn_cordblood_B0891


title: ss3_23_056s_J01_accepted_hits_sorted_deduplicated.bam

description:
Library name: Single cell sample 141
Smart-seq3


title: P7657_1049

description:
single cell library
Smart-Seq2

tag: genotype

tag: individual

tag: type of_sequencing


title: ss3_23_056s_I24_accepted_hits_sorted_deduplicated.bam

description:
Library name: Single cell sample 140
Smart-seq3

tag: tissue


title: hapo_newborn_cordblood_B0874

tag: Sex

tag: developmental stage


title: P7657_1048

description:
single cell library
Smart-Seq2

tag: cell type

tag: sorting date

tag: internal number


title: hapo_newborn_cordblood_B0872


title: ss3_23_056s_I22_accepted_hits_sorted_deduplicated.bam

description:
Library name: Single cell sample 139
Smart-seq3


title: P7657_1047

description:
single cell library
Smart-Seq2

tag: isolation criteria

tag: ercc spike-in_lot_no

tag: n primer


title: hapo_newborn_cordblood_B0861


title: ss3_23_056s_I21_accepted_hits_sorted_deduplicated.bam

description:
Library name: Single cell sample 138
Smart-seq3

tag: group


title: hapo_newborn_cordblood_B0857


title: P7657_1046

description:
single cell library
Smart-Seq2

tag: lane

tag: s primer


title: hapo_newborn_cordblood_B0845


title: hapo_newborn_cordblood_B0901


title: hapo_newborn_cordblood_B0844


title: P7657_1045

description:
single cell library
Smart-Seq2

tag: strain

tag: cdna library_preparation_date


title: hapo_newborn_cordblood_B0843


title: ss3_23_056s_I19_accepted_hits_sorted_deduplicated.bam

description:
Library name: Single cell sample 136
Smart-seq3

tag: batch


title: hapo_newborn_cordblood_B0839


title: P7657_1044

description:
single cell library
Smart-Seq2

tag: genotype

tag: individual

tag: plate well


title: hapo_newborn_cordblood_B0892

tag: Sex

tag: tissue


title: hapo_newborn_cordblood_B0838

tag: developmental stage

tag: cell type


title: ss3_23_056s_I18_accepted_hits_sorted_deduplicated.bam

description:
Library name: Single cell sample 135
Smart-seq3


title: ss3_23_056s_I20_accepted_hits_sorted_deduplicated.bam

description:
Library name: Single cell sample 137
Smart-seq3


title: hapo_newborn_cordblood_B0836


title: P7657_1043

description:
single cell library
Smart-Seq2

tag: sorting date

tag: type of_sequencing

tag: internal number


title: hapo_newborn_cordblood_B0824


title: WT, mESC, allelW, HA, Replicate 2

status: Public on Feb 17 2026

city: Miami

first: Rodrigo

last: Lucena Borges

state: Florida

address: 1501 NW 10th Avenue

department: Department of Human Genetics

institute: Sylvester Comprehensive Cancer Center

description: Library name: WT_mESC_allelW_HA_W_REP2

library_source: genomic

data_processing:
Sequenced reads (FASTQ files) were processed with nf-core pipelines (PMID: 32055031) for read trimming, QC and alignment algainst mm10 using nf-core/cutandrun v3.2.2 (https://github.com/nf-core/cutandrun/tree/3.2.2)  with additional ‘--aligner bowtie2 --read_length 150 --trim_nextseq 20 --blacklist [BED]’
Assembly: mm10, GRCh38
Supplementary files format and content: Bigwig files with average (normalized) signal from replicates and/or alleles (WT/M)
Library strategy: Cut&Run

source_name: WT mESC

growth_protocol: mESCs were cultured in ESC+2i media, while mNPCs were differentiated using a three-stage protocol: 4 days in ESC media, followed by 4 days in EB media, and a final 4 days in EB media supplemented with 5 μM of RA.

extract_protocol:
CUT&RUN assays were performed using the CUTANA kit following the manufacturer's protocol (EpiCypher, 14-1048). Briefly, mESCs Ring1B WT and R70H mutants were trypsinized (0.05%) to obtain a single-cell suspension followed by mild crosslinking with 0.1% formaldehyde for 1 minute. A total of 2 × 10⁵ cells were incubated with ConA beads, followed by overnight incubation with antibodies against HA (EpiCypher, 13-2010), Flag (EpiCypher, 13-2031), H3K27me3 (Active Motif, 39155), H2AK119ub (Cell Signaling D27C4), and IgG (EpiCypher, 13-0042).
E. coli was used as a spike-in control for all samples. Additionally, the SNAP-CUTANA™ K-MetStat Panel (EpiCypher, 19-1002) was included as an additional spike-in control for IgG and H3K27me3. Two biological replicates were used per condition.

treatment_protocol: there was no additional treatments

tag: cell line

value: WT mESC

value: Mouse embryonic stem cells (mESCs)

tag: antibody

value: HA-Tag, EpiCypher (Cat #13-2010)0.5 ug


title: ss3_23_056s_I16_accepted_hits_sorted_deduplicated.bam

description:
Library name: Single cell sample 134
Smart-seq3

tag: group


title: hapo_newborn_cordblood_B0884

value: newborn

value: whole blood cells


title: P7657_1042

description:
single cell library
Smart-Seq2

value: lung

value: Scgb1a1CREERT2; Rosa26R-fGFP

tag: isolation criteria

tag: ercc spike-in_lot_no

tag: lane

tag: n primer

tag: s primer


title: hapo_newborn_cordblood_B0822


title: hapo_newborn_cordblood_B0806


title: ss3_23_056s_I15_accepted_hits_sorted_deduplicated.bam

description:
Library name: Single cell sample 133
Smart-seq3

value: Neuronal/Glia

tag: batch


title: hapo_newborn_cordblood_B0798


title: hapo_newborn_cordblood_B0864


title: hapo_newborn_cordblood_D0143


title: P7657_1041

description:
single cell library
Smart-Seq2

tag: strain

value: lung epithelial secretory cells

tag: genotype

value: WT

tag: individual

value: GFP^pos

tag: cdna library_preparation_date

tag: plate well


title: hapo_newborn_cordblood_B0797

tag: Sex

tag: tissue

tag: developmental stage

tag: cell type


title: ss3_23_056s_I14_accepted_hits_sorted_deduplicated.bam

description:
Library name: Single cell sample 132
Smart-seq3

value: meninges

value: Immune


title: P7657_1040

description:
single cell library
Smart-Seq2

tag: sorting date

tag: type of_sequencing

value: single-end 50bp

tag: internal number


title: hapo_newborn_cordblood_B0778

value: Male


title: hapo_newborn_cordblood_B0783


title: ss3_23_056s_I13_accepted_hits_sorted_deduplicated.bam

description:
Library name: Single cell sample 131
Smart-seq3

tag: group

value: control


title: hapo_newborn_cordblood_B0776

value: Female

value: cord clood


title: P7657_1039

description:
single cell library
Smart-Seq2

tag: isolation criteria

tag: ercc spike-in_lot_no

tag: lane


title: hapo_newborn_cordblood_B0763


title: P7657_1038

description:
single cell library
Smart-Seq2

tag: n primer

tag: s primer


title: hapo_newborn_cordblood_B0771


title: ss3_23_056s_I11_accepted_hits_sorted_deduplicated.bam

description:
Library name: Single cell sample 129
Smart-seq3

tag: batch


title: ss3_23_056s_I12_accepted_hits_sorted_deduplicated.bam

description:
Library name: Single cell sample 130
Smart-seq3

value: BLEC


title: hapo_newborn_cordblood_B0762


title: hapo_newborn_cordblood_B0759


title: hapo_newborn_cordblood_B0755


title: P7657_1037

description:
single cell library
Smart-Seq2

tag: strain

tag: genotype

tag: individual


title: hapo_newborn_cordblood_B0753

tag: Sex


title: ss3_23_056s_I10_accepted_hits_sorted_deduplicated.bam

description:
Library name: Single cell sample 128
Smart-seq3

tag: tissue


title: P7657_1036

description:
single cell library
Smart-Seq2

tag: developmental stage

tag: cdna library_preparation_date

tag: plate well


title: hapo_newborn_cordblood_B0745

description: Illumina Infinium MethylationEPIC BeadChip (850K chip)

tag: cell type


title: U2OS_DHX8_siRNA_O5_biolrep_1

city: London

first: Pradeep

last: Ramagiri

state: Greater London

address: 15 Cotswold Rd

department: Cancer Therapeutics

country: United Kingdom

institute: The Institute of Cancer Research

description: Library name: U2OS_DHX8_siRNA_O5_A

library_source: transcriptomic

data_processing:
Raw FastQ files were processed using nf-core/rnaseq pipeline (version 21.04.3) which comprises the following software:  1. Read QC (FastQC v0.11.9 and MultiQC v1.12) 2. Alignment to the reference genome (GRCh38) using STAR aligner (v.2.7.6a) 3. Sort and index alignments (SAMtools) 4. Duplicate read marking (picard MarkDuplicates)
Once the reads were aligned, HTSeq-count (HTSeq v0.12.4) was used to count the number of reads mapping unambiguously to genomic features in each sample.
Differential expression analysis of the count data was performed in R using the Bioconductor package DESeq2 (v1.20.0). For differential splicing analysis, 1st pass and 2nd pass BAM files were created by mapping raw reads to reference genome (GRCh38) using STAR (v.2.7.6a). Differential local splicing variations (LSV) were detected and quantified using MAJIQ (v2.2-e25c4ac). Pathway and Gene Set Enrichment Analysis was carried out in R using package fgsea (v1.0).
Assembly: GRCh38
Supplementary files format and content: Tab-delimited text file includes raw counts for each sample.

source_name: Bone

growth_protocol: Human cell lines were obtained from ATCC and identity confirmed by short tandem repeat profiling. Cells were cultured in DMEM supplemented with 10% FCS, 2 mM glutamine and non-essential amino acids. All cell lines were maintained at 37 °C, 5% CO2 and tested negative for mycoplasma.

extract_protocol:
RNA extracted using an automated Magnapure (Roche) workstation according to the manufacturer’s instructions and RNA quality assessed using an Agilent bioanalyzer (Agilent)
RNA libraries for RNA-seq were prepared using Novogene NGS Stranded RNA Library Prep Set (PT044)* and sequenced in NovaSeq X Plus.

treatment_protocol: H1299 dTAG cells were treated for 6 hours with 250 nM dTAG-V1. U2OS, HCT116 and H1229 cells were reverse transfected with DHX8 or negative control siRNA using Hiperfect cationic lipid for 72 hours. HCT116 cells transfected with DHX8 or scramble control siRNA were treated +/- doxycyline to induce exogenous wild-type or mutant DHX8. U2OS cells were transfected with DHX8-O5 (GCAGUGGGUUCUUCCGUAA), DHX8-O2 (GGAAUAAAGUGAAGUCUAG) or AllStars negative control siRNA (Quagen).

value: Bone

tag: cell line

value: Osteosarcoma

tag: treatment

value: DHX8 siRNA

tag: time

value: 72 hours


title: hapo_newborn_cordblood_B0734

value: newborn

value: whole blood cells


title: ss3_23_056s_I09_accepted_hits_sorted_deduplicated.bam

description:
Library name: Single cell sample 127
Smart-seq3

tag: group


title: P7657_1035

description:
single cell library
Smart-Seq2

value: lung

value: Scgb1a1CREERT2; Rosa26R-fGFP

value: lung epithelial secretory cells

tag: sorting date

tag: isolation criteria

tag: ercc spike-in_lot_no

tag: type of_sequencing

tag: lane

tag: internal number


title: hapo_newborn_cordblood_B0719


title: ss3_23_056s_I08_accepted_hits_sorted_deduplicated.bam

description:
Library name: Single cell sample 126
Smart-seq3

value: meninges

tag: batch


title: hapo_newborn_cordblood_B0712

tag: Sex


title: ss3_23_056s_I04_accepted_hits_sorted_deduplicated.bam

description:
Library name: Single cell sample 125
Smart-seq3

tag: tissue

value: Neuronal/Glia


title: P7657_1034

description:
single cell library
Smart-Seq2

tag: strain

tag: genotype

value: WT

tag: developmental stage

tag: individual

value: EpCam^pos CD45^neg

value: single-end 50bp

tag: n primer

tag: s primer


title: hapo_newborn_cordblood_B0708

value: Male

tag: cell type


title: hapo_newborn_cordblood_B0697

value: cord clood


title: hapo_newborn_cordblood_B0694

value: Female


title: ss3_23_056s_I03_accepted_hits_sorted_deduplicated.bam

description:
Library name: Single cell sample 124
Smart-seq3

tag: group

value: control


title: P7657_1033

description:
single cell library
Smart-Seq2

tag: sorting date

tag: cdna library_preparation_date

tag: plate well


title: P7657_1032

description:
single cell library
Smart-Seq2

tag: isolation criteria

tag: ercc spike-in_lot_no

tag: type of_sequencing


title: hapo_newborn_cordblood_B0681


title: hapo_newborn_cordblood_B0668


title: ss3_23_056s_I02_accepted_hits_sorted_deduplicated.bam

description:
Library name: Single cell sample 123
Smart-seq3

tag: batch


title: P7657_1031

description:
single cell library
Smart-Seq2

tag: lane

tag: internal number


title: hapo_newborn_cordblood_B0667

tag: Sex

tag: tissue


title: hapo_newborn_cordblood_B0656

tag: developmental stage


title: P7657_1030

description:
single cell library
Smart-Seq2

tag: strain

tag: genotype

tag: individual


title: ss3_23_056s_I01_accepted_hits_sorted_deduplicated.bam

description:
Library name: Single cell sample 122
Smart-seq3

tag: cell type


title: hapo_newborn_cordblood_B0640


title: hapo_newborn_cordblood_B0644


title: hapo_newborn_cordblood_B0639


title: P7657_1029

description:
single cell library
Smart-Seq2

tag: n primer

tag: s primer


title: hapo_newborn_cordblood_B0636


title: ss3_23_056s_H23_accepted_hits_sorted_deduplicated.bam

description:
Library name: Single cell sample 121
Smart-seq3

value: Immune

tag: group


title: ss3_23_056s_H22_accepted_hits_sorted_deduplicated.bam

description:
Library name: Single cell sample 120
Smart-seq3


title: hapo_newborn_cordblood_B0635


title: hapo_newborn_cordblood_B0631


title: hapo_newborn_cordblood_B0619


title: hapo_newborn_cordblood_B0626


title: P7657_1028

description:
single cell library
Smart-Seq2

tag: sorting date

tag: cdna library_preparation_date

tag: plate well


title: ss3_23_056s_H20_accepted_hits_sorted_deduplicated.bam

description:
Library name: Single cell sample 118
Smart-seq3


title: hapo_newborn_cordblood_B0617


title: P7657_1026

description:
single cell library
Smart-Seq2

tag: isolation criteria

tag: ercc spike-in_lot_no

tag: type of_sequencing


title: P7657_1027

description:
single cell library
Smart-Seq2

tag: lane

tag: internal number


title: hapo_newborn_cordblood_B0609

tag: Sex

tag: tissue


title: P7657_1025

description:
single cell library
Smart-Seq2

tag: strain

tag: developmental stage


title: hapo_newborn_cordblood_B0611


title: hapo_newborn_cordblood_B0607


title: ss3_23_056s_H17_accepted_hits_sorted_deduplicated.bam

description:
Library name: Single cell sample 116
Smart-seq3

value: Fibroblast

tag: batch


title: ss3_23_056s_H19_accepted_hits_sorted_deduplicated.bam

description:
Library name: Single cell sample 117
Smart-seq3

tag: cell type


title: hapo_newborn_cordblood_B0610


title: P7657_1024

description:
single cell library
Smart-Seq2

tag: genotype

tag: individual

tag: n primer


title: P7657_1023

description:
single cell library
Smart-Seq2

tag: sorting date

value: GFP^pos

tag: s primer


title: ss3_23_056s_H16_accepted_hits_sorted_deduplicated.bam

description:
Library name: Single cell sample 115
Smart-seq3

tag: group


title: hapo_newborn_cordblood_B0599

value: newborn


title: ss3_23_056s_H15_accepted_hits_sorted_deduplicated.bam

description:
Library name: Single cell sample 114
Smart-seq3


title: hapo_newborn_cordblood_B0597

value: whole blood cells


title: ss3_23_056s_H11_accepted_hits_sorted_deduplicated.bam

description:
Library name: Single cell sample 113
Smart-seq3


title: hapo_newborn_cordblood_B0580


title: hapo_newborn_cordblood_B0578


title: P7657_1021

description:
single cell library
Smart-Seq2

value: lung

tag: isolation criteria

tag: cdna library_preparation_date

tag: plate well


title: hapo_newborn_cordblood_B0575


title: P7657_1020

description:
single cell library
Smart-Seq2

value: Scgb1a1CREERT2; Rosa26R-fGFP

tag: ercc spike-in_lot_no

tag: type of_sequencing

tag: lane


title: hapo_newborn_cordblood_B0573

tag: Sex

tag: tissue


title: ss3_23_056s_H09_accepted_hits_sorted_deduplicated.bam

description:
Library name: Single cell sample 111
Smart-seq3

value: BLEC


title: hapo_newborn_cordblood_B0571

tag: developmental stage


title: hapo_newborn_cordblood_B0567


title: ss3_23_056s_H05_accepted_hits_sorted_deduplicated.bam

description:
Library name: Single cell sample 110
Smart-seq3

value: meninges

tag: batch


title: hapo_newborn_cordblood_B0564

description: Illumina Infinium MethylationEPIC BeadChip (850K chip)

tag: cell type


title: P7657_1019

description:
single cell library
Smart-Seq2

tag: strain

value: lung epithelial secretory cells

tag: genotype

tag: internal number


title: hapo_newborn_cordblood_B0561


title: ss3_23_056s_H21_accepted_hits_sorted_deduplicated.bam

description:
Library name: Single cell sample 119
Smart-seq3


title: ss3_23_056s_H04_accepted_hits_sorted_deduplicated.bam

description:
Library name: Single cell sample 109
Smart-seq3


title: hapo_newborn_cordblood_B0557


title: P7657_1018

description:
single cell library
Smart-Seq2

value: WT

tag: individual

tag: sorting date

tag: n primer


title: P7657_1017

description:
single cell library
Smart-Seq2

tag: isolation criteria

tag: s primer


title: hapo_newborn_cordblood_B0538


title: ss3_23_056s_H01_accepted_hits_sorted_deduplicated.bam

description:
Library name: Single cell sample 108
Smart-seq3

value: Neuronal/Glia

tag: group


title: hapo_newborn_cordblood_B0512


title: P7657_1016

description:
single cell library
Smart-Seq2

tag: ercc spike-in_lot_no

tag: cdna library_preparation_date

value: single-end 50bp

tag: plate well


title: ss3_23_058s_D02_accepted_hits_sorted_deduplicated.bam

description:
Library name: Single cell sample 293
Smart-seq3

value: treated


title: hapo_newborn_cordblood_B0602

tag: Sex

value: Male

value: cord clood


title: hapo_newborn_cordblood_B0500

value: Female

tag: tissue


title: hapo_newborn_cordblood_B0603

tag: developmental stage


title: ss3_23_056s_G23_accepted_hits_sorted_deduplicated.bam

description:
Library name: Single cell sample 107
Smart-seq3

value: control

tag: batch


title: hapo_newborn_cordblood_B0498

tag: cell type


title: hapo_newborn_cordblood_B0497


title: ss3_23_056s_G22_accepted_hits_sorted_deduplicated.bam

description:
Library name: Single cell sample 106
Smart-seq3

value: Immune


title: hapo_newborn_cordblood_B0493


title: P7657_1015

description:
single cell library
Smart-Seq2

tag: strain

value: GFP^pos

tag: type of_sequencing

tag: lane


title: P7657_1014

description:
single cell library
Smart-Seq2

tag: genotype

tag: individual

tag: internal number


title: hapo_newborn_cordblood_B0491

value: newborn


title: hapo_newborn_cordblood_B0482

value: whole blood cells


title: ss3_23_056s_G21_accepted_hits_sorted_deduplicated.bam

description:
Library name: Single cell sample 105
Smart-seq3


title: hapo_newborn_cordblood_B0478


title: P7657_1013

description:
single cell library
Smart-Seq2

value: lung

tag: sorting date

tag: isolation criteria

tag: n primer


title: ss3_23_056s_G20_accepted_hits_sorted_deduplicated.bam

description:
Library name: Single cell sample 104
Smart-seq3

tag: group


title: hapo_newborn_cordblood_B0457


title: P7657_1012

description:
single cell library
Smart-Seq2

value: Scgb1a1CREERT2; Rosa26R-fGFP

tag: ercc spike-in_lot_no

tag: cdna library_preparation_date

tag: s primer


title: ss3_23_056s_G19_accepted_hits_sorted_deduplicated.bam

description:
Library name: Single cell sample 103
Smart-seq3

tag: tissue


title: hapo_newborn_cordblood_B0442

tag: Sex

tag: developmental stage


title: hapo_newborn_cordblood_B0438

tag: cell type


title: hapo_newborn_cordblood_B0437


title: P7657_1011

description:
single cell library
Smart-Seq2

tag: strain

tag: plate well


title: hapo_newborn_cordblood_B0428


title: hapo_newborn_cordblood_B0430


title: ss3_23_056s_G18_accepted_hits_sorted_deduplicated.bam

description:
Library name: Single cell sample 102
Smart-seq3

tag: batch


title: P7657_1010

description:
single cell library
Smart-Seq2

tag: genotype

tag: type of_sequencing

tag: lane


title: ss3_23_056s_G17_accepted_hits_sorted_deduplicated.bam

description:
Library name: Single cell sample 101
Smart-seq3


title: hapo_newborn_cordblood_B0425


title: hapo_newborn_cordblood_B0422


title: ss3_23_056s_G16_accepted_hits_sorted_deduplicated.bam

description:
Library name: Single cell sample 100
Smart-seq3


title: P7657_1009

description:
single cell library
Smart-Seq2

tag: individual

tag: sorting date

tag: internal number


title: hapo_newborn_cordblood_B0418


title: hapo_newborn_cordblood_B0417


title: P7657_1008

description:
single cell library
Smart-Seq2

tag: isolation criteria

tag: n primer


title: hapo_newborn_cordblood_B0411


title: ss3_23_056s_G15_accepted_hits_sorted_deduplicated.bam

description:
Library name: Single cell sample 99
Smart-seq3

tag: group


title: hapo_newborn_cordblood_B0409


title: P7657_1007

description:
single cell library
Smart-Seq2

tag: ercc spike-in_lot_no

tag: cdna library_preparation_date

tag: s primer


title: hapo_newborn_cordblood_B0407

tag: Sex

tag: tissue

tag: developmental stage


title: hapo_newborn_cordblood_B0406

tag: cell type


title: ss3_23_056s_G06_accepted_hits_sorted_deduplicated.bam

description:
Library name: Single cell sample 97
Smart-seq3

tag: batch


title: ss3_23_056s_G14_accepted_hits_sorted_deduplicated.bam

description:
Library name: Single cell sample 98
Smart-seq3


title: hapo_newborn_cordblood_B0403


title: P7657_1006

description:
single cell library
Smart-Seq2

tag: strain

tag: genotype

tag: plate well


title: ss3_23_056s_K10_accepted_hits_sorted_deduplicated.bam

description:
Library name: Single cell sample 164
Smart-seq3


title: ss3_23_056s_G05_accepted_hits_sorted_deduplicated.bam

description:
Library name: Single cell sample 96
Smart-seq3

value: BLEC


title: hapo_newborn_cordblood_B0398

description: Illumina Infinium MethylationEPIC BeadChip (850K chip)


title: hapo_newborn_cordblood_B0386


title: E. coli, 75%wt+25%ΔmiaA, 42°C, rep3

city: Berlin

first: Yu

last: Sun

address: Philippstr. 13

department: Institut für Biologie

country: Germany

institute: Humboldt-Universität zu Berlin

description: Library name: E. coli_75pwt_42_rep3

library_source: other

data_processing:
Read alignment was carried out using Bowtie2 with parameters -N 1 -L 6 to allow up to one mismatch per 6 nt seed. To assess reverse transcription-derived misincorporation patterns, the misincorporation rate at each nucleotide position was quantified using CoverageAnalyzer.
Assembly: Reference curation: The reference for S. pombe tRNATyr contains sequences of all unique mature tRNATyr and intron-containing tRNATyr  from GtRNAdb, and both 5’ and 3’ primer sequences were added. For E. coli, sequences of all unique tRNAs were from GtRNAdb, and primer sequences were added.
Supplementary files format and content: The processed data includes the following information: position, refbase, coverage, mm_ratio, a_mism, g_mism, t_mism, c_mism, and arrest_rate.

molecule: other

organism: Escherichia coli

source_name: strain:BW25113, BW25113 miaADEL

growth_protocol: The S. pombe strains were grown in YES medium with or without 0.1 μM of queuine at 30°C and 140 rpm. The E. coli strains were grown in M9 medium at 37°C or 42°C and 180 rpm.

extract_protocol:
Extraction of small RNAs from cells: Small RNAs were extracted according to the manufacturer’s protocol (PureLink™ miRNA Isolation Kit (Invitrogen)) with some adjustments. Briefly, cells were suspended in 1 ml Trizol (Ambion). The samples were vortexed for 2 min after adding 0.2 ml chloroform and glass beads, and then were centrifuged at 16 000 rcf, 4°C for 15 min. After adding 215 µl ethanol to the upper phase, the samples were transferred to a spin cartridge and centrifuged at 12 000 rcf for 1 min. 700 µl of ethanol was added to the flow-through, and the samples were transferred to a new spin cartridge followed by centrifugation at 12 000 rcf for 1 min. After washing the cartridge with wash buffer, small RNAs were eluted with 50 µl of DEPC-treated water.
For ms2i6A modification detection, in brief, 500 ng of deacylated small RNAs were hybridized with 1 μl of 10 μM tRNATyr stem-loop primer using the following thermocycling program: 95°C for 2 min, 65°C for 30 s, followed by a gradual ramp to 4°C at 5°C per 30 s. After incubation on ice for 1 min, reverse transcription was performed in 20 μl reactions containing 100 μM dA/C/GTP, 12.5 μM dTTP, 100 nM RT-KTq I614Y enzyme, and RT buffer [50 mM Tris-HCl (pH 9.2), 16 mM (NH₄)₂SO₄, 2.5 mM MgCl₂, 0.1% Tween-20], and incubation at 55°C for 1 hour. Following reverse transcription, 5 μl of cDNA was used for PCR amplification in a 50 μl reaction containing 0.5 µM forward and reverse primers, 250 μM dNTPs, 2 mM MgCl2, 1 x Taq buffer with KCl, and 1.25 U Taq polymerase (Thermo Fisher). The thermal cycling conditions were: 96°C for 3 min; 40 cycles of 96°C for 30 s, 50°C for 45 s, and 72°C for 45 s; followed by a final extension at 72°C for 5 min. 3′-end primers included sample-specific barcodes for multiplexing. PCR products were resolved on a 2% agarose gel and purified using the QIAquick Gel Extraction Kit (Qiagen). The purified PCR products were pooled and submitted for Next-generation sequencing. For i6A modification detection, deacylated small RNAs were further treated with 0.5 M I2 for 20 min on ice. Following iodine treatment, saturated Na2S2O3 was added to the reaction mixture until the solution became colorless. Subsequently, saturated Na2CO3 was added dropwise until effervescence ceased. Upon completion of the reaction, small RNAs were purified using the RNA Clean & Concentrator Kit (ZYMO Research) according to the manufacturer’s instructions. Iodine-treated samples were then used for sequencing library preparation following the same protocol as described above for ms2i6A detection.

value: strain:BW25113, BW25113 miaADEL

tag: treatment

value: grown in M9 medium  at 42°C


title: ss3_23_056s_G04_accepted_hits_sorted_deduplicated.bam

description:
Library name: Single cell sample 95
Smart-seq3

value: meninges


title: P7657_1003

description:
single cell library
Smart-Seq2

value: lung epithelial secretory cells

value: WT

tag: individual

tag: sorting date

tag: type of_sequencing

tag: lane


title: P7657_1002

description:
single cell library
Smart-Seq2

tag: isolation criteria

value: single-end 50bp

tag: internal number

tag: n primer


title: P7657_1004

description:
single cell library
Smart-Seq2

tag: ercc spike-in_lot_no

tag: cdna library_preparation_date

tag: s primer


title: hapo_newborn_cordblood_B0376

tag: Sex

value: Male

tag: tissue

tag: developmental stage


title: E. coli, 75%wt+25%ΔmiaA, 42°C, rep2

description: Library name: E. coli_75pwt_42_rep2


title: ss3_23_056s_G01_accepted_hits_sorted_deduplicated.bam

description:
Library name: Single cell sample 93
Smart-seq3

tag: cell type

value: Neuronal/Glia

tag: group

tag: batch


title: hapo_newborn_cordblood_B0365

value: cord clood


title: hapo_newborn_cordblood_B0371


title: P7657_1001

description:
single cell library
Smart-Seq2

tag: strain

tag: genotype

tag: plate well


title: E. coli, 50%wt+50%ΔmiaA, 42°C, rep3

description: Library name: E. coli_50pwt_42_rep3

tag: treatment


title: hapo_newborn_cordblood_B0364


title: P4730_1048

description:
single cell library
Smart-Seq2

tag: individual

tag: sorting date

value: EpCam^pos CD45^neg

tag: type of_sequencing

tag: lane


title: ss3_23_056s_F21_accepted_hits_sorted_deduplicated.bam

description:
Library name: Single cell sample 91
Smart-seq3

value: Immune

value: control


title: hapo_newborn_cordblood_B0363

value: newborn


title: P4730_1047

description:
single cell library
Smart-Seq2

tag: isolation criteria

tag: ercc spike-in_lot_no

tag: internal number

tag: n primer


title: E. coli, 50%wt+50%ΔmiaA, 42°C, rep1

description: Library name: E. coli_50pwt_42_rep1

tag: tissue


title: ss3_23_056s_F20_accepted_hits_sorted_deduplicated.bam

description:
Library name: Single cell sample 90
Smart-seq3


title: hapo_newborn_cordblood_B0352

tag: Sex

tag: developmental stage

value: whole blood cells


title: P4730_1046

description:
single cell library
Smart-Seq2

value: lung

tag: cell type

tag: cdna library_preparation_date

tag: s primer


title: E. coli, 25%wt+75%ΔmiaA, 42°C, rep3

description: Library name: E. coli_25pwt_42_rep3


title: ss3_23_056s_F19_accepted_hits_sorted_deduplicated.bam

description:
Library name: Single cell sample 89
Smart-seq3

value: Fibroblast

tag: group

tag: batch


title: hapo_newborn_cordblood_B0351


title: P4730_1045

description:
single cell library
Smart-Seq2

tag: strain

value: Scgb1a1CREERT2; Rosa26R-fGFP

tag: genotype

tag: plate well


title: E. coli, 25%wt+75%ΔmiaA, 42°C, rep2

description: Library name: E. coli_25pwt_42_rep2

value: strain:BW25113, BW25113 miaADEL

tag: treatment


title: ss3_23_056s_F17_accepted_hits_sorted_deduplicated.bam

description:
Library name: Single cell sample 88
Smart-seq3

value: Network


title: P7657_1005

description:
single cell library
Smart-Seq2

tag: individual

tag: sorting date

value: GFP^pos

tag: type of_sequencing

tag: lane


title: E. coli, 25%wt+75%ΔmiaA, 42°C, rep1

description: Library name: E. coli_25pwt_42_rep1

value: grown in M9 medium  at 42°C


title: ss3_23_056s_F16_accepted_hits_sorted_deduplicated.bam

description:
Library name: Single cell sample 87
Smart-seq3

value: meninges


title: hapo_newborn_cordblood_B0346


title: P4730_1043

description:
single cell library
Smart-Seq2

value: lung epithelial secretory cells

value: WT

tag: isolation criteria

tag: ercc spike-in_lot_no

value: single-end 50bp

tag: internal number

tag: n primer


title: E. coli, 12.5%wt+87.5%ΔmiaA, 42°C, rep3

description: Library name: E. coli_12p5wt_42_rep3

tag: tissue


title: ss3_23_056s_F15_accepted_hits_sorted_deduplicated.bam

description:
Library name: Single cell sample 86
Smart-seq3

tag: cell type

value: Neuronal/Glia


title: hapo_newborn_cordblood_B0343

tag: Sex

value: Female

value: cord clood

tag: developmental stage


title: P4730_1042

description:
single cell library
Smart-Seq2

value: EpCam^pos CD45^neg

tag: cdna library_preparation_date

tag: s primer


title: E. coli, 12.5%wt+87.5%ΔmiaA, 42°C, rep2

description: Library name: E. coli_12p5wt_42_rep2


title: ss3_23_056s_F14_accepted_hits_sorted_deduplicated.bam

description:
Library name: Single cell sample 85
Smart-seq3

tag: group

value: control

tag: batch


title: hapo_newborn_cordblood_B0342

value: Male

value: newborn

value: whole blood cells


title: P4730_1041

description:
single cell library
Smart-Seq2

value: lung

tag: strain

value: Scgb1a1CREERT2; Rosa26R-fGFP

tag: genotype

tag: plate well


title: E. coli, 12.5%wt+87.5%ΔmiaA, 42°C, rep1

description: Library name: E. coli_12p5wt_42_rep1

value: strain:BW25113, BW25113 miaADEL

tag: treatment


title: ss3_23_056s_F12_accepted_hits_sorted_deduplicated.bam

description:
Library name: Single cell sample 84
Smart-seq3

value: BLEC


title: hapo_newborn_cordblood_B0339


title: P4730_1040

description:
single cell library
Smart-Seq2

tag: individual

tag: sorting date

tag: type of_sequencing

tag: lane


title: hapo_newborn_cordblood_B0349


title: P4730_1044

description:
single cell library
Smart-Seq2

tag: isolation criteria

tag: ercc spike-in_lot_no

tag: internal number

tag: n primer


title: ss3_23_056s_F06_accepted_hits_sorted_deduplicated.bam

description:
Library name: Single cell sample 83
Smart-seq3

tag: tissue

tag: cell type


title: E. coli, ΔmiaA Δtgt, 42°C, rep3

description: Library name: E. coli_ΔmiaA Δtgt_42_rep3

source_name: strain:BW25113 miaADEL tgtDEL

value: strain:BW25113 miaADEL tgtDEL

value: F-, Delta(araD-araB)567, DeltalacZ4787(::rrnB-3), lambda-, DeltamiaA, Deltatgt::kan, rph-1, Delta(rhaD-rhaB)568, hsdR514

value: grown in M9 medium  at 42°C


title: E. coli, ΔmiaA Δtgt, 42°C, rep2

description: Library name: E. coli_ΔmiaA Δtgt_42_rep2


title: ss3_23_056s_F05_accepted_hits_sorted_deduplicated.bam

description:
Library name: Single cell sample 82
Smart-seq3

value: meninges


title: hapo_newborn_cordblood_B0332

tag: Sex

tag: developmental stage


title: hapo_newborn_cordblood_B0335


title: P4730_1038

description:
single cell library
Smart-Seq2

value: lung epithelial secretory cells

value: WT

tag: cdna library_preparation_date

value: single-end 50bp

tag: s primer


title: P4730_1039

description:
single cell library
Smart-Seq2

tag: strain

tag: genotype


title: E. coli, ΔmiaA Δtgt, 42°C, rep1

description: Library name: E. coli_ΔmiaA Δtgt_42_rep1

tag: treatment


title: hapo_newborn_cordblood_B0328

value: Female

value: cord clood


title: P4730_1037

description:
single cell library
Smart-Seq2

tag: individual

value: EpCam^pos CD45^neg

tag: plate well


title: E. coli, ΔmiaA, 42°C, rep3

description: Library name: E. coli_ΔmiaA_42_rep3

source_name: strain:BW25113 miaADEL

value: strain:BW25113 miaADEL

value: F-, Delta(araD-araB)567, DeltalacZ4787(::rrnB-3), lambda-, DeltamiaA::kan, rph-1, Delta(rhaD-rhaB)568, hsdR514


title: ss3_23_056s_F02_accepted_hits_sorted_deduplicated.bam

description:
Library name: Single cell sample 80
Smart-seq3

value: Neuronal/Glia

tag: group

value: control

tag: batch


title: hapo_newborn_cordblood_B0326

description: Illumina Infinium MethylationEPIC BeadChip (850K chip)

value: Male

value: newborn

value: whole blood cells


title: P4730_1036

description:
single cell library
Smart-Seq2

value: lung

value: Scgb1a1CREERT2; Rosa26R-fGFP

tag: sorting date

tag: isolation criteria

tag: type of_sequencing

tag: lane


title: E. coli, ΔmiaA, 42°C, rep2

description: Library name: E. coli_ΔmiaA_42_rep2

tag: tissue

value: grown in M9 medium  at 42°C


title: ss3_23_056s_F01_accepted_hits_sorted_deduplicated.bam

description:
Library name: Single cell sample 79
Smart-seq3

value: meninges

tag: cell type


title: hapo_newborn_cordblood_B0324

tag: Sex


title: P4730_1035

description:
single cell library
Smart-Seq2

value: lung epithelial secretory cells

tag: developmental stage

tag: ercc spike-in_lot_no

tag: internal number

tag: n primer


title: E. coli, ΔmiaA, 42°C, rep1

description: Library name: E. coli_ΔmiaA_42_rep1

tag: genotype


title: ss3_23_056s_E24_accepted_hits_sorted_deduplicated.bam

description:
Library name: Single cell sample 78
Smart-seq3

value: Immune


title: hapo_newborn_cordblood_B0321


title: P4730_1034

description:
single cell library
Smart-Seq2

tag: strain

value: WT

tag: cdna library_preparation_date

value: single-end 50bp

tag: s primer


title: E. coli, ΔqueF, 42°C, rep3

description: Library name: E. coli_ΔqueF_42_rep3

source_name: strain:BW25113 queFDEL

value: strain:BW25113 queFDEL

value: F-, Delta(araD-araB)567, DeltalacZ4787(::rrnB-3), lambda-, DeltaqueF721::kan, rph-1, Delta(rhaD-rhaB)568, hsdR514

tag: treatment


title: ss3_23_056s_E21_accepted_hits_sorted_deduplicated.bam

description:
Library name: Single cell sample 77
Smart-seq3

tag: group

tag: batch


title: hapo_newborn_cordblood_F1077

value: cord clood


title: E. coli, ΔqueF, 42°C, rep2

description: Library name: E. coli_ΔqueF_42_rep2


title: hapo_newborn_cordblood_D0652


title: ss3_23_056s_E20_accepted_hits_sorted_deduplicated.bam

description:
Library name: Single cell sample 76
Smart-seq3


title: hapo_newborn_cordblood_B0316

value: Female


title: P4730_1032

description:
single cell library
Smart-Seq2

tag: individual

tag: sorting date

tag: isolation criteria

value: EpCam^pos CD45^neg

tag: plate well


title: E. coli, ΔqueF, 42°C, rep1

description: Library name: E. coli_ΔqueF_42_rep1

tag: tissue


title: ss3_23_056s_E18_accepted_hits_sorted_deduplicated.bam

description:
Library name: Single cell sample 75
Smart-seq3

tag: cell type

value: control


title: hapo_newborn_cordblood_B0306

tag: Sex

tag: developmental stage


title: hapo_newborn_cordblood_F1138

value: Male


title: P4730_1031

description:
single cell library
Smart-Seq2

tag: ercc spike-in_lot_no

tag: type of_sequencing

tag: lane

tag: internal number


title: E. coli, ΔqueA, 42°C, rep3

description: Library name: E. coli_ΔqueA_42_rep3

source_name: strain:BW25113 queADEL

value: strain:BW25113 queADEL

tag: genotype

value: F-, Delta(araD-araB)567, DeltalacZ4787(::rrnB-3), DeltaqueA769::kan, lambda-, rph-1, Delta(rhaD-rhaB)568, hsdR514


title: ss3_23_056s_E17_accepted_hits_sorted_deduplicated.bam

description:
Library name: Single cell sample 74
Smart-seq3

value: Neuronal/Glia


title: hapo_newborn_cordblood_B0300

value: newborn

value: whole blood cells


title: P4730_1030

description:
single cell library
Smart-Seq2

value: lung

tag: strain

value: Scgb1a1CREERT2; Rosa26R-fGFP

tag: cdna library_preparation_date

tag: n primer

tag: s primer


title: E. coli, ΔqueA, 42°C, rep2

description: Library name: E. coli_ΔqueA_42_rep2

tag: treatment

value: grown in M9 medium  at 42°C


title: hapo_newborn_cordblood_B0298


title: P4730_1029

description:
single cell library
Smart-Seq2

value: lung epithelial secretory cells

value: WT

tag: individual

tag: sorting date

value: GFP^pos


title: E. coli, ΔqueA, 42°C, rep1

description: Library name: E. coli_ΔqueA_42_rep1


title: ss3_23_056s_E14_accepted_hits_sorted_deduplicated.bam

description:
Library name: Single cell sample 72
Smart-seq3

value: meninges

tag: group

tag: batch


title: hapo_newborn_cordblood_B0295

tag: tissue

value: cord clood

tag: cell type


title: ss3_23_056s_E16_accepted_hits_sorted_deduplicated.bam

description:
Library name: Single cell sample 73
Smart-seq3

value: Network


title: P4730_1024

description:
single cell library
Smart-Seq2

tag: developmental stage

tag: isolation criteria

value: EpCam^pos CD45^neg

value: single-end 50bp

tag: plate well


title: E. coli, Δtgt, 42°C, rep3

description: Library name: E. coli_Δtgt_42_rep3

source_name: strain:BW25113 tgtDEL

value: strain:BW25113 tgtDEL

value: F-, Delta(araD-araB)567, DeltalacZ4787(::rrnB-3), Deltatgt::kan, lambda-, rph-1, Delta(rhaD-rhaB)568, hsdR514


title: hapo_newborn_cordblood_B0287

tag: Sex

value: Male


title: P4730_1023

description:
single cell library
Smart-Seq2

tag: ercc spike-in_lot_no

tag: type of_sequencing

tag: lane

tag: internal number


title: E. coli, Δtgt, 42°C, rep2

description: Library name: E. coli_Δtgt_42_rep2

tag: genotype


title: ss3_23_056s_G03_accepted_hits_sorted_deduplicated.bam

description:
Library name: Single cell sample 94
Smart-seq3

value: Neuronal/Glia

value: control


title: ss3_23_056s_E12_accepted_hits_sorted_deduplicated.bam

description:
Library name: Single cell sample 70
Smart-seq3

value: BLEC


title: hapo_newborn_cordblood_B0285

value: Female

value: newborn

value: whole blood cells


title: P4730_1022

description:
single cell library
Smart-Seq2

value: lung

tag: strain

value: Scgb1a1CREERT2; Rosa26R-fGFP

value: lung epithelial secretory cells

tag: cdna library_preparation_date

tag: n primer

tag: s primer


title: ss3_23_056s_E13_accepted_hits_sorted_deduplicated.bam

description:
Library name: Single cell sample 71
Smart-seq3

value: meninges

tag: group


title: E. coli, Δtgt, 42°C, rep1

description: Library name: E. coli_Δtgt_42_rep1

tag: treatment

value: grown in M9 medium  at 42°C


title: ss3_23_056s_E09_accepted_hits_sorted_deduplicated.bam

description:
Library name: Single cell sample 69
Smart-seq3

tag: tissue

tag: batch


title: hapo_newborn_cordblood_B0283

value: cord clood

tag: developmental stage

tag: cell type


title: P4730_1021

description:
single cell library
Smart-Seq2

value: WT

tag: individual

tag: sorting date

tag: isolation criteria

value: EpCam^pos CD45^neg

tag: plate well


title: E. coli, wt, 42°C, rep3

description: Library name: E. coli_wt_42_rep3

value: F-, Delta(araD-araB)567, DeltalacZ4787 (::rrn B-3), lambda-, rph-1, Delta(rhaD-rhaB)568, hsdR5154


title: ss3_23_056s_E07_accepted_hits_sorted_deduplicated.bam

description:
Library name: Single cell sample 68
Smart-seq3


title: hapo_newborn_cordblood_B0280

tag: Sex


title: P4730_1020

description:
single cell library
Smart-Seq2

tag: ercc spike-in_lot_no

tag: type of_sequencing

value: single-end 50bp

tag: lane

tag: internal number


title: E. coli, wt, 42°C, rep2

description: Library name: E. coli_wt_42_rep2

tag: genotype


title: hapo_newborn_cordblood_B0274


title: E. coli, wt, 42°C, rep1

description: Library name: E. coli_wt_42_rep1


title: ss3_23_056s_E05_accepted_hits_sorted_deduplicated.bam

description:
Library name: Single cell sample 66
Smart-seq3


title: hapo_newborn_cordblood_B0268


title: P4730_1018

description:
single cell library
Smart-Seq2

tag: strain

tag: cdna library_preparation_date

tag: n primer

tag: s primer


title: E. coli, 75%wt+25%ΔmiaA, 37°C, rep3

description: Library name: E. coli_75pwt_37_rep3

tag: tissue

value: strain:BW25113, BW25113 miaADEL

tag: treatment

value: grown in M9 medium  at 37°C


title: ss3_23_056s_E04_accepted_hits_sorted_deduplicated.bam

description:
Library name: Single cell sample 65
Smart-seq3

tag: cell type

value: Neuronal/Glia

tag: group

value: control

tag: batch


title: hapo_newborn_cordblood_B0264

value: Female

tag: developmental stage


title: P4730_1017

description:
single cell library
Smart-Seq2

tag: individual

tag: sorting date

tag: isolation criteria

tag: plate well


title: E. coli, 75%wt+25%ΔmiaA, 37°C, rep2

description: Library name: E. coli_75pwt_37_rep2


title: ss3_23_056s_E03_accepted_hits_sorted_deduplicated.bam

description:
Library name: Single cell sample 64
Smart-seq3


title: hapo_newborn_cordblood_B0256

description: Illumina Infinium MethylationEPIC BeadChip (850K chip)

tag: Sex

value: Male

value: newborn


title: P4730_1016

description:
single cell library
Smart-Seq2

value: lung

tag: ercc spike-in_lot_no

tag: type of_sequencing

tag: lane

tag: internal number


title: E. coli, 75%wt+25%ΔmiaA, 37°C, rep1

description: Library name: E. coli_75pwt_37_rep1


title: ss3_23_056s_E02_accepted_hits_sorted_deduplicated.bam

description:
Library name: Single cell sample 63
Smart-seq3


title: P4730_1015

description:
single cell library
Smart-Seq2

tag: strain

value: Scgb1a1CREERT2; Rosa26R-fGFP

tag: genotype

tag: cdna library_preparation_date

tag: n primer


title: E. coli, 50%wt+50%ΔmiaA, 37°C, rep3

description: Library name: E. coli_50pwt_37_rep3

tag: tissue

tag: treatment


title: ss3_23_056s_E01_accepted_hits_sorted_deduplicated.bam

description:
Library name: Single cell sample 62
Smart-seq3

tag: cell type

tag: group

tag: batch


title: hapo_newborn_cordblood_B0252

tag: developmental stage

value: whole blood cells


title: P4730_1014

description:
single cell library
Smart-Seq2

value: lung epithelial secretory cells

tag: individual

tag: sorting date

tag: isolation criteria

tag: s primer


title: E. coli, 50%wt+50%ΔmiaA, 37°C, rep2

description: Library name: E. coli_50pwt_37_rep2


title: ss3_23_056s_D24_accepted_hits_sorted_deduplicated.bam

description:
Library name: Single cell sample 61
Smart-seq3

value: meninges

value: Immune


title: hapo_newborn_cordblood_B0247

tag: Sex

value: cord clood


title: P4730_1013

description:
single cell library
Smart-Seq2

value: WT

value: EpCam^pos CD45^neg

tag: ercc spike-in_lot_no

tag: type of_sequencing

tag: lane

tag: plate well


title: E. coli, 50%wt+50%ΔmiaA, 37°C, rep1

description: Library name: E. coli_50pwt_37_rep1


title: hapo_newborn_cordblood_E1402


title: hapo_newborn_cordblood_B0246


title: P4730_1012

description:
single cell library
Smart-Seq2

tag: strain

tag: genotype

tag: cdna library_preparation_date

value: single-end 50bp

tag: internal number


title: E. coli, 25%wt+75%ΔmiaA, 37°C, rep3

description: Library name: E. coli_25pwt_37_rep3

tag: tissue

value: strain:BW25113, BW25113 miaADEL

tag: treatment


title: ss3_23_056s_D21_accepted_hits_sorted_deduplicated.bam

description:
Library name: Single cell sample 59
Smart-seq3

tag: cell type

tag: group

tag: batch


title: hapo_newborn_cordblood_E0605

tag: developmental stage


title: hapo_newborn_cordblood_B0245


title: P4730_1011

description:
single cell library
Smart-Seq2

tag: individual

tag: sorting date

tag: isolation criteria

tag: n primer


title: E. coli, 25%wt+75%ΔmiaA, 37°C, rep2

description: Library name: E. coli_25pwt_37_rep2

value: grown in M9 medium  at 37°C


title: ss3_23_056s_D20_accepted_hits_sorted_deduplicated.bam

description:
Library name: Single cell sample 58
Smart-seq3


title: hapo_newborn_cordblood_B0244

tag: Sex


title: P4730_1010

description:
single cell library
Smart-Seq2

tag: ercc spike-in_lot_no

tag: type of_sequencing

tag: lane

tag: s primer


title: E. coli, 25%wt+75%ΔmiaA, 37°C, rep1

description: Library name: E. coli_25pwt_37_rep1


title: ss3_23_056s_D19_accepted_hits_sorted_deduplicated.bam

description:
Library name: Single cell sample 57
Smart-seq3


title: hapo_newborn_cordblood_B0240


title: P4730_1009

description:
single cell library
Smart-Seq2

tag: strain

tag: genotype

tag: cdna library_preparation_date

tag: plate well


title: E. coli, 12.5%wt+87.5%ΔmiaA, 37°C, rep3

description: Library name: E. coli_12p5wt_37_rep3

tag: tissue

tag: treatment


title: ss3_23_056s_D17_accepted_hits_sorted_deduplicated.bam

description:
Library name: Single cell sample 56
Smart-seq3

tag: cell type

value: Fibroblast

tag: group

tag: batch


title: P4730_1008

description:
single cell library
Smart-Seq2

tag: developmental stage

tag: individual

tag: sorting date

tag: internal number


title: E. coli, 12.5%wt+87.5%ΔmiaA, 37°C, rep2

description: Library name: E. coli_12p5wt_37_rep2


title: ss3_23_056s_D16_accepted_hits_sorted_deduplicated.bam

description:
Library name: Single cell sample 55
Smart-seq3

value: Neuronal/Glia

value: control


title: hapo_newborn_cordblood_B0229

tag: Sex

value: Female


title: ss3_23_056s_O22_accepted_hits_sorted_deduplicated.bam

description:
Library name: Single cell sample 231
Smart-seq3


title: E. coli, 12.5%wt+87.5%ΔmiaA, 37°C, rep1

description: Library name: E. coli_12p5wt_37_rep1


title: ss3_23_056s_D15_accepted_hits_sorted_deduplicated.bam

description:
Library name: Single cell sample 54
Smart-seq3


title: hapo_newborn_cordblood_B0221

value: Male

value: newborn


title: P4730_1002

description:
single cell library
Smart-Seq2

value: lung

value: Scgb1a1CREERT2; Rosa26R-fGFP

tag: isolation criteria

tag: ercc spike-in_lot_no

tag: type of_sequencing

tag: n primer


title: E. coli, ΔmiaA Δtgt, 37°C, rep3

description: Library name: E. coli_ΔmiaA Δtgt_37_rep3

value: strain:BW25113 miaADEL tgtDEL

tag: genotype

value: F-, Delta(araD-araB)567, DeltalacZ4787(::rrnB-3), lambda-, DeltamiaA, Deltatgt::kan, rph-1, Delta(rhaD-rhaB)568, hsdR514


title: ss3_23_056s_D13_accepted_hits_sorted_deduplicated.bam

description:
Library name: Single cell sample 53
Smart-seq3

value: meninges


title: hapo_newborn_cordblood_B0216

value: cord clood

value: whole blood cells


title: P4730_1001

description:
single cell library
Smart-Seq2

tag: strain

value: lung epithelial secretory cells

value: WT

value: EpCam^pos CD45^neg

tag: cdna library_preparation_date

tag: lane

tag: s primer


title: E. coli, ΔmiaA Δtgt, 37°C, rep2

description: Library name: E. coli_ΔmiaA Δtgt_37_rep2

tag: tissue

tag: treatment

value: grown in M9 medium  at 37°C


title: ss3_23_056s_D12_accepted_hits_sorted_deduplicated.bam

description:
Library name: Single cell sample 52
Smart-seq3

tag: cell type

tag: group

tag: batch


title: hapo_newborn_cordblood_F1062

tag: developmental stage


title: P3504_1192

description:
single cell library
Smart-Seq2

tag: individual

tag: sorting date

value: GFP^pos

value: single-end 50bp

tag: plate well

tag: internal number


title: E. coli, ΔmiaA Δtgt, 37°C, rep1

description: Library name: E. coli_ΔmiaA Δtgt_37_rep1


title: ss3_23_056s_D09_accepted_hits_sorted_deduplicated.bam

description:
Library name: Single cell sample 51
Smart-seq3

value: Neuronal/Glia

value: control


title: hapo_newborn_cordblood_B0211

description: Illumina Infinium MethylationEPIC BeadChip (850K chip)

tag: Sex

value: Female


title: P3504_1191

description:
single cell library
Smart-Seq2

tag: isolation criteria

tag: ercc spike-in_lot_no

tag: type of_sequencing

tag: n primer


title: E. coli, ΔmiaA, 37°C, rep3

description: Library name: E. coli_ΔmiaA_37_rep3

value: strain:BW25113 miaADEL

tag: genotype

value: F-, Delta(araD-araB)567, DeltalacZ4787(::rrnB-3), lambda-, DeltamiaA::kan, rph-1, Delta(rhaD-rhaB)568, hsdR514


title: ss3_23_056s_D07_accepted_hits_sorted_deduplicated.bam

description:
Library name: Single cell sample 50
Smart-seq3

value: BLEC


title: hapo_newborn_cordblood_B0198

value: newborn


title: P3504_1190

description:
single cell library
Smart-Seq2

value: lung

tag: strain

value: Scgb1a1CREERT2; Rosa26R-fGFP

tag: cdna library_preparation_date

tag: lane

tag: s primer


title: E. coli, ΔmiaA, 37°C, rep2

description: Library name: E. coli_ΔmiaA_37_rep2

tag: tissue

tag: treatment


title: hapo_newborn_cordblood_B0929

value: Male

value: cord clood

tag: developmental stage

tag: cell type


title: hapo_newborn_cordblood_B0182

value: whole blood cells


title: P3504_1189

description:
single cell library
Smart-Seq2

value: lung epithelial secretory cells

value: WT

tag: individual

tag: sorting date


title: E. coli, ΔmiaA, 37°C, rep1

description: Library name: E. coli_ΔmiaA_37_rep1

value: grown in M9 medium  at 37°C


title: ss3_23_056s_D05_accepted_hits_sorted_deduplicated.bam

description:
Library name: Single cell sample 48
Smart-seq3

value: meninges

tag: group

tag: batch


title: hapo_newborn_cordblood_B0171

tag: Sex


title: P3504_1188

description:
single cell library
Smart-Seq2

tag: isolation criteria

value: EpCam^pos CD45^neg

tag: ercc spike-in_lot_no

value: single-end 50bp

tag: plate well

tag: internal number


title: E. coli, ΔqueF, 37°C, rep3

description: Library name: E. coli_ΔqueF_37_rep3

value: strain:BW25113 queFDEL

tag: genotype

value: F-, Delta(araD-araB)567, DeltalacZ4787(::rrnB-3), lambda-, DeltaqueF721::kan, rph-1, Delta(rhaD-rhaB)568, hsdR514


title: ss3_23_056s_D04_accepted_hits_sorted_deduplicated.bam

description:
Library name: Single cell sample 47
Smart-seq3

value: Neuronal/Glia

value: control


title: hapo_newborn_cordblood_B0170


title: P3504_1187

description:
single cell library
Smart-Seq2

tag: strain

tag: cdna library_preparation_date

tag: type of_sequencing

tag: n primer


title: P4730_1007

description:
single cell library
Smart-Seq2

tag: tissue

tag: lane

tag: s primer


title: ss3_23_056s_D03_accepted_hits_sorted_deduplicated.bam

description:
Library name: Single cell sample 46
Smart-seq3

tag: cell type

value: Fibroblast


title: hapo_newborn_cordblood_B0168

value: Female

tag: developmental stage

value: newborn


title: P3504_1185

description:
single cell library
Smart-Seq2

value: lung

value: Scgb1a1CREERT2; Rosa26R-fGFP

tag: individual

tag: sorting date


title: E. coli, ΔqueF, 37°C, rep1

description: Library name: E. coli_ΔqueF_37_rep1

tag: treatment


title: ss3_23_056s_D02_accepted_hits_sorted_deduplicated.bam

description:
Library name: Single cell sample 45
Smart-seq3

tag: group

tag: batch


title: hapo_newborn_cordblood_B0167

tag: Sex

value: Male

value: cord clood


title: P3504_1184

description:
single cell library
Smart-Seq2

value: lung epithelial secretory cells

tag: isolation criteria

tag: ercc spike-in_lot_no

tag: plate well

tag: internal number


title: E. coli, ΔqueA, 37°C, rep3

description: Library name: E. coli_ΔqueA_37_rep3

value: strain:BW25113 queADEL

tag: genotype

value: F-, Delta(araD-araB)567, DeltalacZ4787(::rrnB-3), DeltaqueA769::kan, lambda-, rph-1, Delta(rhaD-rhaB)568, hsdR514


title: ss3_23_056s_D01_accepted_hits_sorted_deduplicated.bam

description:
Library name: Single cell sample 44
Smart-seq3

value: meninges


title: hapo_newborn_cordblood_B0157

value: whole blood cells


title: ss3_23_056s_F04_accepted_hits_sorted_deduplicated.bam

description:
Library name: Single cell sample 81
Smart-seq3


title: E. coli, ΔqueA, 37°C, rep2

description: Library name: E. coli_ΔqueA_37_rep2

value: grown in M9 medium  at 37°C


title: ss3_23_056s_C24_accepted_hits_sorted_deduplicated.bam

description:
Library name: Single cell sample 43
Smart-seq3

value: Immune


title: hapo_newborn_cordblood_B0156


title: P3504_1182

description:
single cell library
Smart-Seq2

tag: strain

value: WT

value: EpCam^pos CD45^neg

tag: cdna library_preparation_date

tag: type of_sequencing

value: single-end 50bp

tag: n primer


title: E. coli, ΔqueA, 37°C, rep1

description: Library name: E. coli_ΔqueA_37_rep1

tag: tissue


title: ss3_23_056s_C23_accepted_hits_sorted_deduplicated.bam

description:
Library name: Single cell sample 42
Smart-seq3

tag: cell type

value: control


title: hapo_newborn_cordblood_B0155

tag: developmental stage


title: P3504_1181

description:
single cell library
Smart-Seq2

tag: individual

tag: sorting date

tag: lane

tag: s primer


title: E. coli, Δtgt, 37°C, rep3

description: Library name: E. coli_Δtgt_37_rep3

value: strain:BW25113 tgtDEL

value: F-, Delta(araD-araB)567, DeltalacZ4787(::rrnB-3), Deltatgt::kan, lambda-, rph-1, Delta(rhaD-rhaB)568, hsdR514

tag: treatment


title: ss3_23_056s_C22_accepted_hits_sorted_deduplicated.bam

description:
Library name: Single cell sample 41
Smart-seq3

tag: group

tag: batch


title: hapo_newborn_cordblood_G0619

tag: Sex

value: newborn


title: P3504_1180

description:
single cell library
Smart-Seq2

value: lung

value: Scgb1a1CREERT2; Rosa26R-fGFP

tag: isolation criteria

value: GFP^pos

tag: ercc spike-in_lot_no

tag: plate well

tag: internal number


title: E. coli, Δtgt, 37°C, rep2

description: Library name: E. coli_Δtgt_37_rep2

tag: genotype


title: ss3_23_056s_C21_accepted_hits_sorted_deduplicated.bam

description:
Library name: Single cell sample 40
Smart-seq3


title: hapo_newborn_cordblood_B0148

value: Male

value: cord clood


title: P3504_1179

description:
single cell library
Smart-Seq2

tag: strain

value: lung epithelial secretory cells

tag: cdna library_preparation_date

tag: type of_sequencing

tag: n primer


title: E. coli, Δtgt, 37°C, rep1

description: Library name: E. coli_Δtgt_37_rep1

tag: tissue


title: ss3_23_056s_C20_accepted_hits_sorted_deduplicated.bam

description:
Library name: Single cell sample 39
Smart-seq3

value: meninges

tag: cell type


title: hapo_newborn_cordblood_B0143

tag: developmental stage

value: whole blood cells


title: P3504_1178

description:
single cell library
Smart-Seq2

tag: individual

tag: sorting date

tag: lane

tag: s primer


title: E. coli, wt, 37°C, rep3

description: Library name: E. coli_wt_37_rep3

value: F-, Delta(araD-araB)567, DeltalacZ4787 (::rrn B-3), lambda-, rph-1, Delta(rhaD-rhaB)568, hsdR5154

tag: treatment

value: grown in M9 medium  at 37°C


title: P4730_1019

description:
single cell library
Smart-Seq2

value: WT

tag: isolation criteria


title: hapo_newborn_cordblood_B0140

tag: Sex


title: P3504_1176

description:
single cell library
Smart-Seq2

tag: ercc spike-in_lot_no

tag: plate well


title: E. coli, wt, 37°C, rep2

description: Library name: E. coli_wt_37_rep2

tag: genotype


title: ss3_23_056s_C17_accepted_hits_sorted_deduplicated.bam

description:
Library name: Single cell sample 37
Smart-seq3

value: Immune

tag: group

tag: batch


title: hapo_newborn_cordblood_B0139


title: P3504_1175

description:
single cell library
Smart-Seq2

tag: strain

tag: cdna library_preparation_date

tag: type of_sequencing

value: single-end 50bp

tag: internal number


title: E. coli, wt, 37°C, rep1

description: Library name: E. coli_wt_37_rep1

tag: tissue


title: ss3_23_056s_C16_accepted_hits_sorted_deduplicated.bam

description:
Library name: Single cell sample 36
Smart-seq3

tag: cell type

value: Fibroblast

value: control


title: hapo_newborn_cordblood_B0136

value: Female

tag: developmental stage


title: P3504_1174

description:
single cell library
Smart-Seq2

tag: individual

tag: sorting date

tag: lane

tag: n primer


title: ss3_23_056s_E06_accepted_hits_sorted_deduplicated.bam

description:
Library name: Single cell sample 67
Smart-seq3

value: Neuronal/Glia


title: ss3_23_056s_C12_accepted_hits_sorted_deduplicated.bam

description:
Library name: Single cell sample 35
Smart-seq3

value: BLEC


title: hapo_newborn_cordblood_B0134

description: Illumina Infinium MethylationEPIC BeadChip (850K chip)

tag: Sex

value: newborn


title: P3504_1173

description:
single cell library
Smart-Seq2

value: lung

value: Scgb1a1CREERT2; Rosa26R-fGFP

tag: isolation criteria

value: GFP^pos

tag: ercc spike-in_lot_no

tag: s primer


title: RNA-seq of mouse cardiac tissue: AAV9_Irx3_MI_3

city: Changchun

first: BIng

last: Li

address: 130021, No. 1, Xinmin Street, Chaoyang District, Changchun, Jilin Province

country: China

institute: First Hospital of Jilin University

description:
Library name: AAV9_Irx3_MI_3
Transcriptome sequencing of mouse cardiac tissues performed by Novogene (Beijing, China). mRNA was enriched via oligo(dT) magnetic beads, randomly fragmented, and reverse transcribed into double-stranded cDNA. The cDNA was then subjected to end-repair, A-tailing, adapter ligation, and PCR amplification. Qualified libraries were sequenced on the Illumina platform. Raw sequencing data were processed via fastp to remove adapter sequences and low-quality reads, yielding clean reads.

data_processing:
Raw sequencing data were processed using fastp to remove adaptor sequences and low-quality reads, generating clean reads; Q20, Q30, and GC content of clean reads were calculated.
Clean reads were aligned to the mouse reference genome (GRCm39/mm39), and gene expression levels were quantified.
Assembly: GRCm39/mm39 for mouse cardiac tissues.
Supplementary files format and content: GEO_gene_count.xls.csv

source_name: Left ventricle

growth_protocol: C57BL/6J mice were raised under specific pathogen-free (SPF) conditions.

extract_protocol:
Total RNA was extracted using TRIzol reagent and treated with DNase I to remove genomic DNA.
mRNA was enriched from total RNA using Oligo(dT) magnetic beads, randomly fragmented, and reverse-transcribed into double-stranded cDNA. The cDNA was then subjected to end repair, A-tailing, adaptor ligation, and PCR amplification. Qualified libraries (verified by Qubit quantification and Agilent fragment analysis) were sequenced on an Illumina platform (conducted by Novogene, Beijing, China).

treatment_protocol: Mice were injected with AAV9 control or AAV9-Irx3 vector via tail vein, followed by sham or MI surgery.

value: Left ventricle

value: Cardiomyocytes

tag: genotype

value: Wild type

tag: treatment

value: Myocardial infarction (MI) surgery + AAV9-Irx3 overexpression vector


title: ss3_23_056s_C10_accepted_hits_sorted_deduplicated.bam

description:
Library name: Single cell sample 34
Smart-seq3

value: meninges

tag: group

tag: batch


title: hapo_newborn_cordblood_B0131

value: cord clood

value: whole blood cells


title: P3504_1171

description:
single cell library
Smart-Seq2

tag: strain

value: lung epithelial secretory cells

value: WT

tag: cdna library_preparation_date

tag: type of_sequencing

value: single-end 50bp

tag: plate well


title: RNA-seq of mouse cardiac tissue: AAV9_Irx3_MI_2

description:
Library name: AAV9_Irx3_MI_2
Transcriptome sequencing of mouse cardiac tissues performed by Novogene (Beijing, China). mRNA was enriched via oligo(dT) magnetic beads, randomly fragmented, and reverse transcribed into double-stranded cDNA. The cDNA was then subjected to end-repair, A-tailing, adapter ligation, and PCR amplification. Qualified libraries were sequenced on the Illumina platform. Raw sequencing data were processed via fastp to remove adapter sequences and low-quality reads, yielding clean reads.

tag: tissue

tag: cell type


title: ss3_23_056s_C06_accepted_hits_sorted_deduplicated.bam

description:
Library name: Single cell sample 33
Smart-seq3

value: control


title: hapo_newborn_cordblood_B0130

value: Female

tag: developmental stage


title: hapo_newborn_cordblood_B0254

value: Male