title: WAT_TH_24h_3

city: Lyon

first: Yanis

last: ZEKRI

address: 32-34 Avenue Tony Garnier

institute: IGFL-ENS

data_processing:
Reads were mapped on mouse mm10 genome using Bowtie Galaxy version 2.2.6.2 with default parameters
Read were counted using htseqcount Galaxy version 0.6.1galaxy3 using these parameters // Mode : Union / Minimul alignement quality : 10 / Feature type : exon / ID Attribute : gene name
Differential gene expression analysis was performed with DESeq2 (R package, Version 1.34.0) using the following thresholds: adjusted p-value <0.05; average expression > 10 reads per million.
Assembly: mm10
Supplementary files format and content: tab-delimited text file including raw counts of all samples from the same experiment (thus, two files, one for WAT, one for Striatum)

source_name: White adipose tissue

extract_protocol:
RNAs were extracted using Trizol (WAT) or Rneasy mini-kit Qiagen (Striatum). Total RNA was converted to cDNA using MMLV reverse transcriptase. 1ug of total RNA was used for the construction of sequencing libraries
cDNA libraries were prepared using the total RNA SENSE kit (Lexogen, Vienna, Austria) and analyzed on a Nextseq 500 sequencer (Illumina)

value: White adipose tissue

tag: age

value: 8 weeks

tag: Sex

tag: background strain

value: Wild-type

value: TH-treated 24h


title: WAT_TH_24h_2

status: Public on Aug 12 2022

type: SRA

country: France

library_source: transcriptomic

molecule: total RNA

organism: Mus musculus

tag: tissue

value: Male

tag: genotype

tag: treatment


title: WAT_TH_6h_3

value: TH-treated 6h


title: WAT_TH_24h_1


title: Control 14

type: RNA

city: LOS ANGELES

first: Neal

last: Yuan

state: CA

address: 8700 Beverly Blvd, Davis 1015

country: USA

institute: Cedars-Sinai

data_processing: We excluded any miRNA if greater than 80% of samples failed to meet manufacturer quality scores, a sign of either very low miRNA levels and/or failed amplification. We normalized miRNA expression data by subtracting the cycle threshold (Ct) from the global mean across the Ct’s of all miRNAs for that patient, a widely accepted normalization method (see D’haene Methods Mol Biol 2012). Lastly, we excluded any patients if greater than 80% of their samples failed to meet quality scores.

label: EVAGREEN

organism: Homo sapiens

source_name: platelet poor plasma

extract_protocol: miRNeasy Serum Plasma Kit

tag: condition

value: control


title: Control 1


title: WAT_TH_6h_4


title: WAT_TH_6h_2


title: WAT_PTU_4

value: Hypothyroid (PTU-treated 2 weeks)


title: WAT_PTU_3


title: WAT_TH_6h_1


title: WAT_PTU_2


title: WAT_PTU_1


title: Striatum_TH24h_4

source_name: Striatum

value: Striatum


title: WAT_TH_24h_4


title: Striatum_TH24h_2


title: Striatum_TH24h_1


title: Striatum_TH24h_3


title: Control 5


title: Striatum_TH12h_4

value: TH-treated 12h


title: Striatum_TH12h_1


title: Striatum_TH12h_2


title: Striatum_PTU_S3


title: Striatum_PTU_S6


title: Striatum_TH12h_3


title: ChIP_TRa_Striatum_adult_2

library_source: genomic

data_processing:
Reads were mapped on mouse mm10 genome using Bowtie Galaxy version 2.3.2.2 with default parameters
Peaks were called using MACS2 Callpeak version 2.1.1.20160309.0 using input files as control files. Peaks with a score inferior at 60 were filetered out
De novo motif search was performed using the MEME-Suite (5.4.1)
Distance distribution of binding sites around transcription starting sites and functional distribution of binding sites in the genome were assessed using PAVIS (manticore)
Assembly: mm10
Supplementary files format and content: Narrow peaks table of TRa1 ChIP (which was made using the input files as a control files. Thus, this table is relative to the input files)

molecule: genomic DNA

growth_protocol: Adult male mice expressing a GS-tagged version of TRa1 specifically in GABAergic neurons of striatum, under standard housing conditions and diet.

extract_protocol:
Freshly dissected small pieces of striatum were crosslinked during 25min at room temperature under agitation in the crosslink solution (250mM disuccinimidyl glutarate, 50mM HEPES, 100mM NaCl, 1mM EDTA, 0.5mM EGTA). Then, 1% formaldehyde was added for 20 further minutes followed by 50mM glycine addition. The tissue was rinsed several times with PBS. Chromatin immunoprecipitation was then performed as previously described (Chatonnet et al., 2013).
Sequencing libraries were prepared from the immunoprecipitated fraction and the input fraction as control, using the Accel-NGS 2S Plus DNA library kits with single indexing (Swift Biosciences).

tag: cell type

value: GABAergic neurons

value: TRa1 GS-tagged

value: None - Euthyroid


title: ChIP_TRa_Striatum_adult_1


title: Input_Striatum_adult


title: 910: 10wk B6 female, Control limb, Metaphyseal Shell, 7d 4

city: Ithaca

first: Carolyn

last: Chlebek

state: NY

address: 110 Hoy Road

department: Biomedical Engineering

institute: Cornell University

data_processing:
Sequence reads were trimmed for adaptor sequence. 12bp were trimmed from the 5' end for quality assurance.
Trimmed sequence reads were mapped to mm10 using STAR (parameters- outFilterMismatchNmax: 2 - outFilterMultimapNmax: 1)
Fastqc was run for all files and only samples with high quality from both fastqc & RQN were included for analysis
Each sample contained over 1 million reads. Genes with less than 3 counts per million were not included for analysis.
Normalized gene counts were calculated in DESeq2 with Trimmed Mean of M-values correction
Assembly: mm10
Supplementary files format and content: .xlsx file with normalized gene counts and experimental conditions for each samle

source_name: Bone

extract_protocol:
The cortical bone was segmented into three sections: metaphyseal cortex, proximal diaphysis, and mid-diaphysis, resulting in six samples per mouse. All tissues were flash frozen in liquid nitrogen. Samples were pulverized and RNA  isolated using a phenol-chloroform extraction followed by the RNeasy kit (Qiagen).
RNA libraries were prepared for 3' mRNA-seq

treatment_protocol: Female 10-week-old female C57Bl/6J were subjected to in vivo mechanical loading of the left tibia (9N peak load at 4 Hz for 1200 cycles per day). Mice were euthanized by cervical dislocation at 1-hour (n=5), 3-hours (n=4), or 24-hours (n=4) following the completion of one bout of loading. To evaluate long term time points, mice received daily cyclic compressive loading for 7 consecutive days (n=4) and were euthanized 24 hours after the last loading bout. A final group received 5 consecutive days of loading with euthanasia on the eighth day following the first loading session

value: Bone

value: female

value: 10 weeks

value: Contralateral Control Limb


title: 896: 10wk B6 female, Control limb, Mid-Diaphysis, 7d 3


title: 908: 10wk B6 female, Loaded limb, Mid-Diaphysis, 7d 4

value: 9N Tibial loading


title: 912: 10wk B6 female, Control limb, Mid-Diaphysis, 7d 4


title: 911: 10wk B6 female, Control limb, Proximal Diaphysis, 7d 4


title: 895: 10wk B6 female, Control limb, Proximal Diaphysis, 7d 3


title: 907: 10wk B6 female, Loaded limb, Proximal Diaphysis, 7d 4


title: 906: 10wk B6 female, Loaded limb, Metaphyseal Shell, 7d 4


title: 891: 10wk B6 female, Loaded limb, Proximal Diaphysis, 7d 3


title: 892: 10wk B6 female, Loaded limb, Mid-Diaphysis, 7d 3


title: 634: 10wk B6 female, Control limb, Metaphyseal Shell, 7d 2


title: 636: 10wk B6 female, Control limb, Mid-Diaphysis, 7d 2


title: 635: 10wk B6 female, Control limb, Proximal Diaphysis, 7d 2


title: 890: 10wk B6 female, Loaded limb, Metaphyseal Shell, 7d 3


title: 632: 10wk B6 female, Loaded limb, Mid-Diaphysis, 7d 2


title: 628: 10wk B6 female, Control limb, Mid-Diaphysis, 7d 1


title: 5909KO-Day5

city: Shanghai

first: Yingchao

last: Wang

address: 145 Middle Shandong Road

country: China

institute: Shanghai Institute of Digestive Disease

data_processing:
The sequencing data were first assessed using FastQC for quality control.
all sequenced libraries were mapped to the mouse genome (UCSC mm10) using STAR RNA-seq aligner version 2.5
The reads distribution across the genome was assessed using bamutils (from ngsutils) version 0.5.9
Uniquely mapped sequencing reads were assigned to mm10 refGene genes using featureCounts (from subread) version 1.5.1
Differential expression analysis was performed using edgeR version 3.12.1
Assembly: mm10
Supplementary files format and content: Excel files include RPKM and Raw counts values for each Sample

source_name: intestinal organoid culcure

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen).The concentration and quality of total RNA samples was first assessed using Agilent 2100 Bioanalyzer. A RIN (RNA Integrity Number) of five or higher was required to pass the quality control.
Four hundred nanograms of RNA per sample were used to prepared dual-indexed strand-specific cDNA library using TruSeq RNA Access Library Prep Kit (Illumina).

value: intestinal organoid culcure

value: tamoxifen


title: 6180con-Day5


title: 6186KO-Day5


title: 5916con-Day5


title: 894: 10wk B6 female, Control limb, Metaphyseal Shell, 7d 3


title: 630: 10wk B6 female, Loaded limb, Metaphyseal Shell, 7d 2


title: 6181con-Day5


title: 631: 10wk B6 female, Loaded limb, Proximal Diaphysis, 7d 2


title: 6182KO-Day5


title: 626: 10wk B6 female, Control limb, Metaphyseal Shell, 7d 1


title: 627: 10wk B6 female, Control limb, Proximal Diaphysis, 7d 1


title: WT BMDMs,  IL-4 + rCPL1 rep #2

city: San Francisco

first: Eric

middle: V

last: Dang

address: 600 16th Street

institute: UCSF

description:
CPL1_IL4_2
EDHM05_RNAseq_Summary.csv

data_processing:
Sequence reads were mapped to GrCM38/mm10s using STAR
Read counts from aligned files were then generated using HTSeq and differentially expressed genes were determined using DESeq2
Assembly: mm10
Supplementary files format and content: CSV files include RPKM values for each Sample

source_name: Bone marrow

growth_protocol: BMDMS were generated from mouse bone marrow by culturing bone marrow cells in DMEM (10% FCS, HEPES, P/S, glutamine) containing 10% MCSF (from 3T3-MCSF feeder line supernantant) for 7 days in non-TC petri dishes. 3mL of 10% MCSF media was supplemented on day 4.

extract_protocol:
RNA was extracted using a Qiagen Rneasy Mini Plus Kit. Libraries were constructed using 1ug of total RNA.
RNA libraries were generated using a Quantseq 3'End mRNA Library Prep Kit (Lexogen) according to the manufactorer's instructions

treatment_protocol: 2 million BMDMs were seeded in TC-treated 6-well plates overnight. The next day, cells were stimulated with the indicated yeast/PAMPs for the indicated times

value: Bone marrow

value: Macrophage

value: wild type

value: Interleukin-4 10ng/ml + rCPL1 111nM

tag: timepoint

value: 24 hours


title: 623: 10wk B6 female, Loaded limb, Proximal Diaphysis, 7d 1


title: WT BMDMs,  IL-4 + rCPL1 rep #3

description:
CPL1_IL4_3
EDHM05_RNAseq_Summary.csv


title: 512: 10wk B6 female, Control limb, Mid-Diaphysis, 5d 5


title: 622: 10wk B6 female, Loaded limb, Metaphyseal Shell, 7d 1


title: 511: 10wk B6 female, Control limb, Proximal Diaphysis, 5d 5


title: WT BMDMs,  rCPL1 rep #2

description:
CPL1_2
EDHM05_RNAseq_Summary.csv

value: rCPL1 111nM


title: 510: 10wk B6 female, Control limb, Metaphyseal Shell, 5d 5


title: WT BMDMs,  rCPL1 rep #3

description:
CPL1_3
EDHM05_RNAseq_Summary.csv


title: WT BMDMs,  IL-4 + rCPL1 rep #1

description:
CPL1_IL4_1
EDHM05_RNAseq_Summary.csv


title: WT BMDMs,  rCPL1 rep #1

description:
CPL1_1
EDHM05_RNAseq_Summary.csv


title: WT BMDMs,  IL-4 rep #3

description:
IL4_3
EDHM05_RNAseq_Summary.csv

value: Interleukin-4 10ng/ml


title: 508: 10wk B6 female, Loaded limb, Mid-Diaphysis, 5d 5


title: 507: 10wk B6 female, Loaded limb, Proximal Diaphysis, 5d 5


title: WT BMDMs,  IL-4 rep #2

description:
IL4_2
EDHM05_RNAseq_Summary.csv


title: 506: 10wk B6 female, Loaded limb, Metaphyseal Shell, 5d 5


title: 624: 10wk B6 female, Loaded limb, Mid-Diaphysis, 7d 1


title: WT BMDMs,  PBS rep #2

description:
Nil_2
EDHM05_RNAseq_Summary.csv

value: PBS


title: 487: 10wk B6 female, Control limb, Proximal Diaphysis, 5d 4


title: WT BMDMs,  IL-4 rep #1

description:
IL4_1
EDHM05_RNAseq_Summary.csv


title: WT BMDMs,  PBS rep #3

description:
Nil_3
EDHM05_RNAseq_Summary.csv


title: 488: 10wk B6 female, Control limb, Mid-Diaphysis, 5d 4


title: WT BMDMs C. neoformans (CAP60ko) rep #3

description:
K99_CAP60_3_S36
EDHM02_Rawcounts.csv

value: C. neoformans (CAP60ko) MOI=3.0

value: 6 hours


title: 484: 10wk B6 female, Loaded limb, Mid-Diaphysis, 5d 4

value: Bone


title: 483: 10wk B6 female, Loaded limb, Proximal Diaphysis, 5d 4

value: female


title: WT BMDMs C. neoformans (WT) rep #3

description:
K99_WT_3_S33
EDHM02_Rawcounts.csv

value: C. neoformans (WT) MOI=3.0


title: WT BMDMs C. neoformans (CAP60ko) rep #1

description:
K99_CAP60_1_S34
EDHM02_Rawcounts.csv


title: 482: 10wk B6 female, Loaded limb, Metaphyseal Shell, 5d 4

value: 10 weeks


title: 143: 10wk B6 female, Control limb, Proximal Diaphysis, 5d 3

value: Contralateral Control Limb


title: 486: 10wk B6 female, Control limb, Metaphyseal Shell, 5d 4


title: WT BMDMs C. neoformans (WT) rep #1

description:
K99_WT_1_S31
EDHM02_Rawcounts.csv


title: WT BMDMs S. cerevisiae rep #3

description:
s288c_3_S39
EDHM02_Rawcounts.csv

value: S. cerevisiae MOI=3.0


title: WT BMDMs C. neoformans (CAP60ko) rep #2

description:
K99_CAP60_2_S35
EDHM02_Rawcounts.csv


title: WT BMDMs S. cerevisiae rep #1

description:
s288c_1_S37
EDHM02_Rawcounts.csv


title: 138: 10wk B6 female, Loaded limb, Metaphyseal Shell, 5d 3

value: 9N Tibial loading


title: 140: 10wk B6 female, Loaded limb, Mid-Diaphysis, 5d 3


title: 139: 10wk B6 female, Loaded limb, Proximal Diaphysis, 5d 3


title: 128: 10wk B6 female, Control limb, Mid-Diaphysis, 5d 2


title: WT BMDMs S. cerevisiae rep #2

description:
s288c_2_S38
EDHM02_Rawcounts.csv

value: Bone marrow


title: WT BMDMs Zymosan stim rep #3

description:
Zymo_3_S30
EDHM02_Rawcounts.csv

value: Macrophage

value: Zymosan 10ug/ml


title: WT BMDMs,  PBS rep #1

description:
Nil_1
EDHM05_RNAseq_Summary.csv

value: wild type


title: 127: 10wk B6 female, Control limb, Proximal Diaphysis, 5d 2


title: WT BMDMs Zymosan stim rep #2

description:
Zymo_2_S29
EDHM02_Rawcounts.csv


title: WT BMDMs, lipopolysaccharide stim rep #3

description:
LPS_3_S27
EDHM02_Rawcounts.csv

value: lipopolysaccharide 100ng/ml


title: 124: 10wk B6 female, Loaded limb, Mid-Diaphysis, 5d 2


title: 126: 10wk B6 female, Control limb, Metaphyseal Shell, 5d 2


title: WT BMDMs Zymosan stim rep #1

description:
Zymo_1_S28
EDHM02_Rawcounts.csv


title: WT BMDMs, lipopolysaccharide stim rep #2

description:
LPS_2_S26
EDHM02_Rawcounts.csv


title: WT BMDMs C. neoformans (WT) rep #2

description:
K99_WT_2_S32
EDHM02_Rawcounts.csv


title: 142: 10wk B6 female, Control limb, Metaphyseal Shell, 5d 3


title: WT BMDMs, lipopolysaccharide stim rep #1

description:
LPS_1_S25
EDHM02_Rawcounts.csv


title: WT BMDMs, PBS stim rep #3

description:
Nil_3_S24
EDHM02_Rawcounts.csv


title: 104: 10wk B6 female, Control limb, Mid-Diaphysis, 5d 1


title: 123: 10wk B6 female, Loaded limb, Proximal Diaphysis, 5d 2


title: 144: 10wk B6 female, Control limb, Mid-Diaphysis, 5d 3


title: 122: 10wk B6 female, Loaded limb, Metaphyseal Shell, 5d 2


title: WT BMDMs, PBS stim rep #2

description:
Nil_2_S23
EDHM02_Rawcounts.csv


title: 100: 10wk B6 female, Loaded limb, Mid-Diaphysis, 5d 1


title: 102: 10wk B6 female, Control limb, Metaphyseal Shell, 5d 1


title: 103: 10wk B6 female, Control limb, Proximal Diaphysis, 5d 1


title: Media stimulated cDCs donor 3

city: Farmington

first: Djamel

last: Nehar-Belaid

state: CONNECTICUT

address: 10 discovery drive

institute: THE JACKSON LABORATORY

data_processing:
trimmomatic v0.33
alignment using star v2.5.3a
quantification using RSEMv1.3.0
gencode.v25
Supplementary_files_format_and_content: Proccesed data contain the result of the processing steps using the tools described above

source_name: BLOOD

growth_protocol: Human PBMCs, used as source of cDCs, were isolated from leukopaks obtained from healthy adult volunteers (New York Blood Center) by Ficoll gradient centrifugation. Isolation of untouched cDCs was performed using immunomagnetic negative selection (EasySep human myeloid DC enrichment kit, StemCell Technologies). All cells were cultured in RPMI 1640 medium supplemented with 1% L-glutamine, 1% penicillin/streptomycin, 1% sodium pyruvate, 1% non-essential amino acids, and 10% heat-inactivated fetal bovine serum (RPMI complete medium).

extract_protocol:
Total RNA was isolated from activated cDCs using the Qiagen RNeasy Mini Kit (Qiagen) or Arcturus PicoPure (Life Technologies) kits following manufacturer’s protocols. During RNA isolation, DNase treatment was additionally performed using the RNase-free DNase set (Qiagen). RNA quality was checked using an Agilent 2100 Expert bioanalyzer (Agilent Technologies). RNA quality was reported as a score from 1 to 10, samples falling below threshold of 8.0 were omitted from the study.
RNA-seq libraries were prepared with KAPA mRNA HyperPrep kit (Roche) according to manufacturer’s instruction. Poly(A) mRNA was isolated from 60 ng total RNA using oligo(dT) magnetic beads and then fragmented at 85°C for 6 minutes, targeting 250-300 bp-range fragments. Fragmented RNA was reverse transcribed by incubating it for 10 minutes at 25°C followed by 15 minutes at 42°C and finally inactivated for 15 minutes at 70°C. This was followed by second strand synthesis at 16°C for 60 minutes. cDNA was purified using AMPure XP beads (Beckman-Coulter), then A-tailed and ligated with Illumina unique adapters (Illumina). Adapter-ligated cDNA was purified using AMPure XP beads and amplified by 10 cycles of PCR. The final libraries were cleaned up using AMPure XP beads and quantified using real-time qPCR (Thermo Fisher). The libraries were sequenced on Illumina HiSeq4000 platform generating paired end reads of 75bp.

treatment_protocol: cDCs (0.5 x 10^6 per condition) were incubated in 24-well plates for 24 hours in the absence or presence of  rASP-1 (5 µg/ml) . After stimulation, activated cDCs were harvested for downstream applications.

value: DENDRITIC CELLS

tag: stimulation

value: Media


title: rASP-1 stimulated cDCs donor 3


title: 88: 10wk B6 female, Control limb, Mid-Diaphysis, 24h 4


title: 98: 10wk B6 female, Loaded limb, Metaphyseal Shell, 5d 1


title: rASP-1 stimulated cDCs donor 2


title: 83: 10wk B6 female, Loaded limb, Proximal Diaphysis, 24h 4


title: Media stimulated cDCs donor 1


title: 86: 10wk B6 female, Control limb, Metaphyseal Shell, 24h 4


title: 87: 10wk B6 female, Control limb, Proximal Diaphysis, 24h 4


title: 84: 10wk B6 female, Loaded limb, Mid-Diaphysis, 24h 4


title: 82: 10wk B6 female, Loaded limb, Metaphyseal Shell, 24h 4


title: 64: 10wk B6 female, Control limb, Mid-Diaphysis, 24h 3


title: UCD115 E2

city: Aurora

first: Jessica

last: Finlay-Schultz

state: CO

department: Pathology

institute: University of Colorado Denver Anschutz Medical Campus

data_processing:
Generate UMIs for the sample
Convert UMI to a readable format
Normalize the data
Cluster the data
Generate UMAP for each cells in the clusters
Genome_build: GRCh38
Supplementary_files_format_and_content: txt; consists of raw counts of each gene

source_name: Breast tumor xenograft

growth_protocol: Xenografts were grown in NOD/SCID/Il2rgnull mice

extract_protocol:
Xenografts were dissociated using Accumax, depeleted for mouse cells, and submitted as live cells for sequencing. Cells were captured using the 10X Genomics Chromium system.
RNA libraries were prepared for sequencing using standard 10X Genomics Chromium system at the University of Colorado Denver Genomics and Microarray Core facility.
scRNA-Seq

treatment_protocol: Chronic E2 or no treatment upon transplant

tag: xenograft

value: estradiol


title: 62: 10wk B6 female, Control limb, Metaphyseal Shell, 24h 3


title: UCD46 placebo

value: placebo


title: rASP-1 stimulated cDCs donor 1


title: UCD18 placebo


title: UCD15 E2

data_processing:
Generate UMIs for the sample
Convert UMI to a readable format
Normalize the data
Cluster the data
Generate UMAP for each cells in the clusters
Genome_build: GRCh38
Supplementary_files_format_and_content: tsv; consists of raw counts of each genes

extract_protocol:
Xenografts were dissociated using Accumax, depeleted for mouse cells, and submitted as live cells for sequencing. Cells were captured using the 10X Genomics Chromium system.
RNA libraries were prepared for sequencing using standard 10X Genomics Chromium system at the University of Colorado Denver Genomics and Microarray Core facility.

treatment_protocol: Chronic E2 treatment upon transplant

value: Breast tumor xenograft


title: WT BMDMs, PBS stim rep #1

description:
Nil_1_S22
EDHM02_Rawcounts.csv

value: PBS

value: 6 hours


title: 99: 10wk B6 female, Loaded limb, Proximal Diaphysis, 5d 1

value: Bone

value: female


title: porcine Mo-DCs, Nano-11/poly(I:C), pig 3

city: WEST LAFAYETTE

first: Shaojun

last: Xie

state: Indiana

address: 3135 Decatur Street

institute: Purdue University

data_processing:
The quality of the sequence was assessed using the FastQC program.Using HISAT2, clean reads were mapped to the Sus scrofa reference genome. The featureCounts software was used to count the reads assigned to each gene.
The fragments per kilobase of transcripts per million mapped reads (FPKM) were determined to standardize gene expression levels for each gene.
The differential gene expression assessment was performed using the DESeq2 (Bioconductor) software. To decrease the false discovery rate (FDR), the resultant P-values were adjusted using the Benjamini-Hochberg procedure for multiple test correction.
DESeq2 was used to identify the differentially expressed genes (DEGs) using an FDR threshold of 0.05. The clusterProfile R package was used to conduct Gene Ontology (GO) and KEGG enrichment analysis for the study of DEGs induced by Nano-11 and Nano-11/poly(I:C) stimulated porcine Mo-DCs.
Assembly: Sscrofa10.2
Supplementary files format and content: Read count matrix in Excel file

organism: Sus scrofa

source_name: blood

growth_protocol: Porcine monocyte-derived DCs (Mo-DCs) were maintained and generated from the peripheral blood of 8-10-week-old cross-bred (Yorkshire X Landrace) pigs in complete RPMI-1640 (25 mM HEPES, 2 mM L-glutamine, 100 U/ml penicillin, 100 μg/ml streptomycin, 0.25 μg/ml amphotericin B, and 50 μM 2-ME) containing 5% FBS and supplemented with 25 ng/ml swine GM-CSF and 10 ng/ml swine IL-4 at 37°C with 5% CO2.

extract_protocol:
RNA was isolated from porcine Mo-DCs using a RNeasy Plus Kit (Qiagen) and the RNA quality was evaluated using an RNA screentape test (Agilent). The RNA library preparations used approximately 0.8 or 1 μg of RNA per sample as input material.
The sequencing libraries were constructed using the NEBNext Ultra RNA Library Prep Kit for Illumina and assembled in accordance with the manufacturer's instructions.

treatment_protocol: Porcine Mo-DCs from three pigs were divided into three separate treatment groups: Nano-11, Nano-11/poly(I:C), and untreated as the control. Treatment was administered in complete RPMI-1640 containing 5% FBS at 37°C with 5% CO2 for three hours.

value: blood

value: dendritic cell

value: WT


title: porcine Mo-DCs, Nano-11, pig 3


title: 60: 10wk B6 female, Loaded limb, Mid-Diaphysis, 24h 3

value: 10 weeks

value: 9N Tibial loading


title: porcine Mo-DCs, Nano-11/poly(I:C), pig 2


title: Media stimulated cDCs donor 2


title: 59: 10wk B6 female, Loaded limb, Proximal Diaphysis, 24h 3


title: porcine Mo-DCs, Nano-11, pig 2


title: 63: 10wk B6 female, Control limb, Proximal Diaphysis, 24h 3

value: Contralateral Control Limb


title: 58: 10wk B6 female, Loaded limb, Metaphyseal Shell, 24h 3


title: 55: 10wk B6 female, Control limb, Proximal Diaphysis, 24h 2


title: 56: 10wk B6 female, Control limb, Mid-Diaphysis, 24h 2


title: 52: 10wk B6 female, Loaded limb, Mid-Diaphysis, 24h 2


title: porcine Mo-DCs, untreated, pig 2


title: porcine Mo-DCs, Nano-11/poly(I:C), pig 1


title: porcine Mo-DCs, Nano-11, pig 1


title: porcine Mo-DCs, untreated, pig 3


title: 54: 10wk B6 female, Control limb, Metaphyseal Shell, 24h 2


title: porcine Mo-DCs, untreated, pig 1


title: 50: 10wk B6 female, Loaded limb, Metaphyseal Shell, 24h 2


title: 32: 10wk B6 female, Control limb, Mid-Diaphysis, 24h 1


title: 31: 10wk B6 female, Control limb, Proximal Diaphysis, 24h 1


title: Acinar191 (RNA-seq)

city: Heidelberg

first: Ana

last: Martin-Villalba

address: Im Neuenheimer Feld 280

department: Molecular Neurobiology

country: Germany

institute: German Cancer Research Center

description:
single-cell RNA-seq
RNA_readcount_matrix.csv.gz
RNA_UMIcount_matrix.csv.gz

library_source: transcriptomic single cell

data_processing:
mapping with STAR via zUMIs
transcript quantification with featureCounts via zUMIs
Assembly: GRCm38 (mm10)
Supplementary files format and content: Single-cell RNA-seq count matrices (UMI counts and read counts) in csv (comma-separated values) format. Values are not normalized, decimals are due to distribution of multimapping reads.

source_name: exocrine pancreas

extract_protocol:
Primary pancreatic acinar cells were isolated by digestive dissociation of pancreatic tissue and subsequent density gradient centrifugation. After cultivation as 3D matrigel embedded organoids for 9 days, the cells were harvested and subjected to the scNMT-seq protocol. For more information on the generation of pancreatic organoids, see the following papers (Wollny et al., 2016; Krieger et al., 2021).
For profiling the transcriptome and epigenome of single cells we developed and implemented a miniaturized and higher throughput version of the scNMT-seq protocol (Clark et al., 2018). On this new version, the Smart-seq3 (Hagemann-Jensen et al., 2020) method and specific normalization steps were implemented. A detailed version of the protocol is described in Cerrizuela et al., (2022). The samples listed here represent the transcriptomic portion of this multi-omic data set, i.e. transcript UMI counts and read counts assessed with single-cell RNA-seq.
Single-cell RNA-seq (Smart-seq3)

value: exocrine pancreas

value: acinar cell

value: wild type

tag: strain

tag: culture condition

value: 9 days as 3D organoids


title: Acinar192 (RNA-seq)


title: Acinar190 (RNA-seq)


title: Acinar188 (RNA-seq)


title: 28: 10wk B6 female, Loaded limb, Mid-Diaphysis, 24h 1


title: 26: 10wk B6 female, Loaded limb, Metaphyseal Shell, 24h 1


title: 80: 10wk B6 female, Control limb, Mid-Diaphysis, 3h 4


title: Acinar187 (RNA-seq)


title: Acinar189 (RNA-seq)


title: 78: 10wk B6 female, Control limb, Metaphyseal Shell, 3h 4


title: Acinar184 (RNA-seq)


title: Acinar186 (RNA-seq)


title: Acinar183 (RNA-seq)


title: Acinar182 (RNA-seq)


title: 51: 10wk B6 female, Loaded limb, Proximal Diaphysis, 24h 2


title: 76: 10wk B6 female, Loaded limb, Mid-Diaphysis, 3h 4


title: 75: 10wk B6 female, Loaded limb, Proximal Diaphysis, 3h 4


title: 74: 10wk B6 female, Loaded limb, Metaphyseal Shell, 3h 4


title: 72: 10wk B6 female, Control limb, Mid-Diaphysis, 3h 3


title: Acinar179 (RNA-seq)


title: Acinar180 (RNA-seq)


title: 71: 10wk B6 female, Control limb, Proximal Diaphysis, 3h 3


title: 30: 10wk B6 female, Control limb, Metaphyseal Shell, 24h 1


title: Acinar178 (RNA-seq)


title: Acinar177 (RNA-seq)


title: 27: 10wk B6 female, Loaded limb, Proximal Diaphysis, 24h 1


title: Acinar185 (RNA-seq)


title: Acinar176 (RNA-seq)


title: Acinar174 (RNA-seq)


title: 66: 10wk B6 female, Loaded limb, Metaphyseal Shell, 3h 3


title: 68: 10wk B6 female, Loaded limb, Mid-Diaphysis, 3h 3


title: 70: 10wk B6 female, Control limb, Metaphyseal Shell, 3h 3


title: 79: 10wk B6 female, Control limb, Proximal Diaphysis, 3h 4


title: 40: 10wk B6 female, Control limb, Mid-Diaphysis, 3h 2


title: Acinar175 (RNA-seq)


title: Acinar173 (RNA-seq)


title: Acinar172 (RNA-seq)


title: 67: 10wk B6 female, Loaded limb, Proximal Diaphysis, 3h 3


title: 39: 10wk B6 female, Control limb, Proximal Diaphysis, 3h 2


title: Acinar181 (RNA-seq)


title: 38: 10wk B6 female, Control limb, Metaphyseal Shell, 3h 2


title: 36: 10wk B6 female, Loaded limb, Mid-Diaphysis, 3h 2


title: Acinar171 (RNA-seq)


title: 35: 10wk B6 female, Loaded limb, Proximal Diaphysis, 3h 2


title: Acinar169 (RNA-seq)


title: Acinar170 (RNA-seq)


title: Acinar168 (RNA-seq)


title: Acinar167 (RNA-seq)


title: 6: 10wk B6 female, Control limb, Metaphyseal Shell, 3h 1


title: Acinar166 (RNA-seq)


title: 7: 10wk B6 female, Control limb, Proximal Diaphysis, 3h 1


title: 3: 10wk B6 female, Loaded limb, Proximal Diaphysis, 3h 1


title: Acinar165 (RNA-seq)


title: Acinar164 (RNA-seq)


title: Acinar163 (RNA-seq)


title: 4: 10wk B6 female, Loaded limb, Mid-Diaphysis, 3h 1


title: Acinar162 (RNA-seq)


title: 572: 10wk B6 female, Control limb, Mid-Diaphysis, 1h 5


title: Acinar161 (RNA-seq)


title: 570: 10wk B6 female, Control limb, Metaphyseal Shell, 1h 5


title: Acinar160 (RNA-seq)


title: Acinar159 (RNA-seq)


title: 571: 10wk B6 female, Control limb, Proximal Diaphysis, 1h 5


title: Acinar158 (RNA-seq)


title: 2: 10wk B6 female, Loaded limb, Metaphyseal Shell, 3h 1


title: 567: 10wk B6 female, Loaded limb, Proximal Diaphysis, 1h 5


title: 34: 10wk B6 female, Loaded limb, Metaphyseal Shell, 3h 2


title: 568: 10wk B6 female, Loaded limb, Mid-Diaphysis, 1h 5


title: 566: 10wk B6 female, Loaded limb, Metaphyseal Shell, 1h 5


title: 8: 10wk B6 female, Control limb, Mid-Diaphysis, 3h 1


title: Acinar155 (RNA-seq)


title: 548: 10wk B6 female, Control limb, Mid-Diaphysis, 1h 4


title: Acinar156 (RNA-seq)


title: Acinar154 (RNA-seq)


title: 546: 10wk B6 female, Control limb, Metaphyseal Shell, 1h 4


title: Acinar153 (RNA-seq)


title: 547: 10wk B6 female, Control limb, Proximal Diaphysis, 1h 4


title: 543: 10wk B6 female, Loaded limb, Proximal Diaphysis, 1h 4


title: 544: 10wk B6 female, Loaded limb, Mid-Diaphysis, 1h 4


title: 455: 10wk B6 female, Control limb, Proximal Diaphysis, 1h 3


title: Acinar148 (RNA-seq)


title: 454: 10wk B6 female, Control limb, Metaphyseal Shell, 1h 3


title: Acinar151 (RNA-seq)


title: Acinar152 (RNA-seq)


title: Acinar150 (RNA-seq)


title: 542: 10wk B6 female, Loaded limb, Metaphyseal Shell, 1h 4


title: Acinar157 (RNA-seq)


title: 456: 10wk B6 female, Control limb, Mid-Diaphysis, 1h 3


title: Acinar147 (RNA-seq)


title: Acinar146 (RNA-seq)


title: 450: 10wk B6 female, Loaded limb, Metaphyseal Shell, 1h 3


title: Acinar145 (RNA-seq)


title: Acinar143 (RNA-seq)


title: Acinar142 (RNA-seq)


title: Acinar149 (RNA-seq)


title: 446: 10wk B6 female, Control limb, Metaphyseal Shell, 1h 2


title: 448: 10wk B6 female, Control limb, Mid-Diaphysis, 1h 2


title: Acinar141 (RNA-seq)


title: 447: 10wk B6 female, Control limb, Proximal Diaphysis, 1h 2


title: Acinar139 (RNA-seq)


title: 443: 10wk B6 female, Loaded limb, Proximal Diaphysis, 1h 2


title: 442: 10wk B6 female, Loaded limb, Metaphyseal Shell, 1h 2


title: 451: 10wk B6 female, Loaded limb, Proximal Diaphysis, 1h 3


title: 452: 10wk B6 female, Loaded limb, Mid-Diaphysis, 1h 3


title: Acinar138 (RNA-seq)


title: Acinar137 (RNA-seq)


title: 332: 10wk B6 female, Control limb, Mid-Diaphysis, 1h 1


title: 331: 10wk B6 female, Control limb, Proximal Diaphysis, 1h 1


title: Acinar136 (RNA-seq)


title: Acinar144 (RNA-seq)


title: 328: 10wk B6 female, Loaded limb, Mid-Diaphysis, 1h 1


title: 330: 10wk B6 female, Control limb, Metaphyseal Shell, 1h 1


title: Acinar134 (RNA-seq)


title: 327: 10wk B6 female, Loaded limb, Proximal Diaphysis, 1h 1


title: Acinar133 (RNA-seq)


title: Acinar140 (RNA-seq)


title: 326: 10wk B6 female, Loaded limb, Metaphyseal Shell, 1h 1


title: Acinar132 (RNA-seq)


title: Acinar131 (RNA-seq)


title: 444: 10wk B6 female, Loaded limb, Mid-Diaphysis, 1h 2


title: Acinar129 (RNA-seq)


title: Acinar130 (RNA-seq)


title: sci-RNA-seq3 with ETiX mouse embryoids and natural mouse embryos [NextSeq1_PA-12H_S96]

city: Seattle

first: Chengxiang

last: Qiu

state: WA

address: William H. Foege Hall, 3720 15th Ave NE

department: Genome Sciences

institute: University of Washington

description: sci-RNA-seq3 library

data_processing:
Base calls were converted to fastq format using Illumina’s bcl2fastq/v2.20 and demultiplexed based on PCR i5 and i7 barcodes using maximum likelihood demultiplexing package deML (Renaud et al. 2015) with default settings. Downstream sequence processing and single cell digital expression matrix generation were similar to sci-RNA-seq (Cao et al. 2017) except that RT index was combined with hairpin adaptor index, and thus the mapped reads were split into constituent cellular indices by demultiplexing reads using both the RT index and ligation index (Levenshtein edit distance (ED) < 2, including insertions and deletions).
Briefly, demultiplexed reads were filtered based on RT index and ligation index (ED < 2, including insertions and deletions) and adaptor-clipped using trim_galore/v0.6.5 with default settings. Trimmed reads were mapped to the mouse reference genome (mm10) for mouse embryo nuclei, using STAR/v2.6.1d (Dobin et al. 2013) with default settings and gene annotations (GENCODE VM12 for mouse). Uniquely mapping reads were extracted, and duplicates were removed using the unique molecular identifier (UMI) sequence (ED < 2, including insertions and deletions), reverse transcription (RT) index, hairpin ligation adaptor index and read 2 end-coordinate (i.e. reads with UMI sequence less than 2 edit distance, RT index, ligation adaptor index and tagmentation site were considered duplicates).
Finally, mapped reads were split into constituent cellular indices by further demultiplexing reads using the RT index and ligation hairpin (ED < 2, including insertions and deletions). To generate digital expression matrices, we calculated the number of strand-specific UMIs for each cell mapping to the exonic and intronic regions of each gene with python/v2.7.13 HTseq package (Anders, Pyl, and Huber 2015). For multi-mapped reads, reads were assigned to the closest gene, except in cases where another intersected gene fell within 100 bp to the end of the closest gene, in which case the read was discarded. For most analyses we included both expected-strand intronic and exonic UMIs in per-gene single-cell expression matrices.
Assembly: mm10
Supplementary files format and content: Processed data files include a cell annotation csv  file, gene annotation csv file, and a gene count sparse matrix file

molecule: polyA RNA

extract_protocol: We performed a simplified version of sci-RNA-seq3, further optimized for “tiny” samples (Martin et al. 2021). Briefly, to each tube, 100ul of a hypotonic, PBS-based lysis buffer was added with DEPC as an RNase inhibitor. The resulting nuclei were then fixed with 4 volumes of a mix of methanol and dithiobis (succinimidyl propionate) (DSP). After rehydrating and washing the nuclei carefully in a sucrose/PBS/triton/MgCl2 buffer (SPBSTM), the nuclei were distributed to two 96-well plates for reverse transcription, allocating 8 wells per embryo. After reverse transcription, nuclei were pooled, washed in SPBSTM and redistributed to a fresh plate for ligation of the second index primer with T4 DNA ligase. Nuclei were then again pooled, washed, and redistributed to three final plates for second strand synthesis, extraction, tagmentation, and PCR to add the third index plus a plate index. Products were pooled by PCR plate, size-selected and sequenced on two Illumina NextSeq runs (termed “NextSeq-1" and “NextSeq-2”).

tag: developmental stage

value: ETiX mouse embryoids (Day6 and Day8) and natural mouse embryos (E7.5, E8, E8.5, E8.75. and E9)


title: Acinar127 (RNA-seq)


title: sci-RNA-seq3 with ETiX mouse embryoids and natural mouse embryos [NextSeq1_PA-12G_S95]

description: sci-RNA-seq3 library


title: sci-RNA-seq3 with ETiX mouse embryoids and natural mouse embryos [NextSeq1_PA-12F_S94]

description: sci-RNA-seq3 library


title: Acinar128 (RNA-seq)


title: Acinar135 (RNA-seq)


title: iTreg cells, vehicle Control, Day1

city: Seoul

first: Gap Ryol

last: Lee

address: 35 Baekbeom-ro, Mapo-gu

department: Department of Life Science

country: South Korea

institute: Sogang University

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence(using fastx_trimmer), then mapped to mm10 (UCSC) whole genome using Bowtie2
Read count extraction using bedtools.
Assembly: mm10
Supplementary files format and content: tab-delimited text files include read count values for each Sample

source_name: T lymphocyte

extract_protocol:
RNA was harvested using Trizol reagent (Invitrogen). 500 ng of total RNA was used for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using LEXOGEN Quant-Seq Library Prep Kit (Cat#001.24) standard protocols.

value: T lymphocyte

value: DMSO


title: Acinar126 (RNA-seq)


title: sci-RNA-seq3 with ETiX mouse embryoids and natural mouse embryos [NextSeq1_PA-12E_S93]

description: sci-RNA-seq3 library


title: iTreg cells, Tubastatin A, Day1

value: Tubastatin A


title: sci-RNA-seq3 with ETiX mouse embryoids and natural mouse embryos [NextSeq1_PA-12C_S91]

description: sci-RNA-seq3 library


title: sci-RNA-seq3 with ETiX mouse embryoids and natural mouse embryos [NextSeq1_PA-12D_S92]

description: sci-RNA-seq3 library


title: Acinar123 (RNA-seq)


title: Acinar124 (RNA-seq)


title: sci-RNA-seq3 with ETiX mouse embryoids and natural mouse embryos [NextSeq1_PA-11H_S88]

description: sci-RNA-seq3 library


title: sci-RNA-seq3 with ETiX mouse embryoids and natural mouse embryos [NextSeq1_PA-11G_S87]

description: sci-RNA-seq3 library


title: sci-RNA-seq3 with ETiX mouse embryoids and natural mouse embryos [NextSeq1_PA-12A_S89]

description: sci-RNA-seq3 library


title: Acinar122 (RNA-seq)


title: Acinar120 (RNA-seq)


title: sci-RNA-seq3 with ETiX mouse embryoids and natural mouse embryos [NextSeq1_PA-11F_S86]

description: sci-RNA-seq3 library


title: Acinar121 (RNA-seq)


title: Acinar118 (RNA-seq)


title: sci-RNA-seq3 with ETiX mouse embryoids and natural mouse embryos [NextSeq1_PA-11E_S85]

description: sci-RNA-seq3 library


title: Acinar117 (RNA-seq)


title: sci-RNA-seq3 with ETiX mouse embryoids and natural mouse embryos [NextSeq1_PA-11C_S83]

description: sci-RNA-seq3 library


title: Acinar116 (RNA-seq)


title: sci-RNA-seq3 with ETiX mouse embryoids and natural mouse embryos [NextSeq1_PA-12B_S90]

description: sci-RNA-seq3 library


title: Acinar115 (RNA-seq)


title: Acinar125 (RNA-seq)


title: sci-RNA-seq3 with ETiX mouse embryoids and natural mouse embryos [NextSeq1_PA-11B_S82]

description: sci-RNA-seq3 library


title: sci-RNA-seq3 with ETiX mouse embryoids and natural mouse embryos [NextSeq1_PA-11A_S81]

description: sci-RNA-seq3 library


title: Acinar114 (RNA-seq)


title: sci-RNA-seq3 with ETiX mouse embryoids and natural mouse embryos [NextSeq1_PA-10H_S80]

description: sci-RNA-seq3 library


title: Acinar111 (RNA-seq)


title: Acinar113 (RNA-seq)


title: sci-RNA-seq3 with ETiX mouse embryoids and natural mouse embryos [NextSeq1_PA-10F_S78]

description: sci-RNA-seq3 library


title: sci-RNA-seq3 with ETiX mouse embryoids and natural mouse embryos [NextSeq1_PA-10G_S79]

description: sci-RNA-seq3 library


title: Acinar112 (RNA-seq)


title: 4-NGS2016020501P115

city: Caparica

first: Paulo

middle: Jorge Couto

last: Almeida

address: Monte da Caparica

department: NGS

country: Portugal

institute: STAB VIDA

data_processing:
CLC Genomics Workbench 9.0.1.
Sequence reads were trimmed for adaptor sequence/low-quality sequence using CLC genomic benchwork (parameter- Quality limit: 0.01)
Trimmed sequence reads were mapped to GRCz10 using CLC genomic benchwork (parameters- mismath cost: 2 insertion cost: 3 deletion cost: 3 length fraction: 0.95 similarity fraction: 0.95)
Read count extraction and normalization were performed using CLC genomic benchwork
Assembly: GRCz10
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

organism: Danio rerio

source_name: Danio Rerio caudal fin regenerated tissue Control

extract_protocol:
The regenerated tissue was homogenized and a phenolic extraction was performed (as previously described in Chomczynski and Sacchi, 2006)
Illumina TruSeq Stranded mRNA Library Preparation Kit

value: caudal fin regenerated tissue

value: Control


title: Acinar110 (RNA-seq)


title: sci-RNA-seq3 with ETiX mouse embryoids and natural mouse embryos [NextSeq1_PA-10E_S77]

description: sci-RNA-seq3 library


title: 5-NGS2016020501P116


title: sci-RNA-seq3 with ETiX mouse embryoids and natural mouse embryos [NextSeq1_PA-11D_S84]

description: sci-RNA-seq3 library


title: WT_mRNA_rep3

city: Hefei

first: Ge

last: Shan

state: Anhui

address: 443 Huangshan Road

department: School of Life Sciences

institute: University of Science and Technology of China

data_processing:
The Hisat2 and feature counts software were used to map clean reads to reference genome (mm10) and calculate the gene expression level which was normalized to FPKM.
the find_circ software (v 1.2) was utilized to predict the junction of circRNAs.
Genome_build: mm10
Supplementary_files_format_and_content: raw counts
Supplementary_files_format_and_content: circRNA junction counts

source_name: NIH/3T3 cell

extract_protocol:
The peripheral blood samples and TRizol reagent(Invitrogen, USA) are evenly mixed in a ratio of 1:3, total of 12 ml. Total RNA was extracted by using Trizol reagent according to the manufacturer’s instructions.
The RNA samples were utilized to construct whole transcriptome library by the TruSeq Ribo Profile Library Prep Kit (Illumina, United States), following manufacturer’s instructions. For circRNA-sequencing, the RNase R digestion (10U, 1.5h) was conducted before library construction to enrich circRNAs.  The library products with 300-500 length were purified and quantified. These libraries were utilized to 150 nt paired-end sequencing with an Illumina Nova seq 6000 system (Novogene, China). Each library was generated a depth of ~8G basepairs

tag: cell line

value: NIH/3T3 cell (from ATCC)

value: Wild Type

tag: sequencing type

value: mRNA seq


title: Acinar119 (RNA-seq)


title: 3-NGS2016020501P114

source_name: Danio Rerio caudal fin regenerated tissue 24h


title: 2-NGS2016020501P113


title: 1-NGS2016020501P112


title: Acinar109 (RNA-seq)


title: sci-RNA-seq3 with ETiX mouse embryoids and natural mouse embryos [NextSeq1_PA-10D_S76]

description: sci-RNA-seq3 library


title: Acinar108 (RNA-seq)


title: WT_mRNA_rep1


title: KO_mRNA_rep3

value: XPO4 knockout


title: WT_mRNA_rep2


title: sci-RNA-seq3 with ETiX mouse embryoids and natural mouse embryos [NextSeq1_PA-10A_S73]

description: sci-RNA-seq3 library


title: sci-RNA-seq3 with ETiX mouse embryoids and natural mouse embryos [NextSeq1_PA-10C_S75]

description: sci-RNA-seq3 library


title: Acinar106 (RNA-seq)


title: sci-RNA-seq3 with ETiX mouse embryoids and natural mouse embryos [NextSeq1_PA-10B_S74]

description: sci-RNA-seq3 library


title: sci-RNA-seq3 with ETiX mouse embryoids and natural mouse embryos [NextSeq1_PA-09H_S72]

description: sci-RNA-seq3 library


title: Acinar107 (RNA-seq)


title: Acinar105 (RNA-seq)


title: sci-RNA-seq3 with ETiX mouse embryoids and natural mouse embryos [NextSeq1_PA-09G_S71]

description: sci-RNA-seq3 library


title: WT_nuc_circ_rep2

value: circRNA seq


title: WT_cyto_circ_rep2


title: KO_mRNA_rep1


title: WT_nuc_circ_rep1


title: WT_cyto_circ_rep1


title: sci-RNA-seq3 with ETiX mouse embryoids and natural mouse embryos [NextSeq1_PA-09F_S70]

description: sci-RNA-seq3 library


title: WT_whole_cell_circ_rep2


title: WT_whole_cell_circ_rep1


title: Acinar104 (RNA-seq)


title: sci-RNA-seq3 with ETiX mouse embryoids and natural mouse embryos [NextSeq1_PA-09E_S69]

description: sci-RNA-seq3 library


title: Acinar103 (RNA-seq)


title: KO_nuc_circ_rep2


title: KO_cyto_circ_rep2


title: Acinar102 (RNA-seq)


title: KO_nuc_circ_rep1


title: KO_mRNA_rep2


title: sci-RNA-seq3 with ETiX mouse embryoids and natural mouse embryos [NextSeq1_PA-09D_S68]

description: sci-RNA-seq3 library


title: Acinar101 (RNA-seq)


title: KO_cyto_circ_rep1


title: sci-RNA-seq3 with ETiX mouse embryoids and natural mouse embryos [NextSeq1_PA-09C_S67]

description: sci-RNA-seq3 library


title: Acinar100 (RNA-seq)


title: WT_IP_RNaseR+_rep2

data_processing:
Library strategy: DRIP-seq
DRIP-seq reads were aligned to the mm10 genome assembly using Bowties2 default settings
All duplicates, unmapped reads, reads with more than three mismatches and non-uniquely mapped reads were removed by using samtools version 1.1.
MACS2 was used to identify peaks in individual replicates (-q 0.001).
Genome_build: mm10
Supplementary_files_format_and_content: peak files

extract_protocol:
Totally 10^7 cells were trypsinized and centrifuged for the cell pellets. Cells were resuspended by 4 ml TE buffer with 0.5% SDS and 0.1 mg/ml proteinase K, incubated in constant temperature shaker at 37℃ for 16 h. Add 1/4 volume 5 M KAc, mix and place the tube on ice 10 min. Then the DNA was extracted by phenol: chloroform: isoamyl alcohol (25: 24: 1). Precipitate the supernatant by adding 1 volume isopropyl alcohol, 30 min at room temperature, and washed by 1 ml 70% ethanol. Dry the pellet and resuspend by 200 μl ddH2O. A cocktail of restrict enzymes (MseI, DdeI, AluI, MboI; NEB) was used for gDNA digestion in 200 μl system, incubated at 37°C overnight. Fragmented DNA was purified and quantified by Qubit 3.0 (Invitrogen). Mix 1.8 µg DNA with 0.2 µg E. coli DNA (for normalization) in 500 μl 1×TE. For RNase R treated group,  10 U RNase R (Epicentre) incubated at 37℃ for 1.5 h was used to remove linear RNA from DNA Fragment. For control group, the identical amount of reaction buffer was add to DNA Fragment incubated at 37℃ for 1.5 h. Take out 50 μl as Input, the rest 450 μl DNA was immunoprecipitated overnight at 4°C with 1× DRIP binding buffer (10 mM NaPO4 pH 7.0, 140 mM NaCl, 0.05% Triton X-100) and 10 µg S9.6 antibody (ATCC, HB-8730) at 500 μl system. Add 50 µl Protein G Dynabeads (Invitrogen, 10004D) and incubated for 4 h, then wash the beads by 1× DRIP binding buffer for 4 times at room temperature. Add 250 µl elution buffer (50 mM Tris pH 8.0, 10 mM EDTA, 0.5% SDS) and 5 U Proteinase K to the bead-antibody complexes, and incubated for 60 min in an Eppendorf ThermoMixer at 55°C.
DNA from DRIP was purified and subjected to library construction using Accel-NGS® 1S Plus DNA Library Kit (Swift Biosciences). These libraries were utilized to 150 nt paired-end sequencing with an Illumina Nova 6000 PE150 system (Genewiz, China). Each library was generated from 70 to 121 million reads and then adapters were removed with cutadapt software to obtain cleandata.

tag: drip antibody

value: S9.6 antibody (ATCC, HB-8730)

value: Rnase R(Epicentre)


title: Acinar99 (RNA-seq)

value: exocrine pancreas


title: sci-RNA-seq3 with ETiX mouse embryoids and natural mouse embryos [NextSeq1_PA-09B_S66]

description: sci-RNA-seq3 library


title: KO_whole_cell_circ_rep2


title: WT_IP_RNaseR-_rep2

value: S9.6 antibody (ATCC, HB-8731)


title: WT_IP_RNaseR+_rep1


title: WT_input_RNaseR+_rep1


title: Acinar98 (RNA-seq)

value: acinar cell

value: wild type


title: WT_input_RNaseR+_rep2


title: sci-RNA-seq3 with ETiX mouse embryoids and natural mouse embryos [NextSeq1_PA-09A_S65]

description: sci-RNA-seq3 library

value: ETiX mouse embryoids (Day6 and Day8) and natural mouse embryos (E7.5, E8, E8.5, E8.75. and E9)


title: WT_input_RNaseR-_rep2


title: WT_IP_RNaseR-_rep1


title: sci-RNA-seq3 with ETiX mouse embryoids and natural mouse embryos [NextSeq1_PA-08H_S64]

description: sci-RNA-seq3 library


title: Acinar97 (RNA-seq)

value: 9 days as 3D organoids


title: sci-RNA-seq3 with ETiX mouse embryoids and natural mouse embryos [NextSeq1_PA-08G_S63]

description: sci-RNA-seq3 library


title: Acinar96 (RNA-seq)


title: WT_input_RNaseR-_rep1


title: sci-RNA-seq3 with ETiX mouse embryoids and natural mouse embryos [NextSeq1_PA-08F_S62]

description: sci-RNA-seq3 library


title: KO_IP_RNaseR+_rep2

value: S9.6 antibody (ATCC, HB-8733)


title: KO_IP_RNaseR+_rep1

value: S9.6 antibody (ATCC, HB-8732)


title: Acinar95 (RNA-seq)


title: KO_IP_RNaseR-_rep2


title: Acinar94 (RNA-seq)


title: KO_whole_cell_circ_rep1


title: KO_input_RNaseR+_rep2


title: KO_input_RNaseR-_rep2


title: KO_input_RNaseR+_rep1


title: Acinar93 (RNA-seq)


title: Acinar92 (RNA-seq)


title: KO_input_RNaseR-_rep1


title: sci-RNA-seq3 with ETiX mouse embryoids and natural mouse embryos [NextSeq1_PA-08C_S59]

description: sci-RNA-seq3 library


title: sci-RNA-seq3 with ETiX mouse embryoids and natural mouse embryos [NextSeq1_PA-08B_S58]

description: sci-RNA-seq3 library


title: Acinar90 (RNA-seq)


title: sci-RNA-seq3 with ETiX mouse embryoids and natural mouse embryos [NextSeq1_PA-08D_S60]

description: sci-RNA-seq3 library


title: Acinar91 (RNA-seq)


title: sci-RNA-seq3 with ETiX mouse embryoids and natural mouse embryos [NextSeq1_PA-07H_S56]

description: sci-RNA-seq3 library


title: Acinar88 (RNA-seq)


title: sci-RNA-seq3 with ETiX mouse embryoids and natural mouse embryos [NextSeq1_PA-07F_S54]

description: sci-RNA-seq3 library


title: Acinar87 (RNA-seq)


title: sci-RNA-seq3 with ETiX mouse embryoids and natural mouse embryos [NextSeq1_PA-08E_S61]

description: sci-RNA-seq3 library


title: KO_IP_RNaseR-_rep1


title: Acinar89 (RNA-seq)


title: sci-RNA-seq3 with ETiX mouse embryoids and natural mouse embryos [NextSeq1_PA-07E_S53]

description: sci-RNA-seq3 library


title: sci-RNA-seq3 with ETiX mouse embryoids and natural mouse embryos [NextSeq1_PA-08A_S57]

description: sci-RNA-seq3 library


title: Acinar85 (RNA-seq)


title: sci-RNA-seq3 with ETiX mouse embryoids and natural mouse embryos [NextSeq1_PA-07C_S51]

description: sci-RNA-seq3 library


title: Acinar86 (RNA-seq)


title: sci-RNA-seq3 with ETiX mouse embryoids and natural mouse embryos [NextSeq1_PA-07G_S55]

description: sci-RNA-seq3 library


title: sci-RNA-seq3 with ETiX mouse embryoids and natural mouse embryos [NextSeq1_PA-07D_S52]

description: sci-RNA-seq3 library


title: Acinar83 (RNA-seq)


title: Acinar84 (RNA-seq)


title: d30_rep2

city: seattle

first: xueqiu

last: lin

state: wa

address: 1100 Fairview Ave N

institute: FRED HUTCHINSON CANCER CENTER

data_processing:
We calculated the count matrix by exact match for the first 8bp of both ends of each paired end reads. We ensured the high reproducibility of the multiplexed CRISPRi screening by calculating counts between replicates of the same condition (Pearson correlation coefficient R = 0.968 for the day 0 (D0) sample and 0.985 for the day 30 (D30) sample). To obtain sufficient representative reads for the downstream calculation, counts of sgRNA pairs were first filtered by requiring all paired constructors with at least 30 reads in D0.
Genome_build: hg19
Supplementary_files_format_and_content:  Mapping_CountTable.xlsx file: sequenced pairwise sgRNA counts mapped to the sgRNA library at different time points for two biological replicates

source_name: dCas9-KRAB expressing K562 cell line

extract_protocol: We extracted genomic DNA from both the reference and final cell populations using the QIAamp DNA Blood Maxi kit (Qiagen) according to the manufacturer's instructions. We amplified sgRNAs integrations from 500 μg genomic DNA by PCR with indexed sgRNA sequencing library primers containing Illumina adaptors and sequenced them on a Miseq using custom Illumina sequencing and index primers.

treatment_protocol: We transduced K562 cells harboring the doxycycline-inducible dCas9-KRAB at a multiplicity of infection (MOI) of 0.3 at a coverage of 1,000 transduced cells per sgRNA. Forty-eight hours post transduction, we selected transduced cells with 2 μg/mL puromycin for 48 hours and collected 200 million cells as a reference sample. After maintaining cells at 1,000× coverage in 1 μg/mL puromycin and 1 μg/mL doxycycline for 30 population doublings, we collected 200 million cells from the final cell population.

tag: sample type

value: dCas9-KRAB expressing K562 cell line

value: K562 cell line


title: Acinar82 (RNA-seq)


title: Acinar81 (RNA-seq)


title: sci-RNA-seq3 with ETiX mouse embryoids and natural mouse embryos [NextSeq1_PA-07A_S49]

description: sci-RNA-seq3 library


title: sci-RNA-seq3 with ETiX mouse embryoids and natural mouse embryos [NextSeq1_PA-06H_S48]

description: sci-RNA-seq3 library


title: d0_rep2

growth_protocol: maintaining cells at 1,000× coverage in 1 μg/mL puromycin and 1 μg/mL doxycycline


title: Acinar80 (RNA-seq)


title: wildtype rep4

city: Cologne

first: Thorsten

last: Hoppe

state: NRW

address: Joseph-Stelzmann-Str. 26

department: Institut für Genetik

institute: Universität zu Köln

hyb_protocol: Reversely transcribed RNAs were hybridized to Affymetrix EleGene 1.0 ST microarrays, according to the manufacturer's instructions.

scan_protocol: Standard Affyemtrix Protocol

data_processing: R package oligo was used to read Affymetrix CEL files and perform RMA normalization (Irizary et al., 2003) using background adjustment, quantile normalization, and median polish as the summarization method.

label: biotin

organism: Caenorhabditis elegans

source_name: whole organism

label_protocol: Standard Affyemtrix Protocol

growth_protocol: wildtype (N2) and dyf-1(mn335) worms were synchronized by bleaching and grown until day 1 of adulthood.

extract_protocol: The RNA isolation followed the standard procedures using Trizol reagent (Invitrogen). RNA was subsequently purified using the RNeasy kit (Qiagen).

value: wildtype (N2)


title: wildtype rep3


title: dyf-1(mn335) rep4


title: wildtype rep1


title: dyf-1(mn335) rep3


title: wildtype rep2


title: dyf-1(mn335) rep2


title: dyf-1(mn335) rep1


title: d30_rep1


title: Acinar78 (RNA-seq)


title: d0_rep1


title: sci-RNA-seq3 with ETiX mouse embryoids and natural mouse embryos [NextSeq1_PA-07B_S50]

description: sci-RNA-seq3 library


title: Acinar76 (RNA-seq)


title: sci-RNA-seq3 with ETiX mouse embryoids and natural mouse embryos [NextSeq1_PA-06D_S44]

description: sci-RNA-seq3 library


title: sci-RNA-seq3 with ETiX mouse embryoids and natural mouse embryos [NextSeq1_PA-06E_S45]

description: sci-RNA-seq3 library


title: HC#1_T1_single_cell_VDJseq(BCR)

city: Birmingham

first: Min

last: Gao

state: AL

address: 1900 University Blvd, THT Building Suite #130G

institute: University of Alabama at Birmingham

data_processing:
Raw data were processed with the Cell Ranger pipeline (v.2.1.1).
Sequencing reads were aligned using STAR aligner
The cellranger-vdj pipeline was applied for single cell V(D)J BCR data
Genome_build: GRCh38

source_name: T1 B cells from a AA healthy donor, anti-DNA(-)/anti-Sm(-)/anti-SSA(-)/RD(-)

extract_protocol:
Single cells and beads containing barcoded DNA oligos were captured into oil droplets by 10xChromium controller using 10xGenomics 5' VDJ reagent kits. Individual cells were lyzed immediately, mRNA were released, and reverse transcription was performed by plyT primers according to 10xGenomics 5' VDJ standard protocol. Single-stranded cDNA was then captured in the each oil droplet by the barcoded DNA oligos carried by the beads.
Barcoded single cell cDNA were pooled and preamplified, 5' biased transcriptome libraries and BCR libraries were constructed according to the standard protocol of 10xGenomics 5' VDJ reagent kits.

value: African Am

tag: gender

value: Male

value: heparinized blood

value: PBMC Transitional Stage 1 (T1) B cells


title: SLE#2_T1_single_cell_VDJseq(BCR)

source_name: T1 B cells from an AA SLE, anti-DNA(+)/anti-Sm(+)/anti-SSA(-)/RD(+)

value: Female


title: Acinar77 (RNA-seq)


title: sci-RNA-seq3 with ETiX mouse embryoids and natural mouse embryos [NextSeq1_PA-06G_S47]

description: sci-RNA-seq3 library


title: Acinar75 (RNA-seq)


title: HC#1_single_cell_VDJseq(BCR)

source_name: total B cells from a AA healthy donor, anti-DNA(-)/anti-Sm(-)/anti-SSA(-)/RD(-)

value: PBMC B cells


title: sci-RNA-seq3 with ETiX mouse embryoids and natural mouse embryos [NextSeq1_PA-06C_S43]

description: sci-RNA-seq3 library


title: sci-RNA-seq3 with ETiX mouse embryoids and natural mouse embryos [NextSeq1_PA-06B_S42]

description: sci-RNA-seq3 library


title: sci-RNA-seq3 with ETiX mouse embryoids and natural mouse embryos [NextSeq1_PA-06F_S46]

description: sci-RNA-seq3 library


title: sci-RNA-seq3 with ETiX mouse embryoids and natural mouse embryos [NextSeq1_PA-06A_S41]

description: sci-RNA-seq3 library


title: Acinar74 (RNA-seq)

value: exocrine pancreas


title: SLE#2_single_cell_VDJseq(BCR)

source_name: total B cells from an AA SLE, anti-DNA(+)/anti-Sm(+)/anti-SSA(-)/RD(+)


title: SLE#3_single_cell_VDJseq(BCR)

source_name: total B cells from an AA SLE, anti-DNA(+)/anti-Sm(+)/anti-SSA(+)/RD(+)


title: sci-RNA-seq3 with ETiX mouse embryoids and natural mouse embryos [NextSeq1_PA-05H_S40]

description: sci-RNA-seq3 library


title: Acinar73 (RNA-seq)


title: sci-RNA-seq3 with ETiX mouse embryoids and natural mouse embryos [NextSeq1_PA-05G_S39]

description: sci-RNA-seq3 library


title: SLE#1_single_cell_VDJseq(BCR)


title: Acinar71 (RNA-seq)


title: Acinar70 (RNA-seq)


title: sci-RNA-seq3 with ETiX mouse embryoids and natural mouse embryos [NextSeq1_PA-05E_S37]

description: sci-RNA-seq3 library


title: Acinar72 (RNA-seq)


title: Acinar69 (RNA-seq)


title: Acinar68 (RNA-seq)


title: Acinar67 (RNA-seq)


title: sci-RNA-seq3 with ETiX mouse embryoids and natural mouse embryos [NextSeq1_PA-05D_S36]

description: sci-RNA-seq3 library


title: sci-RNA-seq3 with ETiX mouse embryoids and natural mouse embryos [NextSeq1_PA-05B_S34]

description: sci-RNA-seq3 library


title: GSC23_sh-lncEPAT_rep2

city: Richmond

first: LINLIN

last: LI

state: Virginia

address: 401 college street

institute: Massey Cancer Center, VCU Health

description: GSC23 cultured cells

hyb_protocol: Following fragmentation, 5.5 ug cRNA were hybridized at 45℃ for 16 hrs. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: Arrays were subsequently scanned on a GCS3000 7G Scanner.

data_processing: The genes showing altered expression (fold change >1.5) compared with the control shRNA were selected and analyzed using Gene Set Enrichment Analysis (GSEA).

label: Biotin

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 10 ug total RNA (Expression Analysis Technical Manual, 2007, Affymetrix).

growth_protocol: All cells were maintained in DMEM/F-12 (50:50) medium supplemented with B27, EGF (10 ng/mL), and basic fibroblast growth factor (FGF, 10 ng/ml).

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

treatment_protocol: No special treatment.

value: glioblastoma stem cell

value: lncEPAT depletion


title: sci-RNA-seq3 with ETiX mouse embryoids and natural mouse embryos [NextSeq1_PA-05C_S35]

description: sci-RNA-seq3 library


title: GSC23_sh-ctr_rep2

description: GSC23 cultured cells

value: control


title: LTR18A MPRA input DNA [input_DNA_run2]

city: St. Louis

first: Alan

middle: Y

last: Du

state: MO

address: 4515 McKinley Avenue

department: Genetics

institute: Washington University at St. Louis School of Medicine

library_source: other

data_processing:
library strategy: MPRA
Fastq reads (from read 1 only) were filtered to only include reads which contain barcodes that fully matched a synthesized barcode from the library design. The number of reads for each barcode was then counted.
Barcodes for the same associated element were added together to get element-level counts and then normalized to total read depth (counts per million, CPM). Elements with fewer than 5 counts in any sample (DNA or RNA) were filtered out.
Expression of an element was calculated as RNA CPM/DNA CPM. Expression was normalized to the average of Basal construct transfection replicates. Finally, enrichment score was calculated as the log2 of normalized expression.
Assembly: hg19
Supplementary files format and content: TXT file of barcode counts

molecule: other

organism: Escherichia coli DH5[alpha]

growth_protocol: K562 cells were grown in RPMI1640 with L-glutamine supplemented with 10% FBS and 1% penicillin/streptomycin. HepG2 cells were grown in DMEM (with high glucose and L-glutamine, without sodium pyruvate) supplemented with 10% FBS and 1% penicillin/streptomycin.

extract_protocol:
RNA was extracted from cell cultures using PureLink RNA Mini Kit with on-column DNase treatment followed by DNase I treatment using TURBO DNA-free kit. DNA was taken directly from the MPRA library used for transfections.
Barcodes were amplified from the MPRA library (DNA) or from cDNA after first strand cDNA synthesis of extracted RNA. Amplified barcodes were then ligated to Illumina adapters for pooled sequencing.

value: LTR18A MPRA input DNA


title: Acinar66 (RNA-seq)

value: acinar cell

value: wild type

value: 9 days as 3D organoids


title: sci-RNA-seq3 with ETiX mouse embryoids and natural mouse embryos [NextSeq1_PA-05A_S33]

description: sci-RNA-seq3 library

value: ETiX mouse embryoids (Day6 and Day8) and natural mouse embryos (E7.5, E8, E8.5, E8.75. and E9)


title: Acinar65 (RNA-seq)


title: GSC23_sh-lncEPAT_rep1

description: GSC23 cultured cells


title: sci-RNA-seq3 with ETiX mouse embryoids and natural mouse embryos [NextSeq1_PA-04H_S32]

description: sci-RNA-seq3 library


title: sci-RNA-seq3 with ETiX mouse embryoids and natural mouse embryos [NextSeq1_PA-05F_S38]

description: sci-RNA-seq3 library


title: Acinar64 (RNA-seq)


title: GSC23_sh-ctr_rep1

description: GSC23 cultured cells


title: sci-RNA-seq3 with ETiX mouse embryoids and natural mouse embryos [NextSeq1_PA-04F_S30]

description: sci-RNA-seq3 library


title: sci-RNA-seq3 with ETiX mouse embryoids and natural mouse embryos [NextSeq1_PA-04E_S29]

description: sci-RNA-seq3 library


title: PDX2_LT_breast_primary_tumor_MULTI_Seq

first: Juliane

last: Winkler

address: 513 Parnassus Avenue

department: Department of Cell and Tissue Biology

institute: University of California, San Francisco

data_processing:
To generate gene expression data, sequences from Novaseq were de-multiplexed and aligned using CellRanger v.5.0.1, available from 10x Genomics with default parameters.
To generate MULTI-seq UMI count matrices for demultiplexing FASTQs were converted to barcode UMI count matrices using the ‘MULTIseq.preProcess’ and ‘MULTIseq.align’ functions in the deMULTIplex R package31 with default parameters  (https://github.com/chris-mcginnis-ucsf/MULTI-seq). Notably, ‘PDX3’ FASTQs were randomly down-sampled to 1x10^8 total reads prior to UMI count matrix conversion in order to minimize computation time.
For each 10X lane, we first removed the cells with less than 2500 UMI and 250 genes and more than 50% mitochondria reads by using the Scanpy Python package version 1.8.1. In addition, in order to filter out reads from ambient RNA, we ran DecontX 94 separately for each 10X lane by using default parameters. Next, we re-filtered the dataset from every 10X run when cells did not contain a minimum number of genes (250), minimum of counts/UMIs (2500), and/or having more than 50% mitochondria reads. Cells were sample assigned using the MULTI-Seq demultiplexing result, thereby removing doublets but including unassigned ‘negative’ cells. In order to recover MULTI-Seq-unassigned ‘negative’ cells, we used DBSCAN clustering. Negative cells in one DBSCAN cluster were assigned as the same tumor sample as the majority of MULTI-Seq classified cells in that cluster. After completed cell assignment, all 10X runs were combined to one MULTI-Seq dataset and removed genes that were not expressed in at least 20 cells. We then performed normalization, log-transformation, finding highly variable genes, cell cycle regression, principal component analysis, UMAP dimension reduction, and Louvain and Leiden clustering.
Assembly: genecode V30
Supplementary files format and content: comma seperated values (CSV) file for meta data, raw gene count matrix, DecontX modified gene count matrix, normalized and log-transformed gene count matrix, and MULTI-Seq barcode count matrix

source_name: Tumor

extract_protocol:
Live, LIN-/hDC298+ single breast primary tumor and metastatic cells from lung were sorted, pooled, captured and processed in microfluidics droplets via 10x Genomics using MULTI-Seq protocol.
Library was performed according to the manufacter’s instructions (single cell 3’ v2 protocol, 10x Genomics) using custom MULTI-seq library preparation protocols.

value: Tumor

value: patient-derived-xenograft

value: NSG


title: PDX2_POOL_lung_metastasis_MULTI_Seq

source_name: Metastasis

value: Metastasis


title: PDX3B_breast_primary_tumor_MULTI_Seq


title: PDX3A_breast_primary_tumor_MULTI_Seq


title: LTR18A MPRA input DNA [input_DNA_run3]


title: LTR18A MPRA input DNA [input_DNA_run1]


title: Acinar61 (RNA-seq)


title: sci-RNA-seq3 with ETiX mouse embryoids and natural mouse embryos [NextSeq1_PA-04G_S31]

description: sci-RNA-seq3 library


title: sci-RNA-seq3 with ETiX mouse embryoids and natural mouse embryos [NextSeq1_PA-04D_S28]

description: sci-RNA-seq3 library


title: Acinar62 (RNA-seq)


title: PDX1D_breast_primary_tumor_MULTI_Seq


title: Acinar60 (RNA-seq)


title: sci-RNA-seq3 with ETiX mouse embryoids and natural mouse embryos [NextSeq1_PA-04C_S27]

description: sci-RNA-seq3 library


title: Acinar59 (RNA-seq)


title: Acinar58 (RNA-seq)


title: PDX1C_breast_primary_tumor_MULTI_Seq


title: sci-RNA-seq3 with ETiX mouse embryoids and natural mouse embryos [NextSeq1_PA-04A_S25]

description: sci-RNA-seq3 library


title: Acinar63 (RNA-seq)


title: sci-RNA-seq3 with ETiX mouse embryoids and natural mouse embryos [NextSeq1_PA-03H_S24]

description: sci-RNA-seq3 library


title: PDX1A_breast_primary_tumor_MULTI_Seq


title: Acinar56 (RNA-seq)


title: sci-RNA-seq3 with ETiX mouse embryoids and natural mouse embryos [NextSeq1_PA-03G_S23]

description: sci-RNA-seq3 library


title: Acinar57 (RNA-seq)


title: HaCAT cells, siControl-replicate

first: Xin

last: Huang

state: China

address: zhizaoju Road 639

institute: Ninth People's Hospital affiliated to Shanghai Jiao Tong University School of Medicine

data_processing:
Quality control: the image data measured by the high-throughput sequencer are converted into sequence data (reads) by CASAVA base recognition. Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts. In this step, clean data (clean reads) were obtained by removing reads containing adapter, reads containing N base and low quality reads from raw data. At the same time, Q20, Q30 and GC content the clean data were calculated. All the downstream analyses were based on the clean data with high quality.
Reads mapping to the reference genome: Reference genome and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built using Hisat2 (v2.0.5) and paired-end clean reads were aligned to the reference genome using Hisat2 (v2.0.5). We selected Hisat2 as the mapping tool for that Hisat2 can generate a database of splice junctions based on the gene model annotation file and thus a better mapping result than other non-splice mapping tools.
Quantification of gene expression level: featureCounts (v1.5.0-p3) was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene. FPKM, expected number of Fragments Per Kilobase of transcript sequence per Millions base pairs sequenced, considers the effect of sequencing depth and gene length for the reads count at the same time, and is currently the most commonly used method for estimating gene expression levels.
Differential expression analysis: (For DESeq2 with biological replicates) Differential expression analysis of two conditions/groups (two biological replicates per condition) was performed using the DESeq2 R package (1.20.0). DESeq2 provide statistical routines for determining differential expression in digital gene expression data using a model based on the negative binomial distribution. The resulting P-values were adjusted using the Benjamini and Hochberg’s approach for controlling the false discovery rate . padj<0.05 and |log2(foldchange)| > 1 were set as the threshold for significantly differential expression.
Assembly: hg38
Supplementary files format and content: ExpressionProfiles. Txt

source_name: not applicable

growth_protocol: HaCAT cells were maintained in DMEM (Gibco) supplemented with 10% fetal bovine serum (Gibco) and 1% P/S (Gibco) in humidified atmosphere with 5% CO2 at 37℃

extract_protocol:
Total RNA was extracted from cultured HaCAT using TRIzol reagent (Invitrogen, Carlsbad, CA, USA)
Total RNA was used as input material for the RNA sample preparations. Briefly, mRNA was purified from total RNA by using poly-T oligo-attached magnetic beads. Fragmentation was carried out using divalent cations under elevated temperature in First Strand Synthesis Reaction Buffer(5X). First strand cDNA was synthesized using random hexamer primer and M-MuLV Reverse Transcriptase, then use RNaseH to degrade the RNA. Second strand cDNA synthesis was subsequently performed using DNA Polymerase I and dNTP. Remaining overhangs were converted into blunt ends via exonuclease/polymerase activities. After adenylation of 3’ ends of DNA fragments, Adaptor with hairpin loop structure were ligated to prepare for hybridization. In order to select cDNA fragments of preferentially 370~420 bp in length, the library fragments were purified with AMPure XP system (Beckman Coulter, Beverly, USA). Then PCR amplification, the PCR product was purified by AMPure XP beads, and the library was finally obtained.

treatment_protocol: Knockdown of ALKBH5 in HaCAT cells was realized by transfection with siRNAs. Cells grown in six-well plates were transfected with 200 pmol siRNAs using lipofectamine 3000 transfection reagent (Invitrogen, L3000008) according to the manufactuer’s instructions.

value: not applicable

value: HaCAT

value: Keratinocyte cell line

value: WT

value: Transfection of normal control siRNA


title: HaCAT cells, siALKBH5-replicate

value: ALKBH5 knockdown

value: Transfection of ALKBH5 knockdown siRNA


title: sci-RNA-seq3 with ETiX mouse embryoids and natural mouse embryos [NextSeq1_PA-03E_S21]

description: sci-RNA-seq3 library


title: HaCAT cells, siALKBH5


title: HaCAT cells, siControl


title: Acinar53 (RNA-seq)

value: exocrine pancreas


title: Acinar54 (RNA-seq)


title: sci-RNA-seq3 with ETiX mouse embryoids and natural mouse embryos [NextSeq1_PA-04B_S26]

description: sci-RNA-seq3 library


title: Acinar52 (RNA-seq)


title: sci-RNA-seq3 with ETiX mouse embryoids and natural mouse embryos [NextSeq1_PA-03C_S19]

description: sci-RNA-seq3 library


title: A_si

city: Nanjing

first: Rong

middle: Fang

last: Wei

state: Jiangsu

address: 138 Xianlin Road

institute: Nanjing Unveristy of Chinese Medicine

data_processing:
Data filtering steps.Prior to assembly, the low quality reads(1,reads containing sequencing adaptors; 2,reads containing sequencing primer;3, nucleotide with q quality score lower than 20 )were removed .software CutAdapter,parameters -o 5 -p 100
Read alignment software,software HISAT ,version 2.0 ,parameters -l fr-firststrand -mi 20 -mx 500000 -p 2 -b dta -q phred33-quals -x 9
perform expression level for mRNAs by calculating FPKM.stimate the expression levels of all transcripts.software StringTie ,version 1.3.0,parameters -b dta -q phred33-quals.
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

source_name: Mutiple myeloma cells

extract_protocol:
Total RNA was extracted using Trizol reagent (Invitrogen, CA, USA) following the manufacturer's procedure. The total RNA quantity and purity were analysis of Bioanalyzer 2100 and RNA 6000 Nano LabChip Kit (Agilent, CA, USA) with RIN number >7.0. Approximately 10 ug of total RNA representing a specific adipose type was subjected to isolate Poly (A) mRNA with poly-T oligoattached magnetic beads (Invitrogen). Following purification, the poly(A)- or poly(A)+ RNA fractions is fragmented into small pieces using divalent cations under elevated temperature. Then the cleaved RNA fragments were reverse-transcribed to create the final cDNA library in accordance with the protocol for the mRNA-Seq sample preparation kit (Illumina, San Diego, USA), the average insert size for the paired-end libraries was 300 bp (±50 bp). And then we performed the paired-end sequencing on an Illumina Novaseq™ 6000 at the (lc-bio, China) following the vendor's recommended protocol.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Homo MM cells

value: VCP knockdown


title: A_NC

value: control


title: PDX1B_breast_primary_tumor_MULTI_Seq


title: Acinar51 (RNA-seq)

value: acinar cell

value: wild type

value: 9 days as 3D organoids


title: sci-RNA-seq3 with ETiX mouse embryoids and natural mouse embryos [NextSeq1_PA-03B_S18]

description: sci-RNA-seq3 library

value: ETiX mouse embryoids (Day6 and Day8) and natural mouse embryos (E7.5, E8, E8.5, E8.75. and E9)


title: Acinar50 (RNA-seq)


title: sci-RNA-seq3 with ETiX mouse embryoids and natural mouse embryos [NextSeq1_PA-03A_S17]

description: sci-RNA-seq3 library


title: Acinar49 (RNA-seq)


title: sci-RNA-seq3 with ETiX mouse embryoids and natural mouse embryos [NextSeq1_PA-02H_S16]

description: sci-RNA-seq3 library


title: sci-RNA-seq3 with ETiX mouse embryoids and natural mouse embryos [NextSeq1_PA-03F_S22]

description: sci-RNA-seq3 library


title: Acinar55 (RNA-seq)


title: Acinar48 (RNA-seq)


title: Acinar45 (RNA-seq)


title: sci-RNA-seq3 with ETiX mouse embryoids and natural mouse embryos [NextSeq1_PA-03D_S20]

description: sci-RNA-seq3 library


title: sci-RNA-seq3 with ETiX mouse embryoids and natural mouse embryos [NextSeq1_PA-02G_S15]

description: sci-RNA-seq3 library


title: sci-RNA-seq3 with ETiX mouse embryoids and natural mouse embryos [NextSeq1_PA-02F_S14]

description: sci-RNA-seq3 library


title: Acinar46 (RNA-seq)


title: sci-RNA-seq3 with ETiX mouse embryoids and natural mouse embryos [NextSeq1_PA-02E_S13]

description: sci-RNA-seq3 library


title: Acinar44 (RNA-seq)


title: sci-RNA-seq3 with ETiX mouse embryoids and natural mouse embryos [NextSeq1_PA-02C_S11]

description: sci-RNA-seq3 library


title: Acinar43 (RNA-seq)


title: sci-RNA-seq3 with ETiX mouse embryoids and natural mouse embryos [NextSeq1_PA-02D_S12]

description: sci-RNA-seq3 library


title: Acinar42 (RNA-seq)


title: sci-RNA-seq3 with ETiX mouse embryoids and natural mouse embryos [NextSeq1_PA-02B_S10]

description: sci-RNA-seq3 library


title: Acinar41 (RNA-seq)


title: Acinar40 (RNA-seq)


title: Acinar39 (RNA-seq)


title: sci-RNA-seq3 with ETiX mouse embryoids and natural mouse embryos [NextSeq1_PA-01G_S7]

description: sci-RNA-seq3 library


title: sci-RNA-seq3 with ETiX mouse embryoids and natural mouse embryos [NextSeq1_PA-01F_S6]

description: sci-RNA-seq3 library


title: Acinar37 (RNA-seq)


title: sci-RNA-seq3 with ETiX mouse embryoids and natural mouse embryos [NextSeq1_PA-02A_S9]

description: sci-RNA-seq3 library


title: Acinar36 (RNA-seq)


title: Acinar38 (RNA-seq)


title: Acinar35 (RNA-seq)


title: sci-RNA-seq3 with ETiX mouse embryoids and natural mouse embryos [NextSeq1_PA-01D_S4]

description: sci-RNA-seq3 library


title: control_12_non-neoplastic bile duct

type: genomic

first: Stephanie

last: Roessler

address: Im Neuenheimer Feld 224

institute: Heidelberg University Hospital

description: Illumina HumanMethylation450 BeadChip

hyb_protocol: supplier protocol (Illumina)

scan_protocol: supplier protocol (Illumina)

data_processing: Methylation data were processed using the R platform for statistical computing.

label: Cy5 and Cy3

label_protocol: supplier protocol (Illumina)

extract_protocol: Genomic DNA was isolated from fresh frozen tissue using the QIAamp DNA micro kit (Qiagen, Hilden, Germany) for whole exome sequencing according to the manufacturer's instructions. From formalin-fixed paraffin-embedded (FFPE) samples, genomic DNA was extracted using the AllPrep DNA/RNA FFPE Kit (Qiagen), as recommended by the manufacturer with the following modifications: After addition of xylene, samples were incubated at 56°C for 2 minutes followed by two ethanol washes. The first proteinase K digestion was performed with 20 µL at 56°C for 30 minutes. The DNA was eluted twice with 30 µL of H2O.

value: FFPE


title: control_7_non-neoplastic bile duct

description: Illumina HumanMethylation450 BeadChip


title: control_10_non-neoplastic bile duct

description: Illumina HumanMethylation450 BeadChip


title: sci-RNA-seq3 with ETiX mouse embryoids and natural mouse embryos [NextSeq1_PA-01C_S3]

description: sci-RNA-seq3 library


title: sci-RNA-seq3 with ETiX mouse embryoids and natural mouse embryos [NextSeq1_PA-01E_S5]

description: sci-RNA-seq3 library


title: Acinar34 (RNA-seq)


title: control_9_non-neoplastic bile duct

description: Illumina HumanMethylation450 BeadChip


title: control_5_non-neoplastic bile duct

description: Illumina HumanMethylation450 BeadChip


title: control_11_non-neoplastic bile duct

description: Illumina HumanMethylation450 BeadChip


title: control_4_non-neoplastic bile duct

description: Illumina HumanMethylation450 BeadChip


title: sci-RNA-seq3 with ETiX mouse embryoids and natural mouse embryos [NextSeq1_PA-01A_S1]

description: sci-RNA-seq3 library


title: Acinar31 (RNA-seq)


title: control_8_non-neoplastic bile duct

description: Illumina HumanMethylation450 BeadChip


title: control_6_non-neoplastic bile duct

description: Illumina HumanMethylation450 BeadChip


title: E8.5 fraction extra-embryonic compartment

city: Cambridge

first: Florian

last: Hollfelder

address: 80 Tennis court road

country: United Kingdom

institute: University of Cambridge

description:
Mouse embryo at 8.5 days of development, dissected extra-embryonic compartment
Natural mouse embryos at stage E8.5 (scRNA-seq libraries), extra-embryonic cells

data_processing:
BCL to fastq conversion using bcl2fastq (illumina script)
demultiplexing with Pheniqs from biosails
Filtering,mapping,quantification with zUMIs
Integration, normalisation, scaling of the matrix (containing intronic and exonic de-duplicated reads) with Seurat
Batch effect removal with Harmony
Genome_build: Mus_musculus.GRCm38.99
Supplementary_files_format_and_content: de-duplicated gene expression matrix containing merged intronic and exonic counts

source_name: Mouse embryo

growth_protocol: AggreWell plates (STEMCELL Technologies 34415) were prepared as described in (Amadei et al., 2021).To generate ETiX-embryos, Doxycycline was added to tetO-Gata4 ES cells for 6 hours. TS cells were trypsinised and were added to a gelatinised plate to deplete the mouse embryonic fibroblasts for 20 minutes at 37°C. ES cells and tetO-Gata4 ES cells were subsequently trypsinised. Cell suspensions with 19,200 TS cells, 6000 ES cell and 6,000 tetO-Gata4 ES cells were mixed and pelleted by centrifugation. The cell pellet was resuspended in 1ml FC medium with 7.5nM ROCK inhibitor (Y27632, STEMCELL Technologies 72304). After adding the cell mixture drop-wise to the AggreWell, the plate was centrifuged at 100g for 3 minutes. On the next day, media change was performed twice by removing 1ml medium from each well and adding 1ml fresh FC medium without ROCK inhibitor. On Day 2, media change was performed once to replace 1ml medium with 1ml fresh FC medium. On Day 3, 1.2ml medium was removed from each well and 1.5ml IVC1 was added, after equilibrating for 20 minutes in the incubator. IVC1 (Bedzhov et al., 2014) is made of advanced DMEM/F12 (Gibco, 21331-020) supplemented with 20% (v/v) FBS, 2 mM GlutaMax, 1% v/v penicillin–streptomycin, 1X ITS-X Thermo Fisher Scientific, 51500-056), 8 nM β-estradiol, 200 ng/ml progesterone and 25 μM N-acetyl-L-cysteine. On Day 4, ETiX-embryos in the AggreWell were transferred to CELLSTAR 6 well multiwell plate for suspension culture (Greiner Bio-One 657185) with 5ml of IVC1 (with FBS at 30% v/v) per well. On Day 5 IVC1 was replaced with ex utero culture medium (EUCM) (Aguilera-Castrejon et al., 2021). EUCM comprises 25% DMEM (GIBCO 11880) supplemented with 1× Glutamax (GIBCO, 35050061), 100 units/ml penicillin and 100 μg/ml streptomycin and 11 mM HEPES (GIBCO 15630056), plus 50% rat serum (rat whole embryo culture serum, Charles River) and 25% human cord serum obtained from the Cambridge Blood Biobank. Human and rat serum were heat-inactivated for 35 minutes (from frozen) at 56 C and sterilised by filtration. Each ETiX was transferred to a single well of 24-well, non-adherent dish (Greiner 662102) with 250 uL of EUCM . On day 6 each ETiX embryos was fed with an additional 250 uL of EUCM. On day 7, EUCM was supplemented with 3.0 mg/ml of D-Glucose (Sigma G8644) and the samples were moved to a rotating bottle culture chamber apparatus10. Each rotating bottle contained 2 ml of EUCM and 3 ETiX embryos. On day 8 EUCM was supplemented with 3.5 mg/ml of D-Glucose; in each rotating bottle 2 ETiX were cultured with 3 ml of EUCM. NAtural embryos were recovered from pregnant females at the approrpaite timepoint.

extract_protocol:
Samples were dissociated to single cells by cutting with needles and then incubation in TrypLE Express dissociation solution for 15 minutes followed by reaction inactivation with media containing 15% fetal bovine serum, filtration and 2 washes in PBST (0.02% Tween-20.
inDrop v3

treatment_protocol: not applicable

value: Mouse embryos generated by natural mouse mating

value: Mixed strain:CD1/MF1/C57BL/6

tag: developmental day

tag: ploidy

value: Euploid

tag: stem cells of origin

tag: transgenes

value: Brachyury-GFP


title: E8.5 fraction 6

description:
Mouse embryo at 8.5 days of development, dissected embryonic compartment
Natural mouse embryos at stage E8.5 (scRNA-seq libraries), embryonic cells

tag: tissue

value: not applicable


title: K562 e4i [ATAC-seq]

data_processing:
Bowtie2 was used to map raw FASTQ files to hg19, then paired-end reads were filtered  and converted to non-redundant BEDPE files for each sample.
Genome_build: hg19
Supplementary_files_format_and_content: non-redundant BEDPE files: each row is one unique paired reads. The columns are: chromosome1, start1, end1, chromosome2, start2, end2, PairedReadID, MAPQ value from Bowtie2, strand1 and strand2.

growth_protocol: The K562 (human myelogenous leukemia cells, female, ATCC) cells were cultured in RPMI-1640 (Thermo Fisher Scientific, Waltham, MA) with 10% Tet-system-approved FBS (Life Technologies), GlutaMAX (Thermo Fisher Scientific), and Penicillin-Streptomycin (Thermo Fisher Scientific). K562-KRAB-dCas9 cell line was a gift from Dr. Luke Gilbert (University of California San Francisco) and cultured in the same condition(Gilbert et al., 2014).

extract_protocol: For each ATAC-seq assay, 50,000 cells were collected and washed with PBS. After centrifugation, resuspend cell pellet by gently pipetting up and down 10 times with 100 mL cold Lysis Buffer (10 mM Tris-HCl, pH 7.4, 10 mM NaCl, 3 mM MgCl2, 0.1% NP-40, 0.1% Tween-20, 0.01% Digitonin) and then keep on ice for 3 minutes. Add 1 mL Wash Buffer (10 mM Tris-HCl, pH 7.4, 10 mM NaCl, 3 mM MgCl2, 0.1% Tween-20) to the tube and mix gently. The nuclei were then pelleted by centrifuging at 1000 x g for 10 minutes at 4 °C. Resuspend nuclei pellet with 1 x Transposition Reaction Buffer (50 mM Tris-acetate, pH 7.5, 150 mM potassium acetate, 10mM magnesium acetate, 4 mM spermidine, 0.1% Tween-20, 0.01% Digitonin). Add 5 mL homemade ATAC-seq Tnp complex, then mix well gently and place in a 37 °C thermomixer with 1000 rpm shaking for 30 minutes. After the reaction, DNA was purified with MinElute Reaction Cleanup Kit (QIAGEN, Cat. 28206). Elute DNA with 15 mL elution buffer, then set up PCR reaction by mixing with 2.5 mL each indexed primer (25 mM) and 20 mL NEBNext High-Fidelity 2X PCR Master Mix (NEB, M0541S). Run the following PCR program: 72 °C for 5 minutes; 98 °C for 30 seconds; 11 cycles of 98 °C for 10 seconds, 63 °C for 30 seconds, and 72 °C for 1 minute; 72 °C for 5 minutes. Purify 200-650 bp DNA fragments for sequencing.

treatment_protocol: dCas9-KRAB expressing K562 cells were infected with lentiviruses expressing sgRNAs against e3, e7, e3&e7, e1, e4, or e1&e4.

tag: genotype/variation

value: dCas9-KRAB expressing K562 cell line

tag: cell type

value: K562 cell line

tag: treatment

value: e4 inhibition


title: K562 e1i&e4i [ATAC-seq]

value: e1 and e4 dual inhibition


title: E8.5 fraction 5


title: control_3_non-neoplastic bile duct

description: Illumina HumanMethylation450 BeadChip


title: Acinar30 (RNA-seq)

data_processing:
mapping with STAR via zUMIs
transcript quantification with featureCounts via zUMIs
Assembly: GRCm38 (mm10)
Supplementary files format and content: Single-cell RNA-seq count matrices (UMI counts and read counts) in csv (comma-separated values) format. Values are not normalized, decimals are due to distribution of multimapping reads.

source_name: exocrine pancreas

extract_protocol:
Primary pancreatic acinar cells were isolated by digestive dissociation of pancreatic tissue and subsequent density gradient centrifugation. After cultivation as 3D matrigel embedded organoids for 9 days, the cells were harvested and subjected to the scNMT-seq protocol. For more information on the generation of pancreatic organoids, see the following papers (Wollny et al., 2016; Krieger et al., 2021).
For profiling the transcriptome and epigenome of single cells we developed and implemented a miniaturized and higher throughput version of the scNMT-seq protocol (Clark et al., 2018). On this new version, the Smart-seq3 (Hagemann-Jensen et al., 2020) method and specific normalization steps were implemented. A detailed version of the protocol is described in Cerrizuela et al., (2022). The samples listed here represent the transcriptomic portion of this multi-omic data set, i.e. transcript UMI counts and read counts assessed with single-cell RNA-seq.
Single-cell RNA-seq (Smart-seq3)

value: exocrine pancreas

tag: genotype


title: Acinar29 (RNA-seq)

tag: strain


title: control_2_non-neoplastic bile duct

description: Illumina HumanMethylation450 BeadChip


title: Acinar28 (RNA-seq)

tag: culture condition


title: iCCA_52_iCCA

description: Illumina HumanMethylation450 BeadChip

value: male


title: control_1_non-neoplastic bile duct

description: Illumina HumanMethylation450 BeadChip


title: E8.5 fraction 4


title: Acinar33 (RNA-seq)


title: K562 WT (For e1 and e4 inhibition experiment) [ATAC-seq]

value: WT


title: iCCA_51_iCCA

description: Illumina HumanMethylation450 BeadChip

value: female


title: sci-RNA-seq3 with ETiX mouse embryoids and natural mouse embryos [NextSeq1_PA-01H_S8]

description: sci-RNA-seq3 library

data_processing:
Base calls were converted to fastq format using Illumina’s bcl2fastq/v2.20 and demultiplexed based on PCR i5 and i7 barcodes using maximum likelihood demultiplexing package deML (Renaud et al. 2015) with default settings. Downstream sequence processing and single cell digital expression matrix generation were similar to sci-RNA-seq (Cao et al. 2017) except that RT index was combined with hairpin adaptor index, and thus the mapped reads were split into constituent cellular indices by demultiplexing reads using both the RT index and ligation index (Levenshtein edit distance (ED) < 2, including insertions and deletions).
Briefly, demultiplexed reads were filtered based on RT index and ligation index (ED < 2, including insertions and deletions) and adaptor-clipped using trim_galore/v0.6.5 with default settings. Trimmed reads were mapped to the mouse reference genome (mm10) for mouse embryo nuclei, using STAR/v2.6.1d (Dobin et al. 2013) with default settings and gene annotations (GENCODE VM12 for mouse). Uniquely mapping reads were extracted, and duplicates were removed using the unique molecular identifier (UMI) sequence (ED < 2, including insertions and deletions), reverse transcription (RT) index, hairpin ligation adaptor index and read 2 end-coordinate (i.e. reads with UMI sequence less than 2 edit distance, RT index, ligation adaptor index and tagmentation site were considered duplicates).
Finally, mapped reads were split into constituent cellular indices by further demultiplexing reads using the RT index and ligation hairpin (ED < 2, including insertions and deletions). To generate digital expression matrices, we calculated the number of strand-specific UMIs for each cell mapping to the exonic and intronic regions of each gene with python/v2.7.13 HTseq package (Anders, Pyl, and Huber 2015). For multi-mapped reads, reads were assigned to the closest gene, except in cases where another intersected gene fell within 100 bp to the end of the closest gene, in which case the read was discarded. For most analyses we included both expected-strand intronic and exonic UMIs in per-gene single-cell expression matrices.
Assembly: mm10
Supplementary files format and content: Processed data files include a cell annotation csv  file, gene annotation csv file, and a gene count sparse matrix file

extract_protocol: We performed a simplified version of sci-RNA-seq3, further optimized for “tiny” samples (Martin et al. 2021). Briefly, to each tube, 100ul of a hypotonic, PBS-based lysis buffer was added with DEPC as an RNase inhibitor. The resulting nuclei were then fixed with 4 volumes of a mix of methanol and dithiobis (succinimidyl propionate) (DSP). After rehydrating and washing the nuclei carefully in a sucrose/PBS/triton/MgCl2 buffer (SPBSTM), the nuclei were distributed to two 96-well plates for reverse transcription, allocating 8 wells per embryo. After reverse transcription, nuclei were pooled, washed in SPBSTM and redistributed to a fresh plate for ligation of the second index primer with T4 DNA ligase. Nuclei were then again pooled, washed, and redistributed to three final plates for second strand synthesis, extraction, tagmentation, and PCR to add the third index plus a plate index. Products were pooled by PCR plate, size-selected and sequenced on two Illumina NextSeq runs (termed “NextSeq-1" and “NextSeq-2”).

tag: developmental stage


title: iCCA_49_iCCA

description: Illumina HumanMethylation450 BeadChip


title: Acinar27 (RNA-seq)

value: acinar cell

value: wild type


title: E8.5 fraction 3


title: K562 e1i [ATAC-seq]

value: e1 inhibition


title: sci-RNA-seq3 with ETiX mouse embryoids and natural mouse embryos [NextSeq1_PA-01B_S2]

description: sci-RNA-seq3 library

value: ETiX mouse embryoids (Day6 and Day8) and natural mouse embryos (E7.5, E8, E8.5, E8.75. and E9)


title: K562 WT [ATAC-seq]


title: K562 e3i [ATAC-seq]

value: e3 inhibition


title: K562 e1i&e4i rep1 [ChIP-seq]

data_processing:
Bowtie2 was used to map raw FASTQ files to hg19, then paired-end reads were filtered  and converted to non-redundant BEDPE files for each sample.
Genome_build: hg19
Supplementary_files_format_and_content:  non-redundant BEDPE files: each row is one unique paired reads. The columns are: chromosome1, start1, end1, chromosome2, start2, end2, PairedReadID, MAPQ value from Bowtie2, strand1 and strand2.

extract_protocol: Cells were fixed with 1% Formaldehyde in culture medium at room temperature for 10 minutes. Quench the reaction by adding 250 mM Glycine, then wash cells twice with cold PBS. Three million fixed cells were used for each H3K9me3 ChIP-seq assay. Resuspend cells with 1 x TE buffer plus 1 x protease inhibitor cocktail and 1 mM PMSF. Chromatin was sheared by sonication on a Diagenode Bioruptor Pico device at 4 °C for 18 cycles with 30 seconds on and 30 seconds off. Adjust chromatin solution to 1 x RIPA buffer (1 x TE, 0.1% SDS, 0.1% Sodium Deoxycholate and 1% Triton X-100) plus 500 mM NaCl. After centrifuging at 13, 000 rpm for 10 min at 4 °C, chromatin supernatant was collected and 10% of it was saved at input. Mix 2 mg H3K9me3 antibody (Abcam, Cat. ab8898) with 20 mL Dynabeads Protein A beads (ThermoFischer Scientific, Cat. 10001D), then incubate at room temperature for 1 hour with rotation. Wash beads once with 1 x PBS, then add chromatin solution to beads, and incubate at 4 °C overnight with rotation. Wash beads three times with RIPA buffer plus 500 mM NaCl, then three times with RIPA buffer plus 1 M NaCl, then three times with LiCl buffer (1 x TE, 250 mM LiCl, 0.5% NP-40, 0.5% Sodium Deoxycholate), and finally three times with 1 x TE buffer. Elute DNA and reverse crosslinking with protease K digestion and incubating at 65 °C for over 6 hours. DNA was purified with MinElute Reaction Cleanup Kit (QIAGEN, Cat. 28206). Repair DNA ends with End-It DNA End-Repair Kit (Lucigen, Cat. ER0720), then perform A-tailing with Klenow Fragment (3’ -> 5’ exo-) (NEB, Cat. M0212S) provided with dATP, then followed by adapter ligation with T4 DNA ligase (NEB, Cat. M0202S). Finally, the library was indexed and amplified by PCR, and DNA fragments between 200 bp and 600 bp were purified and sequenced.


title: K562 e1i&e4i rep2 [ChIP-seq]


title: Acinar22 (RNA-seq)

value: 9 days as 3D organoids


title: Acinar20 (RNA-seq)


title: Acinar19 (RNA-seq)


title: E7.5 fraction 2

description:
Mouse embryo at 7.5 days of development
Natural mouse embryos at stage E7.5 (scRNA-seq libraries)

value: Mouse embryos generated by natural mouse mating

value: Mixed strain:CD1/MF1/C57BL/6

value: Euploid


title: E8.5 fraction 1

value: not applicable

value: Brachyury-GFP


title: E7.5 fraction 1


title: Acinar18 (RNA-seq)


title: iCCA_47_iCCA

description: Illumina HumanMethylation450 BeadChip

value: FFPE


title: iCCA_48_iCCA

description: Illumina HumanMethylation450 BeadChip


title: iCCA_50_iCCA

description: Illumina HumanMethylation450 BeadChip


title: iCCA_42_iCCA

description: Illumina HumanMethylation450 BeadChip


title: iCCA_43_iCCA

description: Illumina HumanMethylation450 BeadChip


title: iCCA_46_iCCA

description: Illumina HumanMethylation450 BeadChip


title: iCCA_45_iCCA

description: Illumina HumanMethylation450 BeadChip


title: Acinar16 (RNA-seq)


title: Acinar17 (RNA-seq)


title: K562 e1i rep2 [ChIP-seq]

value: dCas9-KRAB expressing K562 cell line

value: K562 cell line


title: E6.5 fraction 2

description:
Mouse embryo at 6.5 days of development
Natural mouse embryos at stage E6.5 (scRNA-seq libraries)


title: K562 e4i rep1 [ChIP-seq]

value: e4 inhibition


title: E6.5 fraction 1


title: ETiX day 8 extra-embryonic compartment fraction 2

description:
Induced synthetic embryo sample at 8 days of development created with the reported method (Amadei et al. 2021), dissected extra-embryonic compartment
Synthetic ETiX embryo at day 8 (scRNA-seq libraries), extra-embryonic cells

source_name: Stem cell derived embryo

value: Stem cell derived synthetic embryo

value: embryonic stem cells transiently expressing Gata4, embryonic and trophoblast stem cells

value: Embryonic stem cells:Sox2-Venus/Bry-mCherry/Oct4-Cyan;CAG-GFP/tetO-mCherry; Cerl-GFP ES cells; CD1 WT. Trophoblast stem cells:WT CD1; ES cells transiently expressing Gata4:CD1; CAG-GFP/tetO-mCherry; tetO=Gata4; Cerl-GFP


title: E8.5 fraction 2


title: K562 e1i rep1 [ChIP-seq]


title: Acinar15 (RNA-seq)

value: exocrine pancreas

value: acinar cell

value: wild type


title: K562 e3i&e7i rep2 [ChIP-seq]

value: e3 and e7 dual inhibition


title: ETiX day 8 extra-embryonic compartment fraction 1


title: K562 e4i rep2 [ChIP-seq]


title: iCCA_41_iCCA

description: Illumina HumanMethylation450 BeadChip

value: male


title: K562 e3i&e7i rep1 [ChIP-seq]


title: Acinar14 (RNA-seq)

value: 9 days as 3D organoids


title: ETiX day 8 fraction 6

description:
Induced synthetic embryo sample at 8 days of development created with the reported method (Amadei et al. 2021), dissected embryonic compartment
Synthetic ETiX embryo at day 8 (scRNA-seq libraries), embryonic cells

value: Mixed strain:CD1/MF1/C57BL/6


title: Acinar13 (RNA-seq)


title: K562 e7i rep1 [ChIP-seq]

value: e7 inhibition


title: K562 e7i rep2 [ChIP-seq]


title: ETiX day 8 fraction 4

value: Euploid


title: iCCA_37_iCCA

description: Illumina HumanMethylation450 BeadChip


title: iCCA_38_iCCA

description: Illumina HumanMethylation450 BeadChip


title: iCCA_39_iCCA

description: Illumina HumanMethylation450 BeadChip


title: iCCA_40_iCCA

description: Illumina HumanMethylation450 BeadChip

value: female


title: Acinar8 (RNA-seq)


title: ETiX day 8 fraction 3


title: Acinar7 (RNA-seq)


title: ETiX day 8 fraction 5


title: Acinar6 (RNA-seq)


title: Acinar5 (RNA-seq)


title: K562 e3i rep2 [ChIP-seq]

value: e3 inhibition


title: K562 e3i rep1 [ChIP-seq]

value: dCas9-KRAB expressing K562 cell line


title: iCCA_44_iCCA

description: Illumina HumanMethylation450 BeadChip

value: FFPE


title: iCCA_35_iCCA

description: Illumina HumanMethylation450 BeadChip


title: ETiX day 8 fraction 2


title: K562 WT rep2 [ChIP-seq]

value: K562 cell line

value: WT


title: Acinar4 (RNA-seq)


title: ETiX day 6 fraction 6

description:
Induced synthetic embryo sample at 6 days of development created with the reported method (Amadei et al. 2021)
Synthetic ETiX embryo at day 6 (scRNA-seq libraries)

value: Stem cell derived synthetic embryo

value: embryonic stem cells transiently expressing Gata4, embryonic and trophoblast stem cells


title: iCCA_33_iCCA

description: Illumina HumanMethylation450 BeadChip