title: E180A_4_S8_R1_001

city: Cambridge

first: Rishav

last: Mitra

state: Massachusetts

address: 16 Divinity Avenue

institute: Harvard University

data_processing:
Reads were aligned to the genome using HISAT2 (Kim et al., 2015, 2019)
Mapped sequence reads were aligned to the genome to obtain read counts using Featurecounts (Liao et al., 2014)
Differential expression analysis was performed using three independent methods: DESeq2, limma-voom, and edgeR
Assembly: dm6
Supplementary files format and content: tab-delimited text files include read counts for each Sample

organism: Drosophila melanogaster

source_name: THD' neurons

growth_protocol: Drosophila strains were grown on standard cornmeal medium supplemented with yeast (ND) at 25°C under a light-dark cycle of 12h and 12h

extract_protocol:
RNA from at least 600  THD’ neurons from the relevant genotypes was subjected to 14 cycles of PCR amplification (SMARTer Seq V4 Ultra Low Input RNA Kit; Takara Bio). 1 ng of amplified RNA was used to prepare cDNA libraries (Nextera XT DNA library preparation kit; Illumina)
RNA libraries for RNA-seq were prepared using SMARTER mRNA-Seq Library Prep Kit following manufacturer's protocols.

value: THD' neurons

value: 72 hrs APF


title: human_DLBCL_region_43

status: Public on Jan 25 2024

type: SRA

city: Singapore

first: Min

last: Liu

address: 13-02, 14 Medical Drive, Singapore

country: Singapore

institute: National University of Singapore

description: DLBCL B2|001|CD20

library_source: transcriptomic

data_processing:
The GeoMx® NGS Pipeline is used to process FASTQ sequencing files from Nanostring GeoMx libraries to produce digital count conversion (.dcc) files. Once complete, all DCC files are packed into a zip file and available to download. This zip file can be uploaded into the GeoMx Digital Spatial Profiler (DSP) system for quality control and normalizaton.
Raw reads were trimmed, stitched, aligned, and deduplicated to transform digital counts data with unique targets. AOIs with fewer than 10,000 raw reads or sequencing saturation <50% were filtered out of the analysis. AOIs with less than 5% of all target genes (18,000+) and target genes that do not achieve the limit of quantitation were removed. The data was then processed with the Q3 normalization method for all the remaining targets. Q3 normalization divides the counts in one segment by the 3rd quartile value for that segment, then subsequently multiplies that value by the geometric mean of the 3rd quartile values of all segments. Q3 normalization rescales the gene expression data such that all segments have similar gene expression ranges. It reduces variance from segment size, segment cellularity, and other technical factors. Underlying the Q3 method is an assumption that, despite biological variation, segments should have similar gene expression count distributions. Thus, Q3 is only appropriate when a probe panel is large and diverse, such as one that targets the full transcriptome.
Assembly: hg38
Supplementary files format and content: The file named processed data (DSP_gene_matrix) showed the genes expression of all DLBCL tissues and 12 tonsil samples, sequencing by illimina hiseq3000.
Supplementary files format and content: The file named processed data2 (DSP_gene_matrix) showed the genes expression of the rest of tonsil samples, sequencing by illimina novaseq 6000.

molecule: total RNA

organism: Homo sapiens

source_name: DLBCL

extract_protocol:
The slides were incubated with blocking Buffer W (200 ?L/slide, NanoString) for 30 min in the humidity chamber at room temperature after hybridization.Each slide was stained with corresponding morophology markers. After immunofluorescent staining, the slides were visualized using the GeoMx® DSP instrument to select regions of interest (ROIs). To acquire representative regions, ROI selection was performed by an expert pathologist. The pathologist was blinded to the group assignment during the ROIs selection. Based on fluorescent staining, each ROI was segmented into corresponding areas of interest (AOIs) - CD68+ regions, CD3+ regions, and CD20+ regions. Subsequently, each AOI was exposed to UV light and photocleaved oligos were aspirated from the solution into the wells of a collection plate.
Collected photocleaved oligos were PCR amplified with the corresponding GeoMx® Seq Code Primer Plate and Master Mix (NanoString). PCR products were pooled and cleaned with AMPure XP beads (Agilent, Santa Clara, California, USA) twice to obtain the libraries. The quality and concentration of libraries were assessed using a high sensitivity DNA Kit (Agilent) and Bioanalyzer. Subsequently, libraries were sequenced on an illumina sequencing platform (Hiseq or NovaSeq) with standard workflow specifications (dual-indexing and paired-end reads (2?×?27?bp)).

tag: tissue

value: DLBCL

tag: region cell_type


title: human_RLT_region_73

description: Tonsil 21-2B+TCP CD20CD68CD3|020|CD20

source_name: reactive lympoid tissues

value: reactive lympoid tissues


title: human_DLBCL_region_49

description: DLBCL B2|003|CD20


title: E180A_2_S6_R1_001

country: USA

tag: cell type

tag: genotype

tag: time


title: LAN233A2

city: London

first: Victor

last: Tybulewicz

address: 1 Midland Road

country: United Kingdom

institute: Francis Crick Institute

description: DS model heart defects

data_processing:
Read trimming and adaptor removal with Trimmomatic (v 0.36)
Read alignment with STAR ( v 2.5.2a) and gene quantification with RSEM( v 1.2.31)
Differential expression analysis DESeq2
Genome_build: GRCm38 Ensembl release 86
Supplementary_files_format_and_content: table of normalized counts per gene  per sample obtained from DESeq

organism: Mus musculus

source_name: Heart

extract_protocol:
Hearts were dissected and snap frozen and kept at -80C. Samples were lysed (buffer RLT Qiagen RNeasy Minikit) and homogenised using a battery-operated pestle motor mixer followed by RNA extraction using Qiagen RNeasy Mini kit using the standard protocol.
cDNA library synthesis using KAPA mRNA HyperPrep Kit (Illumina) and libraries were sequenced on the Illumina HiSeq 4000  following manufacturer's protocols.

tag: developmental stage


title: E180A_1_S5_R1_001


title: human_DLBCL_region_47

description: DLBCL B2|003|CD68


title: human_RLT_region_77

description: Tonsil1+2 CD3CD20CD68|003|CD68


title: human_RLT_region_74

description: Tonsil 21-2B+TCP CD20CD68CD3|021|CD20


title: human_DLBCL_region_44

description: DLBCL B2|002|CD68


title: human_RLT_region_70

description: Tonsil 21-2B+TCP CD20CD68CD3|019|CD68


title: human_DLBCL_region_38

description: DLBCL A3|013|CD68


title: Ctrl_3_S3_R1_001

value: WT


title: human_RLT_region_72

description: Tonsil 21-2B+TCP CD20CD68CD3|020|CD68


title: human_RLT_region_68

description: Tonsil 21-2B+TCP CD20CD68CD3|018|CD68


title: human_DLBCL_region_41

description: DLBCL B2|001|CD68


title: human_RLT_region_71

description: Tonsil 21-2B+TCP CD20CD68CD3|019|CD20


title: human_DLBCL_region_35

description: DLBCL A3|012|CD68


title: human_RLT_region_78

description: Tonsil1+2 CD3CD20CD68|003|CD20


title: Ctrl_1_S1_R1_001


title: E180A_3_S7_R1_001


title: human_DLBCL_region_40

description: DLBCL A3|013|CD20


title: human_RLT_region_65

description: Tonsil 21-2B+TCP CD20CD68CD3|014|CD68


title: human_RLT_region_69

description: Tonsil 21-2B+TCP CD20CD68CD3|018|CD20


title: human_DLBCL_region_37

description: DLBCL A3|012|CD20


title: human_DLBCL_region_32

description: DLBCL A3|011|CD68


title: human_DLBCL_region_46

description: DLBCL B2|002|CD20


title: RNAseq_ZSCAN4_KO_DUX4_rep1

city: Yokohama

first: Tomohiko

last: Akiyama

state: Kanagawa

address: 3-9 Fuku-ura

department: School of medicine

country: Japan

institute: Yokohama city university

data_processing:
Fastq files were processed and analyzed on the Biowardrobe platform
Heat maps were generated by Morpheus
Assembly: hg19
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

molecule: polyA RNA

source_name: Embryonic cells

extract_protocol:
Total RNA was extracted using TRIzol solution (Roche) according to the manufacturer's instructions
The cDNA library was prepared from 500ng of each total RNA sample for massive parallel sequencing using an NEBNext Poly(A) mRNA Magnetic Isolation Module and an Ultra Directional RNA Library Prep Kit for Illumina (NEB). The cDNA library produced ranged from 400 to 1000 bp, including the adaptor sequences

value: Embryonic cells

tag: cell line

value: ES cells (SEES3)

value: Pluripotent stem cells

value: Male

tag: treatment

tag: replication

value: Biological replicate 1


title: human_DLBCL_region_31

description: DLBCL A3|010|CD20


title: human_RLT_region_63

description: Tonsil 21-2B+TCP CD20CD68CD3|013|CD68


title: human_DLBCL_region_34

description: DLBCL A3|011|CD20


title: human_DLBCL_region_29

description: DLBCL A3|010|CD68


title: human_RLT_region_66

description: Tonsil 21-2B+TCP CD20CD68CD3|014|CD20


title: human_RLT_region_64

description: Tonsil 21-2B+TCP CD20CD68CD3|013|CD20


title: RNAseq_ZSCAN4_KO_Ctrl_rep1

value: Ctrl


title: RNAseq_ZSCAN4_KO_DUX4_rep2

value: Biological replicate 2


title: human_DLBCL_region_28

description: DLBCL A3|009|CD20


title: human_RLT_region_60

description: Tonsil 21-2B+TCP CD20CD68CD3|011|CD20


title: Ctrl_4_S4_R1_001


title: RNAseq_ZSCAN4_KO_Ctrl_rep2


title: human_DLBCL_region_26

description: DLBCL A3|009|CD68


title: human_RLT_region_59

description: Tonsil 21-2B+TCP CD20CD68CD3|011|CD68


title: ChIP-seq,  preproBRag1CreT/+;ErgΔ/Δ-AbCAM

city: Melbourne

first: Ashley

middle: P

last: Ng

state: VIC

address: 1G Royal Parade, Parkville

country: Australia

institute: The Walter and Eliza Hall Institute of Medical Research

library_source: genomic

data_processing:
Illumina Casava 1.8.2 software was used for basecalling.
Sequence reads were mapped to GrCM38/mm10
RNA-seq Read count extraction and normalization were performed using edgeR Bioconductor package version 3.34.15. Peak-calling was performed using MACS2 for ChiP-seq.
Assembly: mm10
Supplementary files format and content: RNA-seq and ChIP-seq: bigwig files created using deepTools version 3.5.0

molecule: genomic DNA

source_name: preproB cells

growth_protocol: Leukemia cells were cultured in IMDM media supplemented with 10% FBS with IL7 at 37C with 10% CO2.

extract_protocol:
preB and leukemia sample RNA was harvested using Qiagen RNA kit (Qiagen) and 500ng-1 ug of total RNA was used for sequencing libraries. ChiP-seq sample lysate were isolated from formaldehyde cross-linked cells and sonicated to release chromatin.
RNA libraries for RNA-seq were prepared using TruSeq RNA Library Prep Kit v2 (Illumina) following manufacturer's protocols. ChIP-seq libraries were prepared with KAPA Hyper Prep Kit (Kapa Biosystems)

value: preproB cells


title: RNAseq_ZSCAN4_GFP_Ctrl_rep2


title: RNAseq_ZSCAN4_GFP_DUX4_rep1


title: human_DLBCL_region_25

description: DLBCL A3|008|CD20


title: Ctrl_2_S2_R1_001


title: human_RLT_region_58

description: Tonsil 21-2B+TCP CD20CD68CD3|010|CD20


title: human_RLT_region_61

description: Tonsil 21-2B+TCP CD20CD68CD3|012|CD68


title: #174 preB leukaemia, Tamoxifen pseudo-replicate

source_name: preB cells

value: preB cells

value: preB leukaemia

value: Tamoxifen


title: Human_ZSCAN4_Mouse_Ab_DUX4_plus

data_processing:
Fastq files were processed and analyzed on the Biowardrobe platform
Sequence reads were aligned using bowtie (version 1.2.0)
MACS2 (version 2.1.1.20160309) was used to estimate fragment size and to find islands of enrichment with q-value threshold less than 0.2
To visualize the data, the data were uploaded to UCSC genome browser
MAnorm was used for comparison of ChIP peaks
Heat maps and average signal profiles were generated by Easeq
Assembly: mm10, hg19
Supplementary files format and content: bigwig

extract_protocol:
Cells were cross-linked with 2 mM disuccinimidyl glutarate in PBS/1 mM MgCl2 for 40 min at room temperature followed by 1% formaldehyde in PBS for 15 min at room temperature. The reaction was stopped by 125 mM glycine. The cells were washed with PBS and stored at –80°C prior to use. The cells were lysed in Lysis buffer (10 mM Tris-HCl, pH8.0, 1 mM EDTA, 0.5 mM EGTA, 100 mM NaCl, 0.1% Na-Deoxycholate, 0.5% N-lauroyl sarcosine) containing proteinase inhibitor cocktail (Roche). Sonication was conducted with the Handy sonicator UR-21P (Tomy) to generate DNA fragments of approximately 150-450 bp. The sonicated lysates from approximately 2 x 106 cells were diluted in ChIP dilution buffer (10 mM HEPES, pH 7.4, 50 mM NaCl, 1% IGEPAL-CA-630, 10% glycerol) containing proteinase inhibitor cocktail and incubated overnight at 4°C with 50 µl of protein G magnetic beads (Invitrogen) that were preincubated with ~2 µg of mouse Zscan4 antibodies. The precipitants were washed once with high salt wash buffer (20 mM Tris-HCl, pH8.0, 400 mM NaCl, 2 mM EDTA, 0.1% SDS, 0.2% Triton-X), three times with LiCl wash buffer (10 mM Tris-HCl, pH 8.0, 1 mM EDTA, 250 mM LiCl, 1% NP40, 1% Na-deoxycholate) and once with 10 mM Tris-HCl, pH 8.0, 5 mM EDTA, 10 mM NaCl. Bound chromatin was eluted in elution buffer (90 mM NaHCO3, 1% SDS), followed by RNase treatment at 37°C for 30 min and crosslink reversal with decross-linking mixture (2 M NaCl, 0.1 M EDTA, 0.4 M Tris-HCl, pH 6.8) containing proteinase K at 65°C for 3 h. DNA was purified by a phenol-chloroform-isoamylalcohol extraction and ethanol precipitation.
ChIP DNA libraries were prepared with the NEBNext ChIP-Seq Library Prep Kit for Illumina (NEB)

tag: antibody

value: Technical replicate 2


title: human_DLBCL_region_22

description: DLBCL A3|007|CD20


title: ChIP-seq,  proBC57BL/6-AbCAM

source_name: proB cells

value: proB cells


title: human_DLBCL_region_23

description: DLBCL A3|008|CD68


title: RNAseq_ZSCAN4_GFP_Ctrl_rep1


title: human_RLT_region_56

description: Tonsil 21-2B+TCP CD20CD68CD3|009|CD68


title: human_DLBCL_region_20

description: DLBCL A3|007|CD68


title: #174 preB leukaemia, Tamoxifen


title: RNAseq_ZSCAN4_GFP_DUX4_rep2


title: human_RLT_region_49

description: Tonsil 21-2B+TCP CD20CD68CD3|003|CD68


title: #174 preB leukaemia, DMSO pseudo-replicate

value: DMSO


title: Human_ZSCAN4_Mouse_Ab_DUX4_minus


title: Human_ZSCAN4_Rabbit_Ab_DUX4_plus


title: human_DLBCL_region_19

description: DLBCL A3|006|CD20

value: DLBCL


title: #174 preB leukaemia, DMSO


title: human_RLT_region_47

description: Tonsil 21-2B+TCP CD20CD68CD3|001|CD20

value: reactive lympoid tissues


title: #162 preB leukaemia, Tamoxifen pseudo-replicate


title: human_DLBCL_region_16

description: DLBCL A3|005|CD20


title: human_RLT_region_57

description: Tonsil 21-2B+TCP CD20CD68CD3|009|CD20


title: human_RLT_region_30

description: Tonsil 17-4B+TCP CD20CD3CD68|024|CD20


title: #162 preB leukaemia, Tamoxifen


title: human_DLBCL_region_14

description: DLBCL A3|005|CD68


title: cmasB, R1

city: Würzburg

first: Alexander

middle: J.

last: Westermann

address: Josef-Schneider-Straße 2/D15

country: Germany

institute: Helmholtz Institute for RNA-based Infection Research (HIRI), Helmholtz Centre for Infection Research (HZI),

description: c201_R1_mapped_sorted.bam (column name in MS2_counts.csv)

data_processing:
Generated reads were quality-checked using FastQC (v0.11.8) and adapters were trimmed using Cutadapt (v1.16) with Python (v3.6.6), using the following parameters: -j 6 -a Illumina Read 1 adapter=AAGATCGGAAGAGCACACGTCTGAACTCCAGTCA -a Poly A=AAAAAAAAAAA --output=out1.fq.gz --error-rate=0.1 --times=1 --overlap=3 --minimum-length=20 --nextseq-trim=20 3_1.
For the both sequencing data types (dRNA-seq and conventional RNA-seq), READemption (v0.4.5) was used to map reads.
ANNOgesic pipeline (v0.7.33) was used to annotate transcriptomic features prior to manual curation.
Assembly: B. thetaiotaomicron VPI-5482 reference genome (NC_004663.1) and plasmid (NC_004703.1)
Supplementary files format and content: Count tables as excel files

organism: Bacteroides thetaiotaomicron

source_name: Bacteria

growth_protocol: Growth assays in the presence of diverse carbon sources were carried out in minimal medium (MM), supplemented with 0.5% of a suitable carbon source. Stress response assays were performed in TYG medium containing the indicated concentration of a stressor and incubated for a further 2 h. MS2 affinity purification was performed on cultures grown in TYG medium until an OD of 2.0, followed by 2 h  incubation with inducer, anhydrotetracycline (aTC).

extract_protocol:
Total RNA was isolated by the hot phenol method. Traces of genomic DNA were removed by treatment with DNase I (Fermentas) and Superase-In RNase Inhibitor (Ambion)
For conventional RNA-seq, libraries were prepared with the NEBNext Multiplex Small RNA Library Prep kit for Illumina according to the manufacturer’s instructions. For differential RNA-seq (dRNA-seq) and MS2 affinity purification and sequencing, libraries were prepared with the TruSeq Library Prep kit for Illumina.

tag: strain

value: Bacteria

value: masB+

tag: condition

value: masB control


title: cmasB, R2

description: c201_R2_mapped_sorted.bam (column name in MS2_counts.csv)


title: human_RLT_region_29

description: Tonsil 17-4B+TCP CD20CD3CD68|023|CD20


title: human_RLT_region_28

description: Tonsil 17-4B+TCP CD20CD3CD68|022|CD20


title: human_DLBCL_region_13

description: DLBCL A3|004|CD20


title: MS2-cmasB, R2

description: MS2_c201_R2_mapped_sorted.bam (column name in MS2_counts.csv)

value: MS2 aptamer tagged masB


title: #162 preB leukaemia, DMSO


title: #86 preB leukaemia, Tamoxifen pseudo-replicate


title: human_DLBCL_region_11

description: DLBCL A3|004|CD68


title: MS2-cmasB, R1

description: MS2_c201_R1_mapped_sorted.bam (column name in MS2_counts.csv)


title: human_RLT_region_27

description: Tonsil 17-4B+TCP CD20CD3CD68|022|CD68


title: human_RLT_region_46

description: Tonsil 21-2B+TCP CD20CD68CD3|001|CD68


title: human_DLBCL_region_17

description: DLBCL A3|006|CD68


title: human_DLBCL_region_08

description: DLBCL A3|003|CD68


title: human_DLBCL_region_10

description: DLBCL A3|003|CD20


title: #86 preB leukaemia, DMSO pseudo-replicate


title: human_RLT_region_26

description: Tonsil 17-4B+TCP CD20CD3CD68|021|CD20


title: Pooled samples - TEX, R2

description: Cutadapt_3_34_plus_TEX_S22_R1_001.fastq.gz.fastqsanger (column name in Pool_counts.csv)

value: WT

value: Pool


title: #86 preB leukaemia, DMSO


title: Pooled samples - noTEX, R2

description: Cutadapt_3_34_minus_TEX_S23_R1_001.fastq.gz.fastqsanger (column name in Pool_counts.csv)


title: human_DLBCL_region_07

description: DLBCL A3|002|CD20


title: Pooled samples - TEX, R1

description: Cutadapt_3_17_plus_TEX_S20_R1_001.fastq.gz.fastqsanger (column name in Pool_counts.csv)


title: human_RLT_region_22

description: Tonsil 17-4B+TCP CD20CD3CD68|014|CD20


title: Pooled samples - noTEX, R1

description: Cutadapt_3_17_minus_TEX_S21_R1_001.fastq.gz.fastqsanger (column name in Pool_counts.csv)


title: human_DLBCL_region_05

description: DLBCL A3|002|CD68


title: human_RLT_region_23

description: Tonsil 17-4B+TCP CD20CD3CD68|017|CD20


title: #86 preB leukaemia, Tamoxifen


title: #87 preB leukaemia, Tamoxifen pseudo-replicate


title: human_DLBCL_region_04

description: DLBCL A3|001|CD20


title: #87 preB leukaemia, DMSO pseudo-replicate


title: human_DLBCL_region_02

description: DLBCL A3|001|CD68


title: human_RLT_region_21

description: Tonsil 17-4B+TCP CD20CD3CD68|013|CD20


title: TYG-Aerobe, R2

description: Cutadapt_on_3_32.fq.gz.fastqsanger (column name in RNAseq_counts.csv)

value: Stress condition


title: human_RLT_region_20

description: Tonsil 17-4B+TCP CD20CD3CD68|011|CD20


title: #87 preB leukaemia, DMSO


title: human_DLBCL_region_01

description:
For this template control, it is only for quality control when we run it on the GeoMx DSP instrument. It will not be converted in processed file .
No Template Control

value: template control


title: TYG-Control, R2

description: Cutadapt_on_3_33.fq.gz.fastqsanger (column name in RNAseq_counts.csv)


title: human_RLT_region_25

description: Tonsil 17-4B+TCP CD20CD3CD68|019|CD68


title: #87 preB leukaemia, Tamoxifen


title: TYG-Acid, R2

description: Cutadapt_on_3_31.fq.gz.fastqsanger (column name in RNAseq_counts.csv)


title: human_RLT_region_19

description: Tonsil 17-4B+TCP CD20CD3CD68|011|CD68


title: TYG-Heat, R2

description: Cutadapt_on_3_30.fq.gz.fastqsanger (column name in RNAseq_counts.csv)


title: Female wild-type non-breeders

city: Philadelphia

first: Apoorva

last: Babu

state: PA

address: SCTR, 3400 Civic Center Blvd

department: Cardiovascular Institute

institute: University of Pennsylvania

library_source: transcriptomic single cell

data_processing:
Fastq files were aligned to the mm39 reference genome using STARSolo V2.7.9a
Downstream processing was performed using Seurat V4
Assembly: mm39
Supplementary files format and content: tab separated matrix files, barcode and features tsv files

source_name: lung

extract_protocol:
No treatments to WT versus KO mice; KO were generated by crossing Tsc2loxP/loxP mice with Tbx4LME_Cre mice. Murine lungs were inflated under constant pressure (25 cm H2O) and the pulmonary circulation was flushed with 2cc of PBS. Lungs were collected and mechanically minced prior to enzymatic digestion with collagenase, dispase and DNase. Samples were then filtered, RBC lysed with ACK lysis buffer and processed into single cell suspension.  CD45+ immune cells were depleted using MACS LS columns with CD45-microbeads with 2 × 10^6 cells per column to enhance purity and viability.
Libraries were prepared for sequencing using standard Illumina protocols

value: lung

value: CD45 depleted cells + 10% CD45+ cells

value: Tbx4Tsc2 WT


title: TYG-Cold, R2

description: Cutadapt_on_3_29.fq.gz.fastqsanger (column name in RNAseq_counts.csv)


title: human_RLT_region_17

description: Tonsil 17-4B+TCP CD20CD3CD68|010|CD68


title: human_RLT_region_18

description: Tonsil 17-4B+TCP CD20CD3CD68|010|CD20


title: Female Knockout non-breeders

value: Tbx4Tsc2 KO


title: human_RLT_region_16

description: Tonsil 17-4B+TCP CD20CD3CD68|009|CD20


title: TYG-Deoxycholic acid, R2

description: Cutadapt_on_3_27.fq.gz.fastqsanger (column name in RNAseq_counts.csv)


title: Mouse_Zscan4_RA

value: Embryonic cells

value: ES cells (MC1)

value: Pluripotent stem cells

value: Male

value: Retinoic acid

value: Technical replicate 2


title: human_RLT_region_15

description: Tonsil 17-4B+TCP CD20CD3CD68|008|CD20

value: reactive lympoid tissues


title: Mouse_Zscan4_ES

value: No treat


title: human_RLT_region_14

description: Tonsil 17-4B+TCP CD20CD3CD68|007|CD20


title: #162 preB leukaemia, DMSO pseudo-replicate

value: preB cells

value: preB leukaemia

value: DMSO


title: Human_ZSCAN4_Rabbit_Ab_DUX4_minus

value: ES cells (SEES3)


title: TYG-Gentamicin, R2

description: Cutadapt_on_3_26.fq.gz.fastqsanger (column name in RNAseq_counts.csv)

value: Bacteria

value: WT

value: Stress condition


title: PFC from F2 sGC sample, biological rep 6

type: RNA

city: Toronto

first: Christopher

last: Casciaro

state: ON

address: 1 King's College Circle

department: Department of Physiology

country: Canada

institute: University of Toronto

description: miRNA levels in F2 female PFC

hyb_protocol: 16 hours at 48C

scan_protocol: Affymetrix GeneChip Scanner 3000

data_processing: The data were analyzed with the Affymetrix Transcriptome Analysis Console 4.0.1(TAC) software using RMA+DMG. Differential analysis was conducted between control and sGC groups for each generation (F1-F3) in adult male germ cells, and for the F2 female PFC data, for a total of 4 analyses. All differential expression analyses were calculated using one-way ANOVA with Benjamini-Hochberg Step-UP FDR correction

label: Biotin

organism: Cavia porcellus

source_name: F2 female PFC germ cells, guinea pigs generated from F1 males that were generated from F0 females exposed to  sGC  in late pregnancy

label_protocol: 1000ng of total RNA was used. Samples were labelled with FlashTag Biotin according to the manufacturer’s instructions

growth_protocol: Guinea pigs were singly housed  on a 12-hour light-dark cycle. F0 females were mated with males to produce the F1 generation. F1 and F2 males were left undisturbed until adulthood and were mated with naiive females to generate F2 and F3 offspring, respectively.  F1-F3 offspring were assigned to juvenile or breeding streams. Litters were weaned on PND 20 and pair-housed with an age-, sex- and treatment-matched partner. Food and water were available ad libitum.

extract_protocol: Total RNA was extracted from germ cells and PFC using Trizol, according to the manufacturer’s recommendations, with some modifications.  RNA was extracted from a total of 49 samples. Germ cells in F1-F3 adult male guinea pigs : F1_Ctrl(n=7), F1_sGC(n=6), F2(n=6/gp), and F3 (n=6/gp). PFC from F2 female guinea pigs (n=6/group).

treatment_protocol: Females (F0) were mated with males and once pregnant were treated with three courses of a clinically-relevant dose (1mg/kg) of betamethasone (Beta) or saline (Ctrl) on GD 40&41, 50&51, 60&61. Germ cells from  F1 -F3 adult male offspring were collected using a density gradient followed by chemical and mechanical digestion  F1_Ctrl(n=7), F1_sGC(n=6), F2(n=6/gp), and F3 (n=6/gp). Prefrontal cortext from adult female F2 (PND40) offspring was isolated and was stored in -80C prior to RNA extraction.

value: PFC from F2 female guinea pigs

tag: Sex

value: female

value: SGC


title: PFC from F2 sGC sample, biological rep 5

description: miRNA levels in F2 female PFC


title: TYG-Hydrogen peroxide, R2

description: Cutadapt_on_3_25.fq.gz.fastqsanger (column name in RNAseq_counts.csv)


title: preB leukaemia #5


title: preB leukaemia #4


title: MM-Starvation, R2

description: Cutadapt_on_3_24.fq.gz.fastqsanger (column name in RNAseq_counts.csv)

value: Carbon source


title: human_RLT_region_11

description: Tonsil 17-4B+TCP CD20CD3CD68|006|CD68


title: PFC from F2 sGC sample, biological rep 4

description: miRNA levels in F2 female PFC


title: PFC from F2 sGC sample, biological rep 3

description: miRNA levels in F2 female PFC


title: Mouse_Zscan4_MEF

value: Embryonic cells

value: ES cells (MC1)

value: Pluripotent stem cells


title: MM-Mucin, R2

description: Cutadapt_on_3_23.fq.gz.fastqsanger (column name in RNAseq_counts.csv)


title: TYG-Bile salts, R2

description: Cutadapt_on_3_28.fq.gz.fastqsanger (column name in RNAseq_counts.csv)


title: preB leukaemia #3


title: human_RLT_region_09

description: Tonsil 17-4B+TCP CD20CD3CD68|005|CD68


title: MM-GlcNAc, R2

description: Cutadapt_on_3_22.fq.gz.fastqsanger (column name in RNAseq_counts.csv)


title: human_RLT_region_07

description: Tonsil 17-4B+TCP CD20CD3CD68|004|CD68


title: preB leukaemia #2


title: human_RLT_region_06

description: Tonsil 17-4B+TCP CD20CD3CD68|003|CD20


title: MM-Maltose, R2

description: Cutadapt_on_3_21.fq.gz.fastqsanger (column name in RNAseq_counts.csv)


title: human_RLT_region_13

description: Tonsil 17-4B+TCP CD20CD3CD68|007|CD68


title: MM-Arabinose, R2

description: Cutadapt_on_3_20.fq.gz.fastqsanger (column name in RNAseq_counts.csv)


title: preB leukaemia #1


title: human_RLT_region_05

description: Tonsil 17-4B+TCP CD20CD3CD68|003|CD68


title: preB #2

value: preB


title: MM-Xylose, R2

description: Cutadapt_on_3_19.fq.gz.fastqsanger (column name in RNAseq_counts.csv)


title: human_RLT_region_03

description: Tonsil 17-4B+TCP CD20CD3CD68|002|CD68

value: reactive lympoid tissues


title: preB #1


title: MM-Glucose, R2

description: Cutadapt_on_3_18.fq.gz.fastqsanger (column name in RNAseq_counts.csv)


title: human_RLT_region_02

description: Tonsil 17-4B+TCP CD20CD3CD68|001|CD20


title: preB #4


title: human_RLT_region_01

description: Tonsil 17-4B+TCP CD20CD3CD68|001|CD68


title: TYG-Aerobe, R1

description: Cutadapt_on_3_15.fq.gz.fastqsanger (column name in RNAseq_counts.csv)


title: preB #3


title: LAN326A9_S38_L006

description: rescue

extract_protocol:
Hearts were dissected and snap frozen and kept at -80C. Samples were lysed (buffer RLT Qiagen RNeasy Minikit) and homogenised using a battery-operated pestle motor mixer followed by RNA extraction using Qiagen RNeasy Mini kit using the standard protocol.
cDNA library synthesis using KAPA mRNA HyperPrep Kit (Illumina) and libraries were sequenced on the Illumina HiSeq 2500  following manufacturer's protocols.


title: MDA-MB-231 cells, siCCR5 (KD3)

city: Shanghai

first: Ling

last: Chen

state: Shanghai

address: 800 Dingchuan Road

country: China

institute: Shanghai Jiao Tong univesity

data_processing:
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.
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).
Differential expression analysis of two conditions/groups (two biological replicates per condition) was performed using the DESeq2 R package (1.20.0). 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 expression.
Gene Ontology (GO) enrichment analysis of differentially expressed genes was implemented by the clusterProfiler R package (3.8.1), in which gene length bias wascorrected. GO terms with corrected Pvalue less than 0.05 were considered significantly enriched by differential expressed genes.
ClusterProfiler R package (3.8.1) to test the statistical enrichment of differential expression genes in KEGG pathways. The Reactome database brings together the various reactions and biological pathways of human model species. Reactome pathways with corrected Pvalue less than 0.05 were considered significantly enriched by differential expressed genes.
Pheatmap was used to display heatmaps of the expression levels of differentially expressed genes, which normalized by z-score.
Assembly: GRCh38/hg38
Supplementary files format and content: GOenrich_significant excel file include Category, GOID, Description, GeneRatio, BgRatio, pvalue, padj, geneID, geneName and Count.
Supplementary files format and content: KEGG_downregulated/upregulated_KEGGenrich_significant excel files include KEGGID, Description, GeneRatio, BgRatio, pvalue, padj, geneID, geneName, keggID and Count.
Supplementary files format and content: Leukocyte migration-Union_for_cluster and Positive regulation of cell migration-Union_for_cluster excel files include FPKM values for each Sample.
Supplementary files format and content: siCCR5vssiNC_deg_all excel file include gene_id, FPKM values for each Sample,  log2FoldChange, pvalue, padj, gene_name, gene_chr, gene_start, gene_end, gene_strand, gene_length, gene_biotype, gene_description and tf_family.

extract_protocol:
RNAs from the control (siNC) and CCR5 knockdown (siCCR5) MDA-MB-231 cells were extracted by using TRIzol reagent (Invitrogen, Cat#15596026).
RNA-seq libraries were constructed by NEBNext® Ultra RNA Library Prep Kit for Illumina (NEB, Cat# E7530L) according to the manufacturer’s protocol.

treatment_protocol: Wild type cells were transfected with CCR5-targeted siRNA by using lipofectamineTM 2000 transfection reagent following the manufacturer’s instructions. Total RNA was extracted 48 h post transfection.

value: Triple-negative breast cancer cells

value: CCR5 knockdown


title: TYG-Acid, R1

description: Cutadapt_on_3_14.fq.gz.fastqsanger (column name in RNAseq_counts.csv)


title: MDA-MB-231 cells, siCCR5 (KD2)


title: LAN326A18_S47_L007

description: rescue


title: TYG-Heat, R1

description: Cutadapt_on_3_13.fq.gz.fastqsanger (column name in RNAseq_counts.csv)


title: LAN326A17_S46_L007

description: rescue


title: TYG-Control, R1

description: Cutadapt_on_3_16.fq.gz.fastqsanger (column name in RNAseq_counts.csv)


title: TYG-Cold, R1

description: Cutadapt_on_3_12.fq.gz.fastqsanger (column name in RNAseq_counts.csv)


title: MDA-MB-231 cells, siNC (NC2)

treatment_protocol: Wild type cells were transfected with negative control siRNA by using lipofectamineTM 2000 transfection reagent following the manufacturer’s instructions. Total RNA was extracted 48 h post transfection.

value: scramble knockdown


title: sn_OA_1

city: Shenyang

first: Lutian

last: Yao

address: 155 Nanjing st

department: Department of Orthopedic

institute: the First Affiliated Hospital of China Medical University

description: 10x Genomics

data_processing:
Cell Ranger (Version 6.0.2) was used to demultiplex the reads, which was followed by extraction of the cell barcodes and unique molecular identifiers (UMIs). The cDNA insert sequence was aligned to the human reference genome (GRCh38-2020).
Assembly: GRCh38-2020
Supplementary files format and content: Tab-separated values files and matrix files

molecule: nuclear RNA

source_name: joint

extract_protocol:
The fresh specimens were subjected to collagenase digestion to isolate the cells. For snRNA, fresh specimens were snap frozen by liquid nitrogen, then 10X protocol of isolating nuclei were applied. Then, approximately 20,000 cells/nuclei were used to acquire a single library of 10,000 cells/nuclei by a Chromium controller.
Library was performed according to the manufacter’s instructions (single cell 3’ v3 protocol, 10x Genomics).

value: joint

value: IPFP/synovium cell

tag: disease state

value: osteoarthritis


title: LAN326A20_S49_L007

description: control

value: WT


title: TYG-Deoxycholic acid, R1

description: Cutadapt_on_3_10.fq.gz.fastqsanger (column name in RNAseq_counts.csv)

value: Bacteria

value: Stress condition


title: TYG-Gentamicin, R1

description: Cutadapt_on_3_9.fq.gz.fastqsanger (column name in RNAseq_counts.csv)


title: PFC from F2 sGC sample, biological rep 1

description: miRNA levels in F2 female PFC

value: PFC from F2 female guinea pigs

value: female


title: LAN326A15_S44_L007

description: rescue


title: TYG-Hydrogen peroxide, R1

description: Cutadapt_on_3_8.fq.gz.fastqsanger (column name in RNAseq_counts.csv)


title: sn_OA_2

description: 10x Genomics


title: PFC from F2 sGC sample, biological rep 2

description: miRNA levels in F2 female PFC

value: SGC


title: LAN326A14_S8_L003

description: rescue


title: TYG-Bile salts, R1

description: Cutadapt_on_3_11.fq.gz.fastqsanger (column name in RNAseq_counts.csv)


title: PFC from F2 control sample, biological rep 6

description: miRNA levels in F2 female PFC

source_name: F2 female PFC germ cells, guinea pigs generated from F1 males that were generated from F0 females exposed to  Control (saline)  in late pregnancy

value: Ctrl


title: LAN326A19_S9_L003

description: control


title: sc_OA_3

description: 10x Genomics


title: PFC from F2 control sample, biological rep 3

description: miRNA levels in F2 female PFC


title: Germ cell from F3 control sample, biological rep 6

description: miRNA levels in F3 germ cells

source_name: F3 male germ cells, guinea pigs generated from F2 males that were generated from F1 males that were generated from F0 females exposed to control (saline)  in late pregnancy

value: Germ cells from F3 male guinea pigs

value: male


title: Germ cell from F3 sGC sample, biological rep 3

description: miRNA levels in F3 germ cells

source_name: F3 male germ cells, guinea pigs generated from F2 males that were generated from F1 males that were generated from F0 females exposed to sGC  in late pregnancy


title: Germ cell from F3 sGC sample, biological rep 6

description: miRNA levels in F3 germ cells


title: PFC from F2 control sample, biological rep 2

description: miRNA levels in F2 female PFC


title: Germ cell from F3 sGC sample, biological rep 2

description: miRNA levels in F3 germ cells


title: Germ cell from F3 sGC sample, biological rep 4

description: miRNA levels in F3 germ cells


title: PFC from F2 control sample, biological rep 4

description: miRNA levels in F2 female PFC


title: Germ cell from F3 control sample, biological rep 4

description: miRNA levels in F3 germ cells


title: LAN326A16_S45_L007

description: control


title: Germ cell from F3 sGC sample, biological rep 1

description: miRNA levels in F3 germ cells


title: PFC from F2 control sample, biological rep 1

description: miRNA levels in F2 female PFC


title: PFC from F2 control sample, biological rep 5

description: miRNA levels in F2 female PFC


title: Germ cell from F3 control sample, biological rep 5

description: miRNA levels in F3 germ cells


title: Germ cell from F3 sGC sample, biological rep 5

description: miRNA levels in F3 germ cells


title: sn_healthy_1

description: 10x Genomics

value: healthy


title: MM-Starvation, R1

description: Cutadapt_on_3_7.fq.gz.fastqsanger (column name in RNAseq_counts.csv)

value: Carbon source


title: MM-GlcNAc, R1

description: Cutadapt_on_3_5.fq.gz.fastqsanger (column name in RNAseq_counts.csv)


title: LAN326A10_S39_L006

description: control


title: Germ cell from F3 control sample, biological rep 3

description: miRNA levels in F3 germ cells


title: sc_OA_1

description: 10x Genomics


title: LAN326A13_S7_L003

description: control


title: sc_OA_2

description: 10x Genomics


title: MM-Mucin, R1

description: Cutadapt_on_3_6.fq.gz.fastqsanger (column name in RNAseq_counts.csv)


title: LAN326A7_S5_L003

description: DS


title: MDA-MB-231 cells, siNC (NC3)

value: Triple-negative breast cancer cells


title: Germ cell from F3 control sample, biological rep 1

description: miRNA levels in F3 germ cells


title: MM-Xylose, R1

description: Cutadapt_on_3_2.fq.gz.fastqsanger (column name in RNAseq_counts.csv)


title: LAN326A4_S33_L006

description: DS


title: Germ cell from F3 control sample, biological rep 2

description: miRNA levels in F3 germ cells


title: bri_1622_vdj

city: Boston

first: JAE WON

last: CHO

state: MA

address: 60 Fenwood Road

department: Neurology

institute: Brigham and Women's Hospital

description: 10x Genomics

data_processing:
Sample demultiplexing, barcode processing, alignment, filtering, UMI counting, and aggregation of multiple sequencing runs were performed using the Cell Ranger analysis pipeline (v6.1.2)
Background and non-cellular barcodes are removed
Assembly: GRCh38
Supplementary files format and content: .tsv: barcodes, genes, .mtx: count matrix, .csv: tcr sequence

source_name: tumor

extract_protocol:
Renal tumor samples were dissociated into single cells by a semi-automated combined mechanical/enzymatic process. The tumor tissue was cut into pieces of (2-3mm) in size and transferred to C Tubes (Miltenyi Biotech) containing a mix of Enzymes H, R and A (Tumor Dissociation Kit, human; Miltenyi Biotech). Mechanical dissociation was accomplished by performing a program (37C_h_TDK_1) on the gentleMAC Octo Dissociator with Heaters (Miltenyi Biotech). Single cell suspensions generated from ccRCC tumor samples were FACS sorted on a SONY MA900 sorter (SONY) for viable human CAR-T cells (Zombie- mCD45- hCD45+ CD3+, BioLegend).
Sorted cells were stained with a distinct barcoded antibody (Cell-Hashing antibody, TotalSeq-A, Biolegend). Next, 7,500 cells from each condition were resuspended in 0.4% BSA in PBS at a concentration of 1,000 cells per μl, pooled together, then loaded onto a single lane (Chromium chip B, 10X Genomics) followed by encapsulation in a lipid droplet (Single Cell 5′ kit V3, 10X Genomics) followed by cDNA and library generation according to the manufacturer’s protocol. mRNA library was sequenced to an average of 50,000 reads per cell, and HTO (Cell Hashing antibodies) library sequenced to an average of 5,000 reads per cell, both using Illumina Novaseq.

value: CD45+ immune cells

value: tumor


title: sc_healthy_3

description: 10x Genomics

value: joint


title: LAN326A3_S3_L003

description: DS


title: MM-Glucose, R1

description: Cutadapt_on_3_1.fq.gz.fastqsanger (column name in RNAseq_counts.csv)


title: LAN326A6_S35_L006

description: DS


title: Germ cell from F2 sGC sample, biological rep 6

description: miRNA levels in F2 germ cells

source_name: F2 male germ cells, guinea pigs generated from F1 males that were generated from F0 females exposed to sGC  in late pregnancy

value: Germ cells from F2 male guinea pigs


title: MM-Maltose, R1

description: Cutadapt_on_3_4.fq.gz.fastqsanger (column name in RNAseq_counts.csv)


title: bri_1621_gex

description: 10x Genomics


title: sc_healthy_2

description: 10x Genomics

value: IPFP/synovium cell


title: bri_1620_vdj

description: 10x Genomics


title: MM-Arabinose, R1

description: Cutadapt_on_3_3.fq.gz.fastqsanger (column name in RNAseq_counts.csv)

value: WT


title: LAN326A5_S4_L003

description: control


title: bri_1619_gex

description: 10x Genomics


title: Heart_Inp_14dpi_r2

city: Mannheim

first: Gergana

last: Dobreva

state: Baden Württemberg

address: Ludolf-Krehl-Str. 7-11

department: Cardiovascular Genomics and Epigenomics

institute: Medical Faculty Mannheim/University of Heidelberg

data_processing:
Raw reads were trimmed with Trimmomatic-0.36 with the parameters (ILLUMINACLIP:${ADAPTERS}:2:30:10 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:20 CROP:70 HEADCROP:10.
The trimmed reads were mapping using Bowtie2 (default settings) to the zebrafish genome from ucsc version danRer11.
Mapped reads were converted to from sam to bam by the help of samtools.
PCR duplicates were removed from the bam files with the help of MarkDuplicates.jar from Picard1.119.
Bam files were merged by the help of bamtools merge and from the merged files the bigwig files were created. We used bamCoverage from deptools (-bs 20 --smoothLength 40 -p max --normalizeUsing RPKM -e 150)
for Peak calling, for H3K27me3, (--broad -g 1.4e+9 -q 0.01 --keep-dup 1 --fix-bimodal --nomodel --extsize 520 ) for the other histone marks the settings were similar to H3K27me3, but with -d 200.  Peaks were annotated using annotatePeaks.pl (danRer11 -gtf custom.gtf). We used a custom gtf file that combined genes presented in the UCSC tables from EMSEMBL, REFSEQ and from NONCODE version5. The NONCODE data was liftover to danRer11 from danRer10 by the help of liftOver script from UCSC
Assembly: danRer11
Supplementary files format and content: BigWig files

organism: Danio rerio

source_name: heart

growth_protocol: All animal experiments have been performed in accordance with the guidelines of the state of Baden Württemberg by the approved by the Regierungspräsidium in Heidelberg

extract_protocol:
Nuclei of embryos were disrupted and sonicated to yield fragment size ranging from 200-500bp. Lysates were incubated with the respective antibodies and bound DNA after washes was extracted using Qiagen PCR cleanup kit.
Libraries were prepared according to Illumina's instructions accompanying the Ovation Ultra Low Kit

treatment_protocol: Cryoinjury of the fished was performed accoring to Schnabel et al 2011.

tag: age

value: 3–6 months old fish

value: heart

value: wt


title: LAN326A12_S41_L007

description: DS


title: LAN326A8_S37_L006

description: control


title: Heart_Inp_14dpi_r1


title: Heart_Inp_45dpi_r2


title: Heart_Inp_45dpi_r1


title: LAN326A11_S6_L003

description: control


title: LAN326A1_S30_L006

description: control


title: Heart_Inp_04dpi_r1


title: LAN326A2_S31_L006

description: control


title: Heart_Inp_01dpi_r2


title: MRW_P6_Dex_in vivo

first: Lijian

last: Hui

address: yueyang road 320

department: SIBCB

institute: CEMCS, CAS

data_processing:
All sequencing reads from RNA-seq were mapped to the human reference genome (GRCh38.84) using hisat2-2.10.
FPKM (fragments per kilobase of exon per million fragments mapped) values were calculated by Cufflinks v.2.2.1 using default parameters for gene expression levels.
We used htseq-count to count reads on genes.
Differential expression analysis was performed using DESeq2 (R package).
Genome_build: GRCh38.84
Supplementary_files_format_and_content: excel files include FPKM values for each Sample.

source_name: MRW P6 after repopulating 5months in Dex-treated FRG mouse

growth_protocol: Primary human hepatocytes or proliferating human hepatocytes were seeded at 2 x 104 cells/cm2 on collagen-coated plates (Corning) in HM. The medium was changed every 3 days. At day 9 of culture, cells cultured in the presence of HM were harvested via trypsinization

extract_protocol:
Proliferaitng human hepatocyte or mouse liver were removed, flash frozen on dry ice, total RNA was extracted using Trizol (Invitrogen) according to the manufacturer’s instructions.
RNA libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: For Dexamethasone treatment, mice were administered 10mg/kg Dex by intraperitoneal injection 5 minutes before transplantation at the first day and for the next two days. 5x105 lc-ProliHH in 100 ul PBS were intrasplenically transplanted into FRG mice. After transplantation, NTBC was withdrawn and transiently put on for two days when mice lost 20% of their body weights. Mice were sacrificed 5 months later and collect liver samples.

value: fresh human hepatocytes isolated from lc-ProliHH-repopulated Fah-/-Rag2-/-IL4rg-/- mouse liver

tag: tag

value: mouse liver

tag: passages

value: fresh  isolated human hepatocyte


title: bri_1618_vdj

description: 10x Genomics

tag: tissue


title: Germ cell from F2 sGC sample, biological rep 5

description: miRNA levels in F2 germ cells

value: SGC


title: sc_healthy_1

description: 10x Genomics


title: Germ cell from F2 sGC sample, biological rep 2

description: miRNA levels in F2 germ cells

value: male


title: Germ cell from F2 sGC sample, biological rep 4

description: miRNA levels in F2 germ cells


title: M01, JAK2VF_homozygous

city: Aachen

first: Martin

last: Zenke

address: Pauwelsstrasse 30

department: Hematology, Oncology and Stem Cell Transplantation

institute: RWTH Aachen University

description:
M21_minus_S21
bulk RNA-seq of human induced pluripotent stem cells

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

source_name: IPSC

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

value: blood

value: iPS cell-derived CD61+ megakaryocyte


title: bri_1617_gex

description: 10x Genomics


title: Germ cell from F2 control sample, biological rep 6

description: miRNA levels in F2 germ cells

source_name: F2 male germ cells, guinea pigs generated from F1 males that were generated from F0 females exposed to  Control (saline)  in late pregnancy

value: Ctrl


title: Germ cell from F2 sGC sample, biological rep 1

description: miRNA levels in F2 germ cells


title: Heart_Inp_04dpi_r2


title: Germ cell from F2 control sample, biological rep 5

description: miRNA levels in F2 germ cells


title: bri_1066_vdj

description: 10x Genomics

value: CD45+ immune cells


title: Germ cell from F2 control sample, biological rep 4

description: miRNA levels in F2 germ cells


title: bri_1064_gex

description: 10x Genomics

value: tumor


title: K01, JAK2VF_homozygous

description:
K_JAK2VF_minus_S11
bulk RNA-seq of human induced pluripotent stem cells


title: M03, JAK2_WT

description:
M72_minus_S23
bulk RNA-seq of human induced pluripotent stem cells


title: Heart_Inp_00dpi_r1


title: Germ cell from F1 sGC sample, biological rep 6

description: miRNA levels in F1 germ cells

source_name: F1 male germ cells, guinea pigs generated from F0 females that were exposed to sGC in late pregnancy

value: Germ cells from F1 male guinea pigs


title: Germ cell from F2 control sample, biological rep 3

description: miRNA levels in F2 germ cells

value: Germ cells from F2 male guinea pigs


title: J03, JAK2_WT

description:
J_JAK2_minus_S3
bulk RNA-seq of human induced pluripotent stem cells


title: Germ cell from F2 control sample, biological rep 1

description: miRNA levels in F2 germ cells


title: Heart_Inp_01dpi_r1


title: K03, JAK2_WT

description:
K_JAK2_minus_S13
bulk RNA-seq of human induced pluripotent stem cells


title: Heart_Inp_00dpi_r2


title: Germ cell from F1 sGC sample, biological rep 4

description: miRNA levels in F1 germ cells


title: Germ cell from F2 control sample, biological rep 2

description: miRNA levels in F2 germ cells


title: YJX_P5_Dex_in vivo

source_name: YJX P5 after repopulating 5months in Dex-treated FRG mouse

value: fresh human hepatocytes isolated from lc-ProliHH-repopulated Fah-/-Rag2-/-IL2rg-/- mouse liver


title: Heart_H3K4me3_14dpi_r2

tag: vendor/catalogue#

value: cell signaling (9751S)


title: Germ cell from F2 sGC sample, biological rep 3

description: miRNA levels in F2 germ cells

tag: cell type


title: Heart_H3K4me3_14dpi_r1

value: 3–6 months old fish

tag: genotype


title: Heart_H3K4me3_45dpi_r2

value: heart


title: TVR_P1

source_name: TVR at P1 cultured for 9days in HM

value: short-term cultured Proliferting human hepatocytes

value: human liver


title: TVR_P5

source_name: TVR at P5 cultured for 9days in HM

value: long-term cultured Proliferting human hepatocytes


title: J01, JAK2VF_homozygous

description:
J_JAK2VF_minus_S1
bulk RNA-seq of human induced pluripotent stem cells


title: Germ cell from F1 sGC sample, biological rep 2

description: miRNA levels in F1 germ cells


title: Heart_H3K4me3_45dpi_r1

value: wt


title: Germ cell from F1 sGC sample, biological rep 5

description: miRNA levels in F1 germ cells

value: SGC


title: HSC biol rep 1 [TCR-10]

city: Gainesville

first: Duane

last: Mitchell

state: Florida

address: 1333 Center Drive, BSB B1-150

institute: University of Florida

description: CD45+ immune cell were selected from GBM tumor microenvironment following tissue dissociation and positive cell selection. SMARTer Mouse TCR a/b Profiling Kit (Takara Bio) was utilized to amplify TCR beta chains using PCR and sequencing libraries were generated following the manufacturers instructions. RNA-sequencing was performed using Illumina MiSeq x 300.

library_source: other

data_processing:
*library strategy: RNA seq of TCR
TCR vb data alignment and analysis were performed using MixCR 4.0
Assembly: mm10
Supplementary files format and content: Processed text files contains count values for each sample

molecule: other

source_name: brain tumor

extract_protocol:
RNA was extracted using Zymo mini/midi RNA extraction kit.
Celero™ EZ DNA-Seq, 24 reactions kit (Tecan Genomics) was utilized to generate sequencing libraries following the manufacturer’s instructions. RNA-sequencing was performed using Illumina NovaSeq 6000, SP 2 x 50.

value: brain tumor

tag: time

value: Day 21 post implantation

value: immune cells

value: WT

value: HSCs


title: YJX_P1

source_name: YJX at P1 cultured for 9days in HM


title: Germ cell from F1 sGC sample, biological rep 3

description: miRNA levels in F1 germ cells

value: male


title: TVR_P6_Dex_in vivo

source_name: TVR P6 after repopulating 5months in Dex-treated FRG mouse

value: fresh human hepatocytes isolated from lc-ProliHH-repopulated Fah-/-Rag2-/-IL3rg-/- mouse liver

value: mouse liver

value: fresh  isolated human hepatocyte


title: HSC biol rep 3 [TCR-12]


title: HSC biol rep 2 [TCR-11]


title: YJX_P5

source_name: YJX at P5 cultured for 9days in HM


title: YJX_PHH

source_name: fresh primary human hepatocytes

value: fresh primary human hepatocytes


title: Heart_H3K4me3_04dpi_r2

value: 3–6 months old fish

value: cell signaling (9751S)


title: Heart_H3K4me3_01dpi_r2

value: heart


title: TOFU ACT biol rep 5 [TCR-6]

value: KR158 loaded DCs + KR158 specific T cells + HSCs


title: TVR_PHH

value: human liver


title: Germ cell from F1 control sample, biological rep 6

description: miRNA levels in F1 germ cells

source_name: F1 male germ cells, guinea pigs generated from F0 females that were exposed to Control (saline) in late pregnancy

value: Germ cells from F1 male guinea pigs

value: Ctrl


title: Untreated biol rep 6 [TCR-3]

value: brain tumor


title: Heart_H3K4me3_04dpi_r1

value: wt


title: Germ cell from F1 sGC sample, biological rep 1

description: miRNA levels in F1 germ cells

value: SGC


title: Heart_H3K4me3_00dpi_r2


title: Germ cell from F1 control sample, biological rep 7

description: miRNA levels in F1 germ cells


title: Germ cell from F1 control sample, biological rep 4

description: miRNA levels in F1 germ cells


title: X1046_BL

city: Bellinzona

first: Luciano

last: Cascione

state: Ticino

address: Via Chiesa 5

department: Lymphoma & Genomics Research Program

country: Switzerland

institute: IOR

hyb_protocol: RNA was hybridized to capture probes and detection probes using the NanoString nCounter system according to the manufacturer's protocol. Detection probes were provided by the manufacturer and were labeled with a proprietary fluorescent barcode system.

scan_protocol: Scanning was conducted using the NanoString confocal microscope scanner/Digital Analyzer according to manufacturer's instructions.

data_processing:
Data were collected as NanoString RCC files and provided as an Excel spreadsheet. Sample-specific background was calculated by adding the average of all the negative controls to their standard deviation multiplied by two and then subtracting this value from the raw values for each gene. Biological normalization was performed to correct for differences in sample abundances. Quantile normalization was applied to the dataset and revealed homogenous distribution and comparability of our samples.
Raw values are the number of copies of a feature-specific molecular barcode that is attached to a detection probe and counted by a confocal system.

label: not provided

source_name: blood

label_protocol: RNA was not labeled; instead, RNA (33 ng/ul) was pre-processed following the NanoString manufacturer's protocol.

extract_protocol: RNA was isolated from FFPE tissue using Recover ALL kit (Ambion)

value: liquid biopsies

tag: status

value: chemo-refractory mCRC patient

tag: time point

value: baseline


title: TOFU ACT biol rep 3 [TCR-5]

value: Day 21 post implantation

value: immune cells

value: WT

tag: treatment


title: Untreated biol rep 2 [TCR-1]


title: TOFU ACT biol rep 2 [TCR-4]


title: Germ cell from F1 control sample, biological rep 3

description: miRNA levels in F1 germ cells

value: male


title: Heart_H3K4me3_01dpi_r1

value: 3–6 months old fish


title: X1049_BL


title: Germ cell from F1 control sample, biological rep 5

description: miRNA levels in F1 germ cells


title: Untreated biol rep 3 [TCR-2]


title: Heart_H3K4me1_45dpi_r1


title: Germ cell from F1 control sample, biological rep 2

description: miRNA levels in F1 germ cells


title: X1045_BL


title: Heart_H3K4me3_00dpi_r1

value: cell signaling (9751S)


title: Heart_H3K4me1_14dpi_r2

value: heart


title: X1043_BL


title: X1044_BL


title: E12.5, replicate 2, scRNAseq

city: Jamaica Plain

first: Xiaoran

last: Zhang

address: 14 Perkins Square, Apt 11

department: Cardiology

institute: Boston Children's Hospital

description: 10x Genomics

data_processing:
Sequencing data from 10x Genomics were processed with the CellRanger software.
Data were mapped to the mm10 reference data.
Potential doublets were filtered by Scrublet.
Further advanced analysis was performed with the Seurat package.
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: whole embryo without tail, limbs and liver

extract_protocol:
Embryos were harvested at E9.5, E12.5, E15.5, and embryos from the same stages were pooled together. The tail, limbs, and liver were removed from E12.5 and E15.5 embryos. The rest tissue or whole E9.5 embryos were dissected into small pieces using sterile scalpels and washed three times with Hank’s Balanced Salt Solution (HBSS) to remove most blood cells, then were incubated in 2 mg/ml Collagenase Type II (Worthington, Cat# LS004174) and 50% (v/v) Accutase (StemCell Technologies, Cat# 07920) solution for 15 mins at 37℃. The sample was further treated with gentleMACS Dissociator (Miltenyi Biotec, Germany) twice to get single-cell suspension. The enzyme was neutralized by 2% FBS -HBSS. The cell suspension was filtered through a 40-µm cell strainer (Corning). After centrifugation (300g, 5 min, 4 °C) the supernatant was removed and the pellet was resuspended in flow buffer (1× phosphate-buffered saline buffer [PBS], 0.5% bovine serum albumin) and then incubated with Rat anti-human/mouse CD31-FITC (Thermo Fisher, Cat# 11-0311-82) for 15 mins at room temperature. Then Magnetic-Activated Cell Sorting (MACS) was performed with EasySep™ FITC Positive Selection Kit II (StemCell Technologies, Cat# 17682) to enrich ECs. The purified cells were resuspended in DMEM + 10% FBS. The viability and cell number of enriched cellular samples were determined by Countess Automated Cell Counter (Thermo Fisher).
Library was performed according to the manufacter’s instructions (single cell 3’ v1 or v2 protocol, 10x Genomics). Briefly, ECs were resuspended in the master mix and loaded together with partitioning oil and gel beads into the A chip to generate the gel bead-in-emulsion (GEM). The poly-A RNA from the cell lysate contained in every single GEM was retrotranscripted to cDNA, which contains an Ilumina R1 primer sequence, Unique Molecular Identifier (UMI) and the 10x Barcode. The pooled barcoded cDNA was then cleaned up with Silane DynaBeads, amplified by PCR and the apropiated sized fragments were selected with SPRIselect reagent for subsequent library construction. During the library construction Ilumina R2 primer sequence, paired-end constructs with P5 and P7 sequences and a sample index were added.

value: endothelial cells

tag: developmental stage


title: E15.5, replicate 2, scRNAseq

description: 10x Genomics

value: whole embryo without tail, limbs and liver


title: E12.5, replicate 1, scRNAseq

description: 10x Genomics


title: X1047_BL


title: E15.5, replicate 1, scRNAseq

description: 10x Genomics


title: Heart_H3K4me1_04dpi_r2

tag: antibody


title: Heart_H3K4me1_45dpi_r2


title: Germ cell from F1 control sample, biological rep 1

description: miRNA levels in F1 germ cells

value: Germ cells from F1 male guinea pigs


title: Heart_H3K4me1_04dpi_r1


title: X1039_BL


title: X1042_BL


title: Heart_H3K4me1_14dpi_r1


title: E9.5, replicate 1, scRNAseq

description: 10x Genomics

source_name: whole embryo

tag: strain

value: whole embryo


title: Heart_H3K4me1_01dpi_r2

source_name: heart


title: HCC1395 cell, drug-resistant, 6 months, clone 1

city: Seoul

first: MINWOO

last: KIM

state: Seoul

address: 50-1 Yonsei-ro, Seodaemum-gu

country: South Korea

institute: Yonsei University College of Medicine

description: Gene expression data from small RNA-containing total RNA were isolated using mirVana™ miRNA Isolation Kit (Invitrogen™, AM1560)

hyb_protocol: Biotylated RNA was hybridized to the Affymetrix GeneChip® miRNA 4.0 Array at 48℃ and 60 rpm for 16-18 hrs in a hybridization oven.

scan_protocol: miRNA 4.0 Array was sccaned using Affymetrix GeneChip® Scanner 3000 7G.

data_processing: The data were analyzed with RMA+DABG normalization using Affymetrix Expression console v1.4.1.46 default settings. The analysis of the microarray data was performed by DNA Link, Inc. (Korea)

label: biotin

source_name: Breast cancer cell lines

label_protocol: Total RNA was labeled using the FlashTag™ Biotin HSR RNA Labeling kit

growth_protocol: following the protocol decribed in ATCC

extract_protocol: RNA was harvested following the protocol desribed in mirVana™ miRNA Isolation Kit

treatment_protocol: adriamycin, taxotere, cytoxan treatment for 6 months

value: Breast; Mammary gland

tag: cell line

tag: phenotype

value: drug resistant


title: X1041_BL


title: X1037_BL


title: X1040_BL


title: HCC1395 cell, drug-resistant, 6 months, clone 2


title: HCC1395 cell, wild-type, clone 1

value: wild type


title: HCC1395 cell, wild-type, clone 2


title: E9.5, replicate 2, scRNAseq

description: 10x Genomics


title: HPAFII_SPDEFKO, 4

city: Cold Spring Harbor

first: David

middle: A

last: Tuveson

state: New York

address: 1 Bungtown Road

department: Cancer Center

institute: Cold Spring Harbor Laboratory

description: SPDEF KO clone of human PDA cell line HPAFII grown in NSG mouse

data_processing:
The quality of the RNA-seq reads was first confirmed using FastQC version 0.11.8.
Reads were mapped to merge transcript annotation of GENCODE M17 (mouse) and GENCODE v28 (human) using STAR version 2.6.0c.
RSEM version 1.3.3 was used to calculate expression estimates per gene and per isoform.
Assembly: Genome Reference Consortium Mouse Build 38 patch release 6 (GRCm38.p6) and Human NCBI genome build 38.p12 (GRCh38.p12)
Supplementary files format and content: The gene.results files are tab-delimited text files that include expected counts, TPM and FKPM values per gene for each sample as generated by RSEM. The isoforms.results files are tab-delimited text files that include expected counts, TPM and FKPM values per isoform for each sample as generated by RSEM.

source_name: HPAFII orthotopically grafted tumor of SPDEF KO clone

growth_protocol: human PDA cells were orthotopically transplanted in NSG mice

extract_protocol:
total RNA from fresh frozen tumor chuncks was extracted using the TRIzol Plus RNA Purification Kit (ThermoFisher) per manufacturer’s instructions. RNA samples were treated on column with PureLink DNase (ThermoFisher). The quality of purified RNA samples was determined using a Bioanalyzer 2100 (Agilent) with an RNA 6000 Nano Kit.
Libraries for RNA-Seq were prepared with the TruSeq Stranded Total RNA Library Prep Human/Mouse/Rat (Illumina) following manufacturer instructions.

value: NSG

value: NOD scid gamma

value: HPAF-II human PDA cell line

tag: genetic manipulation

value: SPDEF knock-out

tag: histological type

value: pancreatic ductal adenocarcinoma

tag: sample type

value: xenograft

tag: sequencing batch identifier

value: batch 3


title: X1036_BL

tag: tissue

value: liquid biopsies

value: chemo-refractory mCRC patient

value: baseline


title: MDA-MB-468 cell, drug-resistant, 6 months, clone 2


title: MDA-MB-468 cell, wild-type, clone 2


title: Heart_H3K27me3_45dpi_r2

tag: age

value: 3–6 months old fish

value: heart

value: wt

tag: vendor/catalogue#

value: cell signaling (9733S)


title: Heart_H3K4me1_01dpi_r1

tag: genotype


title: Heart_H3K4me1_00dpi_r2


title: Heart_H3K27me3_45dpi_r1


title: HPAFII_SPDEFKO, 3

tag: cell type


title: HPAFII_SPDEFKO, 5


title: endothelial cells, WT, 24 weeks, biol. rep3

city: Munich

first: Antje

last: Grosche

address: Grosshaderner Str. 9

institute: Ludwig-Maximilian University Munich

data_processing:
Tuxedo Suite (Trapnell et al. 2012) was used for preprocessing of the data.
Alignment with HISAT2
Quantification with StringTie
Assembly: mm10
Supplementary files format and content: .xlsx Excel file containing samples x genes FPKM values

source_name: retina

extract_protocol:
PureLink® RNA Micro Scale Kit (Thermo Fisher Scientific)
TruSeq RNA Library Prep Kit (Illumina)

value: retina

value: endothelial cells

value: WT

value: 24 weeks


title: HPAFII_hRosa26, 5

description: hRosa26 KO clone of human PDA cell line HPAFII grown in NSG mouse

source_name: HPAFII orthotopically grafted tumor of hRosa26 clone

value: NSG

value: NOD scid gamma

value: hRosa26 knock-out


title: Heart_H3K4me1_00dpi_r1


title: X1034_BL

tag: status


title: X1033_BL

tag: time point


title: HPAFII_SPDEFKO, 2

value: HPAF-II human PDA cell line

value: SPDEF knock-out

value: pancreatic ductal adenocarcinoma


title: HPAFII_SPDEFKO, 1

value: xenograft

value: batch 3


title: Heart_H3K27me3_14dpi_r2


title: X1032_BL

value: liquid biopsies

value: chemo-refractory mCRC patient

value: baseline


title: MDA-MB-468 cell, drug-resistant, 6 months, clone 1

value: Breast; Mammary gland

value: drug resistant


title: X1029_BL


title: MDA-MB-468 cell, wild-type, clone 1

value: wild type


title: Müller cells, WT, 24 weeks, biol. rep3

value: retina

value: Muller cells


title: MDA-MB-231 cell, drug-resistant, 6 months, clone 2


title: Heart_H3K27me3_04dpi_r2

value: 3–6 months old fish

value: heart

value: wt

value: cell signaling (9733S)


title: X1027_BL


title: MDA-MB-231 cell, drug-resistant, 6 months, clone 1


title: MDA-MB-231 cell, wild-type, clone 2


title: HPAFII_hRosa26, 2

value: NSG

value: NOD scid gamma

value: HPAF-II human PDA cell line

value: hRosa26 knock-out


title: HPAFII_hRosa26, 3

value: pancreatic ductal adenocarcinoma

value: xenograft

value: batch 3


title: X1024_BL

value: liquid biopsies

value: chemo-refractory mCRC patient

value: baseline


title: X1026_BL


title: X1023_BL


title: HPAFII_hRosa26, 4


title: microglia, WT, 24 weeks, biol. rep3

value: microglia

value: WT

value: 24 weeks


title: neurons, WT, 24 weeks, biol. rep3

value: retina

value: neurons


title: Heart_H3K27me3_04dpi_r1

value: 3–6 months old fish

value: heart

value: wt


title: X1025_BL


title: MDA-MB-231 cell, wild-type, clone 1

value: Breast; Mammary gland

value: wild type


title: CFPAC1_SPDEFKO, 5

description: SPDEF KO clone of human PDA cell line CFPAC1 grown in NSG mouse

source_name: CFPAC1 orthotopically grafted tumor of SPDEF KO clone

value: NSG

value: NOD scid gamma

value: CFPAC1 human PDA cell line

value: SPDEF knock-out

value: batch 2


title: Heart_H3K27me3_01dpi_r2

value: cell signaling (9733S)


title: HPAFII_hRosa26, 1

value: HPAF-II human PDA cell line

value: hRosa26 knock-out

value: pancreatic ductal adenocarcinoma

value: xenograft

value: batch 3


title: Heart_H3K27me3_14dpi_r1


title: CFPAC1_SPDEFKO, 4


title: Müller cells, WT, 24 weeks, biol. rep2

value: retina

value: Muller cells

value: WT

value: 24 weeks


title: X1022_BL

value: liquid biopsies

value: chemo-refractory mCRC patient

value: baseline


title: Heart_H3K27me3_01dpi_r1

value: 3–6 months old fish

value: heart

value: wt


title: CFPAC1_SPDEFKO, 3

value: NSG

value: NOD scid gamma

value: CFPAC1 human PDA cell line

value: SPDEF knock-out

value: batch 2


title: endothelial cells, dbdb, 24 weeks, biol. rep3

value: endothelial cells

value: dbdb


title: Heart_H3K27me3_00dpi_r1

value: cell signaling (9733S)


title: neurons, WT, 24 weeks, biol. rep2

value: retina

value: neurons


title: Heart_H3K27me3_00dpi_r2


title: X1018_BL


title: X1020_BL


title: endothelial cells, WT, 24 weeks, biol. rep2

value: WT

value: 24 weeks


title: microglia, WT, 24 weeks, biol. rep2

value: microglia


title: CFPAC1_SPDEFKO, 2

value: pancreatic ductal adenocarcinoma

value: xenograft


title: Müller cells, dbdb, 24 weeks, biol. rep3

value: Muller cells


title: Heart_H3K27ac_45dpi_r1

value: 3–6 months old fish

value: heart

value: wt


title: CFPAC1_SPDEFKO, 1

value: NSG

value: NOD scid gamma

value: CFPAC1 human PDA cell line


title: X1019_BL

value: liquid biopsies

value: chemo-refractory mCRC patient

value: baseline


title: neurons, dbdb, 24 weeks, biol. rep3

value: retina

value: dbdb


title: Heart_H3K27ac_14dpi_r2


title: CFPAC1_hRosa26, 4

description: hRosa26 KO clone of human PDA cell line CFPAC1 grown in NSG mouse

source_name: CFPAC1 orthotopically grafted tumor of hRosa26 clone

value: hRosa26 knock-out

value: batch 2


title: microglia, dbdb, 24 weeks, biol. rep3

value: microglia

value: 24 weeks


title: Heart_H3K27ac_04dpi_r2


title: CFPAC1_hRosa26, 3

value: pancreatic ductal adenocarcinoma

value: xenograft


title: X1017_BL


title: endothelial cells, dbdb, 24 weeks, biol. rep2

value: endothelial cells


title: CFPAC1_hRosa26, 5


title: X1015_BL


title: X1016_BL


title: CFPAC1_hRosa26, 2


title: Müller cells, dbdb, 24 weeks, biol. rep2

value: Muller cells


title: Heart_H3K27ac_45dpi_r2

value: 3–6 months old fish

value: heart

value: wt


title: Heart_H3K27ac_14dpi_r1


title: Heart_H3K27ac_04dpi_r1


title: neurons, dbdb, 24 weeks, biol. rep2

value: neurons


title: X1013_BL

value: liquid biopsies


title: Heart_H3K27ac_01dpi_r2


title: microglia, dbdb, 24 weeks, biol. rep2


title: Heart_H3K27ac_01dpi_r1


title: CFPAC1_hRosa26, 1

value: NSG

value: NOD scid gamma

value: CFPAC1 human PDA cell line

value: batch 1


title: endothelial cells, WT, 24 weeks, biol. rep1

value: retina

value: WT


title: hF27_SPDEFKO, 3

description: SPDEF KO clone of human PDA organoids hF27 grown in NSG mouse

source_name: hF27 orthotopically grafted tumor of SPDEF KO clone

value: hF27 human PDA organoids

value: SPDEF knock-out


title: Heart_H3K27ac_00dpi_r2


title: hF27_SPDEFKO, 2

value: pancreatic ductal adenocarcinoma


title: X1009_BL

value: chemo-refractory mCRC patient

value: baseline


title: X1010_BL


title: X1011_BL


title: Heart_H3K27ac_00dpi_r1


title: Müller cells, WT, 24 weeks, biol. rep1

value: Muller cells

value: 24 weeks


title: hF27_SPDEFKO, 1

value: xenograft


title: hF27_hRosa26, 5

description: hRosa26 KO clone of human PDA organoids hF27 grown in NSG mouse

source_name: hF27 orthotopically grafted tumor of hRosa26 clone

value: hRosa26 knock-out


title: X1006_BL


title: X1012_BL


title: adult male small intestine,sham,rep3

city: Yunnnan province

first: kunmei

last: Gong

address: Jinbi Road 157

institute: The first People's Hospital of Yunnan Province

data_processing:
ACGT101-miR （LC Sciences, Houston, Texas, USA）
Raw reads were subjected to an in-house program, ACGT101-miR (LC Sciences, Houston, Texas, USA) to remove adapter dimers, junk, low complexity, common RNA families (rRNA, tRNA, snRNA, snoRNA) and repeats. Subsequently, unique sequences with length in 18~26 nucleotide were mapped to specific species precursors in miRBase 22.0 by BLAST search to identify known miRNAs and novel 3p- and 5p- derived miRNAs. Length variation at both 3’ and 5’ ends and one mismatch inside of the sequence were allowed in the alignment. The unique sequences mapping to specific species mature miRNAs in hairpin arms were identified as known miRNAs. The unique sequences mapping to the other arm of known specific species precursor hairpin opposite to the annotated mature miRNA-containing arm were considered to be novel 5p- or 3pderived miRNA candidates. The remaining sequences were mapped to other selected species precursors (with the exclusion of specific species) in miRBase 22.0 by BLAST search, and the mapped pre-miRNAs were further BLASTed against the specific species genomes to determine their genomic locations. The above two we defined as known miRNAs. The unmapped sequences were BLASTed against the specific genomes, and the hairpin RNA structures containing sequences were predicated from the flank 80 nt sequences using RNAfold software (http://rna.tbi.univie.ac. at/cgi-bin/RNAfold.cgi). The criteria for secondary structure prediction were: (1) number of nucleotides in one bulge in stem (≤12) (2) number of base pairs in the stem region of the predicted hairpin (≥16) (3) cutoff of free energy (kCal/mol ≤-15) (4) length of hairpin (up and down stems + terminal loop ≥50) (5) length of hairpin loop (≤20). (6) number of nucleotides in one bulge in mature region (≤8) (7) number of biased errors in one bulge in mature region (≤4) (8) number of biased bulges in mature region (≤2) (9) number of errors in mature region (≤7) (10) number of base pairs in the mature region of the predicted hairpin (≥12) (11) percent of mature in stem (≥80).
Raw reads were subjected to an in-house program, ACGT101-miR (LC Sciences, Houston, Texas, USA) to remove adapter dimers, junk, low complexity, common RNA families (rRNA, tRNA, snRNA, snoRNA) and repeats. Subsequently, unique sequences with length in 18~26 nucleotide were mapped to specific species precursors in miRBase 22.0 by BLAST search to identify known miRNAs and novel 3p- and 5p- derived miRNAs. Length variation at both 3’ and 5’ ends and one mismatch inside of the sequence were allowed in the alignment. The unique sequences mapping to specific species mature miRNAs in hairpin arms were identified as known miRNAs. The unique sequences mapping to the other arm of known specific species precursor hairpin opposite to the annotated mature miRNA-containing arm were considered to be novel 5p- or 3pderived miRNA candidates. The remaining sequences were mapped to other selected species precursors (with the exclusion of specific species) in miRBase 22.0 by BLAST search, and the mapped pre-miRNAs were further BLASTed against the specific species genomes to determine their genomic locations. The above two we defined as known miRNAs. The unmapped sequences were BLASTed against the specific genomes, and the hairpin RNA structures containing sequences were predicated from the flank 80 nt sequences using RNAfold software (http://rna.tbi.univie.ac. at/cgi-bin/RNAfold.cgi). The criteria for secondary structure prediction were: (1) number of nucleotides in one bulge in stem (≤12) (2) number of base pairs in the stem region of the predicted hairpin (≥16) (3) cutoff of free energy (kCal/mol ≤-15) (4) length of hairpin (up and down stems + terminal loop ≥50) (5) length of hairpin loop (≤20). (6) number of nucleotides in one bulge in mature region (≤8) (7) number of biased errors in one bulge in mature region (≤4) (8) number of biased bulges in mature region (≤2) (9) number of errors in mature region (≤7) (10) number of base pairs in the mature region of the predicted hairpin (≥12) (11) percent of mature in stem (≥80).
Raw reads were subjected to an in-house program, ACGT101-miR (LC Sciences, Houston, Texas, USA) to remove adapter dimers, junk, low complexity, common RNA families (rRNA, tRNA, snRNA, snoRNA) and repeats. Subsequently, unique sequences with length in 18~26 nucleotide were mapped to specific species precursors in miRBase 22.0 by BLAST search to identify known miRNAs and novel 3p- and 5p- derived miRNAs. Length variation at both 3’ and 5’ ends and one mismatch inside of the sequence were allowed in the alignment. The unique sequences mapping to specific species mature miRNAs in hairpin arms were identified as known miRNAs. The unique sequences mapping to the other arm of known specific species precursor hairpin opposite to the annotated mature miRNA-containing arm were considered to be novel 5p- or 3pderived miRNA candidates. The remaining sequences were mapped to other selected species precursors (with the exclusion of specific species) in miRBase 22.0 by BLAST search, and the mapped pre-miRNAs were further BLASTed against the specific species genomes to determine their genomic locations. The above two we defined as known miRNAs. The unmapped sequences were BLASTed against the specific genomes, and the hairpin RNA structures containing sequences were predicated from the flank 80 nt sequences using RNAfold software (http://rna.tbi.univie.ac. at/cgi-bin/RNAfold.cgi). The criteria for secondary structure prediction were: (1) number of nucleotides in one bulge in stem (≤12) (2) number of base pairs in the stem region of the predicted hairpin (≥16) (3) cutoff of free energy (kCal/mol ≤-15) (4) length of hairpin (up and down stems + terminal loop ≥50) (5) length of hairpin loop (≤20). (6) number of nucleotides in one bulge in mature region (≤8) (7) number of biased errors in one bulge in mature region (≤4) (8) number of biased bulges in mature region (≤2) (9) number of errors in mature region (≤7) (10) number of base pairs in the mature region of the predicted hairpin (≥12) (11) percent of mature in stem (≥80).
Raw reads were subjected to an in-house program, ACGT101-miR (LC Sciences, Houston, Texas, USA) to remove adapter dimers, junk, low complexity, common RNA families (rRNA, tRNA, snRNA, snoRNA) and repeats. Subsequently, unique sequences with length in 18~26 nucleotide were mapped to specific species precursors in miRBase 22.0 by BLAST search to identify known miRNAs and novel 3p- and 5p- derived miRNAs. Length variation at both 3’ and 5’ ends and one mismatch inside of the sequence were allowed in the alignment. The unique sequences mapping to specific species mature miRNAs in hairpin arms were identified as known miRNAs. The unique sequences mapping to the other arm of known specific species precursor hairpin opposite to the annotated mature miRNA-containing arm were considered to be novel 5p- or 3pderived miRNA candidates. The remaining sequences were mapped to other selected species precursors (with the exclusion of specific species) in miRBase 22.0 by BLAST search, and the mapped pre-miRNAs were further BLASTed against the specific species genomes to determine their genomic locations. The above two we defined as known miRNAs. The unmapped sequences were BLASTed against the specific genomes, and the hairpin RNA structures containing sequences were predicated from the flank 80 nt sequences using RNAfold software (http://rna.tbi.univie.ac. at/cgi-bin/RNAfold.cgi). The criteria for secondary structure prediction were: (1) number of nucleotides in one bulge in stem (≤12) (2) number of base pairs in the stem region of the predicted hairpin (≥16) (3) cutoff of free energy (kCal/mol ≤-15) (4) length of hairpin (up and down stems + terminal loop ≥50) (5) length of hairpin loop (≤20). (6) number of nucleotides in one bulge in mature region (≤8) (7) number of biased errors in one bulge in mature region (≤4) (8) number of biased bulges in mature region (≤2) (9) number of errors in mature region (≤7) (10) number of base pairs in the mature region of the predicted hairpin (≥12) (11) percent of mature in stem (≥80).
Assembly: mRatBN7.2
Supplementary files format and content: "seq_template_with_sra_accessions.xlsx" is a metadata spreadsheet
Supplementary files format and content: "Table5_All_Expressed_miRNA.txt" is processed data files.

organism: Rattus

source_name: tissue

growth_protocol: 6-8 weeks male Sprague Dawley rats (weight, 300–350 g) were supplied by the Hunan SJA Laboratory Animal Co., Ltd and housed individually in a temperature-controlled barrier facility with light-dark (12:12) cycles at 22 ℃ with 50% humidity, and received ad libitum food and water.

extract_protocol:
Total RNA was extracted from three tissues each group. The RNA amount and purity of each sample was quantified using NanoDrop ND-1000 (NanoDrop, Wilmington, DE, USA). The RNA integrity was assessed by Agilent 2100 with RIN number >7.0.
Micro RNA sequencing library was prepared by TruSeq Small RNA Sample Prep Kits (Illumina, San Diego, USA).

treatment_protocol: The ASMVT rat model was established according to the method described in a previous study:Early Elevation of Cell-Free DNA After Acute Mesenteric Ischemia in Rats(PMID:34517186).Specifically,the rats were fasted for 12 hours before the operation and were given free access to water. In the lower abdomen of the rat, the rat was anesthetized with 5% ketamine 2 ml + 0.05% atropine 1 ml + 2.5% promethazine 2 ml at 5% ketamine 2 ml + 0.05% atropine 1 ml + 2.5% promethazine 2 ml at 2 ml/kg, and a midline incision of approximately 2 cm in length was made in the upper abdomen. The position of the cecum was determined after entering the abdominal cavity. The small intestine was pulled 5 cm away from the ileocecal region and the mesentery was exposed. The main branches of the mesenteric vein and the ends of the arch vein are ligated with 7-0 nylon thread. During mesenteric vein clamping, approximately 15-20 ml/kg of saline is injected intraperitoneally intermittently to prevent transient hypovolemia after loosening of the arterial clamp. Mesenteric vein dilatation and intestinal congestion were dark red, indicating successful modeling. After closing the abdomen, 25-30 m/kg of saline (containing gentamicin 320,000 U/L) was added into the abdominal cavity to prevent abdominal surgical infection. After surgery, the rats were placed back into the feeding cage for observation, one rat per cage, and were allowed to eat and drink freely.

value: tissue

value: Sprague Dawley

value: 6-8 weeks

tag: Sex

value: male

tag: treatment

value: sham


title: microglia, WT, 24 weeks, biol. rep1

value: microglia


title: hF27_hRosa26, 4

value: NSG

value: NOD scid gamma

value: batch 1


title: endothelial cells, dbdb, 24 weeks, biol. rep1

value: retina

value: endothelial cells

value: dbdb


title: Müller cells, dbdb, 24 weeks, biol. rep1


title: adult male small intestine,sham,rep2


title: hF27_hRosa26, 3

value: hF27 human PDA organoids

value: pancreatic ductal adenocarcinoma


title: X1021_BL

value: liquid biopsies

value: chemo-refractory mCRC patient

value: baseline


title: X1002_BL


title: adult male small intestine,Rat ASMVT surgical model,rep3

value: tissue

value: ASMVT


title: X1014_BL


title: neurons, dbdb, 24 weeks, biol. rep1

value: neurons

value: 24 weeks


title: X1008_BL


title: neurons, WT, 24 weeks, biol. rep1

value: WT


title: microglia, dbdb, 24 weeks, biol. rep1

value: microglia


title: adult male small intestine,Rat ASMVT surgical model,rep2

value: Sprague Dawley

value: 6-8 weeks

value: male


title: adult male small intestine,Rat ASMVT surgical model,rep1


title: hF27_hRosa26, 1

value: NSG

value: NOD scid gamma

value: hRosa26 knock-out

value: xenograft

value: batch 1


title: hF27_hRosa26, 2

value: hF27 human PDA organoids

value: pancreatic ductal adenocarcinoma


title: X1001_BL

value: liquid biopsies

value: chemo-refractory mCRC patient

value: baseline


title: E. coli BW25113 replicate 1

status: Public on Jan 24 2024

city: Tübingen

first: Kay

last: Nieselt

state: DE

address: Sand 14

department: Department for Computer Science

institute: Institute for Bioinformatics and Medical Informatics

data_processing:
All reads mappings were performed against the reference strain of E. coli K12 substr. BW25113 (RefSeq ID NZ_CP009273.1).
The mappings of all samples were conducted with HISAT2 v2.1.0. Spliced alignment of reads was disabled (HISAT2 parameter --no-spliced-alignment). Library type was set to reverse (--rna-strandness).
resulting mapping files in SAM format were converted to BAM format using SAMtools v1.9
Gene counts for all samples were computed with featureCounts v1.6.443 based on the annotation of the respective reference genome, where the selected feature type was set to transcript records (featureCounts parameter -t transcript)
Assembly: E. coli BW251113  (RefSeq ID NZ_CP009273.1)
Supplementary files format and content: counts_for_publication.txt: A tab separated matrix with samples as columns and genes as rows

organism: Escherichia coli BW25113

source_name: bacterial cells

growth_protocol: Overnight cultures of E. coli BW25113 were diluted in LB medium supplemented with 25 µg/ml of G6P to a final OD600 of 0.05 (OD600 of 0.09 in the Epoch2 microplate reader), and let grow until an OD600 of 1.9 was reached (OD600 = 0.3 in the Epoch2). Samples were collected and centrifuged (13.500 rpm, 10 min), and the pellet was frozen at -80 °C.

extract_protocol:
The cellular RNA was extracted using the Quick-RNA™ Fungal/Bacterial Miniprep kit (Zymo Research, Freiburg, Germany), according to the producer’s instructions and finally eluted in 50 μL of DNase/RNase-free water.
For library preparation, Illumina Stranded Total RNA Prep Ligation with Ribo-Zero Plus was used according to manufacturer's instructions together with IDT for Illumina DNA/RNA UD Indexes Set A. The input amount was 300 ng RNA in 11µl, QC measurements were performed using Qubit (Qubit™ RNA BR Assay Kit, Qubit™ dsDNA HS Assay Kit) and Bioanaylzer (Bioanalyzer High sensitivity DNA Kit). Sequencing was run on a NextSeq 500 (1x75bp single-end reads, NextSeq™ 500 High Output Kit v2.5 (75 cycles)).

treatment_protocol: No specific treatment

value: bacterial cells


title: P91

city: Novosibirsk

first: Nikita

last: Torgunakov

address: Prospekt Lavrentyeva 10

country: Russia

institute: Institute of Cytology and Genetics

description: Chromatin fragmentation by S1. Raw data not provided due to patient privacy concerns

data_processing:
merged_nodups.txt files were obtained using modified version of the Juicer 1.6 (https://github.com/genomech/juicer1.6_compact)
Assembly: hg19
Supplementary files format and content: merged_nodups.txt.gz files containing valid Hi-C pairs (described as "Long format" in Juicer documentation here: https://github.com/aidenlab/juicer/wiki/Pre#long-format), modified to remove fields <cigar1> <sequence1> <cigar2> <sequence2> <readname1> <readname2> due to patient privacy concerns. Fields <str1> <chr1> <pos1> <frag1> <str2> <chr2> <pos2> <frag2> <mapq1> <mapq2> remain.

extract_protocol:
Extraction protocol was performed as described in Gridina. et. al 2021 (PMID: 33743768).
Exo-C protocol includes a 3C part followed by exome enrichment. The 3C part was performed either following DNase I protocol as described in Gridina. et. al 2021 (PMID: 33743768), or S1 as described in Gridina. et. al 2023 (PMID: 38072950).

value: blood

value: Lymphocytes


title: E. coli BW25113 replicate 3


title: E. coli BW25113 replicate 2


title: P114


title: P112


title: X1003_BL


title: adult male small intestine,sham,rep1

value: tissue

value: sham


title: TAF16

source_name: skin fibroblasts

value: skin fibroblasts

value: Fibroblasts


title: P88


title: P108


title: P104


title: P107


title: P65

value: iPSC


title: P86


title: P84


title: P83


title: P82


title: P103


title: P113


title: P109


title: hF27_SPDEFKO, 4

value: NSG

value: NOD scid gamma

value: SPDEF knock-out


title: PitNET56

type: genomic

city: Hamburg

first: Matthias

last: Dottermusch

address: Martinistr. 52

department: Institute of Neuropathology

institute: University Medical Center Hamburg-Eppendorf

description: Somatotroph PitNET

hyb_protocol: Bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium MethylationEPIC BeadChip using standard Illumina protocol

scan_protocol: Arrays were imaged using the iScan System and standard recommended Illumina scanner setting

data_processing: Data analyses were conducted using the minfi package (v1.46.0), IlluminaHumanMethylationEPICanno.ilm10b4.hg19 (v.0.6.0) and IlluminaHumanMethylationEPICmanifest (v.0.3.0) in R (v4.3.1). The data was read into an RGChannelSet. P-values for every individual probe were calculated using the detectionP()-function of minfi. Methylated and unmethylated signal intensities were extracted without using normalization (preprocessRaw). Functional normalization (preprocessFunnorm) was applied in order to obtain normalized beta-values.

label: Cy3, Cy5

source_name: PitNET

label_protocol: Standard Illumina Protocol

extract_protocol: DNA was isolated from FFPE tissue using the ReliaPrep™ FFPE gDNA Miniprep System (Promega) according to manufacturer’s instructions. About 100-500 ng DNA was used for bisulfite conversion by the EZ DNA Methylation Kit (Zymo Research). Afterwards, the DNA Clean & Concentrator-5 (Zymo Research) and the Infinium HD FFPE DNA Restore Kit (Illumina) were employed to clean and restore the converted DNA. Finally, the Infinium MethylationEPIC BeadChip Kit Illumina) was used to quantify the methylation status of 850,000 CpG sites on an iScan device (Illumina).

value: female

tag: granulation

value: sparse

tag: sf1 immunostaining

value: negative


title: PitNET64

description: Somatotroph PitNET

value: male


title: PitNET57

description: Somatotroph PitNET


title: PitNET74

description: Somatotroph PitNET


title: Treatment CD45

city: St. Louis

first: Michelle

last: Brennan

state: MO

address: 1100 South Grand Blvd

department: Biochemistry & Molecular Biology

institute: Saint Louis University School of Medicine

data_processing:
Raw reads were aligned to the mm10 genome and feature-barcode matrices were generated using CellRanger 6.0.2.
Assembly: mm10
Supplementary files format and content: Tab separated values files and matrix files

source_name: tumor

growth_protocol: The mouse oral cancer cells, MOC2, was obtained from Kerafast, Inc., and were maintained in 2:1 IMDM-Hams Nutrient Mixture F10-F12 medium supplemented with insulin, hydrocortisone, EGF, FBS, and 1% penicillin/streptomycin  at 370C. MOC2 cells (1×106) containing 40% Matrigel were injected subcutaneously into the flank of C57BL/6 female mice (6 -7 weeks old).

extract_protocol:
At the endpoint, mice were euthanized humanely, tumors were collected, parts of the MOC2 tumors were processed for scRNA-seq, and the remaining tumors were snap-frozen in liquid nitrogen for further analysis. Tumors (3 mice per group-pooled) were processed for single-cell isolation followed by cell sorting using FITC-conjugated CD45 antibody and propidium iodide (PI) staining, as described previously (22), with modifications.
Libraries were generating as directed by the manufacturer using the 10X Genomics Chromium™ Next GEM Single Cell 3' Kit v3.1.

treatment_protocol: When palpable tumors developed (> 80-100 mm3), mice were randomly divided into two groups, with 10 mice in each group. The treatment group received 30 mg/kg/mouse of M-I  (100 uL- M-I was dissolved in 5% DMSO/95% of a 30% w:v Captisol solution) intraperitoneally once daily, and the control group received the vehicle, as described previously (15). Bodyweight was monitored, tumor size was measured using a slide caliper, and tumor volume was calculated using the formula ½ L × W2.

value: tumor

tag: cell line

value: Momordicine-I


title: Control CD45

value: Vehicle


title: PitNET14

description: Somatotroph PitNET

value: dense


title: PitNET26

description: Somatotroph PitNET

value: positive


title: PitNET4

description: Somatotroph PitNET


title: PitNET13

description: Somatotroph PitNET


title: PitNET22

description: Somatotroph PitNET


title: PitNET21

description: Somatotroph PitNET


title: PitNET45

description: Somatotroph PitNET


title: PitNET37

description: Somatotroph PitNET


title: PitNET6

description: Somatotroph PitNET


title: PitNET44

description: Somatotroph PitNET


title: PitNET68

description: Somatotroph PitNET


title: PitNET8

description: Somatotroph PitNET


title: PitNET39

description: Somatotroph PitNET


title: IP_yeastTimeCourse_11

city: Rehovot

first: Ran

last: Shachar

address: 234 Herzl St.

department: Department of Molecular Genetics

country: Israel

institute: Weizmann Institute of Science

description: Synaptic Systems (Cat# 202003; RRID: AB_2279214)  + Cell Signaling D9D9W

data_processing:
alignment using STAR (V. 2.5.3a)
Read coverages were obtained using the R package txtools (https://github.com/AngelCampos/txtools)
Assembly: SK1-YPS138, hg19-mm9, CAST-HOUS
Supplementary files format and content: rds

organism: Saccharomyces cerevisiae x Saccharomyces paradoxus

source_name: Saccharomyces Hybrid: sk1-YPS138

growth_protocol: All yeast strains used in this work were grown in YPD (2% dextrose) at 30C. To induce synchronous sporulation, cells were grown for 24 h in 1% yeast extract, 2% peptone, 4% dextrose at 30C, diluted in BYTA (1% yeast extract, 2% tryptone, 1% potassium acetate, 50 mM potassium phthalate) to OD600 = 0.2 and grown for another 16 h at 30C, 250 rpm. Cells were then washed two times with water and re-suspended in Sporulation medium (0.3% potassium acetate) at OD600 = 2.0 and incubated at 30C at 190 rpm. Human monochromosome hybrid cells JCRB2201, JCRB2202 and JCRB2203 were purchased from the Japanese Collection of Research Bioresources (JCRB), and cultured in DMEM (GIBCO) supplemented with 10% fetal bovine serum (FBS) and 0.8mg/ml G418(Gibco,79N9555) 37. mESCs, BJ, and NIH 3T3 cells were cultured in DMEM (GIBCO) supplemented with 10% FBS and 1% Penicillin and Streptomycin.

extract_protocol:
Yeast total RNA samples were prepared by adjusting previously published protocols. After fast freezing the yeast cells in liquid nitrogen, yeast cells were resuspended in equal amounts of phenol:Chloroform:Isoamyl alcohol (Sigma Aldrich), buffer AE (50mM sodium acetate, 10mM EDTA 1% SDS), and glass beads in Eppendorf tube. The tube was vortexed for 15 minutes in a bullet blender, heated to 65 °C for 30 minutes, followed by another round of 5 minutes vortex and 30 minutes heating to 65 °C. Samples were placed on ice for 5 minutes and centrifuged for 10 minutes (12000g, 4 °C). The supernatant was isolated, re-extracted with phenol:Chloroform:Isoamyl alcohol, and precipitated with sodium acetate and isopropanol. For all types of mammalian cell lines, total RNA was extracted with BIO TRI RNA reagent (Bio-lab). Enrichment for mRNA was done by two rounds of poly-A selection using Oligo(dT) beads (Dynabeads mRNA DIRECT) in both total RNAs from yeast and mammals.
m6A-seq2: Fragmentation, 3' adapter ligation, pooled(m6A-IP, cDNA synthesis, second adapter ligation and enrichment)
m6A-seq2

value: yeast cell

tag: fraction

value: IP


title: PitNET40

description: Somatotroph PitNET


title: PitNET34

description: Somatotroph PitNET


title: CTX_Ift88_cKO

city: Calgary

first: Jiami

last: Guo

address: 2500 University Dr NW

department: Cell Biology and Anatomy

institute: University of Calgary

description: 10x Genomics

data_processing:
The demultiplexing, barcode processing, gene counting and aggregation was done using CellRanger3.1.0 pipeline
Assembly: mm10
Supplementary files format and content: Comma-separated file: gene expression matrix
Supplementary files format and content: Comma-separated file: metadata

source_name: Brain Cortex

extract_protocol:
Aldh1l1-CreERT2 (Control), Arl13blox/lox; Aldh1l1-CreERT2 (Arl13bcKO), Smolox/lox; Aldh1l1-CreERT2 (SmocKO), and SmoM2lox/+; Arl13blox/lox; Aldh1l1-CreERT2 (SmoM2-Arl13bcKO) mice were administrated with tamoxifen (20mg/mL) from P7 to P9. Cortices and the cerebellum were dissected at P52~55. Samples from two male mice of each genotype were combined. Tissue was cut into small pieces and digested in 5mL enzyme buffer (1 x EBSS media, 0.36% D(+) glucose, 26mM NaHCO3, 0.5mM EDTA) containing papain (~34 units/mL, Worthington), DNase I (20 units/ml, Sigma) for 30 min at 37 °C in a cell culture incubator (5% CO2, 95% air). Tissue pieces were then gently triturated into single cells after stopping the enzyme reaction by adding 10mL DMEM (Gibco) supplied with 10% FBS (Gibco). Cells were spun down and resuspended in 13mL of Percoll solution [23% Percoll (Sigma), 36mM NaCl in PBS], and carefully topped with 8mL of PBS. Cells were then centrifuged at 900g (accelerate: 4, break: 0), resuspended and washed once with FACS buffer (PBS supplied with 3% FBS). Blocked with FcBlock (Biorad) for 5 min at room temperature, cells were then stained with ACSA2-PE (Miltenyi Biotec) for 30min at 4 °C, followed by Viability Dye eFluor™ 780 (eBioscience) incubation for 5 min at room temperature. Cells were then washed with PBS solution supplied with 3% FBS (Gbico) once, and live ACSA2+ cells were sorted using flow cytometry. The RNase inhibitor (Sigma) was supplied in the solutions from the staining to the end of sorting.
A total of 15, 000 single cells of each sample were loaded for partitioning using 10x Genomics NextGEM Gel Bead emulsions (3’ gene expression kit, version 3.1) and processed according to the manufacturer’s protocol. The PCR amplification steps were run 12x.

value: Brain Cortex


title: CTX_Control_Mutant

description: Split-seq

data_processing:
The demultiplexing, barcode processing, gene counting and aggregation was done using pipeline provided by Parse Biosciences.
Assembly: mm10
Supplementary files format and content: Comma-separated file: gene expression matrix
Supplementary files format and content: Comma-separated file: metadata

extract_protocol:
Nuclei were isolated from mouse (P52) cortices with cell fixation and nuclei fixation kit (Parse Biosciences) from both Arl13bcKO (Arl13blox/lox; Aldh1l1-CreERT2, tamoxifen: P7 ~ P9) and control (Arl13b+/+; Aldh1l1-CreERT2, tamoxifen: P7 ~ P9) mice. Cortices of two male mice were combined in each group.
A total of 10,000 cells per group were used for library construction using the EvercodeTM Whole Transcriptome Mini kit (Parse Bioscience) as per the manufacturer’s protoco
Split-seq


title: PitNET32

description: Somatotroph PitNET


title: PitNET25

description: Somatotroph PitNET


title: IP_yeastTimeCourse_7


title: PitNET46

description: Somatotroph PitNET


title: IP_yeastTimeCourse_6


title: CB_SmoM2-ARL13B_cKO

description: 10x Genomics

source_name: Cerebellum

value: Cerebellum


title: PitNET7

description: Somatotroph PitNET


title: IP_yeastTimeCourse_8


title: IP_yeastTimeCourse_5


title: PitNET9

description: Somatotroph PitNET


title: CTX_SmoM2-ARL13B_cKO

description: 10x Genomics


title: IP_yeastTimeCourse_4


title: PitNET76

description: Somatotroph PitNET


title: CB_Smo_cKO

description: 10x Genomics


title: IP_yeastTimeCourse_1


title: PitNET3

description: Somatotroph PitNET


title: CTX_Smo_cKO

description: 10x Genomics


title: IP_yeastTimeCourse_0


title: IP_yeastTimeCourse_KO


title: IP_yeastTimeCourse_WT


title: CB_Arl13b_cKO

description: 10x Genomics


title: CTX_Arl13b_cKO

description: 10x Genomics


title: IP_yeastTimeCourse_3


title: IP_yeastCrispr_Hybrid_RS184


title: IP_yeastCrispr_Hybrid_RS185


title: eS6A-Δ6SA_rep3

city: Philadelphia

first: Aman

middle: Yebio

last: Husbands

address: 103B Caroline Lynch Bldg, 433 S University Ave

department: Biology

institute: The University of Pennsylvania

data_processing:
Reads were aligned using STAR 2.7.6a intron size was set to 6000nt
Reads were counted using featureCounts 2.0.0 at the meta feature (gene) level, chimeric reads and multimapping reads were filtered out
Genes without at least one count in all three replicates of a single condition were removed
Read counts were normalized using DESeq2_1.26.0 with a pairwise comparison design between all genotypes
Assembly: TAIR10.1 (Genome) Araport 11 (Reference)
Supplementary files format and content: Processed data file is a matrix containing the DESeq2 normalized counts for each sample. Each row is a gene (AGI) and each column is a sample.

organism: Arabidopsis thaliana

source_name: Seedling Shoot

growth_protocol: Seedlings were grown for 12 days  on 1/2-strength MS medium under long-day (16h light, 8h dark) conditions (80uE/m2/sec fluorescent white light).

extract_protocol:
Seedling shoots were harvested by flooding the plants with liquid nitrogen and scraping off the seedling shoots. Total RNA was extracted using a commercial kit
Illumina total RNA with Ribo-Zero depletion plus ERCC spike in RNAs, Paired-end 75 chemistry

value: Seedling Shoot

value: rps6a rps6b; eS6A-{delta}6SA