title: E18 premature alveolar macrophages Csf2rb KO rep3 [preAM_Csf2rbKO_3]

description:
RNAseq_lungE18_Csf_14_1_S41
processed data file: RNAseq_samples_gene_counts.csv

extract_protocol:
lung digestion in RPMI complete with 1mM collagenase IV and 2mg/ml DNase I at 37°C for 30 min
Cells for RNA-Seq or ATAC-Seq were isolated by FACS. Cells for RNA-Seq (500-20,000 sorted cells) were lysed with 50-200µl of lysis/binding buffer (Life Technologies), frozen on dry ice and stored at -80°C until further use. The mRNA was purified using a Dynabeads mRNA DIRECT Purification Kit (Life Technologies) according to the manufacturer’s guidelines. Reverse transcription was performed with oligo(dT) primers (Thermo Scientific) or MARS-seq barcoded RT primers and the Affinity Script cDNA Synthesis Kit (Agilent) in a 10µl reaction volume.
mRNA was subjected to reverse transcription using an Affinity Script cDNA Synthesis Kit (Agilent) and MARS-seq barcoded RT primers. Samples were analyzed by qPCR and up to 8 samples with similar Ct values were combined. Pooled samples were then treated with Exonuclease I (New England BioLabs (NEB)) and incubated at 37°C for 30min and 80°C for 10min followed by a 1.2X AMPure XP beads (Beckman Coulter) cleanup. Second strand synthesis of the cDNA was performed using a second strand synthesis kit (NEB) at 16°C for 2h and samples were cleaned with 1.4X volumes of AMPure XP beads. Afterwards samples were subjected to in vitro transcription (IVT) with a HiScribe T7 RNA Polymerase kit (NEB) at 37°C for 13-16h. The DNA template was removed by Turbo DNase I (Life Technologies) treatment at 37°C for 15min and the samples were cleaned with 1.2X volumes of AMPure XP beads. Subsequently, the RNA was fragmented at 70°C using RNA fragmentation buffer (Invitrogen), after 3min the reaction was stopped with Stop buffer (Invitrogen) and samples were purified by 2X SPRI cleanup. Afterwards T4 RNA ligase (NEB) was used to ligate the fragmented RNA to the MARS-seq ligation adapter (22°C 2h) and samples were purified with a 1.5X AMPure XP beads cleanup. In a second reverse transcription reaction (reaction volume 20µl) using the MARS-seq RT2 primer and an Affinity Script cDNA Synthesis Kit (Agilent Technologies) the RNA was transcribed into cDNA followed by another 1.5X AMPure XP beads purification. As final step the library was amplified in a nested PCR with P5_Rd1 and P7_Rd2 primers and Kapa HiFi Hotstart ready mix (Kapa Biosystems) and purified with a 0.7X AMPure XP beads cleanup. The fragment size of the final libraries was measured using a TapeStation (Agilent Technologies) and library concentrations were quantified with a Qubit fluorometer (Life Technologies). The samples were sequenced using a NextSeq 500 system (Illumina).
For the preparation of ATAC-seq libraries 15,000-20,000 cells were used as described earlier (Lara-Astiaso et al., 2014; Buenrostro et al., 2013). Briefly, nuclei were isolated by lysis with cold lysis buffer (10mM Tris-HCl pH7.4, 10mM MgCl2, 0.1% Igepal CA-630) and centrifuged for 25min at 500xg and 4°C with low acceleration and brake using a swing-out rotor. The supernatant was carefully removed and nuclei were resuspended in 25μl reaction buffer containing 2μl of Tn5 transposase and 12.5μl of TD buffer (Nextera DNA library preparation kit; Illumina). The mix was incubated at 37°C for 1hr. Afterwards, the DNA was purified by adding 5μl of cleanup buffer (900mM NaCl, 30mM EDTA), 2μl of proteinase K (NEB) and 2μl of 5% SDS. After an incubation phase of 30min at 40°C, the tagmented DNA was enriched using AMPure XP beads (Beckman Coulter). The DNA was PCR-amplified with indexed primers and Kapa HiFi Hotstart ready mix (Kapa Biosystems). After the PCR, tagmented DNA fragments were selected for fragments smaller than 600bp and purified using AMPure XP beads. Libraries were subjected to a second PCR amplification with Kapa HiFi Hotstart ready mix (Kapa Biosystems), indexing primers and an appropriate number of reaction cycles depending on the library concentration. Library sizes were determined using a TapeStation (Agilent Technologies) and measurement of DNA concentration was performed with a Qubit fluorometer (Life Technologies). Libraries where sequenced with an average of 20 million reads per sample on a NextSeq500 system (Illumina).

value: Csf2rb -/-

value: whole lung tissue

value: premature alveolar macrophages


title: GTEX-15CHR-1426-SM-GW22K

status: Public on Sep 16 2022

type: genomic

city: Chicago

first: Meritxell

last: Oliva

state: Illinois

address: 5841 S. Maryland Ave

department: Public Health Sciences

country: USA

institute: University of Chicago

description:
sample name:
GTEX-15CHR-1426-SM-GW22K

hyb_protocol: All samples were  prepared and analyzed in accordance with the manufacturer guidelines and protocol for the Illumina Infinium HumanMethylationEPIC array (Illumina, San Diego, CA, USA). That is, bisulphite converted DNA was amplified, fragmented and hybridised to IIllumina Infinium HumanMethylationEPIC BeadChip using standard Illumina protocol

scan_protocol: Arrays were imaged using BeadArray Reader using standard recommended Illumina scanner setting

data_processing:
Raw DNAm data was processed with ChAMP software. For sample quality control (QC), we excluded (1) 3 samples with undetectable or missing methylation values (detection P > 0.01) in ≥ 5% of CpGs and (2) 6 samples with mismatched sex. For CpG QC, we excluded (1) CpGs that had detection P > 0.01 in ≥ 1 samples (N = 44,135) and that had a beadcount < 3 in ≥ 5% samples (N = 660), (2) cross-reactive CpGs (N = 40,812), (3) variant-overlapping CpGs or within a single base pair extension (N = 7,708) and (4) CpGs mapping to sex chromosomes. For filters (2) and (3), we selected CpG probes overlapping variants defined at MAF > 5% in 1000G. A total of 754,054 CpGs passed QC, could be mapped and lifted over from GRCh37 to GRCh38 human genome build and were retained for further analysis. Raw DNAm values were background-adjusted using the single sample normal-exponential out-of-band (ssnoob) method with dye bias correction. DNAm β values were normalized using the beta mixture quantile (BMIQ) method, adjusting for type I/II probe bias; output β values for each CpG were used in downstream analysis. After normalization, we removed one additional sample with array-derived genotype profile not matching the WGS-derived one. Principal component analysis (PCA) was conducted on DNAm β values within each tissue type, and 3 samples were removed for being outliers with respect to the top 5 principal components (PCs) of the corresponding tissue. A total of 987 samples passed final QC and were retained for further analysis.
Processed data file contains: Normalized Average Beta

label: Cy5 and Cy3

molecule: genomic DNA

organism: Homo sapiens

source_name: Colon - Transverse

label_protocol: Standard Illumina Protocol

extract_protocol: DNA samples were extracted from GTEx tissue samples using Qiagen Gentra Puregene method at GTEx Laboratory Data, Analysis and Coordinating Center (LDACC), and sent to the Institute for Population and Precision Health Laboratory on 96-well plates. Tissue types were not batched by plate. Bisulfite conversion was applied to 500 ng of DNA using EZ-96 DNA methylation kit (Zymo Research, Irvine, CA, USA).

tag: Sex

value: Mild

tag: tissue

value: Colon - Transverse

tag: age

value: Never


title: GTEX-15D79-2626-SM-GW1RH

description:
sample name:
GTEX-15D79-2626-SM-GW1RH

value: Severe


title: GTEX-15DDE-2726-SM-GW1TP

description:
sample name:
GTEX-15DDE-2726-SM-GW1TP

value: Current


title: GTEX-15CHQ-2526-SM-GW1E3

description:
sample name:
GTEX-15CHQ-2526-SM-GW1E3

value: Former


title: GTEX-15DYW-2326-SM-GW1RO

description:
sample name:
GTEX-15DYW-2326-SM-GW1RO


title: GLAST176 pD

type: SRA

city: Heidelberg

first: Ana

last: Martin-Villalba

address: Im Neuenheimer Feld 280

department: Molecular Neurobiology

country: Germany

institute: German Cancer Research Center

description: single-cell RNA-seq

library_source: transcriptomic single cell

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

molecule: total RNA

organism: Mus musculus

source_name: ventricular-subventricular zone

extract_protocol:
For the ischemia experiment, the vSVZ and striatum were isolated. For the naïve experiments, vSVZ, striatum, and olfactory bulb were isolated. Depending on the plate, individual or pooled mice were used to sort cells on plate. Tissues were processed and sorted in a BD FACSAria II at the DKFZ Flow Cytometry Facility. Cells were stained with the following antibodies (all conditions and tissues together): O4-APC and O4-APC-Vio770 (Miltenyi; diluted 1:50), Ter119-APC-Cy7 (Biolegend; 1:100), CD45-APC-Cy7 (BD; 1:200), GLAST (ACSA-1)-PE (Miltenyi: 1:20), PSA-NCAM-PE-Vio770 (Miltenyi; 1:75), Prominin1-A488 (eBioscience; 1:75), and Sytox Blue (Life Technologies, 1:1000), CD9-eFluo450 (eBioscience, 1:300).
For profiling the transcriptome and epigenome of single cells we developed and implemented a miniaturized and higher throughput version of the scNMT-seq protocol (Clark et al., 2018). On this new version, the Smart-seq3 (Hagemann-Jensen et al., 2020) method and specific normalization steps were implemented. A detailed version of the protocol is described in Cerrizuela et al., (2022). The samples listed here represent the transcriptomic portion of this multi-omic data set.
Single-cell RNA-seq (Smart-seq3)

treatment_protocol: Two months old TiCY mice were intraperitoneally injected with tamoxifen. In these mice, tamoxifen-induced Cre recombination takes place in neural stem cells in the vSVZ, which express Tlx (Nr2e1) and will stably activate the production of enhanced YFP, labeling NSCs and their progeny. Two weeks after injection, an injury by bilateral carotid artery occlusion (BCCAO) was performed as described (Llorens-Bobadilla et al., 2015). The animals were sacrificed for single cell sorting either 48 h or 3 weeks after ischemia. WT mice were not subjected to tamoxifen or ischemia.

value: ventricular-subventricular zone

tag: cell type

tag: genotype

value: WT

tag: treatment

value: naive


title: GLAST173 pD

description: single-cell RNA-seq

value: TAP


title: GLAST175 pD

description: single-cell RNA-seq


title: GLAST177 pD

description: single-cell RNA-seq


title: GLAST174 pD

description: single-cell RNA-seq


title: GTEX-14LZ3-2726-SM-GW1WK

description:
sample name:
GTEX-14LZ3-2726-SM-GW1WK


title: GTEX-14BIN-3026-SM-GW1QX

description:
sample name:
GTEX-14BIN-3026-SM-GW1QX

value: Moderate


title: GTEX-14PN3-1826-SM-GW1UC

description:
sample name:
GTEX-14PN3-1826-SM-GW1UC


title: GTEX-14H4A-1926-SM-GW1DE

description:
sample name:
GTEX-14H4A-1926-SM-GW1DE


title: GTEX-14E7W-2526-SM-GW1AR

description:
sample name:
GTEX-14E7W-2526-SM-GW1AR


title: GTEX-14BMV-2426-SM-GW1RK

description:
sample name:
GTEX-14BMV-2426-SM-GW1RK


title: GTEX-14DAQ-2726-SM-GW1E6

description:
sample name:
GTEX-14DAQ-2726-SM-GW1E6


title: GTEX-14PK6-1726-SM-GW1WH

description:
sample name:
GTEX-14PK6-1726-SM-GW1WH


title: GTEX-14PJ4-1926-SM-GW1DO

description:
sample name:
GTEX-14PJ4-1926-SM-GW1DO


title: GTEX-14DAR-1526-SM-GW1WG

description:
sample name:
GTEX-14DAR-1526-SM-GW1WG


title: GTEX-14E6D-2226-SM-GW1DI

description:
sample name:
GTEX-14E6D-2226-SM-GW1DI


title: GTEX-14PJM-2626-SM-GW1RJ

description:
sample name:
GTEX-14PJM-2626-SM-GW1RJ


title: GTEX-14BIM-2426-SM-GW1QP

description:
sample name:
GTEX-14BIM-2426-SM-GW1QP


title: GLAST169 pD

description: single-cell RNA-seq

value: aNSC


title: GLAST170 pD

description: single-cell RNA-seq


title: GLAST168 pD

description: single-cell RNA-seq


title: GLAST167 pD

description: single-cell RNA-seq


title: GLAST172 pD

description: single-cell RNA-seq


title: GTEX-14ABY-2426-SM-GW1UN

description:
sample name:
GTEX-14ABY-2426-SM-GW1UN


title: GLAST165 pD

description: single-cell RNA-seq


title: GLAST164 pD

description: single-cell RNA-seq


title: GTEX-14AS3-1126-SM-GW1UG

description:
sample name:
GTEX-14AS3-1126-SM-GW1UG


title: GTEX-14A6H-1826-SM-GW1RY

description:
sample name:
GTEX-14A6H-1826-SM-GW1RY


title: GLAST162 pD

description: single-cell RNA-seq


title: GLAST161 pD

description: single-cell RNA-seq


title: GLAST163 pD

description: single-cell RNA-seq


title: GLAST160 pD

description: single-cell RNA-seq


title: GTEX-14A5I-2626-SM-GW1R2

description:
sample name:
GTEX-14A5I-2626-SM-GW1R2


title: GTEX-1477Z-1826-SM-GW1TG

description:
sample name:
GTEX-1477Z-1826-SM-GW1TG


title: GTEX-147GR-2726-SM-GW1TI

description:
sample name:
GTEX-147GR-2726-SM-GW1TI


title: GTEX-145MH-2526-SM-GW19X

description:
sample name:
GTEX-145MH-2526-SM-GW19X


title: GTEX-13OW7-2426-SM-GW1Z7

description:
sample name:
GTEX-13OW7-2426-SM-GW1Z7


title: GTEX-13QJC-2026-SM-GW23U

description:
sample name:
GTEX-13QJC-2026-SM-GW23U


title: GTEX-13X6I-2626-SM-GW1U3

description:
sample name:
GTEX-13X6I-2626-SM-GW1U3


title: GTEX-13SLW-2726-SM-GW1FX

description:
sample name:
GTEX-13SLW-2726-SM-GW1FX


title: GTEX-13QIC-2726-SM-GW2B8

description:
sample name:
GTEX-13QIC-2726-SM-GW2B8


title: GTEX-13SLX-2826-SM-GW1YI

description:
sample name:
GTEX-13SLX-2826-SM-GW1YI


title: GTEX-13OW8-2626-SM-GW1R9

description:
sample name:
GTEX-13OW8-2626-SM-GW1R9


title: GTEX-13PL6-1826-SM-GW243

description:
sample name:
GTEX-13PL6-1826-SM-GW243


title: GLAST16 pD

description: single-cell RNA-seq


title: GLAST158 pD

description: single-cell RNA-seq


title: GLAST159 pD

description: single-cell RNA-seq


title: GLAST157 pD

description: single-cell RNA-seq


title: GLAST156 pD

description: single-cell RNA-seq


title: GLAST154 pD

description: single-cell RNA-seq


title: E18 premature alveolar macrophages Csf2rb KO rep1 [preAM_Csf2rbKO_1]

city: Turku

first: alexander

last: mildner

address: Tykistökatu 6A

department: Biomedicine

country: Finland

institute: University of Turku / Medicity

description:
RNAseq_lungE18_Csf_11_1_S35
processed data file: RNAseq_samples_gene_counts.csv

library_source: transcriptomic

data_processing:
RNA-seq:
We used fastuniq to collapse PCR duplicates
STAR v2.6.1a was used to align unique reads to the mouse genome (GRCm38).
Gene expression was quantified using featureCounts v1.6.3 and the Gencode vM12 reference
ATAC-seq:
ATAC-seq reads were aligned to the mouse genome v. GRCm38 using the BWA-MEM algorithm implemented in the bwa program (Li, 2013), v. 0.7.17.
peaks were called with MACS2 v. 2.2.7.1
Peak calling was done with the R package DiffBind v. 2.14
Differential binding was done using the R package DESeq2 v. 1.26
Peaks were annotated using ChIPseeker v. 1.22.1
Genome_build: GRCm38
Supplementary_files_format_and_content: gene counts (featureCounts) as csv file
Supplementary_files_format_and_content: Annotation file peak_annotation.xlsx contains the PrimaryIDs and the output of ChIPseeker. Count matrix count_matrix.xlsx contains the counts collected from DiffBind.

molecule: polyA RNA

growth_protocol: no growth protocol; ex vivo isolation

treatment_protocol: no treatment

tag: strain

tag: background

tag: sample/tissue type


title: E18 premature alveolar macrophages Csf2rb WT rep4 [preAM_Csf2rbWT_4]

description:
RNAseq_lungE18_Csf_23_1_S53
processed data file: RNAseq_samples_gene_counts.csv

value: Csf2rb +/+


title: E18 premature alveolar macrophages Csf2rb KO rep2 [preAM_Csf2rbKO_2]

description:
RNAseq_lungE18_Csf_12_1_S38
processed data file: RNAseq_samples_gene_counts.csv


title: adult alveolar macrophages Lip CD11b low rep4 [LipCD11blow_4]

description:
AL_DD_229_S40
processed data file: RNAseq_samples_gene_counts.csv

extract_protocol:
bronchoalveolar lavage with 5x 1ml PBS with 2mM EDTA and 1% FBS
Cells for RNA-Seq or ATAC-Seq were isolated by FACS. Cells for RNA-Seq (500-20,000 sorted cells) were lysed with 50-200µl of lysis/binding buffer (Life Technologies), frozen on dry ice and stored at -80°C until further use. The mRNA was purified using a Dynabeads mRNA DIRECT Purification Kit (Life Technologies) according to the manufacturer’s guidelines. Reverse transcription was performed with oligo(dT) primers (Thermo Scientific) or MARS-seq barcoded RT primers and the Affinity Script cDNA Synthesis Kit (Agilent) in a 10µl reaction volume.
mRNA was subjected to reverse transcription using an Affinity Script cDNA Synthesis Kit (Agilent) and MARS-seq barcoded RT primers. Samples were analyzed by qPCR and up to 8 samples with similar Ct values were combined. Pooled samples were then treated with Exonuclease I (New England BioLabs (NEB)) and incubated at 37°C for 30min and 80°C for 10min followed by a 1.2X AMPure XP beads (Beckman Coulter) cleanup. Second strand synthesis of the cDNA was performed using a second strand synthesis kit (NEB) at 16°C for 2h and samples were cleaned with 1.4X volumes of AMPure XP beads. Afterwards samples were subjected to in vitro transcription (IVT) with a HiScribe T7 RNA Polymerase kit (NEB) at 37°C for 13-16h. The DNA template was removed by Turbo DNase I (Life Technologies) treatment at 37°C for 15min and the samples were cleaned with 1.2X volumes of AMPure XP beads. Subsequently, the RNA was fragmented at 70°C using RNA fragmentation buffer (Invitrogen), after 3min the reaction was stopped with Stop buffer (Invitrogen) and samples were purified by 2X SPRI cleanup. Afterwards T4 RNA ligase (NEB) was used to ligate the fragmented RNA to the MARS-seq ligation adapter (22°C 2h) and samples were purified with a 1.5X AMPure XP beads cleanup. In a second reverse transcription reaction (reaction volume 20µl) using the MARS-seq RT2 primer and an Affinity Script cDNA Synthesis Kit (Agilent Technologies) the RNA was transcribed into cDNA followed by another 1.5X AMPure XP beads purification. As final step the library was amplified in a nested PCR with P5_Rd1 and P7_Rd2 primers and Kapa HiFi Hotstart ready mix (Kapa Biosystems) and purified with a 0.7X AMPure XP beads cleanup. The fragment size of the final libraries was measured using a TapeStation (Agilent Technologies) and library concentrations were quantified with a Qubit fluorometer (Life Technologies). The samples were sequenced using a NextSeq 500 system (Illumina).
For the preparation of ATAC-seq libraries 15,000-20,000 cells were used as described earlier (Lara-Astiaso et al., 2014; Buenrostro et al., 2013). Briefly, nuclei were isolated by lysis with cold lysis buffer (10mM Tris-HCl pH7.4, 10mM MgCl2, 0.1% Igepal CA-630) and centrifuged for 25min at 500xg and 4°C with low acceleration and brake using a swing-out rotor. The supernatant was carefully removed and nuclei were resuspended in 25μl reaction buffer containing 2μl of Tn5 transposase and 12.5μl of TD buffer (Nextera DNA library preparation kit; Illumina). The mix was incubated at 37°C for 1hr. Afterwards, the DNA was purified by adding 5μl of cleanup buffer (900mM NaCl, 30mM EDTA), 2μl of proteinase K (NEB) and 2μl of 5% SDS. After an incubation phase of 30min at 40°C, the tagmented DNA was enriched using AMPure XP beads (Beckman Coulter). The DNA was PCR-amplified with indexed primers and Kapa HiFi Hotstart ready mix (Kapa Biosystems). After the PCR, tagmented DNA fragments were selected for fragments smaller than 600bp and purified using AMPure XP beads. Libraries were subjected to a second PCR amplification with Kapa HiFi Hotstart ready mix (Kapa Biosystems), indexing primers and an appropriate number of reaction cycles depending on the library concentration. Library sizes were determined using a TapeStation (Agilent Technologies) and measurement of DNA concentration was performed with a Qubit fluorometer (Life Technologies). Libraries where sequenced with an average of 20 million reads per sample on a NextSeq500 system (Illumina).

value: mixed background

value: Lip Lip/Lip

value: adult

value: bronchoalveolar lavage

value: alveolar macrophages


title: adult alveolar macrophages Lip CD11b low rep3 [LipCD11blow_3]

description:
AL_DD_227_S38
processed data file: RNAseq_samples_gene_counts.csv


title: adult alveolar macrophages Lip CD11b high rep3 [LipCD11bhigh_3]

description:
AL_DD_228_S39
processed data file: RNAseq_samples_gene_counts.csv


title: adult alveolar macrophages Lip CD11b high rep2 [LipCD11bhigh_2]

description:
AL_DD_226_S37
processed data file: RNAseq_samples_gene_counts.csv


title: adult alveolar macrophages Lip CD11b high rep1 [LipCD11bhigh_1]

description:
AL_DD_224_S35
processed data file: RNAseq_samples_gene_counts.csv


title: adult alveolar macrophages Lip CD11b high rep4 [LipCD11bhigh_4]

description:
AL_DD_230_S41
processed data file: RNAseq_samples_gene_counts.csv


title: GLAST153 pD

description: single-cell RNA-seq


title: GLAST152 pD

description: single-cell RNA-seq


title: adult alveolar macrophages Lip CD11b low rep1 [LipCD11blow_1]

description:
AL_DD_223_S34
processed data file: RNAseq_samples_gene_counts.csv


title: adult alveolar macrophages Lip CD11b low rep2 [LipCD11blow_2]

description:
AL_DD_225_S36
processed data file: RNAseq_samples_gene_counts.csv


title: GLAST149 pD

description: single-cell RNA-seq


title: GTEX-13O3P-2326-SM-GW19Y

description:
sample name:
GTEX-13O3P-2326-SM-GW19Y

value: Colon - Transverse


title: GTEX-13OW5-2626-SM-GW1SS

description:
sample name:
GTEX-13OW5-2626-SM-GW1SS


title: GTEX-13NZB-1826-SM-GW1AH

description:
sample name:
GTEX-13NZB-1826-SM-GW1AH


title: GTEX-13NYS-2726-SM-GW1GE

description:
sample name:
GTEX-13NYS-2726-SM-GW1GE


title: GTEX-13N1W-2326-SM-GW1FV

description:
sample name:
GTEX-13N1W-2326-SM-GW1FV


title: E18 premature alveolar macrophages Cebpb WT rep2 [preAM_CebpbWT_2]

description:
RNAseq_lungE18_11_1_S21
processed data file: RNAseq_samples_gene_counts.csv

value: C/EBPb tm1Pfj

value: Cebpb +/+

value: whole lung tissue

value: premature alveolar macrophages


title: E18 premature alveolar macrophages Cebpb WT rep1 [preAM_CebpbWT_1]

description:
RNAseq_lungE18_10_1_S17
processed data file: RNAseq_samples_gene_counts.csv


title: E18 premature alveolar macrophages Cebpb KO rep2 [preAM_CebpbKO_2]

description:
RNAseq_lungE18_3_1_S5
processed data file: RNAseq_samples_gene_counts.csv

value: Cebpb -/-


title: E18 premature alveolar macrophages Cebpb WT rep3 [preAM_CebpbWT_3]

description:
RNAseq_lungE18_15_1_S25
processed data file: RNAseq_samples_gene_counts.csv


title: E18 premature alveolar macrophages Csf2rb WT rep1 [preAM_Csf2rbWT_1]

description:
RNAseq_lungE18_Csf_20_1_S44
processed data file: RNAseq_samples_gene_counts.csv


title: E18 premature alveolar macrophages Cebpb KO rep1 [preAM_CebpbKO_1]

description:
RNAseq_lungE18_1_1_S1
processed data file: RNAseq_samples_gene_counts.csv


title: E18 premature alveolar macrophages Csf2rb WT rep3 [preAM_Csf2rbWT_3]

description:
RNAseq_lungE18_Csf_22_1_S50
processed data file: RNAseq_samples_gene_counts.csv


title: E18 premature alveolar macrophages Cebpb KO rep4 [preAM_CebpbKO_4]

description:
RNAseq_lungE18_7_1_S13
processed data file: RNAseq_samples_gene_counts.csv


title: E18 premature alveolar macrophages Cebpb KO rep3 [preAM_CebpbKO_3]

description:
RNAseq_lungE18_4_1_S9
processed data file: RNAseq_samples_gene_counts.csv


title: E18 premature alveolar macrophages Csf2rb WT rep2 [preAM_Csf2rbWT_2]

description:
RNAseq_lungE18_Csf_21_1_S47
processed data file: RNAseq_samples_gene_counts.csv


title: GLAST147 pD

description: single-cell RNA-seq

value: ventricular-subventricular zone

value: WT


title: GLAST146 pD

description: single-cell RNA-seq

value: naive


title: GLAST144 pD

description: single-cell RNA-seq


title: GLAST143 pD

description: single-cell RNA-seq


title: GLAST142 pD

description: single-cell RNA-seq


title: adult alveolar macrophages CD11cCre Cebpb KO rep3 [CD11cCreCebpbKO_3]

description:
C11C6_S28
processed data file: RNAseq_samples_gene_counts.csv

value: Cebpbtm1.1Elgaz/J crossed with Tg(Itgax-cre,-EGFP)4097Ach/J

value: CD11c +/Cre Cebpb flox/flox


title: adult alveolar macrophages Lip WT rep1 [LipWT_1]

description:
AL_DD_220_S31
processed data file: RNAseq_samples_gene_counts.csv

source_name: adult alveolar macrophages Lip WT

value: Lip +/+


title: adult alveolar macrophages CD11cCre Cebpb KO rep2 [CD11cCreCebpbKO_2]

description:
C11C5_S27
processed data file: RNAseq_samples_gene_counts.csv


title: adult alveolar macrophages CD11cCre Cebpb KO rep4 [CD11cCreCebpbKO_4]

description:
C11C7_S29
processed data file: RNAseq_samples_gene_counts.csv


title: adult alveolar macrophages Lip WT rep2 [LipWT_2]

description:
AL_DD_221_S32
processed data file: RNAseq_samples_gene_counts.csv

value: mixed background


title: adult alveolar macrophages Lip WT rep3 [LipWT_3]

description:
AL_DD_222_S33
processed data file: RNAseq_samples_gene_counts.csv


title: GLAST141 pD

description: single-cell RNA-seq


title: adult alveolar macrophages CD11cCre Cebpb KO rep1 [CD11cCreCebpbKO_1]

description:
C11C4_S26
processed data file: RNAseq_samples_gene_counts.csv


title: adult alveolar macrophages CD11cCre WT rep3 [CD11cCreWT_3]

description:
C11C3_S25
processed data file: RNAseq_samples_gene_counts.csv

source_name: adult alveolar macrophages CD11cCre WT

value: CD11c +/Cre


title: GLAST140 pD

description: single-cell RNA-seq


title: GLAST139 pD

description: single-cell RNA-seq


title: adult alveolar macrophages CD11cCre WT rep2 [CD11cCreWT_2]

description:
C11C2_S24
processed data file: RNAseq_samples_gene_counts.csv

value: adult


title: adult alveolar macrophages CD11cCre WT rep1 [CD11cCreWT_1]

description:
C11C1_S23
processed data file: RNAseq_samples_gene_counts.csv

value: bronchoalveolar lavage


title: adult alveolar macrophages LyzMCre Cebpb KO rep2 [LyzMCreCebpbKO_2]

description:
AL_DD_245_S56
processed data file: RNAseq_samples_gene_counts.csv

value: Cebpbtm1.1Elgaz/J crossed with Lyz2tm1(cre)Ifo/J

value: LyzM Cre/Cre Cebpb flox/flox

value: alveolar macrophages


title: GLAST137 pD

description: single-cell RNA-seq

value: TAP


title: adult alveolar macrophages LyzMCre Cebpb KO rep1 [LyzMCreCebpbKO_1]

description:
AL_DD_244_S55
processed data file: RNAseq_samples_gene_counts.csv


title: GLAST136 pD

description: single-cell RNA-seq


title: GTEX-11TTK-2426-SM-GW24B

description:
sample name:
GTEX-11TTK-2426-SM-GW24B

value: Severe

value: Colon - Transverse

value: Former


title: GTEX-1211K-1726-SM-GW1U8

description:
sample name:
GTEX-1211K-1726-SM-GW1U8

value: Mild

value: Never


title: GTEX-11EMC-1526-SM-GW23O

description:
sample name:
GTEX-11EMC-1526-SM-GW23O

value: Current


title: GTEX-12696-2126-SM-GW1BJ

description:
sample name:
GTEX-12696-2126-SM-GW1BJ

value: Moderate


title: GTEX-139YR-2126-SM-GW1G2

description:
sample name:
GTEX-139YR-2126-SM-GW1G2


title: GTEX-11TT1-1026-SM-GW1AF

description:
sample name:
GTEX-11TT1-1026-SM-GW1AF


title: GTEX-1399R-2226-SM-GW21Z

description:
sample name:
GTEX-1399R-2226-SM-GW21Z


title: GTEX-11ZTT-1326-SM-GW19N

description:
sample name:
GTEX-11ZTT-1326-SM-GW19N


title: GTEX-13CF2-1926-SM-GW22O

description:
sample name:
GTEX-13CF2-1926-SM-GW22O


title: GTEX-12ZZX-2626-SM-GW2BU

description:
sample name:
GTEX-12ZZX-2626-SM-GW2BU


title: GTEX-12WSE-2626-SM-GW1VB

description:
sample name:
GTEX-12WSE-2626-SM-GW1VB


title: GTEX-139TT-2026-SM-GW1YB

description:
sample name:
GTEX-139TT-2026-SM-GW1YB


title: GTEX-11ZU8-2226-SM-GW2B5

description:
sample name:
GTEX-11ZU8-2226-SM-GW2B5


title: GTEX-12ZZY-2826-SM-GW29L

description:
sample name:
GTEX-12ZZY-2826-SM-GW29L


title: GTEX-11P82-1026-SM-GW1XX

description:
sample name:
GTEX-11P82-1026-SM-GW1XX


title: GTEX-12ZZW-2526-SM-GW1AB

description:
sample name:
GTEX-12ZZW-2526-SM-GW1AB


title: GTEX-11ZUS-2226-SM-GW1Z3

description:
sample name:
GTEX-11ZUS-2226-SM-GW1Z3


title: GTEX-13111-0726-SM-GW1Z8

description:
sample name:
GTEX-13111-0726-SM-GW1Z8


title: GTEX-11ZTS-1726-SM-GW2BJ

description:
sample name:
GTEX-11ZTS-1726-SM-GW2BJ


title: GTEX-11I78-1226-SM-GW192

description:
sample name:
GTEX-11I78-1226-SM-GW192


title: GTEX-12ZZZ-2426-SM-GW24E

description:
sample name:
GTEX-12ZZZ-2426-SM-GW24E


title: GTEX-12WSF-2826-SM-GW1FS

description:
sample name:
GTEX-12WSF-2826-SM-GW1FS


title: GTEX-11UD2-2426-SM-GW1BM

description:
sample name:
GTEX-11UD2-2426-SM-GW1BM


title: GTEX-13112-1826-SM-GW1TV

description:
sample name:
GTEX-13112-1826-SM-GW1TV


title: GTEX-12584-2626-SM-GW1ZC

description:
sample name:
GTEX-12584-2626-SM-GW1ZC


title: GTEX-11GS4-1926-SM-GW2CA

description:
sample name:
GTEX-11GS4-1926-SM-GW2CA


title: GTEX-11WQC-2126-SM-GW1Z4

description:
sample name:
GTEX-11WQC-2126-SM-GW1Z4


title: GTEX-12KS4-2426-SM-GW1BA

description:
sample name:
GTEX-12KS4-2426-SM-GW1BA


title: GTEX-12WSI-1626-SM-GW1AC

description:
sample name:
GTEX-12WSI-1626-SM-GW1AC


title: GTEX-11ONC-2026-SM-GW1YJ

description:
sample name:
GTEX-11ONC-2026-SM-GW1YJ


title: GTEX-11EM3-1526-SM-GW249

description:
sample name:
GTEX-11EM3-1526-SM-GW249


title: GTEX-11DXZ-1726-SM-GW1EW

description:
sample name:
GTEX-11DXZ-1726-SM-GW1EW


title: GTEX-11DXX-1826-SM-GW1UB

description:
sample name:
GTEX-11DXX-1826-SM-GW1UB


title: GTEX-1192X-2626-SM-GW1EK

description:
sample name:
GTEX-1192X-2626-SM-GW1EK


title: GTEX-1192W-1826-SM-GW248

description:
sample name:
GTEX-1192W-1826-SM-GW248


title: GLAST135 pD

description: single-cell RNA-seq

value: ventricular-subventricular zone

value: WT

value: naive


title: GTEX-111YS-1626-SM-GW23H

description:
sample name:
GTEX-111YS-1626-SM-GW23H


title: GTEX-113JC-1826-SM-GW29S

description:
sample name:
GTEX-113JC-1826-SM-GW29S


title: GLAST13 pD

description: single-cell RNA-seq


title: GLAST129 pD

description: single-cell RNA-seq

value: aNSC


title: GLAST128 pD

description: single-cell RNA-seq


title: GLAST134 pD

description: single-cell RNA-seq


title: GLAST133 pD

description: single-cell RNA-seq


title: GLAST131 pD

description: single-cell RNA-seq

value: neuroblast


title: GLAST132 pD

description: single-cell RNA-seq


title: GLAST130 pD

description: single-cell RNA-seq


title: GTEX-1117F-2726-SM-GW1F9

description:
sample name:
GTEX-1117F-2726-SM-GW1F9


title: GTEX-XUW1-2326-SM-GW2AA

description:
sample name:
GTEX-XUW1-2326-SM-GW2AA

source_name: Breast - Mammary Tissue

value: Breast - Mammary Tissue


title: GTEX-WRHU-0326-SM-GW1U1

description:
sample name:
GTEX-WRHU-0326-SM-GW1U1

value: PT-WRHU

value: GTEX-WRHU


title: GTEX-X8HC-0826-SM-GW2B2

description:
sample name:
GTEX-X8HC-0826-SM-GW2B2


title: GTEX-XUZC-1626-SM-GW1CI

description:
sample name:
GTEX-XUZC-1626-SM-GW1CI

value: PT-XUZC

value: GTEX-XUZC


title: GTEX-111FC-2326-SM-GW2AK

description:
sample name:
GTEX-111FC-2326-SM-GW2AK

value: Severe


title: GTEX-ZXES-0826-SM-GW2BT

description:
sample name:
GTEX-ZXES-0826-SM-GW2BT

value: PT-ZXES

value: GTEX-ZXES


title: GTEX-111VG-2226-SM-GW1XW

description:
sample name:
GTEX-111VG-2226-SM-GW1XW

value: Colon - Transverse


title: GTEX-ZC5H-2626-SM-GW1G6

description:
sample name:
GTEX-ZC5H-2626-SM-GW1G6

value: Mild

value: Never


title: GTEX-YFC4-1426-SM-GW1SR

description:
sample name:
GTEX-YFC4-1426-SM-GW1SR

value: Current


title: GTEX-X15G-1626-SM-GW1D9

description:
sample name:
GTEX-X15G-1626-SM-GW1D9

value: Former


title: adult alveolar macrophages Cebpb WT female facility2 rep3 [AM_WT_F2_female_3]

description:
RNAseq_AM_C15_S31
processed data file: RNAseq_samples_gene_counts.csv

value: C/EBPb tm1Pfj

value: mixed background

value: Cebpb +/+

value: adult

value: bronchoalveolar lavage

value: alveolar macrophages


title: adult alveolar macrophages Cebpb KO female facility2 rep1 [AM_KO_F2_female_1]

description:
RNAseq_AM_C5_S23
processed data file: RNAseq_samples_gene_counts.csv

value: Cebpb -/-


title: adult alveolar macrophages Cebpb WT male rep1 [AM_WT_male_1]

description:
RNAseq_AM_MAM1_S13
processed data file: RNAseq_samples_gene_counts.csv


title: GTEX-XV7Q-2326-SM-GW1VQ

description:
sample name:
GTEX-XV7Q-2326-SM-GW1VQ

value: Breast - Mammary Tissue


title: adult alveolar macrophages Cebpb KO female facility2 rep2 [AM_KO_F2_female_2]

description:
RNAseq_AM_C6_S24
processed data file: RNAseq_samples_gene_counts.csv


title: adult alveolar macrophages Cebpb WT male rep2 [AM_WT_male_2]

description:
RNAseq_AM_MAM2_S14
processed data file: RNAseq_samples_gene_counts.csv


title: GTEX-U3ZN-1926-SM-GW1U4

description:
sample name:
GTEX-U3ZN-1926-SM-GW1U4


title: GTEX-UJHI-1426-SM-GW1SO

description:
sample name:
GTEX-UJHI-1426-SM-GW1SO

value: PT-UJHI

value: GTEX-UJHI


title: GTEX-WI4N-1426-SM-GW1FZ

description:
sample name:
GTEX-WI4N-1426-SM-GW1FZ


title: GTEX-T6MO-0326-SM-GW1ZU

description:
sample name:
GTEX-T6MO-0326-SM-GW1ZU


title: GLAST125 pD

description: single-cell RNA-seq

value: ventricular-subventricular zone

value: TAP

value: WT

value: naive


title: GLAST126 pD

description: single-cell RNA-seq


title: adult alveolar macrophages Cebpb KO male rep2 [AM_KO_male_2]

description:
RNAseq_AM_MAM5_S17
processed data file: RNAseq_samples_gene_counts.csv


title: adult alveolar macrophages LyzMCre WT rep1 [LyzMCreWT_1]

description:
AL_DD_242_S53
processed data file: RNAseq_samples_gene_counts.csv

source_name: adult alveolar macrophages LyzMCre WT

value: Cebpb flox/flox


title: adult alveolar macrophages Cebpb KO male rep1 [AM_KO_male_1]

description:
RNAseq_AM_MAM4_S16
processed data file: RNAseq_samples_gene_counts.csv


title: adult alveolar macrophages LyzMCre WT rep2 [LyzMCreWT_2]

description:
AL_DD_243_S54
processed data file: RNAseq_samples_gene_counts.csv


title: GTEX-S4P3-1326-SM-GW2AH

description:
sample name:
GTEX-S4P3-1326-SM-GW2AH

value: Mild


title: GLAST123 pD

description: single-cell RNA-seq


title: GLAST122 pD

description: single-cell RNA-seq


title: adult alveolar macrophages Cebpb WT female facility2 rep2 [AM_WT_F2_female_2]

description:
RNAseq_AM_C13_S30
processed data file: RNAseq_samples_gene_counts.csv


title: adult alveolar macrophages Cebpb KO female facility1 rep2 [AM_KO_F1_female_2]

description:
RNAseq_AM_C4_S22
processed data file: RNAseq_samples_gene_counts.csv


title: adult alveolar macrophages Cebpb WT female facility2 rep1 [AM_WT_F2_female_1]

description:
RNAseq_AM_C12_S29
processed data file: RNAseq_samples_gene_counts.csv


title: GTEX-SE5C-2126-SM-GW1G8

description:
sample name:
GTEX-SE5C-2126-SM-GW1G8

value: Current


title: GLAST119 pD

description: single-cell RNA-seq


title: GLAST12 pD

description: single-cell RNA-seq


title: GLAST118 pD

description: single-cell RNA-seq


title: GLAST117 pD

description: single-cell RNA-seq


title: GLAST115 pD

description: single-cell RNA-seq


title: GLAST120 pD

description: single-cell RNA-seq


title: adult alveolar macrophages Cebpb heterozygous female facility1 rep1 [AM_het_F1_female_1]

description:
RNAseq_AM_C7_S25
processed data file: RNAseq_samples_gene_counts.csv

value: C/EBPb tm1Pfj

value: Cebpb +/-


title: adult alveolar macrophages Cebpb KO female facility1 rep1 [AM_KO_F1_female_1]

description:
RNAseq_AM_C3_S21
processed data file: RNAseq_samples_gene_counts.csv

value: mixed background


title: adult alveolar macrophages Cebpb heterozygous female facility1 rep3 [AM_het_F1_female_3]

description:
RNAseq_AM_C11_S28
processed data file: RNAseq_samples_gene_counts.csv

value: adult


title: GLAST114 pD

description: single-cell RNA-seq


title: adult alveolar macrophages Cebpb heterozygous female facility1 rep2 [AM_het_F1_female_2]

description:
RNAseq_AM_C8_S26
processed data file: RNAseq_samples_gene_counts.csv

value: bronchoalveolar lavage


title: GLAST113 pD

description: single-cell RNA-seq


title: GLAST110 pD

description: single-cell RNA-seq

value: aNSC


title: GLAST109 pD

description: single-cell RNA-seq

value: neuroblast


title: GTEX-15EU6-2426-SM-GW1RL

description:
sample name:
GTEX-15EU6-2426-SM-GW1RL

value: Breast - Mammary Tissue


title: GTEX-17HG3-0126-SM-GW1R6

description:
sample name:
GTEX-17HG3-0126-SM-GW1R6

value: Moderate


title: GTEX-16NGA-0826-SM-GW1UD

description:
sample name:
GTEX-16NGA-0826-SM-GW1UD

value: Never


title: GTEX-1F88E-0326-SM-GW1CC

description:
sample name:
GTEX-1F88E-0326-SM-GW1CC

value: Former


title: GTEX-1GMR3-2626-SM-GW1E8

description:
sample name:
GTEX-1GMR3-2626-SM-GW1E8


title: GTEX-1F5PL-1026-SM-GW1AX

description:
sample name:
GTEX-1F5PL-1026-SM-GW1AX


title: GTEX-1GZ2Q-2626-SM-GW1PZ

description:
sample name:
GTEX-1GZ2Q-2626-SM-GW1PZ


title: GTEX-1GZ4H-0326-SM-GW1RT

description:
sample name:
GTEX-1GZ4H-0326-SM-GW1RT


title: GTEX-1IKOH-2326-SM-GW1T3

description:
sample name:
GTEX-1IKOH-2326-SM-GW1T3


title: GTEX-1AYD5-2526-SM-GW1DB

description:
sample name:
GTEX-1AYD5-2526-SM-GW1DB


title: GTEX-1GPI6-0626-SM-GW1S3

description:
sample name:
GTEX-1GPI6-0626-SM-GW1S3


title: GTEX-1H3VE-2226-SM-GW1S4

description:
sample name:
GTEX-1H3VE-2226-SM-GW1S4


title: GTEX-1GN1W-1926-SM-GW1DD

description:
sample name:
GTEX-1GN1W-1926-SM-GW1DD


title: GTEX-S341-1526-SM-GW24F

description:
sample name:
GTEX-S341-1526-SM-GW24F


title: GTEX-1C6WA-2426-SM-GW1RG

description:
sample name:
GTEX-1C6WA-2426-SM-GW1RG


title: GTEX-18QFQ-0826-SM-GW1CA

description:
sample name:
GTEX-18QFQ-0826-SM-GW1CA


title: GTEX-15SHU-0826-SM-GW21B

description:
sample name:
GTEX-15SHU-0826-SM-GW21B


title: GTEX-1GTWX-2826-SM-GW1E9

description:
sample name:
GTEX-1GTWX-2826-SM-GW1E9


title: GTEX-18D9U-2326-SM-GW1S1

description:
sample name:
GTEX-18D9U-2326-SM-GW1S1


title: GTEX-1IDJE-0826-SM-GW1GS

description:
sample name:
GTEX-1IDJE-0826-SM-GW1GS


title: GTEX-15ER7-1626-SM-GW1VP

description:
sample name:
GTEX-15ER7-1626-SM-GW1VP


title: GLAST108 pD

description: single-cell RNA-seq

value: ventricular-subventricular zone


title: GLAST107 pD

description: single-cell RNA-seq

value: WT


title: GTEX-147F3-1626-SM-GW1DU

description:
sample name:
GTEX-147F3-1626-SM-GW1DU


title: GTEX-14H4A-2526-SM-GW1GY

description:
sample name:
GTEX-14H4A-2526-SM-GW1GY


title: GTEX-14BIL-2526-SM-GW1SZ

description:
sample name:
GTEX-14BIL-2526-SM-GW1SZ


title: GTEX-14PK6-1526-SM-GW21C

description:
sample name:
GTEX-14PK6-1526-SM-GW21C


title: GTEX-14PHY-1926-SM-GW2A6

description:
sample name:
GTEX-14PHY-1926-SM-GW2A6


title: GTEX-14E6C-1326-SM-GW1D1

description:
sample name:
GTEX-14E6C-1326-SM-GW1D1


title: GTEX-14BIN-1826-SM-GW1X6

description:
sample name:
GTEX-14BIN-1826-SM-GW1X6


title: GTEX-14PJ6-2026-SM-GW1R5

description:
sample name:
GTEX-14PJ6-2026-SM-GW1R5


title: GTEX-13PL6-2926-SM-GW1SN

description:
sample name:
GTEX-13PL6-2926-SM-GW1SN


title: GLAST101 pD

description: single-cell RNA-seq

value: naive


title: OLIGO8 pC

description: single-cell RNA-seq

value: oligodendrocyte


title: GLAST102 pD

description: single-cell RNA-seq


title: GLAST105 pD

description: single-cell RNA-seq

value: TAP


title: GLAST106 pD

description: single-cell RNA-seq


title: GLAST104 pD

description: single-cell RNA-seq


title: adult alveolar macrophages Cebpb KO CD11b low rep4 [CebpbKOCD11blow_4]

description:
AL_DD_238_S49
processed data file: RNAseq_samples_gene_counts.csv

value: Cebpb -/-

value: alveolar macrophages


title: adult alveolar macrophages Cebpb KO CD11b high rep3 [CebpbKOCD11bhigh_3]

description:
AL_DD_235_S46
processed data file: RNAseq_samples_gene_counts.csv

value: C/EBPb tm1Pfj


title: adult alveolar macrophages Cebpb KO CD11b high rep4 [CebpbKOCD11bhigh_4]

description:
AL_DD_237_S48
processed data file: RNAseq_samples_gene_counts.csv

value: mixed background


title: adult alveolar macrophages Cebpb WT female facility1 rep1 [AM_WT_F1_female_1]

description:
RNAseq_AM_C1_S19
processed data file: RNAseq_samples_gene_counts.csv

value: Cebpb +/+

value: adult


title: adult alveolar macrophages Cebpb KO CD11b high rep2 [CebpbKOCD11bhigh_2]

description:
AL_DD_233_S44
processed data file: RNAseq_samples_gene_counts.csv

value: bronchoalveolar lavage


title: adult alveolar macrophages Cebpb WT female facility1 rep2 [AM_WT_F1_female_2]

description:
RNAseq_AM_C2_S20
processed data file: RNAseq_samples_gene_counts.csv


title: adult alveolar macrophages Cebpb KO CD11b high rep1 [CebpbKOCD11bhigh_1]

description:
AL_DD_231_S42
processed data file: RNAseq_samples_gene_counts.csv


title: GTEX-13D11-1026-SM-GW1D7

description:
sample name:
GTEX-13D11-1026-SM-GW1D7

value: Current


title: GTEX-11GSP-0926-SM-GW21X

description:
sample name:
GTEX-11GSP-0926-SM-GW21X

value: Mild

value: Breast - Mammary Tissue


title: GTEX-11EM3-1326-SM-GW24C

description:
sample name:
GTEX-11EM3-1326-SM-GW24C

value: Never


title: GTEX-11EMC-2026-SM-GW242

description:
sample name:
GTEX-11EMC-2026-SM-GW242


title: OLIGO7 pC

description: single-cell RNA-seq


title: OLIGO6 pC

description: single-cell RNA-seq


title: GTEX-15CHR-1026-SM-GW218

description:
sample name:
GTEX-15CHR-1026-SM-GW218


title: GTEX-15DDE-0726-SM-GW1RC

description:
sample name:
GTEX-15DDE-0726-SM-GW1RC


title: GTEX-15CHQ-0426-SM-GW1QF

description:
sample name:
GTEX-15CHQ-0426-SM-GW1QF

value: Former


title: OLIGO32 pC

description: single-cell RNA-seq

value: ventricular-subventricular zone


title: OLIGO5 pC

description: single-cell RNA-seq

value: WT


title: OLIGO4 pC

description: single-cell RNA-seq

value: naive


title: Case 21 Be-exosme

type: RNA

city: Kanagawa

first: Satoko

last: Takizawa

state: Kamakura

country: Japan

institute: Toray Industries, Inc.

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

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

data_processing:
Fluorescent value excited at 635 nm was degitalized as the data.
Each fluorescent raw value was run in batches from standardization (in the sample direction by Z-score) to principal component analysis.

source_name: Primary hepatobiliary tumor

label_protocol: microRNA was labeled using 3D-Gene® miRNA Labeling kit (Toray Industries, Inc.) in accordance with the manufacturer's instructions.

extract_protocol: Total RNA was extracted and purified each from 5 ul samples of tissue (or serum exosome) using an miRNeasy mini kit (Qiagen, Inc.).

tag: histology

value: Inflammatory pseudotumor (benign)

value: F

tag: molecule

value: miRNA


title: Case 22 Be-exosme

value: Angiomyolipoma (benign)


title: Case 20 HCC-exosme

value: Hepatocellular carcinoma

value: M


title: OLIGO31 pC

description: single-cell RNA-seq

value: oligodendrocyte


title: Case 23 Be-exosme

value: Adenomyomatous hyperplasia of gallbladder (benign)


title: Case 19 HCC-exosme


title: Case 24 Be-exosme

value: Focal nodular hyperplasia of liver (benign)


title: NTERA2 siIQGAP3 rep3

city: Singapore

first: Khine

last: Myint

address: 14 Medical Drive

department: Medicine

country: Singapore

institute: Cancer Science Institute/NUS

data_processing:
RNA-seq reads were mapped by STAR to the human reference genome GRCh37 with reference gene annotation GENCODE 26.
Reads with low mapping quality <20 were not used for further analysis.
Next, PCR duplicates were removed in the paired-end alignments using SAMtools.
Gene expression levels of individual genes/transcripts were generated using featureCounts.
Cross-sample normalization of reads counts was based on total mappable counts using RPKM.
Genome_build: GRCh37
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample …
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: NTERA2 cells

growth_protocol: NTERA2 cells were grown and maintained in DMEM supplemented with 10% FBS.

extract_protocol:
RNA were extracted from total cell lysates usign RNAeasy Kit (Qiagen).
RNA libraries were prepared for sequencing using standard protocols. BGISEQ(DNBSEQ) Pair-end 100bp Sequencing/40 Million Pair-end reads was done.

treatment_protocol: Cells were treated with siRNAs twice for 7 days.

value: Human embryonic carcinoma cell

tag: cell line

tag: sirna


title: Case 18 HCC-exosme


title: NTERA2 siIQGAP3 rep2


title: NTERA2 siIQGAP3 rep1


title: Case 17 HCC-exosme


title: OLIGO30 pC

description: single-cell RNA-seq


title: NTERA2 siFOXM1 rep3


title: NTERA2 siFOXM1 rep2


title: NTERA2 siFOXM1 rep1


title: Case 16 HCC-exosme


title: OLIGO29 pC

description: single-cell RNA-seq


title: Case 15 HCC-exosme


title: NTERA2 siSRF rep3

value: siSRF


title: NTERA2 siSRF rep2


title: OLIGO28 pC

description: single-cell RNA-seq


title: Case 14 HCC-exosme


title: NTERA2 siIGF2BP1 rep3


title: NTERA2 siIGF2BP1 rep2


title: Case 13 HCC-exosme


title: OLIGO27 pC

description: single-cell RNA-seq


title: NTERA2 siIGF2BP1 rep1


title: NTERA2 siSRF rep1


title: OLIGO25 pC

description: single-cell RNA-seq


title: OLIGO26 pC

description: single-cell RNA-seq


title: Case 12 HCC-exosme


title: OLIGO24 pC

description: single-cell RNA-seq


title: NTERA2 siControl rep3

value: siControl


title: NTERA2 siControl rep2


title: Case 11 HCC-exosme


title: OLIGO23 pC

description: single-cell RNA-seq


title: NTERA2 siControl rep1


title: Case 10 YCC-exosme

value: Cholangiocarcinoma (less than 40 generations)


title: FLAG-IP rep2

data_processing:
Reads from the RIP-Seq samples and the corresponding controls were mapped against human reference genome GRCh37 by STAR with GENCODE 26 for transcriptome annotation.
First, peak calling was performed by MACS2 to identify RIP binding enriched regions.
For reads mapped to multiple exons or peaks presented in neighbouring exons, the peaks were merged together.
Sequences covered by the reproducible peaks of the duplicated samples were extracted for motif finding. The upstream and downstream sequences of reproducible peaks were also extracted and served as the background sequences in the motif finding.
Motif discovery is performed with MEME suite using differential enrichment mode.
Genome_build: GRCh37
Supplementary_files_format_and_content: peak

extract_protocol:
RNA were extracted from pulled down samples using Trizol method.
RNA libraries were prepared for sequencing using standard protocols. BGISEQ(DNBSEQ) DNBseq RipSeq Library was done.

treatment_protocol: Cells were overexpressed with FLAG-IGF2BP1 for 72 hours and cell lysates were used for RNA-IP using FLAG affinity beads.

tag: antibody

value: FLAG

value: FLAG-IGF2BP1 overexpressed cells


title: Input rep2


title: adult alveolar macrophages Cebpb KO CD11b low rep3 [CebpbKOCD11blow_3]

description:
AL_DD_236_S47
processed data file: RNAseq_samples_gene_counts.csv

value: C/EBPb tm1Pfj

value: mixed background

value: Cebpb -/-

value: adult

value: bronchoalveolar lavage

value: alveolar macrophages


title: adult alveolar macrophages Cebpb KO CD11b low rep1 [CebpbKOCD11blow_1]

description:
AL_DD_232_S43
processed data file: RNAseq_samples_gene_counts.csv


title: Input rep1


title: adult alveolar macrophages Cebpb KO CD11b low rep2 [CebpbKOCD11blow_2]

description:
AL_DD_234_S45
processed data file: RNAseq_samples_gene_counts.csv


title: Case 9 CC-exosme

value: Cholangiocarcinoma

value: F

value: miRNA


title: Case 8 YCC-exosme

value: M


title: adult alveolar macrophages Cebpb WT rep2 [CebpbWT_2]

description:
AL_DD_239_S50
processed data file: RNAseq_samples_gene_counts.csv

source_name: adult alveolar macrophages Cebpb WT

value: Cebpb +/+


title: adult alveolar macrophages Cebpb WT rep4 [CebpbWT_4]

description:
AL_DD_241_S52
processed data file: RNAseq_samples_gene_counts.csv


title: adult alveolar macrophages Cebpb WT rep1 [CebpbWT_1]

description:
AL_DD_212_S23
processed data file: RNAseq_samples_gene_counts.csv


title: adult alveolar macrophages Cebpb WT rep3 [CebpbWT_3]

description:
AL_DD_240_S51
processed data file: RNAseq_samples_gene_counts.csv


title: FLAG-IP rep1

value: Human embryonic carcinoma cell


title: Case 7 YCC-exosme


title: OLIGO22 pC

description: single-cell RNA-seq

value: ventricular-subventricular zone

value: oligodendrocyte

value: WT

value: naive


title: OLIGO19 pC

description: single-cell RNA-seq


title: OLIGO21 pC

description: single-cell RNA-seq


title: RNA_seq_minu_rep2

city: Valencia

first: Jaime

last: Pérez

address: Calle del Ingeniero Fausto Elio, s/n

country: Spain

institute: IBMCP

data_processing:
Read quality control was performed using FastQC v0.11.9. Reads were aligned to TAIR10 using STAR v2.7.9 with default parameters. Gene counts were obtained with featureCounts v2.0.1, specifying "-Q 5 -s 2 -B" and using the Araport11 annotation. Differential expression analyses were carried out using DESeq2 v1.32.0. Library size factors were saved for normalizing coverage bedgraphs, which were generated using bedtools genomecov v2.30.9 with parameters “-split -bga -scale <size_factor>”. Bedgraphs were then converted to bigwigs using the bedGraphToBigwig command from UCSC tools.
Assembly: TAIR10
Supplementary files format and content: DESeq2-normalized coverage tracks in bigwig format
Supplementary files format and content: Gene-level raw counts in tab-separated text file

organism: Arabidopsis thaliana

source_name: inflorescences

growth_protocol: Inflorescences of plants grown on soil in long days condition

extract_protocol:
Total RNA from inflorescences of Col-0, minu1-2 minu2-1 and tpf1-1 tpf2-1 plants
Libraries for sequencing were prepared at BGI following the strand-specific mRNA libraries protocol for DNBSEQ platform.

value: inflorescences

value: minu1-2 minu2-1


title: RNA_seq_minu_rep1


title: RNA_seq_tpf_rep3

value: tpf1-1 tpf1-2


title: OLIGO17 pC

description: single-cell RNA-seq


title: RNA_seq_minu_rep3


title: RNA_seq_tpf_rep2


title: OLIGO16 pC

description: single-cell RNA-seq


title: RNA_seq_col0_rep2


title: OLIGO15 pC

description: single-cell RNA-seq


title: Case 5 CC-exosme


title: RNA_seq_col0_rep1


title: RNA_seq_col0_rep3


title: OLIGO14 pC

description: single-cell RNA-seq


title: RNA_seq_tpf_rep1


title: OLIGO12 pC

description: single-cell RNA-seq


title: Case 6 CC-exosme


title: AML94

city: Nottingham

first: Sergio

last: Rutella

address: Clifton Campus

department: John van Geest Cancer Research Centre

country: United Kingdom

institute: Nottingham Trent University

description: Pan Cancer Immune panel

hyb_protocol: Hybridisation was performed in a PCR for 20 hours at 65°C.

scan_protocol: Scanned with NanoString Digital analyser with 555 FOV

data_processing: Data was normalised using the nSolver software, version 4.0.

label: Nanostring bar coding

source_name: Bone Marrow

label_protocol: RNA ispecies were identified and counted using the NanoString PanCancer Immune Profiling Panel.

growth_protocol: Human Samples

extract_protocol: RNA extraction was carried out using Qiagen RNeasy RNA isolation kits. Quantitation of RNA was performed using Nanodrop and Qubit RNA high sensitivity assay.

treatment_protocol: At time of initial diagnosis, achievement of complete remission and relapse.

tag: age (years)

tag: disease stage at sampling

value: Diagnosis

tag: disease type

value: De novo


title: AML93

description: Pan Cancer Immune panel


title: AML92

description: Pan Cancer Immune panel


title: AML95

description: Pan Cancer Immune panel


title: OLIGO11 pC

description: single-cell RNA-seq


title: Case 2 YCC-exosme

value: Cholangiocarcinoma (less than 40 generations)

tag: Sex


title: Case 3 CC-exosme


title: Case 4 CC-exosme


title: Case 1 CC-exosme


title: AML90

description: Pan Cancer Immune panel


title: OLIGO10 pC

description: single-cell RNA-seq

tag: tissue


title: AML91

description: Pan Cancer Immune panel


title: AML89

description: Pan Cancer Immune panel


title: NSC8 pC

description: single-cell RNA-seq


title: AML88

description: Pan Cancer Immune panel

value: sAML


title: AML87

description: Pan Cancer Immune panel


title: Case 23 Be-NT

value: Adenomyomatous hyperplasia of gallbladder (benign), non-tumor part

tag: age


title: Case 24 Be-NT

value: Focal nodular hyperplasia of liver (benign), non-tumor part

value: F


title: NSC32 pC

description: single-cell RNA-seq

tag: cell type


title: AML86

description: Pan Cancer Immune panel


title: Case 22 Be-NT

value: Angiomyolipoma (benign), non-tumor part

value: miRNA


title: S01101159_Genomic DNA from human placenta tissue with low exposure (SOD = 32.99)

city: Chiayi County

first: Mita

last: Tran

address: 168 University Road

department: Biomedical Sciences

country: Taiwan

institute: National Chung Cheng University

hyb_protocol: according to Illumina's instructions accompanying the DNA Sample Kit.

data_processing: NOT PROVIDED; REQUETED

source_name: placenta tissue with low exposure

extract_protocol: Pregnant women attending E-Da Hospital for routine prenatal examinations in their first trimesters were consecutively recruited. We excluded pregnant women: 1) who had history of systematic diseases such as cancer, hypertension and diabetes, chronic use of corticosteroids or immunosuppressant drugs; 2) whose age was older than 45 years; and 3) whose pregnancy was multiparous. Then, the eligible study women were interviewed by a standardized questionnaire and blood and one-spot urine specimens were collected. The same study protocol was also applied to their second and third trimesters, during delivery, and 2-3 weeks after delivery, except the questionnaire was changed to one short diet questionnaire. During delivery, additional specimens of maternal stool, amniotic fluid, placenta, cord blood, and baby meconium were also collected and, 2-3 weeks after delivery, another additional specimen of breast milk was collected. All these different biospecimens have been aliquoted and stored frozen at -70oC for different studies of gene-environmental effect on pregnant women and their offspring.

tag: subject group

value: low DEHP exposure

value: human placenta tissue

tag: sum of dehp metabolites (sod)


title: NSC3 pC

description: single-cell RNA-seq

value: ventricular-subventricular zone

tag: genotype

tag: treatment


title: AML82

description: Pan Cancer Immune panel


title: AML83

description: Pan Cancer Immune panel


title: AML85

description: Pan Cancer Immune panel


title: AML81

description: Pan Cancer Immune panel


title: AML84

description: Pan Cancer Immune panel


title: AML80

description: Pan Cancer Immune panel


title: Case 23 Be-T

value: Adenomyomatous hyperplasia of gallbladder (benign), tumor part

value: M


title: S01101009_Genomic DNA from human placenta tissue with low exposure (sum of DEHP metabolites (SOD) is 24.49)

scan_protocol: according to Illumina's instructions accompanying the DNA Sample Kit.


title: S01101161_Genomic DNA from human placenta tissue with high exposure (SOD = 562.07)

source_name: placenta tissue with high exposure

label_protocol: according to Illumina's instructions accompanying the DNA Sample Kit.

value: high DEHP exposure


title: Case 21 Be-NT

value: Inflammatory pseudotumor (benign), non-tumor part


title: S01101122_Genomic DNA from human placenta tissue with low exposure (SOD = 40.2)


title: NSC27 pC

description: single-cell RNA-seq

value: WT

value: naive


title: Case 22 Be-T

value: Angiomyolipoma (benign), tumor part


title: S01101084_Genomic DNA from human placenta tissue with low exposure (SOD = 38.89)


title: S01101135_Genomic DNA from human placenta tissue with high exposure (SOD = 1414.77)


title: S01101101_Genomic DNA from human placenta tissue with low exposure (SOD = 23.09)


title: NSC25 pC

description: single-cell RNA-seq


title: NSC24 pC

description: single-cell RNA-seq


title: AML79

description: Pan Cancer Immune panel


title: S01101158_Genomic DNA from human placenta tissue with high exposure (SOD = 1378.98)


title: S01101061_Genomic DNA from human placenta tissue with low exposure (SOD = 35.98)


title: S01101121_Genomic DNA from human placenta tissue with high exposure (SOD = 472.27)


title: AML75

description: Pan Cancer Immune panel


title: AML77

description: Pan Cancer Immune panel


title: AML73

description: Pan Cancer Immune panel


title: AML74

description: Pan Cancer Immune panel

value: Diagnosis

value: De novo


title: AML70

description: Pan Cancer Immune panel


title: AML71

description: Pan Cancer Immune panel


title: NSC23 pC

description: single-cell RNA-seq


title: AML72

description: Pan Cancer Immune panel


title: Case 20 HCC-NT

value: Hepatocellular carcinoma, non-tumor part


title: Case 21 Be-T

value: Inflammatory pseudotumor (benign), tumor part


title: Case 19 HCC-NT


title: S01101013_Genomic DNA from human placenta tissue with high exposure (SOD = 1592.24)


title: NSC28 pC

description: single-cell RNA-seq

value: aNSC


title: AML68

description: Pan Cancer Immune panel


title: NSC20 pC

description: single-cell RNA-seq


title: AML76

description: Pan Cancer Immune panel

value: sAML


title: NSC17 pC

description: single-cell RNA-seq


title: S01101172_Genomic DNA from human placenta tissue with high exposure (SOD = 729.14)


title: Case 18 HCC-NT

value: miRNA


title: NSC16 pC

description: single-cell RNA-seq


title: AML69

description: Pan Cancer Immune panel


title: NSC31 pC

description: single-cell RNA-seq


title: NSC15 pC

description: single-cell RNA-seq


title: Case 24 Be-T

value: Focal nodular hyperplasia of liver (benign), tumor part

value: F


title: NSC14 pC

description: single-cell RNA-seq

value: ventricular-subventricular zone


title: Case 17 HCC-NT


title: AML67

description: Pan Cancer Immune panel


title: AML63

description: Pan Cancer Immune panel


title: AML65

description: Pan Cancer Immune panel


title: AML64

description: Pan Cancer Immune panel


title: AML66

description: Pan Cancer Immune panel


title: NSC12 pC

description: single-cell RNA-seq


title: NSC11 pC

description: single-cell RNA-seq


title: AML60

description: Pan Cancer Immune panel


title: AML61

description: Pan Cancer Immune panel


title: Case 16 HCC-NT


title: AML62

description: Pan Cancer Immune panel


title: Case 15 HCC-NT


title: AML59

description: Pan Cancer Immune panel


title: Case 14 HCC-NT


title: AML58

description: Pan Cancer Immune panel


title: AML57

description: Pan Cancer Immune panel


title: Case 13 HCC-NT


title: Case 12 HCC-NT


title: Case 11 HCC-NT


title: AML56

description: Pan Cancer Immune panel


title: AML54

description: Pan Cancer Immune panel


title: AML55

description: Pan Cancer Immune panel


title: AML51

description: Pan Cancer Immune panel


title: AML53

description: Pan Cancer Immune panel


title: NB7 pC

description: single-cell RNA-seq

value: neuroblast


title: AML48

description: Pan Cancer Immune panel


title: NB8 pC

description: single-cell RNA-seq


title: Case 18 HCC-T

value: Hepatocellular carcinoma, tumor part

value: M


title: Case 20 HCC-T


title: NSC10 pC

description: single-cell RNA-seq


title: AML52

description: Pan Cancer Immune panel


title: Case 19 HCC-T


title: AML49

description: Pan Cancer Immune panel


title: NB6 pC

description: single-cell RNA-seq


title: NB4 pC

description: single-cell RNA-seq


title: AML46

description: Pan Cancer Immune panel


title: AML47

description: Pan Cancer Immune panel


title: Case 17 HCC-T


title: NB9 pC

description: single-cell RNA-seq


title: AML43

description: Pan Cancer Immune panel


title: AML45

description: Pan Cancer Immune panel


title: NB32 pC

description: single-cell RNA-seq

value: TAP


title: AML44

description: Pan Cancer Immune panel


title: Case 15 HCC-T


title: Case 14 HCC-T


title: Case 16 HCC-T


title: NB31 pC

description: single-cell RNA-seq

value: WT


title: AML50

description: Pan Cancer Immune panel


title: AML78

description: Pan Cancer Immune panel


title: Case 13 HCC-T


title: NB30 pC

description: single-cell RNA-seq

value: naive


title: NB28 pC

description: single-cell RNA-seq


title: Case 11 HCC-T


title: NB27 pC

description: single-cell RNA-seq


title: AML38

description: Pan Cancer Immune panel


title: AML40

description: Pan Cancer Immune panel


title: AML34

description: Pan Cancer Immune panel


title: Case 12 HCC-T


title: AML41

description: Pan Cancer Immune panel


title: AML37

description: Pan Cancer Immune panel


title: AML35

description: Pan Cancer Immune panel


title: AML42

description: Pan Cancer Immune panel


title: AML36

description: Pan Cancer Immune panel


title: AML32

description: Pan Cancer Immune panel


title: AML30

description: Pan Cancer Immune panel


title: AML31

description: Pan Cancer Immune panel


title: NB26 pC

description: single-cell RNA-seq


title: AML33

description: Pan Cancer Immune panel


title: NB25 pC

description: single-cell RNA-seq


title: NB29 pC

description: single-cell RNA-seq


title: Case 10 YCC-NT

value: Cholangiocarcinoma (less than 40 generations), non-tumor part


title: AML29

description: Pan Cancer Immune panel

value: Diagnosis


title: Case 9 CC-NT

value: Cholangiocarcinoma, non-tumor part


title: Case 8 YCC-NT


title: Case 7 YCC-NT


title: AML28

description: Pan Cancer Immune panel


title: NB24 pC

description: single-cell RNA-seq


title: AML27

description: Pan Cancer Immune panel


title: AML26

description: Pan Cancer Immune panel


title: NB23 pC

description: single-cell RNA-seq


title: NB22 pC

description: single-cell RNA-seq


title: NB20 pC

description: single-cell RNA-seq


title: AML23

description: Pan Cancer Immune panel

value: De novo


title: AML24

description: Pan Cancer Immune panel


title: AML19

description: Pan Cancer Immune panel


title: Case 5 CC-NT


title: Case 4 CC-NT


title: AML20

description: Pan Cancer Immune panel


title: AML18

description: Pan Cancer Immune panel


title: Case 3 CC-NT


title: NB18 pC

description: single-cell RNA-seq


title: AML16

description: Pan Cancer Immune panel


title: NB17 pC

description: single-cell RNA-seq


title: Case 1 CC-NT


title: Case 2 YCC-NT


title: AML25

description: Pan Cancer Immune panel


title: Case 10 YCC-T

value: Cholangiocarcinoma (less than 40 generations), tumor part


title: AML17

description: Pan Cancer Immune panel


title: Case 6 CC-NT


title: NB21 pC

description: single-cell RNA-seq


title: AML21

description: Pan Cancer Immune panel


title: AML22

description: Pan Cancer Immune panel


title: NB16 pC

description: single-cell RNA-seq


title: AML14

description: Pan Cancer Immune panel


title: AML13

description: Pan Cancer Immune panel


title: AML12

description: Pan Cancer Immune panel


title: AML11

description: Pan Cancer Immune panel


title: NB14 pC

description: single-cell RNA-seq


title: NB13 pC

description: single-cell RNA-seq


title: Case 9 CC-T

value: Cholangiocarcinoma, tumor part


title: AML15

description: Pan Cancer Immune panel

value: sAML


title: AML7

description: Pan Cancer Immune panel


title: AML6

description: Pan Cancer Immune panel


title: AML10

description: Pan Cancer Immune panel


title: Case 8 YCC-T

value: miRNA


title: NB12 pC

description: single-cell RNA-seq


title: NB19 pC

description: single-cell RNA-seq


title: AML3

description: Pan Cancer Immune panel


title: NB10 pC

description: single-cell RNA-seq


title: AML5

description: Pan Cancer Immune panel


title: AML2

description: Pan Cancer Immune panel


title: mgSCZ5_biolrep3

city: Reutlingen

first: Hansjuergen

last: Volkmer

address: Markwiesenstr 55

institute: NMI at the University of Tuebingen

data_processing:
Illumina bcl2fastq (version 2.20) was used to demultiplex sequenced reads.
Sequence reads were trimmed for adaptor sequence using Skewer (version 0.2.2).
Trimmed sequence raw reads were mapped to the reference genome hg19.
Assembly: hg19
Supplementary files format and content: tab-delimited text files include raw reads per gene
Supplementary files format and content: tab-delimited text files include DESeq2 normalized reads

growth_protocol: iPSCs were differentiated towards mesodermal lineage by a differential and time-sensitive addition of cytokines and growth factors (BMP4, Activin A, CHIR99021, VEGF, SCF, IL-6, IL-3, TPO).

extract_protocol:
Microglia were harvested using Accutase and pelleted. RNA was extracted using Rneasy Micro Kit (Qiagen).
RNA libraries for RNA-seq were prepared using SMART-Seq stranded total RNA Kit (Takara) following manufacturer's protocols.

treatment_protocol: Maturation into microglia was induced by high-dose application of IL-34, TGFβ1 and GM-CSF.

value: differentiated microglia from induced pluripotent stem cells

tag: gender

value: female

value: untreated microglia

tag: time

value: Day 21


title: AML9

description: Pan Cancer Immune panel


title: Case 7 YCC-T

tag: histology

tag: molecule


title: AML4

description: Pan Cancer Immune panel


title: Case 6 CC-T


title: AML1

description: Pan Cancer Immune panel


title: Case 3 CC-T


title: Case 5 CC-T


title: Case 4 CC-T

value: F


title: ASTRO9 pC

description: single-cell RNA-seq

value: ventricular-subventricular zone

value: neuroblast


title: AML8

description: Pan Cancer Immune panel


title: mgSCZ5_biolrep2

tag: cell line


title: NB11 pC

description: single-cell RNA-seq

value: WT


title: ASTRO7 pC

description: single-cell RNA-seq

value: naive


title: Case 2 YCC-T

value: M


title: mgSCZ4_biolrep1

value: male


title: Case 1 CC-T


title: AML39

description: Pan Cancer Immune panel

value: Diagnosis


title: ASTRO6 pC

description: single-cell RNA-seq

value: TAP


title: JHU_030

tag: disease state

value: acute myeloid leukaemia

value: Bone Marrow

tag: collection timepoint

value: Pretreatment

tag: eln cytogenetic risk

value: Adverse

tag: survival status

value: Dead


title: JHU_032

tag: age (years)


title: NTU/JHU_033

tag: tissue


title: JHU_031


title: ASTRO5 pC

description: single-cell RNA-seq


title: mgSCZ2_biolrep1

value: differentiated microglia from induced pluripotent stem cells

value: female


title: mgSCZ1_biolrep3

value: untreated microglia

value: Day 21


title: mgSCZ5_biolrep1


title: JHU_029


title: ASTRO4 pC

description: single-cell RNA-seq

value: ventricular-subventricular zone


title: ASTRO30 pC

description: single-cell RNA-seq

value: aNSC


title: ASTRO8 pC

description: single-cell RNA-seq

value: WT


title: ASTRO32 pC

description: single-cell RNA-seq

value: naive


title: mgSCZ1_biolrep1


title: mgSCZ1_biolrep2


title: JHU_025


title: JHU_027

value: Alive


title: mgCTR2_biolrep3

value: male


title: ASTRO28 pC

description: single-cell RNA-seq


title: mgSCZ2_biolrep2


title: JHU_026


title: mgCTR2_biolrep2


title: ASTRO27 pC

description: single-cell RNA-seq


title: JHU_024


title: JHU_023


title: mgCTR2_biolrep1


title: mgCTR1_biolrep3


title: JHU_028


title: HCT116-NUP93-mAC,HiChIP,H3K27ac,MboI,IAA,biological replicate 1

city: HOUSTON

first: chuangye

last: Qi

state: Texas

address: One plaza

department: Huffington Center

institute: Baylor College of Medicine

description: HCT116-NUP93-mAC_IAA_H3K27ac_HiChIP_Rep1

library_source: genomic

data_processing:
library strategy: in situ HiC and HiChIP
FASTQ data were trimmed by Cutadapt and Trimmomatic.
RNASeq Reads were aligned using STAR with the hg19 build of the human genome. Read counts for Refseq mRNAs were determined using HTSeq-count.
HiC-Pro was used to process Hi-C and HiChIP data.
Identification of significant chromatin contacts(loops interaction) from HiChIP data by using FitHiChIP.
Assembly: hg19
Supplementary files format and content: pairs, bigwig

source_name: colorectal cancer cells

extract_protocol:
RNA-seq:
Total cellular RNA was extracted with TRIzol (Invitrogen, 15596-018) following the manufacturer’s instructions.   Ploy A RNA was selected by using NEBNext® Poly(A) mRNA Magnetic Isolation Module.
RNAseq  library construction using NEBNext® Ultra™ II DNA Library Prep Kit for Illumina (NEB, E7645L).
in situ HiC and HiChIP:
5-10 million cells were cross-linked using 1% formaldehyde for 10mins at room temperature, quenched with 0.125M glycine for 10mins at room temperature, and were washed with cold PBS. Cross-linked cell pellets were resuspended in 1ml iced-cold Hi-C lysis buffer (10 mM Tris-HCl, pH 8.0; 10mM NaCl, 0.2% NP-40 and protease inhibitor cocktail), and rotated at 4°C for 30 mins. After pelleting down the nuclei, 100 ul of 0.5% SDS was used to resuspend and permeabilize the nuclei at 62 °C for 10 mins.  Then 260 ul H20 and 50 ul 10% Triton-X100 were added to quench the SDS at 37 °C for 15 mins. Subsequently, enzyme digestion of chromatin was performed at 37 °C overnight by adding an additional 50 ul of 10X NEB buffer 2 and 400U MboI (NEB, R0147M). After overnight incubation, the MboI in solution was inactivated at 62 °C for 20 mins. To fill-in the DNA overhangs and mark the ends with biotin, 35U DNA polymerase I (Klenow, NEB, M0210) together with 10 ul of 1mM biotin-dATP (Jeana Bioscience), 1ul 10mM dCTP/dGTP/dTTP were added and incubated at 37°C for 1 hour with rotation. Blunt end Hi-C DNA ligation was performed using 5000 U NEB T4 DNA ligase with 10X NEB T4 Ligase buffer with 10mM ATP, 90 ul 10% Triton X-100, 2.2 ul 50mg/ml BSA at room temperature for four hours with rotation. After ligation, nuclei were pelleted down and resuspended with 440 ul Hi-C nuclear lysis buffer (50mM Tris-HCl pH7.5; 10mM EDTA, 1% SDS and protease inhibitor cocktail), and further sheared using the parameter of 10/20 secs ON/OFF cycle, 25% Amp, 5mins by a QSonica 800R sonicator. Hi-C will use 5-10% of the sonicated chromatin in the next section. For HiChIP, the sonicated chromatin was incubated with appropriate antibody (here by 4ug H3K27ac polyclonal antibody) overnight, and the immunocomplex was captured by dynabeads protein G in the next day. The immunocomplex was washed 2 times by low salt wash buffer (20 mM Tris-HCl pH 7.5, 0.1% SDS, 1% Triton X-100, 2 mM EDTA, 150 mM NaCl), 2 times by high salt wash buffer (20 mM Tris-HCl pH 7.5, 0.1% SDS, 1% Triton X-100, 2 mM EDTA, 500 mM NaCl), 1 time with Tris-EDTA buffer + 0.1% triton-100, and one more time with TE only. The immunocomplex was subjected to overnight decrosslinking at 65°C, protein K treatment, and DNA extraction
For both Hi-C and HiChIP library making , after DNA extraction, they were used for biotin DNA enrichment by 20 ul Dynabeads® MyOne™ Streptavidin C1 beads (Thermo Fisher 65002). The biotin bound DNA on beads was used to perform on-beads library making with KAPA Hyper DNA library kit, or using NEBNext® Ultra™ II DNA Library Prep Kit for Illumina (NEB, E7645L).

tag: antibody

value: treated with IAA for 8hr (500uM indole-3-acetic acid (IAA, Sigma Aldrich, catalog#:87514))


title: HCT116-NUP93-mAC,HiChIP,H3K27ac,MboI,UT,biological replicate 2

value: untreated


title: ASTRO3 pC

description: single-cell RNA-seq

tag: cell type

value: TAP


title: HCT116-NUP93-mAC,HiChIP,H3K27ac,MboI,UT,biological replicate 1


title: HCT116-NUP93-mAC,HiChIP,H3K27ac,MboI,IAA,biological replicate 2

description: HCT116-NUP93-mAC_IAA_H3K27ac_HiChIP_Rep2


title: ASTRO24 pC

description: single-cell RNA-seq


title: ASTRO25 pC

description: single-cell RNA-seq

value: neuroblast


title: mgCTR1_biolrep1


title: JHU_021

value: acute myeloid leukaemia

value: Bone Marrow

value: Pretreatment

value: Intermediate


title: JHU_020

value: Adverse

value: Dead


title: mgCTR1_biolrep2

value: differentiated microglia from induced pluripotent stem cells

value: female

value: untreated microglia

value: Day 21


title: iPSC_rep3

value: naive induced pluripotent stem cells

value: untreated iPSC

value: Day 0


title: JHU_019


title: F17-CHigh-S3_709

city: Lawrence

first: Jennifer

middle: L

last: Robinson

state: Kansas

department: Department of Chemical and Petroleum Engineering

institute: University of Kansas

data_processing:
Base calling was carried out by the Illumina NextSeq 550 Real Time Analysis (RTA) software.
Raw reads were filtered using fastp (Experiment 1) or trimmomatic 0.39 (Experiment 2) and aligned to the reference transcriptome using Kallisto 0.46.1-1.
Kallisto 0.46.1-1 was used for transcript abundance estimates
tximport was used to import Kallisto transcript abundance estimates into DeSeq2 1.3 for differential expression analysis
Assembly: ENSEMBL Homo sapiens reference transcriptome build GRCh38 release 101
Supplementary files format and content: .tsv files containing raw quantified counts and TPM counts

source_name: Meniscal Fibrochondrocytes

growth_protocol: Cells were cultured in tissue culture flasks in DMEM supplemented with 10% Premium FBS (Atlanta Biologicals, 511150) and 1% penicillin/streptomycin and passaged at 70-80% confluency using trypsin (Sigma, T4174, diluted to 1x before use). When passage 1 cells reached 70-80% confluency, cells were washed with PBS (Gibco, 20012-207) and cultured in phenol red-free DMEM (pfDMEM, Gibco, 31053-028) with 15% charcoal/dextran treated FBS (Atlanta Biologicals, S11650) for 3 days to starve them of endogenous hormones. Cells were then passaged and seeded in 24 well plates in pfDMEM and allowed to adhere overnight.

extract_protocol:
For Experiment 1 cells were collected in TRIzol, and total RNA was purified using a PureLink RNA Mini Kit (Life Technologies, 12183025) according to the manual. DNA was removed using a DNA-free DNA Removal Kit (Life Technologies, AM1906) according to the manual. For Experiment 2 cells were collected and total RNA was purified using a QIAGEN RNeasy Mini Kit (QIAGEN, 74104) with no DNase treatment.
Sequencing libraries were constructed using the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina (NEB, E7760). The sequencing library construction process included mRNA purification with polyA selection beads, fragmentation to inserts of ~200 bp, strand specific cDNA synthesis, end repair, 3’ end adenylation, adapter ligation, and PCR amplification. Samples were run across 3 flow cells (Experiment 1: A, B, and C; Experiment 2: 708, 709, and 710).

treatment_protocol: Cells were treated in triplicate with 17β-estradiol (E2, Sigma, E2758) in pfDMEM supplemented with 15% charcoal/dextran treated FBS and 1% penicillin/streptomycin under pulsed or continuous dosing. For pulsed dosing, cells were exposed to E2 for 1 h, after which the E2 media was replaced with E2-free media for 23 h. This pattern was repeated for the length of the experiment. For continuous dosing, cells were exposed to E2 for the entire treatment period.

value: Meniscus

value: Meniscal Fibrochondrocytes

tag: experiment

value: Experiment 2

tag: age

value: Female

value: 1.0 nM E2, Continuous

tag: treatment duration

tag: flow cell


title: F17-CHigh-S3_710

tag: gender

tag: treatment


title: F17-CHigh-S3_708


title: ASTRO23 pC

description: single-cell RNA-seq

value: ventricular-subventricular zone

value: aNSC

tag: genotype

value: WT

value: naive


title: ASTRO22 pC

description: single-cell RNA-seq


title: ASTRO26 pC

description: single-cell RNA-seq


title: F17-CHigh-S2_710


title: iPSC_rep2

value: male

tag: time


title: JHU_018

value: acute myeloid leukaemia

value: Bone Marrow

value: Pretreatment

value: Adverse

value: Alive


title: ASTRO18 pC

description: single-cell RNA-seq

value: TAP


title: F17-CHigh-S2_709


title: iPSC_rep1

tag: cell line

value: naive induced pluripotent stem cells

value: female

value: untreated iPSC

value: Day 0


title: JHU_022

tag: disease state


title: ASTRO17 pC

description: single-cell RNA-seq


title: ASTRO16 pC

description: single-cell RNA-seq


title: JHU_017

tag: collection timepoint

value: Dead


title: F17-CHigh-S1_710

value: Meniscus

value: Meniscal Fibrochondrocytes

value: Experiment 2

value: Female

value: 1.0 nM E2, Continuous


title: JHU_015

tag: eln cytogenetic risk

value: Favorable


title: JHU_016

value: acute myeloid leukaemia

tag: survival status


title: ASTRO15 pC

description: single-cell RNA-seq

value: ventricular-subventricular zone

value: aNSC

value: WT

value: naive


title: F17-CHigh-S1_709


title: JHU_014

value: Bone Marrow

tag: age (years)

value: Pretreatment

value: Adverse


title: FHs74Int, HDAC8+PCI34051+LPS

city: Shanghai

first: Ting

last: Guo

state: Shanghai

address: Shanghai Putuo District,Luding road No.355

department: Department of General surgery

country: China

institute: Shanghai Children's Hospital

data_processing:
Paired‐end reads were aligned to human genome hg38 using the BWA program (Cambridge, MA, USA)
To create cut-tag coverage plots, the locations of the mapped cut-tag reads were extended to 150 bp to represent sequenced fragments, renormalized (to reads per million, rpm) and reformatted in the bigWig file format.
For annotation, MACS2 software was used for peak calling with a cutoff q value < 0.05.
bigWig files were generated using the genomicRanges R package. Score represents the normalized coverage of DNA fragments at a given genomic coordinate. narrowPeak files were generated using MACS v2 with default settings.
Assembly: hg38
Supplementary files format and content: bigWig files
Supplementary files format and content: narrow peaks
Library strategy: CUT&Tag

growth_protocol: FHs74Int cells were incubated in Hybri-Care Medium (ATCC-46X) supplemented with 10% fetal bovine serum, 1% antibiotic-antimycotic and 30ng/ml rhEGF in humidified atmosphere with 5% CO2 at 37C.

extract_protocol:
Lysates were clarified from nuclei and histone-DNA complexes were isolated with antibody.
Libraries were prepared according to Illumina's instructions accompanying the DNA Sample Kit (Part# 0801-0303). Briefly, DNA was end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment (32 to 52 exo minus) and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3’ end. After adapter ligation DNA was PCR amplified with Illumina primers for 15 cycles and library fragments of ~250 bp (insert plus adaptor and PCR primer sequences) were band isolated from an agarose gel. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Illumina HiSeq 2500 following the manufacturer's protocols.

treatment_protocol:
The FHs74Int cells (control, LPS, PCI34051+LPS, HDAC8+PCI34051+LPS) were incubated with PCI34051 (10 µmol/L for 24 h) or LPS (10 µg/ml for 48 h) as indicated.
Then PCI34051 group and HDAC8+PCI34051+LPS group cells were treated with PCI34051 (10 µmol/L for 24 h) in the presence of 10% FBS until for 24 h. Then LPS group and HDAC8+PCI34051+LPS group cells treated with 10 μg/ml LPS in the presence of 10% FBS until for 48h.

value: Small intestinal epithelial cells

tag: chip antibody


title: FHs74Int, HDAC8+PCI34051+LPS_IgG

value: IgG


title: F17-CHigh-S1_708

tag: tissue


title: ASTRO13 pC

description: single-cell RNA-seq

tag: cell type

value: neuroblast


title: FHs74Int, PCI34051+LPS_IgG


title: ASTRO12 pC

description: single-cell RNA-seq


title: F17-CLow-S3_710

value: Meniscus

tag: experiment

value: 0.1 nM E2, Continuous


title: JHU_013

value: Dead


title: F17-CLow-S3_709

value: Meniscal Fibrochondrocytes

value: Experiment 2

tag: age

value: Female


title: FHs74Int, Lps

value: Lps


title: FHs74Int, PCI34051+LPS


title: ASTRO11 pC

description: single-cell RNA-seq

value: ventricular-subventricular zone


title: FHs74Int, Lps _IgG


title: JHU_011

value: acute myeloid leukaemia

value: Favorable


title: JHU_012


title: STRASTRO9 pE

description: single-cell RNA-seq

source_name: striatum & ventricular-subventricular zone

value: astrocyte (striatum)

value: WT

value: naive


title: F17-CLow-S3_708

tag: treatment duration


title: F17-CHigh-S2_708

value: 1.0 nM E2, Continuous

tag: flow cell


title: STRASTRO6 pE

description: single-cell RNA-seq

value: striatum & ventricular-subventricular zone


title: FHs74Int, Con_IgG

value: Small intestinal epithelial cells

value: Con

value: IgG


title: JHU_010

value: Bone Marrow

value: Pretreatment

value: Adverse


title: JHU_009

value: Dead


title: FHs74Int, Con


title: STRASTRO23 pE

description: single-cell RNA-seq


title: F17-CLow-S2_709

value: Meniscus

value: Meniscal Fibrochondrocytes

value: Experiment 2

tag: gender

value: Female

value: 0.1 nM E2, Continuous


title: JHU_008

value: acute myeloid leukaemia


title: JHU_007


title: F17-CLow-S2_708

tag: treatment


title: STRASTRO13 pE

description: single-cell RNA-seq

value: astrocyte (striatum)

tag: genotype

value: WT


title: STRASTRO15 pE

description: single-cell RNA-seq

value: naive


title: STRASTRO12 pE

description: single-cell RNA-seq

value: striatum & ventricular-subventricular zone

value: oligodendrocyte


title: F17-CLow-S1_708


title: JHU_006


title: F17-CLow-S1_710


title: JHU_005


title: F17-CLow-S1_709


title: AQ9697

city: Madrid

first: Jose Maria

middle: Moreno

last: Navarrete

state: (None)

address: Calle de Monforte de Lemos nº 5

institute: CIBER

data_processing:
RNA-seq reads mapped with STAR software v2.5.3a with ENCODE parameters.
Annotated genes quantified with RSEM v1.3.0
Assembly: GRCh38
Supplementary files format and content: Matrix with samples as columns and raw gene counts as rows

source_name: Visceral adipose tissue

extract_protocol:
RNA purification was performed using RNeasy Lipid Tissue Mini Kit (QIAgen, Izasa SA, Barcelona, Spain)
RNA libraries were prepared using TruSeq Stranded total RNA kit (Ribozero)

value: Visceral adipose tissue

tag: condition

value: morbidly obese


title: AQ9701


title: AQ9706


title: AQ9699


title: AQ9704


title: AQ9695


title: F17-PHigh-S4_710

value: 24 nM E2, Pulsed


title: F17-CLow-S2_710


title: STRASTRO10 pE

description: single-cell RNA-seq


title: F17-PHigh-S4_709


title: JHU_004

value: Bone Marrow

value: Pretreatment


title: JHU_002

value: Intermediate

value: Dead


title: STRASTRO-B7 pE

description: single-cell RNA-seq


title: AQ9693


title: AQ9691


title: F17-PHigh-S4_708

value: Meniscus

value: Meniscal Fibrochondrocytes


title: STRASTRO21 pE

description: single-cell RNA-seq


title: JHU_001

value: Adverse


title: STRASTRO-B6 pE

description: single-cell RNA-seq


title: AQ9689


title: F17-PHigh-S2_710

value: Experiment 2

value: Female


title: STRASTRO11 pE

description: single-cell RNA-seq

value: astrocyte (striatum)


title: STRASTRO-B22 pE

description: single-cell RNA-seq

value: WT


title: AQ9687


title: AQ9683


title: F17-PHigh-S2_708


title: STRASTRO-B2 pE

description: single-cell RNA-seq

value: naive


title: AQ9681


title: NSC9 pE

description: single-cell RNA-seq

value: striatum & ventricular-subventricular zone


title: F17-PHigh-S1_710


title: JHU_003

value: acute myeloid leukaemia


title: F17-PHigh-S2_709


title: NSC8 pE

description: single-cell RNA-seq


title: AQ9679

value: Visceral adipose tissue


title: F17-PHigh-S1_709


title: NSC7 pE

description: single-cell RNA-seq


title: 2N

city: Wuhu

first: Xueqin

last: Li

address: 2 Western Zheshan Road

institute: wannan medical college

description: Gene expression data from adjacent non-tumor tissues

hyb_protocol: Following fragmentation, aRNA were hybridized for 16 hr at 45C on GeneChip Hybridization Oven 645. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the GeneChip Scanner 3000.

data_processing: The data were analyzed with RMA using Affymetrix default analysis settings and global scaling as normalization method.

label: biotin

source_name: adjacent non-tumor tissues

label_protocol: Biotinylated aRNA were prepared according to the GeneChip 3’IVT Express Kit protocol.

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

value: brain


title: AQ9675

value: morbidly obese


title: 5N


title: F17-PHigh-S1_708

value: 24 nM E2, Pulsed


title: 4N


title: 3N


title: AQ9673


title: 1N


title: F17-PLow-S4_710

value: 2.4 nM E2, Pulsed


title: NSC6 pE

description: single-cell RNA-seq


title: NSC5 pE

description: single-cell RNA-seq


title: AQ9671


title: F17-PLow-S4_709


title: F17-PLow-S4_708


title: F17-PLow-S3_710


title: AQ9667


title: NSC23 pE

description: single-cell RNA-seq


title: AQ9669


title: NSC3 pE

description: single-cell RNA-seq


title: 5T

description: Gene expression data from glioma tissues

source_name: glioma tissues


title: AQ9665


title: F17-PLow-S3_709


title: 4T


title: M1 biol rep 3

city: Taipei City

first: Yi-Fan

last: Jiang

address: No.1, Sec. 4, Roosevelt Road

institute: National Taiwan University

description: cycle disrupted P20_M1_4

data_processing:
The raw data in FASTQ format were firstly checked in FastQC and MultiQC
The adaptor sequences, low-quality reads and bases were removed in Trimmomatic (v.0.38)
The clean reads were aligned to the mouse reference genome (GRCm38) in HISAT2 software (v 2.1.0)
The mapped reads for each gene were counted in FeatureCounts (v2.0.0).
Assembly: mm10
Supplementary files format and content: ecxel file include original read count, TPM, and FPKM for each Sample

source_name: ovary

growth_protocol: 8-week-old female ICR mice were housed at 25 ± 2℃, with an approximate 50-60% relative humidity and 12-hour light/12-hour dark cycle. Diets and water are freely accessed. Mice were acclimated for two weeks before the treatments started and placed in cages according to their experimental groups.

extract_protocol:
For each individual, both ovaries were collected and homogenized together for RNA extractions. Total RNA was extracted using the Trizol reagent (Invitrogen, CA, USA).
RNA libraries for RNA-seq were prepared using KAPA mRNA HyperPrep Kit

treatment_protocol: The M1 (SI-SML0629, Sigma-Aldrich, 1 mg/ml in 5% DMSO/ 10% Tween80/ 85% 1xPBS solution, 10 mg / kg BW) treatment was given after the mouse has been smeared at 8:00 a.m. and assured in the proestrus stage. The treatments was given at 9:00 a.m. and 4:00 p.m. and was delivered by IP injection. The ovaries were collected at 8:00 p.m.

value: ovary

tag: strain

value: ICR

value: 10 weeks old

tag: Sex

value: female

tag: time

value: 20:00 on Proestrus


title: M1 biol rep 2

description: cycle disrupted P20_M1_2


title: NSC2 pE

description: single-cell RNA-seq


title: M1 biol rep 1

description: cycle disrupted P20_M1_1


title: AQ9661


title: 1T


title: 3T


title: 2T


title: F17-PLow-S2_710

value: Meniscus

value: Meniscal Fibrochondrocytes

value: Experiment 2


title: NSC4 pE

description: single-cell RNA-seq

value: WT


title: Control biol rep 3

description: normal P20_C_4

value: Control


title: NSC19 pE

description: single-cell RNA-seq

value: striatum & ventricular-subventricular zone

value: naive


title: AQ9659

value: Visceral adipose tissue


title: F17-PLow-S2_709

value: Female


title: NSC18 pE

description: single-cell RNA-seq


title: Control biol rep 2

description: normal P20_C_2


title: AQ9657

value: morbidly obese


title: NSC17 pE

description: single-cell RNA-seq


title: AQ9653


title: Control biol rep 1

description: normal P20_C_1


title: F17-NoE2-S4_709

value: Control (No E2)


title: F17-NoE2-S4_710


title: F17-PLow-S2_708

value: 2.4 nM E2, Pulsed


title: AQ9663


title: F17-PLow-S3_708


title: NSC16 pE

description: single-cell RNA-seq


title: DG-tissue, APPko, biol rep 7

city: Hannover

first: Maximilian

last: Lenz

address: Carl-Neuberg-Straße 1

department: Institute of Neuroanatomy and Cell Biology

institute: Hannover Medical School

data_processing:
Data analysis was performed at the Galaxy platform (usegalaxy.eu; (Galaxy, 2022)). All files contained more than 10 M high-quality reads (after mapping to the reference genome; mm10) with a phred quality of at least 30 (>90% of total reads).
RNA sequencing data were uploaded to the galaxy web platform (public server: usegalaxy.eu; Afgan et al., 2018; Jalili et al., 2020; Afgan et al., 2016) and transcriptome analysis was performed using the Galaxy platform in accordance with the reference-based RNA-seq data analysis tutorial (Batut et al., 2021).
Adapter sequences, low quality, and short reads were removed via the CUTADAPT tool (Galaxy version 3.5+galaxy0).
Reads were mapped using RNA STAR (Galaxy version 2.7.8a+galaxy0) with the mm10 Full reference genome (Mus musculus).
The evidence-based annotation of the mouse genome (GRCm38), version M25 (Ensembl 100) served as gene model (GENCODE). For an initial assessment of gene expression, unstranded FEATURECOUNT (Galaxy version 2.0.1+galaxy2) analysis was performed from RNA STAR output.
Assembly: mm10
Supplementary files format and content: FEATURE COUNT output (tabular files)

source_name: Brain, organotypic entorhino-hippocampal culture, dentate gyrus isolate

growth_protocol: Entorhino-hippocampal tissue cultures were prepared at postnatal day 4 - 5 from C57BL/6J (APP+/+) and APP-deficient (APP-/-; (Li et al., 1996)) animals as previously described (Del Turco and Deller, 2007). Cultivation medium contained 50 % (v/v) MEM, 25 % (v/v) basal medium eagle, 25 % (v/v) heat-inactivated normal horse serum, 25 mM HEPES buffer solution, 0.15 % (w/v) bicarbonate, 0.65 % (w/v) glucose, 0.1 mg ml-1 streptomycin, 100 U ml-1 penicillin, and 2 mM glutamax. The pH was adjusted to 7.3 and the medium was replaced three times per week. All tissue cultures were allowed to mature for at least 18 days in humidified atmosphere with 5 % CO2 at 35 °C, since at this age a steady state in structural and functional properties of the organotypic tissue cultures is reached (Hailer et al., 1996; Humpel, 2015; Vlachos et al., 2012a; Vlachos et al., 2013).

extract_protocol:
RNA library preparations for transcriptome analysis were performed using the NEBNext® Single Cell/Low Input RNA Library Prep Kit for Illumina® (New England Biolabs, #E6420) according to the manufacturer's instructions. Briefly, isolation of the dentate gyrus from individual tissue cultures was performed using a scalpel. One isolated dentate gyrus was transferred to 7.5 µl lysis buffer (supplemented with murine RNase inhibitor) and homogenized using a pestill. Samples were centrifuged for 30 seconds at 10000g and 5 µl of supernatant were collected from individual samples and further processed. After cDNA synthesis, cDNA amplification was performed according to the manufacturer's protocol with 12 PCR cycles. The cDNA yield was subsequently analyzed by a High Sensitivity DNA assay on a Bioanalyzer instrument (Agilent). The amount of cDNA was adjusted to 10 ng for further downstream applications.
After fragmentation and adaptor ligation, dual index primers (New England Biolabs, #E7600S) were ligated in a library amplification step using 10 PCR cycles. Libraries were finally cleaned up with 0.8X SPRI beads following a standard bead purification protocol. Library purity and size distribution were assessed with a High Sensitivity DNA assay on a Bioanalyzer instrument (Agilent). We quantified the libraries using the NEBNext Library Quant Kit for Illumina (New England Biolabs, #E7630) based on the mean insert size provided by the Bioanalyzer. A 10 nM sequencing pool (120 µl in Tris-HCl, pH 8.5) was generated for sequencing on the NovaSeq6000 sequencing platform (Illumina; service provided by CeGaT GmbH, Tübingen, Germany). We performed a paired-end sequencing with 151 bp read length.

value: APP deficient; APP-/-


title: NSC15 pE

description: single-cell RNA-seq


title: AQ9651


title: DG-tissue, APPko, biol rep 8

value: Brain, organotypic entorhino-hippocampal culture, dentate gyrus isolate


title: NSC22 pE

description: single-cell RNA-seq

value: TAP


title: AQ9649


title: F17-NoE2-S4_708


title: DG-tissue, APPko, biol rep 6


title: F17-NoE2-S3_710


title: NSC14 pE

description: single-cell RNA-seq


title: NSC13 pE

description: single-cell RNA-seq


title: AF8388


title: F17-NoE2-S3_709


title: AF8384


title: AF8386


title: NSC12 pE

description: single-cell RNA-seq


title: DG-tissue, APPko, biol rep 4


title: F17-NoE2-S3_708


title: NSC11 pE

description: single-cell RNA-seq


title: DG-tissue, APPko, biol rep 3


title: AF8382


title: DG-tissue, APPko, biol rep 2


title: NSC10 pE

description: single-cell RNA-seq


title: AF8380


title: NSC-B9 pE

description: single-cell RNA-seq


title: DG-tissue, APPko, biol rep 1


title: NSC1 pE

description: single-cell RNA-seq


title: F17-NoE2-S2_709


title: F17-NoE2-S2_708


title: F17-NoE2-S2_710


title: AF8378


title: DG-tissue, APPko, biol rep 5


title: AF8376


title: AF8374


title: DG-tissue, wildtype [C57BL/6], biol rep 6

value: wildtype [C57BL/6]; APP+/+


title: F16-CHigh-S4_710

value: 1.0 nM E2, Continuous


title: DG-tissue, wildtype [C57BL/6], biol rep 5


title: NSC-B4 pE

description: single-cell RNA-seq


title: DG-tissue, wildtype [C57BL/6], biol rep 4


title: F16-CHigh-S4_709

value: Meniscus


title: AF8372


title: NSC-B22 pE

description: single-cell RNA-seq

value: aNSC


title: DG-tissue, wildtype [C57BL/6], biol rep 3


title: AQ9705

source_name: Subcutaneous adipose tissue

value: Subcutaneous adipose tissue


title: F16-CHigh-S4_708

value: Meniscal Fibrochondrocytes

value: Experiment 2


title: F16-CHigh-S2_710


title: DG-tissue, wildtype [C57BL/6], biol rep 2


title: F16-CHigh-S2_709


title: DG-tissue, wildtype [C57BL/6], biol rep 1


title: NSC-B21 pE

description: single-cell RNA-seq

value: striatum & ventricular-subventricular zone

value: WT


title: F16-CHigh-S2_708


title: AQ9698


title: AQ9702


title: NSC-B19 pE

description: single-cell RNA-seq

value: naive


title: NSC-B17 pE

description: single-cell RNA-seq


title: F16-CHigh-S1_710

value: Female


title: AQ9696

value: morbidly obese


title: NSC-B23 pE

description: single-cell RNA-seq


title: NSC-B20 pE

description: single-cell RNA-seq


title: F16-CHigh-S1_709


title: NSC-B16 pE

description: single-cell RNA-seq


title: AQ9694


title: F16-CHigh-S1_708


title: Bleo

city: Cincinnati

first: Yan

last: Xu

state: OH

address: 3333 Burnet Ave

institute: Cincinnati Children's Hospital Medical Center

description: 10x 3' v3 scRNA-seq

data_processing:
Read alignment and gene-expression quantification of mouse single-cell RNA-seq (scRNA-seq) were performed using Cell Ranger version 2.0.0 pipeline (10x Genomics).
For scRNA-seq alignment and quantification, Cell Ranger pre-built mouse (mm10) reference package was used.
Assembly: mm10
Supplementary files format and content: Raw Feature Barcode Matrix and 10x Cell Ranger filtered Feature Barcode Matirx in HDF5 format

source_name: Bleomycin treated mouse lung

growth_protocol: Mice were housed in barrier and all experiments were performed in accordance with approved IACUC protocols

extract_protocol:
Single-cell suspensions were processed through the 10X Chromium to generate single-cell cDNA libraries attached to microbeads.
Microbeads were counted, and amplified by PCR, and the 3' end of the cDNA was prepared for sequencing using a modified Nextera XT protocol.

treatment_protocol: For single cell RNAseq, adult mice were treated or untreated with  bleomycin every week for total 4 weeks. Mice lung were collected. Fresh lung tissue was minced and incubated in an enzymatic cocktail containing 60 ml dispase (5U/ml, Stemcell Technologies), 900 µl liberase (1g/l, Sigma Aldrich), 0.03 g DNase (Sigma Aldrich) at 37 ℃ for 45 minutes.  Suspensions were washed with media, cell counts were performed and cells were resuspended in RPMI at a final concentration of 100 cells/ml.

tag: number

value: lung

value: Bleomycin treated


title: AQ9692


title: intestine, NEC

data_processing:
mRNA sequencing libraries were generated using an NEBNext® UltraTM RNA Library Prep Kit for Illumina® (NEB, USA) following the manufacturer’s recommendations
Clustering of the index-coded samples was performed on a cBot Cluster Generation System using a TruSeq PE Cluster Kit v3-cBot-HS (Illumina) according to the manufacturer’s instructions
Assembly: mm10
Supplementary files format and content: tab-delimited text file includes count values for each Sample

source_name: intestine

growth_protocol: Con group mice were fed with dam. NEC group and PCI34051+NEC group were fed with  40 μl of 33% Esbilac formula (Pet-Ag, Abbott Laboratories) every 4 h for 96 h.PCI34051+NEC group mice were also fed with PCI34051  (10 mg/kg/d,once a day for 5 days).

extract_protocol:
Total RNA was extracted using TRIzol reagent (Invitrogen, Carlsbad, CA) and chloroform, and RNA integrity was assessed using an RNA Nano 6000 Assay Kit for the Agilent Bioanalyzer 2100 system (Agilent Technologies, CA, USA).
The library preparations were sequenced on the Illumina NovaSeq platform, and 150 bp paired-end reads were generated.

treatment_protocol:
NEC group mice was induced using formula gavage every 4 h for 96 h using 40 μl of 33% Esbilac formula (Pet-Ag, Abbott Laboratories). Meanwhile, pups were exposed to hypoxia treatments (99.9% N2 for 100 s), followed by cold stress (4 °C for 10 min) every 12 h. The control group were dam-fed without hypoxia and cold stress. In the PCI34051-treated NEC group, the PCI34051  (10 mg/kg/d) was fed once  from the day before the modle made  to the end. At the same time, the mice in the other two groups were fed with the equal volume of PBS.
All animals were euthanized after 96 h of modling.

tag: cell line

value: intestine

value: Fed with formula and PBS by gavage, hypoxia treatments (99.9% N2 for 100 s), followed by cold stress (4 °C for 10 min)


title: intestine, PCI34051+NEC

value: Fed with formula, hypoxia treatments (99.9% N2 for 100 s), followed by cold stress (4 °C for 10 min), treat with PCI34051  (10 mg/kg/d,once a day for 5 days).