title: SG-258-Rep2

description:
SG-241-cy3 vs SG-258-cy5(1).gpr
Biological replicate 2


title: SG-163-Rep2

status: Public on Jun 04 2024

type: RNA

city: Saskatoom

first: wentao

last: zhang

state: SK

address: 110 Gymnasium Pl

country: Canada

institute: NRC-Canada

description:
SG-242-cy3 vs SG-163-cy5(2).gpr
Biological replicate 2

hyb_protocol: Purified cRNAs (2 µg) were fragmented and hybridized to the Agilent 4x44K Brassica arrays (Parkin et al., 2010) for 17 h at 65°C with a rotation of 10 rpm according to the manufacturer’s protocol.

scan_protocol: Arrays were washed with the Agilent Gene Expression Washing buffers according to the manufacturer’s protocol and scanned with GenePix 4000B as described by Parkin et al. (2010). Four and two biological replications were performed for the parental lines and the SG lines, respectively, with dye-swaps applied to the biological replicates to minimize dye effects from the two colour systems (Lee et al., 2004).

data_processing: The raw array datasets were extracted with Gene Pix Pro 6.0, and were firstly normalized by the lowess LOWNESS (Yang et al., 2002) method within arrays, followed by the quantile (Bolstad et al., 2003) method between arrays, using the R/Bioconductor software (available at http://www.r-project.org/). R package Limma (Smyth, 2005).

molecule: total RNA

organism: Brassica napus

source_name: Seeds at 21 DAF

label_protocol: cRNAs were amplified from total RNA samples (2 µg) and labeled with either cy3 or cy5 using the Quick Amp labeling kit, Two Color (Agilent, Catalogue: 5190-0444) according to the manufacturer’s instructions, followed by purification with the Qiagen RNeasy Mini Kit (Qiagen, Catalogue 74104) and quantification with a NanoDrop ND-1000.

growth_protocol: The B. napus lines used in this study include the two parental lines DH12075, a Canadian spring-type doubled haploid canola line (generated by Dr. Gerhard Rakow and Dr. Ginette Séguin-Swartz, Agriculture and Agri-Food Canada), and PSA12, a resynthesised B. napus line (generated by Dr. Monica Beschorner and Dr. Derek Lydiate, Agriculture and Agri-Food Canada), and 96 doubled haploid segregating (SG) lines generated from the cross of these two parental lines. PSA12 was developed from an interspecific cross between B. oleracea ssp. alboglabra line A12DH and B. rapa line Parkland Sunshine, and DH12075 was derived from a cross between varieties Cresor and Westar (Mayerhofer et al., 2005).

extract_protocol: Total RNA was extracted from the developing seeds using a method modified from that of Oñate-Sánchez and Vicente-Carbajosa (2008) and described in detail by Parkin et al. (2010). Seeds from field grown plants from two trials (2009 and 2010) were harvested for seed quality analysis.

treatment_protocol: The developing seeds at 21 days post-anthesis were collected from B. napus lines grown under field conditions at the AAFC Saskatoon Research Farm in 2009. This time point was selected because approximately 20 days after flowering ( DAF) had previously been identified as a critical stage for cell proliferation and oil deposition (O’Hara et al., 2002; Dong et al., 2004).

tag: sample type

value: tissue

tag: tissue

value: development seeds


title: Sample_81_Neutrophil_APOE3_3_MCI

type: SRA

city: Boston

first: Neta

last: Rosenzweig

state: Massachusetts

address: 60 Fenwood Road, 10002K, Brigham and Women’s Hospital

country: USA

institute: Brigham and Women's Hospital, Harvard Medical School

library_source: transcriptomic

data_processing:
Count files (fastq) were preprocessed for quality control and adapter trimming using fastp. High quality reads were aligned using Salmon (v1.7).
Technical outliers were removed for further analysis. Downstream differential gene expression analysis was carried out using DESeq2 (v.1.34.00). Biological outliers were determined using PCA and heatmap visualization and removed for final analysis.
Comparisons were run using LRT, and the cutoff for significant genes was P < 0.05.
Assembly: GRCh38
Supplementary files format and content: zip file of salmon outputs including plain text quantification file (quant.sf), transcripts used for quantification, parameter settings, version of Salmon, and estimated bias parameters.

organism: Homo sapiens

source_name: Neutrophil

extract_protocol:
Blood was drowned in CPT tubes (BD Bioscience) and centrifuged at 1700g for 30min, to pellet polymorphonuclear leukocytes (neutrophils) below the gel barrier. Following the removal of plasma and peripheral blood mononuclear cells (PBMCs) from the fraction above the gel barrier, a syringe attached to an 18-gauge needle was used to extract the erythrocyte/neutrophil fraction below the gel as previously described. Cells collected in a 50ml tube were washed in PBS and centrifuged at 600g for 5min at 4°C. Cell pellet was resuspended twice in 10ml of ACK (ammonium chloride potassium) to lyse erythrocytes at RT and washed with PBS. Cells were stained with FITC anti-CD66b (1:100, Biolegend, 305103) in PBS supplemented with 2% fetal bovine serum (FBS) for 20min at 4°C. After staining, cells were washed and sorted using BD FACSAriaTM II (BD Bioscience).
Smart-Seq2 libraries were prepared by the Broad Technology Labs and sequenced by the Broad Genomics Platform. cDNA libraries were generated from sorted cells using the Smart-seq2 protocol. RNA sequencing was performed using Illumina NextSeq500 using a High Output v2 kit to generate 2× 25bp reads.

tag: cell type

value: Neutrophil

tag: genotype

tag: disease state

value: MCI

tag: Sex

value: F

tag: age

tag: qrds

tag: mmse


title: Sample_80_Neutrophil_APOE3_4_CN

value: CN

value: M


title: mP4_bb_Week11_101

city: Copenhagen

first: Yifan

last: Dai

address: Ole Maaløes Vej 5

department: Department of Biology

country: Denmark

institute: Copenhagen University

description: Acid Adaptation

data_processing:
Fastqc (version 0.11.5) and Multiqc (version 1.748) were used to investigate potential RNA-Seq library (paired-end) artifacts.
The 13 bp 5' adapter sequences in all the libraries were removed using Trim Galore (0.4.4) with the options '–paired –clip_R1 13 –clip_R2 13'.
Salmon (1.3.0) with the parameters '-l IU' was used to map the adapter-trimmed reads on the mouse transcriptome (M25 GRCm38.p6 Gencode release50).
Read Counts and TPM values are extracted from Salmon output.
Assembly: mm10
Supplementary files format and content: tab-delimited text files with counts values for each sample
Supplementary files format and content: tab-delimited text files with TPM values for each sample

organism: Mus musculus

growth_protocol: Mouse pancreatic organoids were cultured in 24 well plates (BioLite Multidish, Thermo Fisher Scientific, #930186), suspended in a 50 µL dome of Matrigel (Matrigel Growth Factor Reduced, Phenol Red Free, Corning, # 356231). They were fed with 500 µl Mouse Complete Feeding Medium 26 that was changed every 3-4 days. Organoids were split approximately twice a week.

extract_protocol:
Confluent organoid cultures (3-4 50 µl domes/condition) were harvested with cold Cell Recovery Solution (Corning, 354253) and incubated on ice for 30 minutes to dissolve Matrigel and release the cells. RNA from the organoid pellets was isolated and purified using RNeasy Mini Kit (QIAGEN, 74106) according to the manufacturer's protocol, including DNase digestion step. RNA concentration was measured using NanoDrop 2000 spectrophotometer and samples were stored at –80°C.
RNA-seq libraries were prepared following the standard protocol of DNBSEQ

treatment_protocol: Culture medium was acidified by titration with 1M hydrochloric acid (HCl), and then filtered through sterile 0.22 µm filters (Millex®-GP, Millipore express PES membrane Filter Unit, #SLGP033RB). Resulting pH was validated using pH determination strips (Sigma Aldrich) inside the CO2 incubator.

tag: cell line

value: Pancreatic Ductal Cells

value: Kras G12D/-

tag: treatment

tag: time

value: Week 11

tag: ph

tag: batch


title: SG-30-Rep2

description:
SG-240-cy3 vs SG-30-cy5 (1).gpr
Biological replicate 2


title: mP4_bb_Week11_102

description: Acid Adaptation


title: SG-90-Rep2

description:
SG-233-cy3 vs SG-90 cy5 (1).gpr
Biological replicate 2


title: Sample_79_Neutrophil_APOE3_3_CN


title: SG-225-Rep2

description:
SG-24-cy3 vs SG-225-cy5(2).gpr
Biological replicate 2


title: SG-295-Rep2

description:
SG-230-cy3 vs SG-295 cy5 (1).gpr
Biological replicate 2


title: SG-18-Rep2

description:
SG-232-cy3 vs SG-18-cy5 (2).gpr
Biological replicate 2


title: SG-130-Rep2

description:
SG-25-cy3 vs SG-130-cy5 (2).gpr
Biological replicate 2


title: Sample_76_Neutrophil_APOE3_3_MCI


title: mP4_p53KO_AA_Week11_98

description: Acid Adaptation

value: AA


title: mP4_bb_Week11_100

description: Acid Adaptation


title: Sample_78_Neutrophil_APOE3_3_dementia

value: dementia


title: SG-229-Rep2

description:
SG-224-cy3 vs SG-229-cy5(1).gpr
Biological replicate 2


title: SG-330-Rep2

description:
SG-231-cy3 vs SG-330-cy5(2).gpr
Biological replicate 2


title: Sample_77_Neutrophil_APOE3_3_CN


title: SG-224-Rep2

description:
SG-229-cy3 vs SG-224-cy5(2).gpr
Biological replicate 2


title: SG-266-Rep2

description:
SG-270-cy3 vs SG-266-cy5(2).gpr
Biological replicate 2


title: SG-19-Rep2

description:
SG-214-cy3 vs SG-19-cy5 (1).gpr
Biological replicate 2


title: SG-168-Rep2

description:
SG-221-cy3 vs SG-168-cy5 (1).gpr
Biological replicate 2


title: SG-80-Rep2

description:
SG-209-cy3 vs SG-80-cy5 (2).gpr
Biological replicate 2


title: SG-100-Rep2

description:
SG-22-cy3  vs SG-100-cy5 (1).gpr
Biological replicate 2


title: mP4_AA_Week11_93

description: Acid Adaptation


title: SG-243-Rep2

description:
SG-216-cy3 vs SG-243-cy5(1).gpr
Biological replicate 2


title: mP4_AA_Week11_92

description: Acid Adaptation


title: SG-214-Rep2

description:
SG-19-cy3 vs SG-214-cy5 (2).gpr
Biological replicate 2


title: Sample_75_Neutrophil_APOE3_4_dementia


title: mP4_p53KO_AA_Week11_97

description: Acid Adaptation


title: SG-132-Rep2

description:
SG-178-cy3 vs SG-132-cy5(1).gpr
Biological replicate 2


title: Sample_74_Neutrophil_APOE3_3_MCI


title: mP4_p53KO_AA_Week11_99

description: Acid Adaptation


title: SG-150-Rep2

description:
SG-208-cy3 vs SG-150-cy5(1).gpr
Biological replicate 2


title: SG-120-Rep2

description:
SG-204-cy3 vs SG-120-cy5 (2).gpr
Biological replicate 2


title: Sample_73_Neutrophil_APOE3_3_MCI


title: SG-171-Rep2

description:
SG-206-cy3 vs SG-171-cy5 (1).gpr
Biological replicate 2


title: SG-221-Rep2

description:
SG-168-cy3 vs SG-221-cy5 (2).gpr
Biological replicate 2


title: Sample_72_Neutrophil_APOE3_3_CN


title: mP4_AA_Week11_91

description: Acid Adaptation


title: SG-10-Rep2

description:
SG-201-cy3 vs SG-10-cy5 (2).gpr
Biological replicate 2


title: mP4_p53KO_CTRL_Week11_89

description: Acid Adaptation

value: CTRL


title: SG-165-Rep2

description:
SG-175-cy3 vs SG-165-cy5 (2).gpr
Biological replicate 2


title: mP4_CTRL_Week11_84

description: Acid Adaptation


title: Sample_71_Neutrophil_APOE3_4_CN


title: mP4_p53KO_CTRL_Week11_90

description: Acid Adaptation


title: SG-29-Rep2

description:
SG-172-cy3 vs SG-29-cy5(2).gpr
Biological replicate 2


title: mP4_CTRL_Week11_83

description: Acid Adaptation


title: SG-232-Rep2

description:
SG-18-cy3 VS SZG-232-cy5 (1).gpr
Biological replicate 2


title: Sample_67_Neutrophil_APOE3_4_CN


title: SG-208-Rep2

description:
SG-150-cy3 vs SG-208-cy5(2).gpr
Biological replicate 2


title: Sample_70_Neutrophil_APOE3_3_CN


title: Sample_66_Neutrophil_APOE3_4_MCI


title: Sample_69_Neutrophil_APOE3_4_MCI


title: mP4_CTRL_Week11_82

description: Acid Adaptation


title: SG-206-Rep2

description:
SG-171-cy3 vs SG-206-cy5 (2).gpr
Biological replicate 2


title: SG-175-Rep2

description:
SG-165-cy3 vs SG-175-cy5 (1).gpr
Biological replicate 2


title: SG-262-Rep2

description:
SG-166-cy3 vs SG-262-cy5 (1).gpr
Biological replicate 2


title: mP4_p53KO_CTRL_Week11_88

description: Acid Adaptation


title: SG-146-Rep2

description:
SG-135-cy3 vs SG-146-cy5 (2).gpr
Biological replicate 2


title: Sample_68_Neutrophil_APOE3_4_MCI


title: Sample_63_Neutrophil_APOE3_3_CN


title: SG-135-Rep2

description:
SG-146-cy3 vs SG-135-cy5(1).gpr
Biological replicate 2


title: SG-118-Rep2

description:
SG-159-cy3 vs SG-118-cy5(2).gpr
Biological replicate 2


title: SG-25-Rep2

description:
SG-130-cy3 vs SG-25 cy5(1).gpr
Biological replicate 2


title: Sample_62_Neutrophil_APOE3_4_CN


title: Sample_65_Neutrophil_APOE3_4_CN


title: SG-54-Rep2

description:
SG-137-cy3 vs SG-54-cy5(2).gpr
Biological replicate 2


title: SG-242-Rep2

description:
SG-163-cy3 vs SG-242-cy5(1).gpr
Biological replicate 2


title: Sample_61_Neutrophil_APOE3_3_CN


title: Sample_64_Neutrophil_APOE3_4_MCI


title: mP4_p53KO_bb_Week10_81

description: Acid Adaptation

value: Week 10


title: mP4_CTRL_Week1_109

description: Acid Adaptation

value: Week 1


title: mP4_p53KO_bb_Week10_79

description: Acid Adaptation


title: SG-75-Rep2

description:
SG-115-cy3 vs SG-75-cy5(1).gpr
Biological replicate 2


title: SG-178-Rep2

description:
SG-132-cy3 vs SG-178-cy5(2).gpr
Biological replicate 2


title: mP4_bb_Week10_75

description: Acid Adaptation


title: mP4_bb_Week10_74

description: Acid Adaptation


title: Sample_60_Neutrophil_APOE3_4_CN


title: mP4_p53KO_bb_Week10_80

description: Acid Adaptation


title: Sample_56_Neutrophil_APOE3_4_MCI


title: mP4_bb_Week10_73

description: Acid Adaptation


title: Sample_59_Neutrophil_APOE3_3_MCI


title: mP4_p53KO_AA_Week10_72

description: Acid Adaptation


title: SG-306-Rep2

description:
SG-107-cy3 vs SG-306-cy5(1).gpr
Biological replicate 2


title: DH-Rep4

description:
PSA-cy3 vs DH-cy5 (4).gpr
Biological replicate 4


title: DH-Rep3

description:
PSA-cy3 vs DH-cy5 (3).gpr
Biological replicate 3


title: SG-278-Rep2

description:
SG-108-cy3 vs SG-278-cy5(1).gpr
Biological replicate 2


title: SG-303-Rep2

description:
SG-121-cy3 vs SG-303-cy5(2).gpr
Biological replicate 2


title: mP4_AA_Week10_66

description: Acid Adaptation


title: SG-276-Rep2

description:
SG-103-cy3 vs SG-276-cy5(1).gpr
Biological replicate 2


title: SG-80-Rep1

description:
SG-80-cy3 vs SG-209 cy5 (1).gpr
Biological replicate 1


title: PSA-Rep3

description:
DH-cy3 vs PSA-cy5 (1).gpr
Biological replicate 3


title: SG-22-Rep2

description:
SG-100- cy3 vs SG-22- cy5 (2).gpr
Biological replicate 2


title: SG-285-Rep2

description:
SG-122-cy3 vs SG-285-cy5(2).gpr
Biological replicate 2


title: PSA-Rep4

description:
DH-cy3 vs PSA-cy5 (2).gpr
Biological replicate 4


title: SG-201-Rep2

description:
SG-10-cy3 vs SG-201-cy5 (1).gpr
Biological replicate 2


title: SG-204-Rep2

description:
SG-120-cy3 vs SG-204 cy5 (1).gpr
Biological replicate 2


title: SG-159-Rep2

description:
SG-118-cy3 vs SG-159-cy5 (1).gpr
Biological replicate 2


title: SG-225-Rep1

description:
Sg-225-cy3 vs SG-24-cy5(1).gpr
Biological replicate 1


title: Sample_58_Neutrophil_APOE3_3_CN


title: mP4_AA_Week10_65

description: Acid Adaptation


title: mP4_p53KO_AA_Week10_71

description: Acid Adaptation


title: Sample_57_Neutrophil_APOE3_3_CN


title: SG-65-Rep1

description:
SG-65 cy3 vs SG-33 cy5 (2).gpr
Biological replicate 1


title: Sample_54_Neutrophil_APOE3_3_MCI


title: mP4_p53KO_AA_Week10_70

description: Acid Adaptation


title: SG-64-Rep1

description:
SG-64-cy3 vs SG-300-cy5 (2).gpr
Biological replicate 1


title: SG-9-Rep1

description:
SG-9-cy3 vs SG-317-cy5(2).gpr
Biological replicate 1


title: SG-90-Rep1

description:
SG-90-cy3 vs Sg-233-cy5(2).gpr
Biological replicate 1


title: mP4_AA_Week10_64

description: Acid Adaptation


title: Sample_55_Neutrophil_APOE3_4_MCI


title: SG-85-Rep1

description:
SG-85-cy3 vs SG-309-cy5 (1).gpr
Biological replicate 1


title: mP4_CTRL_Week10_57

description: Acid Adaptation


title: Sample_50_Neutrophil_APOE3_3_MCI


title: Sample_53_Neutrophil_APOE3_3_MCI


title: mP4_p53KO_CTRL_Week10_63

description: Acid Adaptation


title: Sample_51_Neutrophil_APOE3_3_CN


title: mP4_p53KO_CTRL_Week10_61

description: Acid Adaptation


title: mP4_p53KO_CTRL_Week10_62

description: Acid Adaptation


title: Sample_52_Neutrophil_APOE3_3_CN


title: SG-5-Rep1

description:
SG-5-cy3 vs SG-351-cy5 (1).gpr
Biological replicate 1


title: SG-33-Rep1

description:
SG-33-cy3 vs SG-65 cy5 (1).gpr
Biological replicate 1


title: mP4_CTRL_Week10_55

description: Acid Adaptation


title: SG-67-Rep1

description:
SG-67-cy3 vs SG-333-cy5(1).gpr
Biological replicate 1


title: SG-351-Rep1

description:
SG-351- cy3 vs SG-5-cy5 (2).gpr
Biological replicate 1


title: SG-333-Rep1

description:
SG-333-cy3 vs SG-67-cy5 (2).gpr
Biological replicate 1


title: Sample_49_Neutrophil_APOE3_3_CN


title: mP4_p53KO_AA_Week8_54

description: Acid Adaptation

value: Week 8


title: Sample_46_Neutrophil_APOE3_4_MCI


title: SG-75-Rep1

description:
SG-75-cy3 vs SG-115-cy5 (2).gpr
Biological replicate 1


title: SG-309-Rep1

description:
SG-309-cy3 vs SG-85-cy5 (2).gpr
Biological replicate 1


title: SG-317-Rep1

description:
SG-317-cy3 vs SG-9-cy5(1).gpr
Biological replicate 1


title: SG-324-Rep1

description:
SG-324-cy3 vs SG-261-cy5(1).gpr
Biological replicate 1


title: SG-303-Rep1

description:
SG-303-cy3 vs SG-121-cy5 (1).gpr
Biological replicate 1


title: SG-321-Rep1

description:
SG-321-cy3 vs SG-259-cy5 (2).gpr
Biological replicate 1


title: SG-54-Rep1

description:
SG-54-cy3 vs SG-137-cy5(1).gpr
Biological replicate 1


title: SG-300-Rep1

description:
SG-300-cy3 vs SG-64-cy5(1).gpr
Biological replicate 1


title: Sample_48_Neutrophil_APOE3_4_CN


title: SG-318-Rep1

description:
SG-318-cy3 vs SG-254-cy5 (1).gpr
Biological replicate 1


title: mP4_CTRL_Week10_56

description: Acid Adaptation


title: SG-330-Rep1

description:
SG-330-cy3 vs SG-231-cy5(1).gpr
Biological replicate 1


title: Sample_47_Neutrophil_APOE3_3_CN


title: SG-295-Rep1

description:
SG-295-cy3 vs SG-230-cy5 (3).gpr
Biological replicate 1


title: SG-294-Rep1

description:
SG-294-cy3 vs SG-267-cy5(1).gpr
Biological replicate 1


title: SG-285-Rep1

description:
SG-285-cy3 vs SG-122-cy5(1).gpr
Biological replicate 1


title: mP4_p53KO_AA_Week8_53

description: Acid Adaptation


title: Sample_45_Neutrophil_APOE3_4_CN


title: SG-30-Rep1

description:
SG-30-cy3 vs SG-240-cy5 (2).gpr
Biological replicate 1


title: mP4_p53KO_AA_Week8_52

description: Acid Adaptation


title: Sample_43_Neutrophil_APOE3_3_CN


title: Sample_44_Neutrophil_APOE3_3_MCI


title: SG-306-Rep1

description:
SG-306-cy3 vs SG-107-cy5 (2).gpr
Biological replicate 1


title: mP4_AA_Week8_48

description: Acid Adaptation


title: SG-278-Rep1

description:
SG-278-cy3 vs SG-108-cy5(2).gpr
Biological replicate 1


title: mP4_p53KO_CTRL_Week8_44

description: Acid Adaptation


title: Sample_42_Neutrophil_APOE3_3_CN


title: Sample_39_Neutrophil_APOE3_3_CN


title: SG-273-Rep1

description:
SG-273-cy3 vs SG-253-cy5 (1).gpr
Biological replicate 1


title: Sample_41_Neutrophil_APOE3_4_CN


title: mP4_AA_Week8_46

description: Acid Adaptation


title: SG-29-Rep1

description:
SG-29-cy3 vs SG-172-cy5(1).gpr
Biological replicate 1


title: mP4_p53KO_CTRL_Week8_45

description: Acid Adaptation


title: SG-271-Rep1

description:
SG-271-cy3 vs SG-284 cy5 (2).gpr
Biological replicate 1


title: SG-281-Rep1

description:
SG-281-cy3 vs SG-249-cy5(2).gpr
Biological replicate 1


title: SG-284-Rep1

description:
SG-284-cy3 vs SG-271 cy5(1).gpr
Biological replicate 1


title: SG-270-Rep1

description:
SG-270-cy3 vs SG-266-cy5(2).gpr
Biological replicate 1


title: SG-269-Rep1

description:
SG-269-cy3 vs SG-247-cy5(1).gpr
Biological replicate 1


title: Sample_40_Neutrophil_APOE3_4_CN


title: SG-267-Rep1

description:
SG-267-cy3 vs SG-294-cy5 (2).gpr
Biological replicate 1


title: mP4_p53KO_CTRL_Week8_43

description: Acid Adaptation


title: mP4_AA_Week8_47

description: Acid Adaptation


title: SG-262-Rep1

description:
SG-262-cy3 vs SG-166-cy5 (2).gpr
Biological replicate 1


title: mP4_CTRL_Week8_39

description: Acid Adaptation


title: Sample_36_Neutrophil_APOE3_4_CN


title: SG-276-Rep1

description:
SG-276-cy3 vs sg-103-cy5 (2).gpr
Biological replicate 1


title: mP4_CTRL_Week8_37

description: Acid Adaptation


title: SG-266-Rep1

description:
SG-266-cy3 vs SG-270-cy5 (1).gpr
Biological replicate 1


title: SG-265-Rep1

description:
SG-265-cy3 vs SG-246-cy5 (1).gpr
Biological replicate 1


title: mP4_CTRL_Week8_38

description: Acid Adaptation


title: Sample_35_Neutrophil_APOE3_4_CN


title: SG-259-Rep1

description:
SG-259-cy3 vs SG-321-cy5(1).gpr
Biological replicate 1


title: SG-25-Rep1

description:
SG-25-cy3 vs SG-130-cy5 (2).gpr
Biological replicate 1


title: mP4_p53KO_AA_Week5_36

description: Acid Adaptation

value: Week 5


title: Sample_34_Neutrophil_APOE3_4_dementia


title: mP4_p53KO_AA_Week5_35

description: Acid Adaptation


title: Sample_33_Neutrophil_APOE3_3_MCI


title: Brain_E15.5_RNA

city: Grand Rapids

first: Gerd

middle: P.

last: Pfeifer

state: Michigan

address: 333 Bostwick Ave. NE.

department: Center for Epigenetics

institute: Van Andel Research Institute

data_processing:
Quality and adaptor trimming of Fastq files were performed using Trim_Galore v.0.6.7
The reads were aligned to the mouse reference genome (mm10) and counted with HISAT2 (version 2.2.1) provided on the Galaxy web platform.
Differential gene expression was analyzed using DESeq2 (Galaxy Version 2.11.40.8) provided on the Galaxy web platform.
Assembly: mm10
Supplementary files format and content: bigwig, counts coverage

molecule: polyA RNA

growth_protocol: J1 mouse embryonic stem cells (mESCs) were grown on gelatin-coated plates without feeder cell layers in knockout DMEM supplemented with 15% (v/v) ES-qualified fetal bovine serum (FBS), 1x non-essential amino acids, 2 mM L-glutamine, 100 mM b-mercaptoethanol, and 1,000 U/ml LIF at 37°C in a 5% CO2 standard incubator.

extract_protocol:
Total RNAs were isolated from the cells with PureLink RNA Mini Kit according to the manufacturer's protocol. RNA quality was evaluated with Bioanalyzer 2100.
The RNA-seq libraries were prepared with the KAPA RNA HyperPrep kit according to the manufacturer’s instructions

treatment_protocol: To neuronal differentiation, mESCs were cultured on bacterial dishes in medium lacking LIF and with 10% FBS to induce the formation of embryoid body (EB) for 4 days followed by additional incubation in culture medium with 5 μM retinoic acid (RA) for 4 days. The RA treated cells were trypsinized and plated on PORN/laminin-coated plates. The cells were further cultured for 2 days in N2 medium (DMEM/F12 mixture, 1:1 with 1x N2 supplement) and 7 days in B27 media.

value: Wildtype


title: SG-258-Rep1

description:
SG-258-cy3 vs SG-241-cy5 (2).gpr
Biological replicate 1

value: tissue

value: development seeds


title: SG-254-Rep1

description:
SG-254-cy3 vs SG-318-cy5(2).gpr
Biological replicate 1


title: Sample_32_Neutrophil_APOE3_3_CN

value: Neutrophil


title: Sample_38_Neutrophil_APOE3_4_MCI

value: MCI

value: F


title: Neuron_Day2_RNA

value: mESC

value: Retinoic Acid treatment


title: mP4_AA_Week5_30

description: Acid Adaptation

value: Pancreatic Ductal Cells

value: Kras G12D/-


title: SG-247-Rep1

description:
SG-247-cy3 vs SG-269-cy5(2).gpr
Biological replicate 1


title: SG-253-Rep1

description:
SG-253-cy3 vs SG-273-cy5(2).gpr
Biological replicate 1


title: SG-243-Rep1

description:
SG-243-cy3 vs SG-216-cy5 (2).gpr
Biological replicate 1


title: Sample_31_Neutrophil_APOE3_4_CN

value: CN

value: M


title: SG-246-Rep1

description:
SG-246-cy3 vs SG-265-cy5(2).gpr
Biological replicate 1


title: mP4_AA_Week5_29

description: Acid Adaptation

value: AA


title: SG-261-Rep1

description:
SG-261 cy3 vs SG-324 cy5 (2).gpr
Biological replicate 1


title: SG-249-Rep1

description:
SG-249-cy3 vs SG-281-cy5 (1).gpr
Biological replicate 1


title: Sample_37_Neutrophil_APOE3_4_CN


title: SG-242-Rep1

description:
SG-242-cy3 vs SG-163-cy5(2).gpr
Biological replicate 1


title: NPC_RNA


title: SG-241-Rep1

description:
SG-241-cy3 vs SG-258-cy5(1).gpr
Biological replicate 1


title: Sample_30_Neutrophil_APOE3_4_CN


title: mP4_p53KO_AA_Week5_34

description: Acid Adaptation


title: EB_RNA


title: SG-240-Rep1

description:
SG-240-cy3 vs SG-30-cy5 (1).gpr
Biological replicate 1


title: Sample_29_Neutrophil_APOE3_4_CN


title: mESC_RNA


title: mP4_AA_Week5_28

description: Acid Adaptation


title: mP4_p53KO_CTRL_Week5_27

description: Acid Adaptation

value: CTRL


title: SG-24-Rep1

description:
SG-24-cy3 vs SG-225-cy5(2).gpr
Biological replicate 1


title: mESC_CXXC5_ChIP_rep2

library_source: genomic

data_processing:
The reads were trimmed using Trim_Galore (version 0.4.0) with default parameters.
The reads were aligned to the mouse reference genome (mm10) with Bowtie2 (version 2.3.5).
SAMtools (version 2.0.5) was used to remove PCR duplicates and for sorting data to BAM files, then the data were used for peak calling with MACS2 (version 2.2.9.1).
To visualize the data, bigwig files were generated using bamCoverage (version 3.5.4) and loaded into IGV viewer (version 2.8.9) for genome browser snapshots of ChIP-seq enrichment.
Assembly: mm10
Supplementary files format and content: bigwig, counts coverage

molecule: genomic DNA

extract_protocol:
J1 mESCs were fixed with 1% formaldehyde for 8 minutes, after quencing and cell lysis, chromatin was sonicated using a Covaris E220 Evo sonicator.
The libraries for Illumina sequencing of ChIP DNA were prepared using TruSeq Sample Prep kit according to the manufacturer’s instructions, and then samples were sequenced on an Illumina HiSeq instrument.


title: mP4_p53KO_CTRL_Week5_26

description: Acid Adaptation


title: Sample_28_Neutrophil_APOE3_4_CN


title: Sample_27_Neutrophil_APOE3_3_MCI


title: mESC_CXXC5_ChIP_rep1


title: mP4_p53KO_CTRL_Week5_25

description: Acid Adaptation


title: mESC_Input_ChIP


title: mP4_CTRL_Week5_20

description: Acid Adaptation


title: Sample_26_Neutrophil_APOE3_4_CN


title: mP4_CTRL_Week5_21

description: Acid Adaptation


title: Sample_25_Neutrophil_APOE3_3_CN


title: HTO library for CEL190419LH_GEX

city: Portland

first: Laura

last: Heiser

state: Oregon

address: 2730 S. Moody Ave

department: BME

institute: OHSU

description:
10x Genomics Single Cell 3' v3 ADT
CEL190419LH_raw_feature_bc_matrix.h5
CEL190419LH_filtered_feature_bc_matrix.h5

library_source: transcriptomic single cell

data_processing:
BCL files were converted to fastq using the bamtofastq tool (Illumina). Reads were aligned to GRCh38-2020-A and counted using CellRange (v6.0.2, 10X Genomics) to produce bam file and count matrices.
Assembly: GRCh38-2020-A
Supplementary files format and content: Both filtered (cell containing) and raw (all droplet) feature_bc_matrix.h5 files output from Cellranger 6.0.2

growth_protocol: Cells were cultured in RPMI supplemented with 10% FBS

extract_protocol:
Media was aspirated and cells were washed twice with PBS. Cells were incubated in TrypLE Express for approximately 5 minutes until detached from the well surface, then gently titurated before enzyme neutralization (10% FBS in PBS). Cells were spun at 300xG for 5 minutes and then resuspended in PBS for library preparation (LH2400, LH2401, LH7200, LH7201) or HTO staining (CEL190419LH) following manufacturer protocol (TotalSeq-A, BioLegend).
LH2400, LH2401, LH7200, LH7201: Libraries were prepared following manufacturer protocol (10X Genomics Single Cell 3' v2). CEL190419LH: Libraries were prepared for both single-cell RNA and antibody feature following manufacturer protocol (10X Genomics Single Cell 3' v3).

treatment_protocol: Cells were plated 24 hours prior to treatment in RPMI supplemented with 2% FBS. At the treatment timepoint, perturbation containing media was added such that it doubled the culture volume and maintained 2% FBS.

value: Ductal Carcinoma

tag: library type

value: HTO

value: 0.1percent  PBS, 1uM NOTCHi, 1uM NOTCHi + 20ng/mL IFNB, 20ng/mL IFNB, 20ng/mL IFNG, 10ng/mL TGFB, 10ng/mL LTA, 10ng/mL OSM


title: Sample_23_Neutrophil_APOE3_3_MCI


title: SG-232-Rep1

description:
SG-232-cy3 vs SG-18-cy5 (2).gpr
Biological replicate 1


title: Fetal lung organoids derived from BU3 PSC

city: Toronto

first: Amy

last: Wong

state: Ontario

address: 686 Bay Street, Toronto

department: Developmental & Stem Cell Biology

institute: The Hospital for Sick Children

description:
hPSC_fetal_lung_organoids.rds
BU3_fetal_lung_organoids

data_processing:
FASTQ files generated from supernova/cellranger mkfastq and bcl2fastq2 v2.20.
Cellranger was used to demultiplex and generate single cell feature counts.
Demultiplexing of MULTI-seq barcodes were done as previously published (McGinnis et al., 2019: https://github.com/chris-mcginnis-ucsf/MULTI-seq)
Barcodes related to specific samples were subsetted. Cells with less than 200 features, greater than 15% mitochondrial transcript, and genes expressed in less than 3 cells were excluded from our analysis. Furthermore, principal component analysis (PCA) for each sample was done to ensure filtering of doublets and high-quality cells. Gene expression levels were log normalized datasets and highly variable features that identify high cell-cell variation within each sample dataset were determined using Seurat‘s FindVariableFeatures. CA1_fetal_lung_cells and BU3_fetal_lung_cells, and CA1_fetal_lung_organoids and BU3_fetal_lung_organoids were integrated using Seurat (v4.0) Integrate function.
Assembly: GRCh38
Supplementary files format and content: hPSC_fetal_lung_cells.rds: integrated seurat object derived from CA1_fetal_lung_cells and BU3_fetal_lung_cells
Supplementary files format and content: hPSC_fetal_lung_organoids.rds:  integrated seurat object derived from CA1_fetal_lung_organoids and BU3_fetal_lung_organoids

extract_protocol:
hPSC-derived cultures were dissociated into single cells using 0.25% trypsin at 37°C for 10 minutes and deactivated using 1% BSA in PBS.
Cells were multiplexed using MULTI-seq and barcode library preparation as previously published (McGinnis et al., 2019) . In brief, pre-designed DNA barcodes were hybridized to the plasma membranes through an anchor lipid-modified oligonucleotide (LMO). Subsequently, library construction was done using the 10X Chromium Next GEM single-cell 3’ Reagent Kits v3.1 (10x Genomics). Library prep was performed as per manufacturer’s protocol. During cDNA amplification, barcode fraction was also collected and a separete library preparation was done for the barcodes.

value: Fetal lung organoids


title: Sample_24_Neutrophil_APOE3_4_CN


title: HCC1143, 72 hour HTO multiplexed ligand, Gene expression

description:
10x Genomics Single Cell 3' v3 GEX
CEL190419LH_raw_feature_bc_matrix.h5
CEL190419LH_filtered_feature_bc_matrix.h5

value: mRNA


title: mP4_CTRL_Week5_19

description: Acid Adaptation

value: Week 5


title: mP4_p53KO_CTRL_Week1_18

description: Acid Adaptation

value: Week 1


title: SG-231-Rep1

description:
SG-231-cy3 vs SG-330-cy5(2).gpr
Biological replicate 1

value: tissue

value: development seeds


title: Fetal lung cells derived from BU3 PSC

description:
hPSC_fetal_lung_cells.rds
BU3_fetal_lung_cells

value: Fetal lung cells


title: SG-233-Rep1

description:
SG-233-cy3 vs SG-90 cy5 (1).gpr
Biological replicate 1


title: SG-229-Rep1

description:
SG-229-cy3 vs SG-224-cy5(2).gpr
Biological replicate 1


title: SG-224-Rep1

description:
SG-224-cy3 vs SG-229-cy5(1).gpr
Biological replicate 1


title: SG-221-Rep1

description:
SG-221-cy3 vs SG-168-cy5 (1).gpr
Biological replicate 1


title: Sample_21_Neutrophil_APOE3_3_dementia

value: Neutrophil

value: dementia


title: Fetal lung organoids derived from CA1 PSC

description:
hPSC_fetal_lung_organoids.rds
CA1_fetal_lung_organoids


title: Sample_22_Neutrophil_APOE3_4_dementia

value: F


title: mP4_p53KO_CTRL_Week1_16

description: Acid Adaptation

value: Pancreatic Ductal Cells


title: Fetal lung cells derived from CA1 PSC

description:
hPSC_fetal_lung_cells.rds
CA1_fetal_lung_cells


title: Sample_19_Neutrophil_APOE3_4_MCI

value: MCI


title: mP4_CTRL_Week1_12

description: Acid Adaptation

value: Kras G12D/-


title: mP4_CTRL_Week1_11

description: Acid Adaptation

value: CTRL


title: SG-230-Rep1

description:
SG-230-cy3 vs SG-295 cy5 (1).gpr
Biological replicate 1


title: Fetal lung tissue derived from GW 19.4

data_processing:
FASTQ files generated from supernova/cellranger mkfastq and bcl2fastq2 v2.20
Seurat v4 was used for subsequent analysis. Cells with less than 200 features, greater than 15% mitochondrial transcript, and genes expressed in less than 3 cells were excluded from our analysis. Furthermore, principal component analysis (PCA) for each sample was done to ensure filtering of doublets and high-quality cells. Gene expression levels were log normalized datasets and highly variable features that identify high cell-cell variation within each sample dataset were determined using Seurat‘s FindVariableFeatures. Subsequently features that were repeatedly variable across each sample dataset were identified as integration features. Data was then scaled (linear transformation) was done using Seurat’s ScaleData and principal component analysis (PCA) (linear dimensional reduction) was done on each sample dataset. Generation of a master dataset was done by integrating all the sample datasets using Seurat’s reciprocal PCA (RPCA) integration (3000 features). Subsequent PCA analysis was done to ensure proper integration and 30 dimensions were retained for further analysis. Further reduction was done through uniform manifold approximation and projection (UMAP) (non-linear dimensional reduction) and cluster analysis was done using Seurat’s FindClusters.
Assembly: GRCh38
Supplementary files format and content: Seurat object containing integrated object of all raw data.

source_name: Fetal lung tissue

extract_protocol:
Human fetal lung tissues were dissociated into single-cell suspension using the Multi Tissue Dissociation Kit 1 and 37C Multi_tissue_dissociation B program. Dissociated cells were collected through a 40 µm pore size cell strainer  and incubated with RBC lysis buffer for two minutes.
Library construction was done using the 10X Chromium Next GEM single-cell 3’ Reagent Kits v3.1 (10x Genomics). Library prep was performed as per manufacturer’s protocol.

value: Fetal lung tissue

value: GW 19


title: SG-22-Rep1

description:
SG-22-cy3  vs SG-100-cy5 (1).gpr
Biological replicate 1


title: Sample_18_Neutrophil_APOE3_4_CN

value: CN


title: mP4_p53KO_CTRL_Week1_17

description: Acid Adaptation


title: mP4_CTRL_Week1_10

description: Acid Adaptation


title: Fetal lung tissue derived from GW 19.2


title: Fetal lung tissue derived from GW 18.1 sample 2B

value: GW 18


title: mP4_p53KO_CTRL_Week1_9

description: Acid Adaptation


title: SG-216-Rep1

description:
SG-216-cy3 vs SG-243-cy5(1).gpr
Biological replicate 1


title: Sample_20_Neutrophil_APOE3_4_dementia


title: mP4_p53KO_CTRL_Week1_8

description: Acid Adaptation


title: SG-209-Rep1

description:
SG-209-cy3 vs SG-80-cy5 (2).gpr
Biological replicate 1


title: SG-208-Rep1

description:
SG-208-cy3 vs SG-150-cy5(1).gpr
Biological replicate 1


title: Fetal lung tissue derived from GW 18.1 sample 2A


title: mP4_p53KO_CTRL_Week1_7

description: Acid Adaptation


title: SG-214-Rep1

description:
SG-214-cy3 vs SG-19-cy5 (1).gpr
Biological replicate 1


title: SG-206-Rep1

description:
SG-206-cy3 vs SG-171-cy5 (1).gpr
Biological replicate 1


title: mP4_CTRL_Week1_3

description: Acid Adaptation


title: Sample_13_Neutrophil_APOE3_3_CN


title: Sample_17_Neutrophil_APOE3_4_MCI


title: Sample_16_Neutrophil_APOE3_4_MCI


title: Fetal lung tissue derived from GW 19.0


title: SG-204-Rep1

description:
SG-204-cy3 vs SG-120-cy5 (2).gpr
Biological replicate 1


title: SG-19-Rep1

description:
SG-19-cy3 vs SG-214-cy5 (2).gpr
Biological replicate 1


title: Fetal lung tissue derived from GW 18.1


title: Sample_15_Neutrophil_APOE3_3_MCI

value: M


title: mP4_CTRL_Week1_2

description: Acid Adaptation


title: Fetal lung tissue derived from GW 18


title: Sample_12_Neutrophil_APOE3_3_dementia


title: Fetal lung tissue derived from GW 16.5

value: GW 16


title: mP4_CTRL_Week1_1

description: Acid Adaptation

value: Week 1


title: Fetal lung tissue derived from GW 18.2


title: Sample_11_Neutrophil_APOE3_3_MCI


title: NAR3

city: Guangzhou

first: Yage

last: Nie

address: No.74 Zhongshan Rd.2, Guangzhou

country: China

institute: Sun Yat-sen University

data_processing:
Cell Ranger V1.2.0
‘cellranger-atac count’ was used to perform read filtering, alignment, peak calling, and count matrix generation from fastq files per sample
Genome_build: mm10
Supplementary_files_format_and_content: tsv file include barcode, peak position and peak signal for each sample

source_name: heart

extract_protocol:
Isolated hearts were washed with DPBS twice, and then collected in 1.5 mL EP tubes. Tissues were minced into pieces (~1 mm) on ice using scissors, and digested into single-cell suspensions with 1 mg/ml type II collagenase (17101015, GIBCO) and 1 mg/ml type IV collagenase (17104019, GIBCO) for 30min at 37 ℃ with intermittent shaking. The dissociated cells were separated and remaining undigested tissue were digested again with fresh digestion buffer. Digested suspension was passed through 70um strainer (Biologix).Dissociated cells were centrifuged at 300 g for 5 min at 4 °C, then re-suspended in 1 mL of cold DPBS with 0.1% BSA. After passing through a 40um cell strainer (Biologix), cells were washed twice, centrifuged at 300 g for 5 min at 4 °C.To isolate nuclei, 500,000 cell pellets were re-suspended in 100 uL chilled lysis buffer (10 mM Tris-HCl, pH 7.4, 10 mM NaCl, 3 mM MgCl2, 0.1% NP40, 0.1% Tween-20, and 0.01% digitonin - from (Corces, Trevino et al. 2017) supplemented with 1% BSA), and pipette mix 10X. After incubation for 5 min on ice, add 1 ml chilled Wash Buffer ((10 mM Tris-HCl, pH 7.4, 10 mM NaCl, 3 mM MgCl2, 0.1% Tween-20, 1% BSA) to the lysed cells. Pipette mix 5x, then centrifuged at 300 g for 5 min at 4 °C. Based on number of cells used for isolation and assuming ~50% nuclei loss during cell lysis, resuspend in chilled Diluted Nuclei Buffer (PN-2000153, 10x Genomics). If cell debris and large clumps are observed, pass through a cell strainer. For low volume, use a 40 µm Flowmi Cell Strainer (H13680-0040, Bel-Art) to minimize volume loss.
The scATAC library was prepared using the 10x Genomics platform with the Chromium Single Cell ATAC Library & Gel Bead Kit (10x Genomics, Pleasanton, California) as instructed by the manufacturer. A total of 15,000 nuclei per sample were used as input for single-cell ATAC-seq following the manufacturer’s instructions. Briefly, after tagmentation, the cells were loaded on a Chromium Controller Single-Cell instrument to generate single-cell Gel Bead-In-Emulsions (GEMs) followed by linear PCR as described in the 10X scATAC-seq protocol using a Veriti 96-well thermal cycler (BioRad, 1851197). After breaking the GEMs, the barcoded tagmented DNA was purified with SPRIselect Reagent Kit (Beckman Coulter, Pasadena, CA) and further amplified to enable sample indexing and enrichment of scATAC-seq libraries. The final libraries were quantified using Bioanalyzer (Agilent) and QuBit (Thermofisher) analysis and then sequenced in MGISeq-2000FCL (MGI Tech Co., Ltd., China) with 100-bp paired-end read length targeting a depth of 30,000–50,000 reads per cell.

value: heart

tag: treatmetn

value: apex resection

value: post natal day 4


title: SG-201-Rep1

description:
SG-201-cy3 vs SG-10-cy5 (2).gpr
Biological replicate 1

value: tissue

value: development seeds


title: Sample_14_Neutrophil_APOE3_4_CN

value: Neutrophil


title: P4

value: sham

value: wild type


title: Fetal lung tissue derived from GW 16.2


title: Sample_9_Neutrophil_APOE3_3_CN

value: F


title: SG-175-Rep1

description:
SG-175-cy3 vs SG-165-cy5 (2).gpr
Biological replicate 1


title: Fetal lung tissue derived from GW 15.5 sample 1

value: GW 15


title: Fetal lung tissue derived from GW 16.1

value: Fetal lung tissue


title: Sample_7_Neutrophil_APOE3_3_MCI

value: MCI


title: Sample_10_Neutrophil_APOE3_3_dementia

value: dementia


title: AR3


title: Fetal lung tissue derived from GW 15.5 sample 2


title: Fetal lung tissue derived from GW 14.3

value: GW 14


title: SG-178-Rep1

description:
SG-178-cy3 vs SG-132-cy5(1).gpr
Biological replicate 1


title: SG-171-Rep1

description:
SG-171-cy3 vs SG-206-cy5 (2).gpr
Biological replicate 1


title: Sample_8_Neutrophil_APOE3_4_MCI

value: M


title: SG-172-Rep1

description:
SG-172-cy3 vs SG-29-cy5(2).gpr
Biological replicate 1


title: Sample_6_Neutrophil_APOE3_4_dementia


title: Fetal lung tissue derived from GW 13.6

value: GW 13


title: Sample_5_Neutrophil_APOE3_3_CN

value: CN


title: Fetal lung tissue derived from GW 13.4


title: Sample_4_Neutrophil_APOE3_4_CN


title: SG-168-Rep1

description:
SG-168-cy3 vs SG-221-cy5 (2).gpr
Biological replicate 1


title: Fetal lung tissue derived from GW 12.3

value: GW 12


title: Sample_3_Neutrophil_APOE3_3_MCI


title: Sample_2_Neutrophil_APOE3_4_MCI


title: SG-163-Rep1

description:
SG-163-cy3 vs SG-242-cy5(1).gpr
Biological replicate 1


title: SG-165-Rep1

description:
SG-165-cy3 vs SG-175-cy5 (1).gpr
Biological replicate 1


title: SG-166-Rep1

description:
SG-166-cy3 vs SG-262-cy5 (1).gpr
Biological replicate 1


title: Sample_1_Neutrophil_APOE3_3_MCI


title: ADAT2 Knock Down, shRNA 4, Rep3

city: Hangzhou

first: Xushen

last: Xiong

state: Zhejiang

address: Wenyi Road West

department: Medical Center

institute: Zhejiang University

description: Small RNA sequencing

data_processing:
Raw sequencing reads were firstly subjected to Trim_galore (version 0.6.7) for quality control and adaptor trimming, with "--stringency" set to 3.
Processed reads were mapped to human tRNA transcriptome using bowtie2 (v2.3.4.3) with the following parameters: --sensitive -N 1, the reads mapped to the minus strand of tRNAs are removed.
Samtools mpileup was used to extract the reads mapping of every nucleotide in the transcriptome and mitochondrial genome.
Mismatch rate was calculated using in-house scripts. RPKM was calculated using in-house scripts following the definition of RPKM.
Assembly: hg38
Supplementary files format and content: Mismatch rate file in tab-delimited format; containing the mismatch rate for every nucleotide in the transcriptome.

source_name: cell line

growth_protocol: LPS853 cells were cultured in IMDM medium supplemented with 15% FBS and 1X penicillin/streptomycin

extract_protocol:
Total RNA was isolated with Trizol Reagent (Invitrogen) and treated with recombinant AlkB and AlkB D135S for demethylation for 2 h as detailed in Lin et al 2019. Demethylated small RNA was purified using the RNA Clean and Concentrator -5 kit (Zymo Research)
NEBnext Multiplex small RNA library prep for Illumina (New England Biolabs)

treatment_protocol: 2 shRNAs for ADAT2. shGFP used as a control

value: cell line

value: ADAT2 Knock Down, shRNA 4


title: Fetal lung tissue derived from GW 10.2

value: GW 10


title: SG-159-Rep1

description:
SG-159-cy3 vs SG-118-cy5(2).gpr
Biological replicate 1

value: tissue

value: development seeds


title: SG-150-Rep1

description:
SG-150-cy3 vs SG-208-cy5(2).gpr
Biological replicate 1


title: SG-137-Rep1

description:
SG-137-cy3 vs SG-54-cy5(2).gpr
Biological replicate 1


title: Fetal lung tissue derived from GW 10.1


title: ADAT2 Knock Down, shRNA 1, Rep3

description: Small RNA sequencing

value: ADAT2 Knock Down, shRNA 1


title: SG-146-Rep1

description:
SG-146-cy3 vs SG-135-cy5(1).gpr
Biological replicate 1


title: ADAT2 Knock Down, shRNA 4, Rep2

description: Small RNA sequencing


title: ADAT2 Knock Down, shRNA 4, Rep1

description: Small RNA sequencing


title: ADAT2 Knock Down, shRNA 1, Rep2

description: Small RNA sequencing


title: R1015-5-siG4-2

city: Houston

first: Carl

last: Gay

state: TX

address: 1515 Holcombe Blvd

department: Thoracic-Head & Neck Med Onc

institute: The University of Texas MD Anderson Cancer Center

data_processing:
Base calling using bcl2fastq v2.17 for Novaseq output
Seqeunces were mapped to hg38 reference genome and transcriptome using RSEM v1.3.3
Assembly: hg38
Supplementary files format and content: tab delimited text file for TPM (tag permillion reads) values for all samples

growth_protocol: H520 cells were grown in RPMI 1640 medium supplemented with 10% FBS and antibiotics.

extract_protocol:
Total cell RNA was extracted using RNeasy mini Kit (Qiagen).
Library was preparated using the Eppendorf EPMotion 5075 and Agilent Bravo Liquid Handlers.

treatment_protocol: Cells were transfected with siRNAs against GOLIM4 or control siRNA using jetPRIME transfection reagent.

value: Squamous lung cancer cell line

value: GOLIM4 siRNA knockdown


title: Static, scRNA-seq

city: Kyoto

first: Kazuo

last: Takayama

state: Kyoto

address: Shogoin Kawaharacho 53, Sakyo-ku

department: Center for iPS Cell Research and Application

country: Japan

institute: Kyoto University

data_processing:
The 10X Genomics Cell Ranger pipeline (version 7.1.0) was used to perform sample demultiplexing, alignment to the hg38 human reference genome, barcode/UMI processing, and gene counting for each cell.
Assembly: hg38
Supplementary files format and content: hdf5 files contain lists of gene names, cell barcodes and UMI counts for each sample.

source_name: Micro-small intestinal tissue

extract_protocol:
Micro-small intestine systems were trypsinized to dissociate into single cells. These cells were mixed and the cell concentration was adjusted to 1,000 cells/μL and applied to a Chromium 10X Single Cell System (10X Genomics) to generate the Gel-Bead in Emulsions (GEMs).
cDNA libraries were prepared using a Chromium Next GEM Single Cell 3’ GEM, Library & Gel Bead Kit v3.1 (10X Genomics) following the manufacturer's instructions.

value: Micro-small intestinal tissue

tag: originating cell line

value: human iPS cells

tag: condition

value: Static


title: Flow, scRNA-seq

tag: tissue

value: Flow


title: ADAT2 Knock Down, shRNA 1, Rep1

description: Small RNA sequencing


title: Fetal lung tissue derived from GW 11.1

value: Fetal lung tissue

value: GW 11


title: SG-130-Rep1

description:
SG-130-cy3 vs SG-25 cy5(1).gpr
Biological replicate 1

tag: sample type


title: Control, Rep2

description: Small RNA sequencing

tag: genotype

value: Control


title: R1015-6-siG4-3

tag: cell type


title: Control, Rep1

description: Small RNA sequencing


title: Control, Rep3

description: Small RNA sequencing


title: R1015-4-siG4-1


title: R1015-2-siCTL-2

value: Control siRNA


title: cAMP + R62D 3

city: Ube

first: Yuichiro

last: Shirafuta

state: Yamaguchi

address: 1-1-1, minami-kogushi

institute: Yamaguchi university

data_processing:
Raw reads were first filtered to get rid of low quality reads using Trimmomatic. Reads of less than 20 bases and unpaired reads were also removed.
Removal of adaptor, polyA, polyT and polyG sequences were performed using Trim Galore! Version 0.6.6.
For mapping of reads, trimmed reads were first aligned to the human genome hg19 using STAR version 2.7.3a.
Gene expression values were calculated as “fragments per kilobase of exon unit per million mapped reads” (FPKM).
Gene counts in triplicate were used to identify differentially expressed genes (DEGs, fulfilling the following criteria: padj<0.05) using DESeq2 version 1.20.0
Assembly: hg19
Supplementary files format and content: gene expression values

source_name: endometrial stromal cells

growth_protocol: Cells were seeded at 3 x 104 cells in 12-well plates. The following day, virus concentrate (mCherry or R62D) was added to the medium with 8 μg/ml final concentration of Polybrene. Then, cells were cultured with DMEM with 10%FBS until 80% confluency.

extract_protocol:
Total RNA was isolated from the cultured cells with NucleoSpin® RNA (TaKaRa).
Complementary DNA (cDNA) libraries for Illumina sequencing were generated with NEBNext Ultra II RNA library Prep kit (NEB) and NEBNextplex Oligos for Illumina.

treatment_protocol: To induce decidualization, cells were incubated with treatment medium (Phenol Red-free DMEM supplemented with glutamine, antibiotics and 2% dextran-coated charcoal-stripped FBS) containing cAMP (0.5 mM) for 4 days.

value: endometrial stromal cells

tag: transfection

value: overexpression of R62D (actin mutant ActinR62D).

tag: agent

value: cAMP treatment


title: SG-122-Rep1

description:
SG-122-cy3 vs SG-285-cy5(2).gpr
Biological replicate 1


title: S4, scBCR

city: Epalinges

first: Mathilde

last: Foglierini-Perez

address: Chemin de Boveresses 155

country: Switzerland

institute: CHUV

description: Singleron

data_processing:
celescope flv_CR pipeline (https://github.com/singleron-RD/CeleScope)
Assembly: hg38
Supplementary files format and content: VDJ: tsv table of cell annotations (AIRR format)

source_name: PBMC

extract_protocol:
Peripheral blood mononuclear cells (PBMC) of different donors were isolated by the standard density-gradient centrifugation and cryopreserved until the day of use.  The CD19+ cell fraction was enriched from PBMCs by positive selection with CD19 magnetic microbeads (Miltenyi Biotech) and subsequently stained on ice for 20 min with the following fluorochrome-labeled mouse monoclonal antibodies: CD20 (clone 2H7, BioLegend) and APC mouse anti-human IgG (Clone: G18-145 BD Pharmingen). Cells were sorted to over 99% purity on a FACSAria III (BD). FACS-sorted cells were collected in 6 μl FCS in Eppendorf tubes that were pre-coated overnight with 2% BSA.
Single-cell suspensions with 1 × 105 cells/mL in PBS were prepared. Then, the suspensions were loaded onto microfluidic devices, and scRNA-seq libraries were constructed according to the Singleron GEXSCOPE protocol in the GEXSCOPE Single-Cell RNA Library Kit (Singleron Biotechnologies) (Dura B. et al. scFTD-seq: freeze-thaw lysis based, portable approach toward highly distributed single-cell 3′ mRNA profiling. Nucleic Acids Res. 2019).  Individual libraries were diluted to 4 nM and pooled for sequencing. Pools were sequenced on an Illumina HiSeq X with 150 bp paired-end reads

value: PBMC

value: memory B cell

tag: antibodies/tag

value: VDJ


title: R1015-1-siCTL-1


title: SG-135-Rep1

description:
SG-135-cy3 vs SG-146-cy5 (2).gpr
Biological replicate 1

value: tissue

value: development seeds


title: SG-121-Rep1

description:
SG-121-cy3 vs SG-303-cy5(2).gpr
Biological replicate 1


title: cAMP + R62D 2


title: R1015-3-siCTL-3

value: Squamous lung cancer cell line


title: cAMP + R62D 1


title: SG-103-Rep1

description:
SG-103-cy3 vs SG-276-cy5(1).gpr
Biological replicate 1


title: SG-132-Rep1

description:
SG-132-cy3 vs SG-178-cy5(2).gpr
Biological replicate 1


title: SG-118-Rep1

description:
SG-118-cy3 vs SG-159-cy5 (1).gpr
Biological replicate 1


title: SG-120-Rep1

description:
SG-120-cy3 vs SG-204 cy5 (1).gpr
Biological replicate 1


title: SG-115-Rep1

description:
SG-115-cy3 vs SG-75-cy5(1).gpr
Biological replicate 1


title: G3, BCRseq

description: 10X genomics

data_processing:
BCL-files were demultiplexed into samples using bcl2fastq 2.20
scRNA: The barcoded processing and gene counting were made using the Cell Ranger v6.0.0 (v6 for D1, D2 and G3, v7 for G4) software with method count
VDJ: The barcoded processing, V(D)J sequences and annotations were made using the Cell Ranger v6.0.0 (v6 for D1, D2 and G3, v7 for G4) software with method vdj
Assembly: VDJ: cellranger-vdj-GRCh38-alts-ensembl-5.0.0 for cellranger-6 and cellranger-vdj-GRCh38-alts-ensembl-7.0.0 for cellranger-7
Assembly: hg38
Supplementary files format and content: VDJ: tsv table of cell annotations (AIRR format)

extract_protocol:
Single cell suspension was performed according to Chromium Next GEM Single cell V(D)J Reagent kits v2. The positive fractions of memory B cells were collected in 6ul of FCS containing eppendorf tubes that were pre-coated overnight with 2 percent BSA.
The 5’scRNA-seq libraries were generated using Chromium Next GEM Single Cell V(D)J Reagent Kit v2 (10X Genomics) according to the manufacturer’s protocol. Paired heavy and light chain BCR libraries were prepared from the sorted B cell populations. All the steps were followed as per the manufacturer’s instructions in user guide recommended for 10X Genomics kit v2.

value: mRNA

tag: disease state

value: HIV infected


title: G4, BCRseq

description: 10X genomics


title: SG-108-Rep1

description:
SG-108-cy3 vs SG-278-cy5(1).gpr
Biological replicate 1


title: SG-107-Rep1

description:
SG-107-cy3 vs SG-306-cy5(1).gpr
Biological replicate 1


title: cAMP 3

value: overexpression of mCherry (as a mock control)


title: cAMP 2


title: cAMP 1


title: D2, BCRseq

description: 10X genomics


title: B3, scRNA

description: BD Rhapsody

data_processing:
The BD Rhapsody Targeted Analysis Pipeline (v1.11) was used to process the sequencing data (fastq files).
Assembly: BD_Rhapsody_Immune_Response_Panel_Hs.fasta
Supplementary files format and content: Comma-separated values files: count matrices (targeted transcripts) and VDJ annotation

extract_protocol:
Peripheral blood mononuclear cells (PBMC) of different donors were isolated by the standard density-gradient centrifugation and cryopreserved until the day of use.  The CD19+ cell fraction was enriched from PBMCs by positive selection with CD19 magnetic microbeads (Miltenyi Biotech) and subsequently stained on ice for 20 min with the following fluorochrome-labeled mouse monoclonal antibodies: CD20 (clone 2H7, BioLegend) and APC mouse anti-human IgG (Clone: G18-145 BD Pharmingen). Cells were sorted to over 99% purity on a FACSAria III (BD). FACS-sorted cells were collected in 6 μl FCS in Eppendorf tubes that were pre-coated overnight with 2% BSA.
Memory B cells were targeted for single-cell RNA-seq analysis using the BD Rhapsody Single-Cell Analysis System (BD Biosciences; Fan et al., 2015). Briefly, the single-cell suspension was loaded into a BD Rhapsody cartridge with >200,000 microwells, and single-cell capture was achieved by random distribution and gravity precipitation. Next, the bead library was loaded into the microwell cartridge to saturation so that the bead was paired with a cell in a microwell. The cells were lysed in a microwell cartridge to hybridize mRNA molecules onto bar-coded capture oligos on the beads. These beads were then retrieved from the microwell cartridge into a single tube for subsequent cDNA synthesis, exonuclease I digestion, and multiplex-PCR–based library construction. Sequencing was performed on NovaSeq paired-end mode.

value: targeted RNA


title: B3, scBCR

description: BD Rhapsody


title: SG-100-Rep1

description:
SG-100- cy3 vs SG-22- cy5 (2).gpr
Biological replicate 1


title: SG-10-Rep1

description:
SG-10-cy3 vs SG-201-cy5 (1).gpr
Biological replicate 1


title: control 3

value: no treatment


title: PSA-Rep1

description:
PSA-cy3 vs DH-cy5 (3).gpr
Biological replicate 1


title: D1, BCRseq

description: 10X genomics

value: healthy


title: DH-Rep2

description:
DH-cy3 vs PSA-cy5 (2).gpr
Biological replicate 2


title: control 2


title: Ahrr_3

city: Bonn

first: Joachim

last: Schultze

state: NRW

address: Carl-Troll-Strasse 31

department: Genomics and Immunoregulation

country: Germany

institute: LIMES (Life and Medical Sciences Center Genomics and Immunoregulation)

data_processing:
Base calling and de-multipexing using CASAVA version 1.8.2.
The 75 bp single-end reads were trimmed using fastp v0.20.0 and aligned to the murine reference genome mm10 vM32 from GENCODE using STAR v2.7.10b with --quantMode GeneCounts.
Aligned reads sorted by coordinates were indexed using samtools v1.16.1.
Downstream data analysis was performed in R version 4.3.1 mainly using the R package DESeq2 version 1.40.2
Assembly: mm10 vM32
Supplementary files format and content: DESeq2_normalized_annotated_expression.csv: comma-separated files holding normalized and annotated expression values
Supplementary files format and content: raw_expression.csv: comma-separated files holding unnormalized and unfiltered expression values

source_name: Fetal liver

growth_protocol: Fetal liver macrophages were isolated from E13.5 fetuses (WT and AhRR-/-). Cells were cultured and kept in continuous culture for 5 weeks in RPMI (10% FCS, 1% P/S, 1% L-Glut) + 2% GM-CSF, adding medium every 2-4 day. Fianlly, 5x10^6 non-adherent cells were collected in Trizol and used for RNA sequencing.

extract_protocol:
RNA was isolated with Qiazol and miRNeasy micro kit (Qiagen) according to the manufacturer’s protocol.
Library construction was performed according to the manufacturer´s instructions using the Tru-Seq RNA library preparation kit v2. 100 ng of RNA was converted into cDNA libraries
75 bp single-end run was performed on a HiSeq1500

value: macrophages

value: Fetal liver

tag: strain

value: C57BL/6 RCC

tag: mouse

tag: age

value: Ahrr


title: Ahrr_2


title: control 1

value: endometrial stromal cells


title: PSA-Rep2

description:
PSA-cy3 vs DH-cy5 (4).gpr
Biological replicate 2

data_processing: The raw array datasets were extracted with Gene Pix Pro 6.0, and were firstly normalized by the lowess LOWNESS (Yang et al., 2002) method within arrays, followed by the quantile (Bolstad et al., 2003) method between arrays, using the R/Bioconductor software (available at http://www.r-project.org/). R package Limma (Smyth, 2005).

extract_protocol: Total RNA was extracted from the developing seeds using a method modified from that of Oñate-Sánchez and Vicente-Carbajosa (2008) and described in detail by Parkin et al. (2010). Seeds from field grown plants from two trials (2009 and 2010) were harvested for seed quality analysis.


title: AML_93

city: Brisbane

first: Jasmin

last: Straube

state: QLD

address: 300 Herston Rd

country: Australia

institute: QIMR Berghofer

data_processing:
All samples raw reads were mapped and counted with cell ranger version 3.0.2 to the Human genome GRCh38.
Genome_build: GRCh38
Supplementary_files_format_and_content: Cell ranger generated one mtx file and two tsv files for gene ID and cell barcode ID

source_name: Immune cell fraction

extract_protocol:
The mononuclear fractions after Ficoll gradient separation were FACS sorted for CD34-CD45+ fraction and processed using 10x Genomics Single Cell Kit (v2 or v3) according to manufacturer’s recommendations.
Reads were sequenced using 150bp PE reads on the Illumina HiSeq 4000 or NextSeq 500/550.

value: bone marrow

value: Denovo acute myeloid leukemia

tag: gender

value: male


title: RP3

first: Zezhen

last: Liu

state: Guangdong

address: #.1 Kangda Road, Haizhu District

institute: The First Affiliated Hospital of Guangzhou Medical University

data_processing:
scRNA-seq data analysis was performed by NovelBio Co.,Ltd. with NovelBrain Cloud Analysis Platform.
We applied fastq with default parameter filtering the adaptor sequence and removed low quality reads to achieve the clean data
UMI-tools were applied for Single Cell Transcriptome Analysis to identify the cell barcode whitelist. The UMI-based clean data was mapped to human genome (Ensemble version 91) utilizing STAR mapping with customized parameter from UMI-tools standard pipeline to obtain the UMIs counts of each sample.
Cells contained over 200 expressed genes and mitochondria UMI rate below 60% passed the cell quality filtering and mitochondria genes were removed in the expression table. Seurat package (version: 3.1.0, https://satijalab.org/seurat/) was used for cell normalization and harmony was used to correct the batch among samples.
PCA was constructed with top 2000 high variable genes and top 10 principals were used for tSNE construction and UMAP construction. Utilizing graph-based cluster method (resolution = 0.8), we acquired the unsupervised cell cluster result based the PCA top 10 principal and we calculated the marker genes by FindAllMarkers function with wilcox rank sum test algorithm under following criteria:1. logFC > 0.25; 2. pvalue<0.05; 3. min.pct>0.1. In order to identify the cell type detailed, the clusters of same cell type were selected for re-tSNE analysis, graph-based clustering and marker analysis.
Genome_build: GRCh38
Supplementary_files_format_and_content: tab-delimited text files include counts for each cell

source_name: kidney stone

growth_protocol: We obtained 3 plaque from consecutive patients with pure or predominantly calcium oxalate (CaOx) stones who had undergone endoscopic stone removal and 3 normal renal papilla tissues from consecutive patients with kidney cancer who had undergone nephrectomy.

extract_protocol:
Single-cell RNA-seq experiment was performed by experimental personnel in the laboratory of NovelBio Co.,Ltd. The tissues were surgically removed and kept in MACS Tissue Storage Solution (Miltenyi Biotec) until processing. The tissue samples were processed as described below. Briefly, samples were first washed with phosphate-buffered saline (PBS), minced into small pieces (approximately 1mm3) on ice and enzymatically digested with collagenase II (Worthington), collagenase IV (Worthington) and DNase I (Worthington) for 40 min at 37°C, with agitation. After digestion, samples were sieved through a 70µm cell strainer, and centrifuged at 300g for 5 min. After the supernatant was removed, the pelleted cells were suspended in red blood cell lysis buffer (Miltenyi Biotec) to lyse red blood cells. After washing with PBS containing 0.04% BSA, the cell pellets were re-suspended in PBS containing 0.04% BSA and re-filtered through a 35μm cell strainer. Dissociated single cells were then stained for viability assessment using Calcein-AM (Thermo Fisher Scientific) and Draq7 (BD Biosciences). The single-cell suspension was further enriched with a MACS dead cell removal kit (Miltenyi Biotec)
Sequencing libraries were conducted using the BD Rhapsody Single-Cell Analysis System (BD Biosciences), following the manufacture's protocol.

value: renal

value: Randall's plaque


title: RP2


title: AML_69


title: WT_2

value: WT


title: NP3

source_name: normal

value: normal renal papillae


title: Ahrr_1


title: AML_104

value: female


title: RP1


title: WT_3


title: NP2


title: AML_114


title: DH-Rep1

description:
DH-cy3 vs PSA-cy5 (1).gpr
Biological replicate 1

value: tissue

value: development seeds


title: WT_1


title: NP1


title: LMM section (spinal cord, medium)

status: Public on Jun 03 2024

city: St. Petersburg

first: Oscar

middle: E

last: Ospina

state: FL

address: 600 5th Street South

department: Health Informatics

institute: Johns Hopkins All Children's Hospital

description:
sample13_LMM_B1
Fresh frozen Visium

data_processing:
*library strategy: Spatial transcriptomics
Two illumina NextSeq 2000 runs were and accompanying tissue H&E images were processed using the Space Ranger mkfastq pipeline to generate demultiplexed .fastq files for each sample.
Sequences in the .fastq files were aligned to the GRCh38-2020-A human genome to generate gene expression counts using Space Ranger count. The .fastq files for the two runs of each sample were combined at this point, resulting in the gene expression count files (.h5 and MEX). The Space Ranger count pipeline also generated the spot X,Y coordinates (_tissue_positions_list.csv).
Assembly: GRCh38-2020-A
Supplementary files format and content: _raw_feature_bc_matrix.h5: Unfiltered gene expression in HDF5 format
Supplementary files format and content: _raw_barcodes.tsv.gz: Spot IDs (spatial barcodes) accompanying unfiltered MEX gene expression matrix
Supplementary files format and content: _raw_features.tsv.gz: Gene IDs accompanying unfiltered MEX gene expression matrix
Supplementary files format and content: _raw_matrix.mtx.gz: Unfiltered gene expresion matrix in Matrix Market Exchange (MEX) format
Supplementary files format and content: _filtered_feature_bc_matrix.h5: Gene expression in HDF5 format
Supplementary files format and content: _filtered_barcodes.tsv.gz: Spot IDs (spatial barcodes) accompanying MEX gene expression matrix
Supplementary files format and content: _filtered_features.tsv.gz: Gene IDs accompanying MEX gene expression matrix
Supplementary files format and content: _filtered_matrix.mtx.gz: Gene expresion matrix in Matrix Market Exchange (MEX) format
Supplementary files format and content: _tissue positions list.csv: X,Y spatial coordinates of the spots in the Visium array
Supplementary files format and content: _tissue_hires_image.png: High-resolution version of the H&E stained tissue image
Supplementary files format and content: _tissue_lowres_image.png: Low-resolution version of the H&E stained tissue image
Supplementary files format and content: _scalefactors_json.json: File containing pixel to spot scaling factors in json format

source_name: Melanoma leptomeningeal metastasis (LMM)

extract_protocol:
Fresh frozen tissue prepared according the Visium Spatial Gene Expression User Guide using reagents from the Visium Spatial Gene Expression Kit.
Spatial transcriptome sequencing libraries were prepared with Visium Spatail Gene Expression Slides & Reagent kit according to manufacturer's construction.

tag: patient id

value: B


title: Melanoma metastasis section (ribcage)

description:
sample16_LMM_A4
Fresh frozen Visium

source_name: Melanoma metastasis

value: A

value: Melanoma metastasis


title: LMM section (left parietal region)

description:
sample12_LMM_B4
Fresh frozen Visium

value: Melanoma leptomeningeal metastasis (LMM)


title: Melanoma metastasis section (right upper chest wall)

description:
sample15_LMM_B6
Fresh frozen Visium


title: Melanoma metastasis section (cecal nodule)

description:
sample14_LMM_B5
Fresh frozen Visium


title: VA-free 2A

city: Ann Arbor

first: Carlos

last: Aguilar

state: MI

address: 2800 Plymouth Rd

department: Biomedical Engineering

institute: University of Michigan

data_processing:
Fastq files were checked for quality using FastQC
Fastq files were aligned to the GRCm38/mm10 reference transcriptome using Kallisto version 0.46.2 with the following parameters:  -b 100 --single -l 76 -s 20 -t 8
Assembly: mm10
Supplementary files format and content: .tsv files containing estimated counts and tpm values for each sample

source_name: skeletal muscle

extract_protocol:
RNA was isolated using the Trizol lysis reagent, followed by the Qiagen Rneasy micro kit.
Takara Bio SMART-Seq v4 Ultra Low Input RNA Kit for Sequencing was used for cDNA synthesis. Illumina library prep was performed with theNexteraXT DNA Library Preparation Kit andNexteraXT Index Kit, using an input of 500pgof full-length cDNA amplicons per sample

value: skeletal muscle

value: muscle stem cells

tag: diet

value: Vitamin A-free

tag: biological replicate

tag: technical replicate


title: CTRL 2A

value: Control


title: LMM section (spinal cord, posterior)

description:
sample2_LMM_B2
Fresh frozen Visium


title: LMM section (right temporal region)

description:
sample7_LMM_A1
Fresh frozen Visium


title: CTRL 2B


title: HK_Flox_Control_2

city: Austin

first: Husniye

last: Kantarci

address: NHB Building,, 100 E 24TH ST, Room 4.358

department: Neuroscience

institute: UT Austin

description: 10 X genomics

data_processing:
Initial gene expression tables for barcodes were generated using CellRanger version 5.0.1 (10X genomics) using default parameters. Gene expression tables were than imported to Phyton and analyzed using Scanpy using scanpy tutorials.
Assembly: mm10-2020-A
Supplementary files format and content: tab seperated matrix files, h5 files including raw barcodes, features and data

source_name: Dorsal root ganglia

extract_protocol:
DRG ganglia from all axial levels were dissected from Ptges3-Flox or Ptges3-cKO mice at P4 postnatal stage and placed in Neurobasal medium supplemented with 12.5 mM D-glucose and 100 U/mL +penicillin and 0.1 mg/mL streptomycin [GibcoTM, 15140122]). Next, dissected DRG ganglia were placed in a collagenase/dispase cocktail composed of 1 mg/mL collagenase (Roche, 10103578001), 2.9 mg/mL dispase (Roche, 101103578001), 40 U of papain (Worthington LS003126), 100  µl DNAse (0.02 mg/mL) in 1X HEPES buffered saline solution (Sigma-Aldrich, 51558) and placed in 37 C for 20 minutes. DRG ganglia were dissociated in Lo-ovomucoid inhibitor solution in PBS. Cells were counter-stained with trypan blue counted under a hemocytometer to assess cell density and health (cell viability was measured as greater than 92%), and subsequently resuspended in Neurobasal medium supplemented with 12.5 mM D-glucose and 100 U/mL +penicillin and 0.1 mg/mL streptomycin [GibcoTM, 15140122]) as 1000 cells per  µl.   Actinomycin-D (Sigma-Aldrich, A9415) was added to inhibit new transcription during preparation steps: 30 µM during dissections, 15 µM during digestion, 3 µM during dissociation, and 0.3 µM in resuspension solutions.
Libraries were prepared using the Single Cell 3ʹ v.3.1 according to the manufacturer’s protocol (10x Genomics), targeting 10,000 cells per sample. 12 cycles of cDNA amplification were done for all samples. Individual libraries were quality checked on an Agilent 4200 Tapestation 827 using D5000 screen tape. Next, KAPA library quantification kit (#KK4923) was used for qPCR on a BioRad CFX96 RT PCR thermal cycler.

value: Dorsal root ganglia

value: Dorsal root ganglion cells

value: Ptges3 flox/flox


title: LMM section (left temporal region)

description:
sample8_LMM_B3
Fresh frozen Visium


title: Melanoma metastasis section (sternum)

description:
sample4_LMM_A5
Fresh frozen Visium


title: VA-free 3B


title: Pooled CSP Library

city: Seattle

first: Albert

middle: C

last: Yeh

state: WA

address: 1100 Fairview Ave N.

department: Translational Sciences and Therapeutics

institute: Fred Hutchinson Cancer Center

description: 10x Genomics

data_processing:
Reads were demultiplexed and processed using cellranger-arc v1.0.1 aligning reads to GENCODE vM23/Ensembl98.
Cells meeting the following criteria were retained for downstream analysis: 3.25 < log10(nCount_RNA) < 4.25 & percent.mt < 5%. Dimensionality reduction using principal components analysis (PCA) was performed and clusters were identified using the standard Seurat workflow. We used the CLR method to normalize HTO data and used HTODemux to ID experimental groups. Two clusters enriched in hemoglobin and myeloid genes were removed, as well as one cluster expressing Trbv29 (non-Marilyn, non-CBir1 TCR), prior to generating the final embedding for analysis.
Assembly: vM23/Ensembl98
Supplementary files format and content: Comma separate values (VDJ), matrix files (GEX), and h5 file (feature)

source_name: Spleen

extract_protocol:
Spleens were harvested at D+6 post-transplant (three mice pooled for group 1, four for group 2, and three for group 3). T cells from each mouse were incubated with APC-labeled CBir1 tetramer (NIH, above), washed, and labeled with TotalSeq C hashtag antibodies (C0301-C0310) along with TotalSeq C0987 (anti-AP). Following staining, T cells were sort-purified (Marilyn: CD45.1neg/CD45.2+/CD90.1+/CD90.2neg/CD4+/CD8neg; CBir1: CD45.1neg /CD45.2+/CD90.1neg/CD90.2+/CD4+/CD8neg) at a 4:1 ratio for cell capture.
Library construction according to the 10x Genomics Chromium User Guide CG000424 (CG000424_ChromiumNextGEMSingleCell5_HTv2_CellSurfaceProtein_UserGuide_RevD.pdf), using Chromium Next GEM Single Cell 5’Kit (v2), Chromium Single Cell Mouse TCR Amplification Kit (v2), and Chromium Next GEM Chip K Single Cell Kit.

treatment_protocol: Naïve CD45.1+ C57BL/6 mice from Taconic Biosciences were transplanted with 5x106 bone marrow cells derived from CD45.1+ C57BL/6 mice and with either 5x105 CD45.2+/CD90.1+ Marilyn Tg CD4 T cells (group 1), 1x106 CD45.2+/CD90.2+ CBir1 Tg CD4 T cells (group 3), or both Tg T cells (group 2). Spleens were harvested at D+6 post-transplant (three mice pooled for group 1, four for group 2, and three for group 3).

value: Spleen

value: Donor T cells

tag: donor sex

tag: treatment

value: Donor T cells included Marilyn T +/- CBir1 T cells. Spleen harvested at day 6 takedown of transplant.

tag: library type

value: CSP/HTO


title: HK_cKO_2

description: 10 X genomics

tag: tissue

tag: genotype

value: Dhh CRE+, Ptges3 flox/flox


title: CTRL 1A

tag: cell type


title: MDA231 resistant -3

city: HOUGHTON

first: TAHIYAT

last: ALOTHAIM

address: DOW 514,1400 Townsend Dr

department: Department of Biological Sciences

institute: Michigan Technological University

description: Clariom 24-plate array

hyb_protocol: standard Affymetrix protocol

scan_protocol: standard Affymetrix protocol

data_processing: The gene expression pattern of the RNA samples were interrogated with Affymetrix U133A genechips and normalized by the RMA (Robust Multi-Array) algorithm

label: biotin

source_name: MDA231  resistant cells challenged with 5µM Erastin

label_protocol: Clariom 24-plate array

growth_protocol: Cells were seeded for 72h before RNA extraction

extract_protocol: Samples were collected on ice and RNA was isolated with QIAGEN’s RNeasy Mini Kit

treatment_protocol: Cells grew in the control full DMEM media supplemet with 10% FBS and Penicillin/ Stertomycin

tag: tissue source

value: Breast tissue of 51-year-old, White, female adenocarcionma patient

tag: tissue type

value: primary tumor

tag: cell line source


title: MDA231 resistant -2

description: Clariom 24-plate array

value: resistant cells challenged with 5µM Erastin


title: VA-free 3A

value: A


title: VA-free 1B

value: B


title: GS243_DMSO

city: Los Angeles

first: Thomas

middle: Jasper

last: Lai

state: CA

address: Gonda Room 1554 695 Charles E. Young Dr.

department: Neurosurgery

institute: University of California; Los Angeles

description: 10x Genomics single cell barcoded mRNA from CD45+ fraction

data_processing:
The reads are first mapped to custom GRCh38 omitting gene locus CTAG1A using cellranger software from 10x Genomics
Single-cell, gene-level raw read counts are read from cellranger output and analyzed using Seurat 4.2.0
Assembly: GRCh38
Supplementary files format and content: Tab separated values files and matrix files

extract_protocol:
Dissociated gliomasphere single cells were processed using Chromium Single Cell GEM, Library & Gel Bead Kit through the Chromium controller from 10x Genomics.
The resulting single cell barcoded mRNA were reverse transcribed and cleaned as per 10x Genomic's protocol.
10x Genomics single cell RNA-Seq

tag: cell line

value: primary patient-derived gliomasphere

value: WT

value: vehicle


title: GS025_DAC

value: 0.5 uM Decitabine


title: MDA231 sensitive-3

description: Clariom 24-plate array

source_name: MDA231 parental cell

value: parental cells


title: MDA231 resistant -1

description: Clariom 24-plate array


title: CTRL 1B

value: skeletal muscle

value: muscle stem cells

value: Control


title: Pooled V(D)J Library

description: 10x Genomics

value: Spleen

tag: strain

value: Donor T cells

value: female

value: VDJ


title: MDA231 sensitive-2

description: Clariom 24-plate array

value: Breast tissue of 51-year-old, White, female adenocarcionma patient


title: Pooled 5'GEX Library

description: 10x Genomics

value: Donor T cells included Marilyn T +/- CBir1 T cells. Spleen harvested at day 6 takedown of transplant.


title: MDA231 sensitive-1

description: Clariom 24-plate array

value: primary tumor


title: U251.DAC.4d.3

data_processing:
Reads were mapped to the Genome Reference Consortium Human Build 38 (GRCh38) reference genome using HISAT2
PCR duplicates were removed with RmDup in Picard
The gene level counts are generated by HTSeq-count
Assembly: GRCh38
Supplementary files format and content: combined matrix containing CPM

extract_protocol:
RNA was isolated using Zymo Research Quick DNA/RNA Miniprep Kit according to manufacturer’s protocol
stranded mRNA poly-A

value: immortalized Glioblastoma Cell Line

value: 1.0uM Decitabine

tag: time

value: 4 day


title: GS351.DAC

value: primary patient-derived gliomasphere

value: WT

value: 0.5uM Decitabine

value: 12 day


title: GS243_DAC

value: 0.5 uM Decitabine


title: GS277.DAC


title: GS351.DMSO

value: vehicle


title: GS243.DMSO.1


title: U251.DMSO.2


title: GS277.DMSO


title: U251.DAC.4d.1


title: GS025_DMSO


title: GS243.DMSO.2


title: GS081.DMSO


title: GS243.DAC.1


title: SG-18-Rep1

city: Saskatoom

first: wentao

last: zhang

address: 110 Gymnasium Pl

institute: NRC-Canada

description:
SG-18-cy3 VS SZG-232-cy5 (1).gpr
Biological replicate 1

source_name: Seeds at 21 DAF

tag: sample type

value: tissue

value: development seeds


title: U251.DAC.4d.2


title: GS025.DMSO.2


title: GS025.DAC.2


title: U251.DAC.2d

value: 2 day


title: GS025.DAC.1


title: GS081.DAC


title: embryo, Chiron, rep3

city: Waltham

first: Yerbol

last: Kurmangaliyev

state: MA

address: 415 South Street, MS 029

department: Biology

institute: Brandeis University

data_processing:
RNA-Seq reads were aligned using STAR aligner (2.5.2b).
Read counts were obtained using STAR and normalized using edgeR.
The reference genome and gene annotations of Xenopus laevis were downloaded from Xenbase (xenbase.org, v10.1).
Assembly: Xenopus_laevis_v10.1
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample

organism: Xenopus laevis

source_name: embryo

extract_protocol:
Total RNA was isolated with the RNAeasy Plus kit (QIAGEN) from 3 Xenopus embryos of each replicate.
Strand-specific and barcode-indexed RNA-seq libraries were generated from 60 ng total RNA each after poly-A enrichment using the Kapa mRNA-seq Hyper kit (Kapa Biosystems, Cape Town, South Africa) following the manufacturer's instructions.

value: embryo

tag: Stage

value: stage 9.5 (early gastrula)

value: Chiron (CHIR 99021)


title: embryo, BIO, rep3

value: BIO (6-bromoindirubin-3'-oxime)


title: embryo, Chiron, rep1


title: embryo, BIO, rep1


title: embryo, BIO, rep2


title: embryo, Genistein, rep2

value: Genistein


title: embryo, Genistein, rep3


title: embryo, Control, rep2

value: Control


title: GS025.DMSO.1


title: embryo, Genistein, rep1


title: embryo, Control, rep1


title: GS243.DAC.2


title: primary mouse oligodendroglia Sox2Sox3_ctrl, 4d diff, biological replicate 1

city: Erlangen

first: Michael

last: Wegner

state: Bavaria

address: Fahrstr. 17

department: Institut of Biochemistry

data_processing:
RNA samples were quantified using Qubit 4.0 Fluorometer (Life Technologies, Carlsbad, CA, USA) and RNA integrity was checked with RNA Kit on Agilent 5300 Fragment Analyzer (Agilent Technologies, Palo Alto, CA, USA).
RNA sequencing libraries were prepared using the TruSeq Stranded mRNA Kit for Illumina following manufacturer’s instructions (NEB, Ipswich, MA, USA)
Sequencing libraries were validated using NGS Kit on the Agilent 5300 Fragment Analyzer (Agilent Technologies, Palo Alto, CA, USA), and quantified by using Qubit 4.0 Fluorometer (Invitrogen, Carlsbad, CA).
The sequencing libraries were multiplexed and loaded on the flow cell on the Illumina HiSeq2500 instrument according to manufacturer’s instructions. The samples were sequenced using a 2x100 bp single-end configuration.
After investigating the quality of the raw data, sequence reads were trimmed to remove possible adapter sequences and nucleotides with poor quality using cutadapt v1.18. The trimmed reads were mapped to the Mus musculus reference genome available on ENSEMBL using the STAR aligner v.2.6.1c.
Unique gene hit counts were calculated by using feature Counts from the Subread package v.1.6.1. Only unique reads that fell within exon regions were counted. To reduce batch effects RuvSeq
DESeq2 was used for differential gene expression analysis.
Assembly: GRCm38
Supplementary files format and content: tab-delimited text files containing counts and DESeq results

source_name: brain

extract_protocol:
Total RNA was extracted using the RNeasy Mini Kit according to QIAGEN protocol. 1µg of total RNA was used for the construction of sequencing libraries.
RNA sequencing libraries for RNA-Seq were prepared using the TruSeq Stranded mRNA Kit for Illumina following manufacturer’s instructions (NEB, Ipswich, MA, USA).

treatment_protocol: Primary mouse OPC were treated with Tat-Cre to induce recombination of floxed alleles and kept under differentiating conditions for four consecutive days.

value: brain

value: primary mouse oligodendroglia derived from brain

value: 4d differentation


title: primary mouse oligodendroglia Sox2Sox3_dko, 4d diff, biological replicate 1


title: M01-20522_3M_Liver_iPCRtag2

city: Cambridge

first: Laura

last: Biggins

address: Babraham Research Campus

department: Bioinformatics

country: United Kingdom

institute: The Babraham Institute

data_processing:
RRBS and WGBS datasets were processed as described previously (RRBS: Stubbs et al., 2017; WGBS: von Meyenn, 2022), aligning reads to the bisulfite converted GRCm38 mouse genome using Bismark v0.22.3 (Krueger and Andrews, 2011).
Assembly: GRCm38
Supplementary files format and content: bismark.cov.gz files are tab separated and contain DNA methylation data with the following columns: chromosome, start, end, methylation, methylated reads, nonmethylated reads.

source_name: Liver

extract_protocol:
Genomic DNA was isolated from ~10 mg frozen tissue using the DNeasy Blood & Tissue Kit (Qiagen)
RRBS libraries were prepared from isolated DNA following published protocols (Stubbs et al 2017). Briefly, RRBS libraries were prepared by MspI digestion of 100–500 ng genomic DNA, followed by end-repair and T-tailing using Klenow Exo- (Fermentas). Adapter ligation was performed overnight (in-house adapters) using T4 DNA Ligase (NEB), followed by a clean-up step using AMPure XP beads (Agencourt, 0.9×). Subsequently, libraries were bisulfite-treated according to the manufacturer’s instructions (Sigma Imprint Kit; 2 step protocol) and purified using an automated liquid handling robotic system (Agilent Bravo). The libraries were amplified using KAPA HiFi Uracil HotStart DNA Polymerase (KAPA Biosystems), indexing the samples with individual primers. All amplified libraries were purified (AMPure XP beads, 0.8×) and assessed for quality and quantity using High-Sensitivity DNA chips on the Agilent Bioanalyzer.

value: Liver

value: C57BL/6 J

tag: age

value: wildtype


title: M01-20525_3M_Liver_iPCRtag4


title: primary mouse oligodendroglia Sox2Sox3_dko, 4d diff, biological replicate 2


title: M01-20527_3M_Liver_iPCRtag6


title: breast tumor tissue.Intraperitoneal injection of PD-1 inhibitor

city: changchun

first: xu

last: xiaoru

address: No1035.Boshuo Street,Jingyue Economic Development District

institute: Changchun University of Chinese Medicine

data_processing:
CLC Genomics Workbench v11.0.1
Sequence reads were trimmed for adaptor sequence/low-quality sequence using CLC genomic benchwork (parameter-Quality limit:0.05)
Trimmed sequence reads were mapped to GRCm39/mm39 using CLC genomic benchwork (parameters-mismath cost:2insertion cost:3 deletion cost:3 length fraction:0.8 similarity fraction:0.8)
Read count extraction and normalization were performed using CLC genomic benchwork
Assembly: mm39
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample

source_name: breast tumor tissue

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen).1.3 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using SMARTER mRNA-Seq Library Prep Kit following manufacturer's protocols.

value: breast tumor tissue


title: breast tumor tissue.Intraperitoneal injection of PD-1 inhibitor+acupuncture


title: embryo, Control, rep3


title: embryo, Chiron, rep2


title: primary mouse oligodendroglia Sox2Sox3_ctrl, 4d diff, biological replicate 2


title: M01-20525_3M_Cortex_iPCRtag28

source_name: Cortex

value: Cortex


title: M01-20527_3M_Heart_iPCRtag22

source_name: Heart

value: Heart


title: M00018360_9M_B_cells_plate1_pool8_iPCRtag61


title: M01-20522_3M_Lung_iPCRtag10

source_name: Lung

value: Lung


title: U251.DMSO.1

value: immortalized Glioblastoma Cell Line

value: WT

value: vehicle

value: 4 day


title: M00018740_6M_Intestinal_Stem_Cells_plate1_pool8_iPCRtag16


title: M00018740_6M_B_cells_plate1_pool8_iPCRtag11


title: M01-20525_3M_Intestinal_Stem_Cells_plate1_pool8_iPCRtag8


title: M00018359_9M_Cerebellum_plate1_pool8_iPCRtag22

source_name: Cerebellum

value: Cerebellum


title: M05-20526_3M_Cerebellum_plate1_pool8_iPCRtag48


title: M00018752_6M_Cerebellum_plate1_pool7_iPCRtag56


title: M01-20522_3M_Cortex_iPCRtag26


title: M00017995_15M_Intestinal_Stem_Cells_plate1_pool8_iPCRtag32


title: M00018740_6M_CD8_T_Cells_plate1_pool8_iPCRtag13


title: M00018011_15M_Testes_plate1_pool8_iPCRtag66

source_name: Testes

value: Testes


title: M00017619_24M_B_cells_plate1_pool6_iPCRtag35


title: M00018752_6M_Kidney_plate1_pool7_iPCRtag87

source_name: Kidney

value: Kidney


title: M00018011_15M_Hind_Muscle_plate1_pool6_iPCRtag26


title: M00018360_9M_CD4_T_Cells_plate1_pool8_iPCRtag62


title: M00018359_9M_Testes_plate1_pool6_iPCRtag58


title: M00017619_24M_Cerebellum_plate1_pool6_iPCRtag38


title: M00018011_15M_B_cells_plate1_pool7_iPCRtag27


title: M00018360_9M_CD8_T_Cells_plate1_pool7_iPCRtag63


title: M05-20526_3M_Kidney_plate1_pool7_iPCRtag86


title: M00018359_9M_Intestinal_Stem_Cells_plate1_pool7_iPCRtag24


title: M00018359_9M_CD8_T_Cells_plate1_pool8_iPCRtag21


title: M05-20526_3M_CD4_T_Cells_plate1_pool6_iPCRtag46


title: M00017619_24M_CD8_T_Cells_plate1_pool6_iPCRtag37


title: M00018359_9M_Kidney_plate1_pool7_iPCRtag57


title: M00018752_6M_CD4_T_Cells_plate1_pool7_iPCRtag54


title: M00018359_9M_CD4_T_Cells_plate1_pool6_iPCRtag20


title: M00018740_6M_Skin_plate1_pool7_iPCRtag9

source_name: Skin

value: Skin


title: M00018359_9M_Hind_Muscle_plate1_pool5_iPCRtag18


title: M04-20526_3M_Testes_plate1_pool6_iPCRtag42


title: M05-20526_3M_CD8_T_Cells_plate1_pool7_iPCRtag47


title: M00018360_9M_Intestinal_Stem_Cells_plate1_pool6_iPCRtag91


title: M00018360_9M_Kidney_plate1_pool7_iPCRtag88


title: M00017619_24M_Intestinal_Stem_Cells_plate1_pool7_iPCRtag40


title: M00018740_6M_Cerebellum_plate1_pool5_iPCRtag14


title: M00018752_6M_CD8_T_Cells_plate1_pool5_iPCRtag55


title: M04-20526_3M_Kidney_plate1_pool5_iPCRtag41


title: M00018011_15M_Cerebellum_plate1_pool5_iPCRtag30


title: M04-20526_3M_B_cells_plate1_pool5_iPCRtag3


title: M00018740_6M_Testes_plate1_pool5_iPCRtag50


title: M00017620_24M_Skin_plate1_pool6_iPCRtag75


title: M00018740_6M_Hind_Muscle_plate1_pool5_iPCRtag10


title: M00017619_24M_CD4_T_Cells_plate1_pool6_iPCRtag36


title: M00018360_9M_Cerebellum_plate1_pool6_iPCRtag64


title: M00017619_24M_Hind_Muscle_plate1_pool5_iPCRtag34


title: M04-20526_3M_Cerebellum_plate1_pool5_iPCRtag6


title: M00018359_9M_B_cells_plate1_pool4_iPCRtag19


title: M00017996_15M_Intestinal_Stem_Cells_plate1_pool4_iPCRtag92


title: M00017912_15M_B_cells_plate1_pool4_iPCRtag69


title: M00017619_24M_Testes_plate1_pool4_iPCRtag74


title: M00018752_6M_B_cells_plate1_pool4_iPCRtag53


title: M00018359_9M_Skin_plate1_pool3_iPCRtag17


title: M00017620_24M_B_cells_plate1_pool4_iPCRtag77


title: M00018752_6M_Lung_Macrophages_plate1_pool4_iPCRtag82


title: M00017620_24M_Intestinal_Stem_Cells_plate1_pool4_iPCRtag93


title: M05-20526_3M_Skin_plate1_pool4_iPCRtag43


title: M00018752_6M_Skin_plate1_pool4_iPCRtag51


title: M00018740_6M_Kidney_plate1_pool4_iPCRtag49


title: M00018011_15M_Skin_plate1_pool3_iPCRtag25


title: M00017619_24M_Skin_plate1_pool3_iPCRtag33


title: M00018011_15M_Lung_Macrophages_plate1_pool3_iPCRtag31


title: M00017620_24M_CD4_T_Cells_plate1_pool3_iPCRtag78


title: M00017912_15M_Skin_plate1_pool3_iPCRtag67


title: M00018360_9M_Skin_plate1_pool3_iPCRtag59


title: M00017620_24M_Lung_Macrophages_plate1_pool3_iPCRtag85


title: M00017912_15M_Cerebellum_plate1_pool3_iPCRtag72


title: M00018360_9M_Lung_Macrophages_plate1_pool5_iPCRtag83


title: M00018740_6M_Lung_Macrophages_plate1_pool3_iPCRtag15


title: M00018011_15M_Kidney_plate1_pool2_iPCRtag65


title: M00017912_15M_Hind_Muscle_plate1_pool2_iPCRtag68


title: M05-20526_3M_Hind_Muscle_plate1_pool2_iPCRtag44


title: M04-20526_3M_Lung_Macrophages_plate1_pool3_iPCRtag7


title: M00018359_9M_Lung_Macrophages_plate1_pool4_iPCRtag23


title: M04-20526_3M_CD8_T_Cells_plate1_pool3_iPCRtag5


title: M00018740_6M_CD4_T_Cells_plate1_pool5_iPCRtag12


title: M00018011_15M_CD4_T_Cells_plate1_pool2_iPCRtag28


title: M00017620_24M_CD8_T_Cells_plate1_pool2_iPCRtag79


title: M00017620_24M_Kidney_plate1_pool2_iPCRtag95


title: M00018011_15M_CD8_T_Cells_plate1_pool1_iPCRtag29


title: M00017912_15M_CD4_T_Cells_plate1_pool2_iPCRtag70


title: M00017620_24M_Cerebellum_plate1_pool2_iPCRtag80


title: M05-20526_3M_B_cells_plate1_pool2_iPCRtag45


title: M00017620_24M_Hind_Muscle_plate1_pool2_iPCRtag76


title: M00017619_24M_Lung_Macrophages_plate1_pool1_iPCRtag39


title: RAW 3hr

first: Apeksha

last: Singh

address: 570 Boyer Hall

institute: University of California, Los Angeles

description:
col 16
RAW-3-2

data_processing:
After adapter trimming with cutadapt, sequences were preprocessed with PRINSEQ using the “dust” method to filter low complexity sequences with the maximum allowed score set to 7 and sequences with more than 10% ambiguous bases were removed.  Single-end reads were mapped to reference mouse genome (mm10) using STAR with the following options: --outFilterMultimapNmax 20 --alignSJoverhangMin 8 --alignSJDBoverhangMin 1 --outFilterMismatchNmax 999 --outFilterMismatchNoverLmax 0.04 --alignIntronMin 20 --alignIntronMax 1000000 --alignMatesGapMax 1000000 --seedSearchStartLmax 30. Only primary mapped reads with alignment score (MAPQ)>30 were then selected by Samtools.  Ribosomal RNA was filtered out using the intersect function in bedtools with a minimal overlap fraction of 0.1 and finally reads mapped to the Y chromosome or mitochondria were removed for downstream analysis.  Transcript abundance was quantified based on GENECODE M4 annotation using featureCounts using option ‘-t exon -g gene_id.
Assembly: mm10
Supplementary files format and content: tab delimited file containing raw counts for all samples

extract_protocol:
For PolyA+ RNA, cells were harvested in TRIzol reagent (Life Technologies, Carlsbad, CA).  Then, DNA-free RNA was extracted from cell using DIRECTzol kit (Zymo Research, Irvine, CA) according to manufacturer’s instructions.
After RNA extraction, libraries for polyA+ RNA were prepared using KAPA Stranded RNA-Seq Kit for Illumina Platforms (KAPA Biosystems, Wilmington, MA) according to the manufacturer’s instructions.

value: LPS


title: M00017912_15M_CD8_T_Cells_plate1_pool1_iPCRtag71


title: M02-20525_3M_Intestinal_Stem_Cells_plate1_pool1_iPCRtag89


title: BMDM 3hr Rep2

description:
col 10
BMDM-3-2

source_name: BMDM

value: BMDM


title: M05-20526_3M_Lung_Macrophages_plate1_pool1_iPCRtag81


title: M00017912_15M_Kidney_plate1_pool1_iPCRtag94


title: RAW 0hr

description:
col 15
RAW-0-2

value: unstimulated


title: BMDM 0hr Rep2

description:
col 8
BMDM-0-2


title: BMDM 3hr Rep1

description:
col 9
BMDM-3-1


title: M00017912_15M_Lung_Macrophages_plate1_pool1_iPCRtag84

value: C57BL/6 J


title: M00018752_6M_Hind_Muscle_plate1_pool1_iPCRtag52

value: wildtype


title: hMPDM 0hr

description:
col 12
hMPDM-0-2

source_name: hMPDM

value: hMPDM


title: hMPDM 3hr

description:
col 14
hMPDM-3-2


title: M00018752_6M_Intestinal_Stem_Cells_plate1_pool1_iPCRtag90


title: BMDM 0hr Rep1

description:
col 7
BMDM-0-1


title: M00017619_24M_Kidney_plate1_pool1_iPCRtag73


title: M02-20525_3M_Heart_iPCRtag17


title: M04-20526_3M_CD4_T_Cells_plate1_pool2_iPCRtag4


title: M04-20526_3M_Hind_Muscle_plate1_pool1_iPCRtag2


title: M04-20526_3M_Skin_plate1_pool2_iPCRtag1


title: KO3

city: St. Louis

first: Michelle

last: Brennan

state: MO

address: 1100 South Grand Blvd

department: Biochemistry & Molecular Biology

institute: Saint Louis University School of Medicine

data_processing:
Raw data were aligned to the mm10 genome. Gene counts for each sample were normalized by read depth, low expressed genes filtered from the data, and t test performed for statistical comparison.
Assembly: mm10
Supplementary files format and content: Excel spreadsheet of normalized gene counts, differential expression, and p values

source_name: left ventricle heart

growth_protocol: 6 fl/fl and 6 CS-Mpc2-/- mice were raised to 30-weeks and fed normal chow.

extract_protocol:
RNA was isolated from ~25 mg of frozen left ventricular tissue using RNA-STAT (Tel-Test, Inc) and cleaned-up using the PureLink RNA Mini Kit (Invitrogen). RNA was then pooled between 2 different fl/fl and CS-Mpc2-/- hearts, resulting in n=3 samples per group.
RNA concentration and quality were determined by 2100 Bioanalyzer RNA 6000 Nano Kit (Agilent) and depleted of rRNA using RiboMinus Eukaryote Kit v2 (Ambion). DNA libraries were constructed using Ion Total RNA-seq Kit v2 (Thermo Fisher Scientific) and sequenced on an Ion Torrent Proton DNA sequencer (Thermo Fisher Scientific).

value: left ventricle heart

value: chow


title: KO2


title: M00017562_24M_Liver_iPCRtag36

value: Liver


title: WT3

value: fl/fl


title: M00018360_9M_Hind_Muscle_plate1_pool1_iPCRtag60


title: KO1


title: WT2


title: M00017549_24M_Liver_iPCRtag33


title: M00017576_24M_Cortex_iPCRtag62

value: Cortex


title: M00017549_24M_Lung_iPCRtag41

value: Lung


title: WT1


title: M02-NB_NewBorn_Heart_iPCRtag15

value: Heart

value: NewBorn


title: M00018011_15M_Lung_iPCRtag70


title: M00018002_15M_Liver_iPCRtag70


title: Rag_control_1

city: Tokyo

first: Takeshi

last: Nitta

address: 7-3-1 Hongo, Bunkyo-ku

department: Department of Immunology,

institute: Graduate School of Medicine and Faculty of Medicine, The University of Tokyo

data_processing:
Data were acquired on an Ion Proton sequencer (Thermo Fisher) and analyzed using CLC genomics Workbench v12 (CLC bio).
Assembly: mm10
Supplementary files format and content: RPKM values for each sample

source_name: thymus

extract_protocol:
Cells were collected by FACS sorting. Total RNA was extracted using RNeasy micro kit (QIAGEN).
cDNA was synthesized and amplified using SMART-seq v4 Ultra Low Input RNA Kit for Sequencing (Clontech Laboratories)

value: thymus

value: FACS-sorted primary cell

value: eosinophil

value: hamster IgG (control), day 10


title: Rag_antiCD3_1

value: anti-CD3 antibody, day 10


title: Rag_antiCD3_2


title: Rag_control_2


title: WT_lung_3

source_name: lung

value: lung

value: wild type


title: WT_lung_2


title: WT_lung_1


title: M00017589_24M_Cortex_iPCRtag48

value: C57BL/6 J

value: wildtype


title: M00017561_24M_Liver_iPCRtag35


title: WT_spleen_3

source_name: spleen

value: spleen


title: M00017578_24M_Heart_iPCRtag56


title: WT_spleen_2


title: M01-20523_3M_Heart_iPCRtag19


title: M00017578_24M_Lung_iPCRtag48


title: WT_spleen_1


title: WT_thymus_3


title: M00017549_24M_Cortex_iPCRtag57


title: M01-20526_3M_Heart_iPCRtag21


title: M00017897_15M_Heart_iPCRtag83


title: WT_thymus_2


title: M00017579_24M_Cortex_iPCRtag40


title: WT_thymus_1


title: M00018001_15M_Cortex_iPCRtag93


title: Stb3-ChIP_CRF1_Control

city: Geneva

first: Sevil

last: Zencir

address: 30, quai Ernest-Ansermet

department: Department of Molecular and Cellular Biology

institute: University of Geneva

data_processing:
For ChIP-Seq raw reads were aligned to the sacCer3 and 972-h pombe genome assembly using Bowtie2 with options "-k 20 --end-to-end --sensitive -X 800". The data were filtered to retain only the mapped reads with at most 5 hits in the reference, reads that mapped to both sacCer3 and 972-h genomes were discarded. The reads mapped uniquely to the sacCer3 genome were used for further analysis.
Assembly: sacCer3
Supplementary files format and content: bigwig files were obtained using Galaxy server (Afgan et al., 2018).

organism: Saccharomyces cerevisiae

growth_protocol:
Cells were grown at 30 degrees in YPED to mid-log phase before treatment
Yeast cells were grown at 30 degrees in YPED to mid-log phase before treatment.

extract_protocol:
ChIP protocol was performed as previously described (Zencir et al., 2020, Ribaud et al., 2012). The cells were crosslinked with 1% formaldehyde for 10 min and quenched by adding 125 mM glycine for 5 min at room temperature. Briefly, crosslinked cells were lysed by bead beating, chromatin was sonicated, and the soluble fraction was incubated with the appropriate antibodies for 1 hr at 4°C. Magnetic beads coupled to IgG against rabbit or mouse (Invitrogen, Dynabeads™ M-280 Sheep Anti-Rabbit or Anti-Mouse IgG) were added into the samples and incubated for additional 3 h at 4°C. A defined amount (5% of total chromatin) of crosslinked and sonicated chromatin from S. pombe was added to S. cerevisiae chromatin prior to the immunoprecipitation step. ChIP was performed using the following antibodies: anti-histone H3 ChIP, (Abcam ab1791); anti-H3K9ac (Millipore 07-352); anti-RNAPII (Abcam ab5131); fanti-Flag (Sigma F3165); anti-Myc (a homemade antibody, clone 9E10). The DNAs were purified using the MinElute PCR Purification Kit (Qiagen) before library preparation.
TruSeq ChIP library preparation kit (Illumina)

treatment_protocol: For stress experiments; cells were incubated in YEPD medium until log phase at 30°C, then the samples were treated with rapamycin at a final concentration of 200 nM for 20 min to inhibit the growth regulator TORC1. The cells were collected following rapamycin treatment at the indicated time points before crosslinking. For conditional depletion of target proteins 'Anchor-away system' was used; log-phase growing cells (OD600 = 0.3–0.4) were treated with 1 μg/mL rapamycin before collection of the cells. For TBP anchor-away, cells were treated with rapamycin for 30 min. For Sfp1 and Ifh1 single and double anchor-way, cells were treated with rapamycin for 60 min.

value: W303 background, deltaifh1::trp pGAL425GPD-CRF1 (leu) STB3-FLAG::KAN

value: No rapamycin


title: Stb3-ChIP_CRF1_Rapamycin

value: 20 min rapamycin


title: Rpd3-ChIP_CRF1_Rapamycin

value: W303 background, deltaifh1::trp pGAL425GPD-CRF1 (leu) RPD3-13-Myc::HIS3


title: M00018001_15M_Lung_iPCRtag77

value: Lung


title: Stb3-ChIP_WT_Control

value: W303 background; leu2-3,112 can1-100 ura3-1 ade2-1 rad5-535 STB3-FLAG::KAN RPD3-13-Myc::HIS3  MATa

tag: chip antibody

value: Anti-Flag® M2 (Sigma, F3165)


title: M00017578_24M_Liver_iPCRtag40

value: Liver


title: M00018002_15M_Lung_iPCRtag78


title: M00018003_15M_Cortex_iPCRtag95

value: Cortex


title: Stb3-ChIP_WT_Rapamycin


title: M00017912_15M_Lung_iPCRtag73


title: M00018001_15M_Heart_iPCRtag85

value: Heart


title: Rpd3-ChIP_CRF1_Control


title: Rpd3-ChIP_WT_Control

value: Anti-Myc (9E10)


title: M01-20526_3M_Lung_iPCRtag13


title: Rpd3-ChIP_WT_Rapamycin


title: M02-20525_3M_Lung_iPCRtag9


title: Sfp1-AA_Ifh1-AA_Rapamycin_RNAPII

value: HHY168 background;  SFP1-FRB::KANMX IFH1-FRB::HIS MATalpha

value: 60 min rapamycin


title: M02-20525_3M_Cortex_iPCRtag25


title: Sfp1-AA_Ifh1-AA_Vehicle_RNAPII

value: Anti-RNA polymerase II CTD repeat YSPTSPS (phospho S5) (Abcam, ab5131)