title: Pool113_RS2_Plate8-1-O19-P14


title: Pool113_RS2_Plate8-1-O19-O2

status: Public on May 04 2023

type: SRA

city: La Jolla

first: Joseph

middle: R

last: Ecker

state: CA

address: 10010 North Torrey Pines Road

department: Genomic Analysis Laboratory

country: USA

institute: HHMI-Salk-Institute

library_source: genomic

data_processing:
Reads trimed with Cutadapt for adapters and low quality bases (Phred score >= 20)
The resulting files are mapped to in-silico bisulfite converted reference genome using Bismark.
The raw BAM file will be filtered using samtools to filter reads by MAPQ > 10 and use Picard to remove PCR duplicates
Tab-delimited files (ALLC files) describing the quantity of unmethylated and methylated cytosine base calls will be generated with in-house developing package using the filtered BAM files
Assembly: mm10
Supplementary files format and content: tab-delimited files (ALLC files) describing the quantity of unmethylated and methylated cytosine base calls. Columns are: 1. Chromosome, 2. Position, 3. Strand, 4. Cytosin Context, 5. methylated base call, 6. total mapped base call, 7. not used, place holder column
Library strategy: snmC-seq2 & 3

molecule: genomic DNA

organism: Mus musculus

source_name: brain

growth_protocol: All experimental procedures using live animals were approved by the Salk Institute Animal Care and Use Committee. The knock-in mouse line, R26R-CAG-loxp-stop-loxp-Sun1-sfGFP-Myc (INTACT) was used for most experiments4 and they were maintained on a C57BL/6J background. 42-49 day old adult male and female INTACT mice were used for the retrograde labeling experiment.

extract_protocol:
Approximately two weeks after the AAVretro injection, brains were extracted from the 56-63 day old INTACT mice, immediately submerged in ice-cold slicing buffer (2.5mM KCl, 0.5mM CaCl2, 7mM MgCl2, 1.25mM NaH2PO4, 110mM sucrose, 10mM glucose and 25mM NaHCO3) that was bubbled with carbogen, and sliced into 0.6 mm coronal sections starting from the frontal pole. From each AAVretro-injected brain, the slices were kept in the ice-cold dissection buffer from which selected brain regions (Supplementary Table 1) were manually dissected under a fluorescent dissecting microscope (Olympus SZX16), following the Allen Mouse Common Coordinate Framework (CCF), Reference Atlas, Version 3 (2015) (Extended Data Fig. 1). The dissected brain tissues were transferred to prelabeled microcentrifuge tubes, immediately frozen in dry ice, and subsequently stored at -80oC.   For each dissected brain region, samples from 2 males and 2 females were pooled separately as biological replicates for nuclei preparation. The 2-mL glass tissue dounce homogenizer and pestles (Sigma-Aldrich D8938-1SET) were pre-chilled on ice. Nuclei were prepared using a modified protocol as reported by Lacar et al., 201622. In summary, the frozen brain tissues were transferred to the dounce homogenizer with 1 mL ice-cold NIM buffer (0.25M sucrose, 25mM KCl, 5mM MgCl2, 10mM Tris-HCl (pH7.4), 1mM DTT (Sigma 646563), 10μl of protease inhibitor (Sigma P8340)), with 0.1% Triton X-100 and 5μM Hoechst 33342 (Invitrogen H3570), and gently homogenized on ice with the pestle 10-15 times. The homogenate was transferred to pre-chilled microcentrifuge tubes and centrifuged at 1000 rcf for 8 min at 4oC to pellet the nuclei. The pellet was resuspended in 1 mL ice-cold NIM buffer, and again centrifuged at 1000 rcf for 8 min at 4oC. The pellet was then resuspended in 450 μL of ice-cold NSB buffer (0.25M sucrose, 5mM MgCl2, 10mM Tris-HCl (pH7.4), 1mM DTT, 9ul of Protease inhibitor), and filtered through 40μM cell strainer. The filtered nuclei suspension was incubated on ice for at least 30 minutes with 50μl of nuclease-free BSA for at least 10 minutes, then incubated with GFP antibody, Alexa Fluor 488 (Invitrogen, A-21311) and anti-NeuN antibody (EMD Millipore MAB377) conjugated with Alexa Fluor 647 (Invitrogen A20173). GFP+/NeuN+ single nuclei were isolated using fluorescence-activated nuclei sorting (FANS) on a BD Influx sorter with 100μm nozzle, and sorted into 384-well plates preloaded with 2μl of digestion buffer for snmC-seq (20 mL digestion buffer consists of 10 mL M-digestion buffer (2×, Zymo D5021-9), 1 ml Proteinase K (20 mg, Zymo D3001-2-20), 9 mL water, and 10 µL unmethylated lambda DNA (100 pg/µL, Promega, D1521)). The collected plates were incubated at 50oC for 20 minutes then stored at -20 oC.
The bisulfite conversion and library preparation were performed following the detailed snmC-seq2 protocol as previously described (Luo, C. et al., Nat. Commun. 2018, 9(1):3824.) or snmC-seq3 protocol described in (Liu, H. et al., Biorxiv. 2023:2023-04.). The libraries were sequenced on Illumina Novaseq 6000 using the S4 flow cell 2 x 150 bp mode.

treatment_protocol: To label neurons projecting to regions of interest, injections of rAAV2-retro-Cre (produced by Salk Vector Core or Vigene, 2x1012 to 1x1013 viral genomes/ml, produced with capsid from Addgene plasmid #81070 packaging pAAV-EF1a-Cre from Addgene plasmid #55636) were made into both hemispheres of the INTACT mice. Animals were anesthetized with either ketamine/xylazine or isoflurane, placed in a stereotaxic frame, and 0.1 to 0.5 microliters of AAV was injected by pressure into stereotaxic coordinates corresponding to the desired projection target.

tag: tissue

value: brain

tag: source

value: ACA

tag: target

value: PTLp

tag: Sex

value: male


title: Pool113_RS2_Plate8-2-I11-A16

value: AI


title: Pool113_RS2_Plate8-1-O19-P1

value: female


title: Pool113_RS2_Plate8-1-O19-O1


title: Pool113_RS2_Plate8-1-O19-M2


title: Pool113_RS2_Plate8-1-O19-L14


title: Pool113_RS2_Plate8-1-O19-K14


title: Pool113_RS2_Plate8-1-O19-K1


title: Pool113_RS2_Plate8-1-O19-M1


title: Pool113_RS2_Plate8-1-O19-M14


title: Pool113_RS2_Plate8-1-O19-N14


title: Pool113_RS2_Plate8-2-I11-F15


title: Pool113_RS2_Plate8-1-O19-J13


title: Pool113_RS2_Plate8-1-O19-J1


title: Pool113_RS2_Plate8-1-O19-J2


title: Pool113_RS2_Plate8-1-O19-I2


title: Pool113_RS2_Plate8-1-O19-I13


title: Pool113_RS2_Plate8-1-O19-H14


title: Pool113_RS2_Plate8-1-O19-F1


title: Pool113_RS2_Plate8-1-O19-G14


title: Pool113_RS2_Plate8-1-O19-G1


title: Pool113_RS2_Plate8-1-O19-E14


title: Pool113_RS2_Plate8-1-O19-E13


title: Pool113_RS2_Plate8-1-O19-C1


title: Pool113_RS2_Plate8-1-O19-C2


title: Pool113_RS2_Plate8-1-O19-A1


title: Pool113_RS2_Plate8-1-O19-G2


title: Pool113_RS2_Plate7-6-N17-P23


title: Pool113_RS2_Plate8-1-O19-A2


title: Pool113_RS2_Plate7-6-N17-P24


title: Pool113_RS2_Plate8-1-O19-B1


title: Pool113_RS2_Plate8-1-O19-K2


title: Pool113_RS2_Plate7-6-N17-N12


title: Pool113_RS2_Plate7-6-N17-N23


title: Pool113_RS2_Plate7-6-N17-L24


title: Pool113_RS2_Plate7-6-N17-O11


title: Pool113_RS2_Plate7-6-N17-M24


title: Pool113_RS2_Plate7-6-N17-M11


title: Pool113_RS2_Plate7-6-N17-M23


title: Pool113_RS2_Plate8-1-O19-E2


title: Pool113_RS2_Plate8-1-O19-G13


title: Pool113_RS2_Plate7-6-N17-O24


title: Pool113_RS2_Plate7-6-N17-L23


title: Pool113_RS2_Plate8-1-O19-F13


title: Pool113_RS2_Plate8-1-O19-C13


title: Pool113_RS2_Plate7-6-N17-J23


title: Pool113_RS2_Plate7-6-N17-J12


title: Pool113_RS2_Plate7-6-N17-K11


title: Pool113_RS2_Plate7-6-N17-I23


title: Pool113_RS2_Plate7-6-N17-J11


title: Pool113_RS2_Plate7-6-N17-I11


title: Pool113_RS2_Plate7-6-N17-H24


title: Pool113_RS2_Plate7-6-N17-H23


title: Pool113_RS2_Plate7-6-N17-K24


title: Pool113_RS2_Plate7-6-N17-H11


title: Pool113_RS2_Plate7-6-N17-H12


title: Pool113_RS2_Plate7-6-N17-G24


title: Pool113_RS2_Plate7-6-N17-G12


title: Pool113_RS2_Plate7-6-N17-E24


title: Pool113_RS2_Plate7-6-N17-D24


title: Pool113_RS2_Plate7-6-N17-F12


title: Pool113_RS2_Plate7-6-N17-E11


title: Pool113_RS2_Plate7-6-N17-E12


title: Pool113_RS2_Plate7-6-N17-F23


title: Pool113_RS2_Plate7-6-N17-D23


title: Pool113_RS2_Plate7-6-N17-K23


title: Pool113_RS2_Plate7-6-N17-F11


title: Pool113_RS2_Plate7-6-N17-D11


title: Pool113_RS2_Plate7-6-N17-G23


title: Pool113_RS2_Plate7-6-N17-A24


title: Pool113_RS2_Plate7-6-N17-B12


title: Pool113_RS2_Plate7-6-N17-B23


title: Pool113_RS2_Plate7-6-N17-C11


title: Pool113_RS2_Plate7-6-N17-F24


title: Pool113_RS2_Plate7-6-N17-B11


title: Pool113_RS2_Plate7-6-N17-B24


title: Pool113_RS2_Plate7-6-N17-D12


title: Pool113_RS2_Plate7-6-N17-A11


title: Pool113_RS2_Plate7-5-M24-P21


title: Pool113_RS2_Plate7-6-N17-A23


title: Pool113_RS2_Plate7-5-M24-P22


title: Pool113_RS2_Plate7-5-M24-O9


title: Pool113_RS2_Plate7-6-N17-C12


title: Pool113_RS2_Plate7-5-M24-M22


title: Pool113_RS2_Plate7-5-M24-N10


title: Pool113_RS2_Plate7-5-M24-N21


title: Pool113_RS2_Plate7-5-M24-L22


title: Pool113_RS2_Plate7-5-M24-M21


title: Pool113_RS2_Plate7-5-M24-N9


title: Pool113_RS2_Plate7-5-M24-L21


title: Pool113_RS2_Plate7-5-M24-O21


title: Pool113_RS2_Plate7-5-M24-K22


title: Pool113_RS2_Plate7-5-M24-L9


title: Pool113_RS2_Plate7-5-M24-N22


title: Pool113_RS2_Plate7-5-M24-O22


title: Pool113_RS2_Plate7-5-M24-K10


title: Pool113_RS2_Plate7-5-M24-I9


title: Pool113_RS2_Plate7-5-M24-I21


title: Pool113_RS2_Plate7-5-M24-J10


title: Pool113_RS2_Plate7-5-M24-J21


title: Pool113_RS2_Plate7-5-M24-J9


title: Pool113_RS2_Plate7-5-M24-M9


title: Pool113_RS2_Plate7-5-M24-J22


title: Pool113_RS2_Plate7-5-M24-H9


title: Pool113_RS2_Plate7-5-M24-I22


title: Pool113_RS2_Plate7-5-M24-H10


title: Pool113_RS2_Plate7-5-M24-H21


title: Pool113_RS2_Plate7-5-M24-F9


title: Pool113_RS2_Plate7-5-M24-F22


title: Pool113_RS2_Plate7-5-M24-F21


title: Pool113_RS2_Plate7-5-M24-E9


title: Pool113_RS2_Plate7-5-M24-F10


title: Pool113_RS2_Plate7-5-M24-D9


title: Pool113_RS2_Plate7-5-M24-E10


title: Pool113_RS2_Plate7-5-M24-E21


title: Pool113_RS2_Plate7-5-M24-D21


title: Pool113_RS2_Plate7-5-M24-C10


title: Pool113_RS2_Plate7-5-M24-B9


title: Pool113_RS2_Plate7-5-M24-B22


title: Pool113_RS2_Plate7-5-M24-D10


title: Pool113_RS2_Plate7-5-M24-B21


title: Pool113_RS2_Plate7-4-L15-P7


title: Pool113_RS2_Plate7-5-M24-B10


title: Pool113_RS2_Plate7-5-M24-A9


title: Pool113_RS2_Plate7-5-M24-D22


title: Pool113_RS2_Plate7-4-L15-N8


title: Pool113_RS2_Plate7-5-M24-H22


title: Pool113_RS2_Plate7-4-L15-M19


title: Pool113_RS2_Plate7-5-M24-A10


title: RNA-seq of Daucus carota BC-2

city: Nanjing

first: Bo

last: mianWang

address: 1 weigang road, Nanjing, China.

department: College of Horticulture

country: China

institute: Nanjing Agricultural University

library_source: transcriptomic

data_processing:
Read count extraction and normalization were performed using rsem.
Assembly: Daucus carota v2.0
Supplementary files format and content: gene.FPKM.matrix.add_info.txt: Tab-delimited text file includes FPKM values and functional annotation for each Sample.

molecule: total RNA

organism: Daucus carota

source_name: fleshy roots

extract_protocol:
Purified mRNA was extracted from BC and WT fleshy roots and fragmented into small pieces with a fragment buffer. 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. Then, first-strand cDNA was generated by random hexamer-primed reverse transcription, followed by a second-strand cDNA synthesis. The fragments of cDNA obtained from previous steps were amplified by PCR, and validated on the Agilent Technologies 2100 bioanalyzer for quality control. The double-strand PCR products were denatured by heating and circularized by the splint oligo sequence to get the final library, and the single stranded circular DNA was formatted as the final library.

value: fleshy roots

tag: genotype

value: betanin-transgenic (BC)


title: Pool113_RS2_Plate7-4-L15-N7


title: Pool113_RS2_Plate7-4-L15-N20


title: Pool113_RS2_Plate7-4-L15-K7


title: RNA-seq of Daucus carota BC-3


title: RNA-seq of Daucus carota WT-3

value: non-transgenic (WT)


title: RNA-seq of Daucus carota BC-1


title: Pool113_RS2_Plate7-4-L15-L7


title: Pool113_RS2_Plate7-4-L15-K19


title: RNA-seq of Daucus carota WT-2


title: Pool113_RS2_Plate7-4-L15-K20


title: Pool113_RS2_Plate7-4-L15-J8


title: Pool113_RS2_Plate7-4-L15-N19


title: Pool113_RS2_Plate7-4-L15-I8


title: RNA-seq of Daucus carota WT-1


title: Pool113_RS2_Plate7-5-M24-A22


title: Pool113_RS2_Plate7-4-L15-I7


title: Pool113_RS2_Plate7-4-L15-P20


title: Pool113_RS2_Plate7-4-L15-J7


title: Pool113_RS2_Plate7-4-L15-I20


title: Pool113_RS2_Plate7-4-L15-J20


title: Pool113_RS2_Plate7-4-L15-L19


title: Pool113_RS2_Plate7-4-L15-H20


title: Pool113_RS2_Plate7-4-L15-H8


title: Pool113_RS2_Plate7-4-L15-G20


title: Pool113_RS2_Plate7-4-L15-H19


title: HPN3

type: RNA

city: Kyoto

first: Mio

last: Namikawa

state: Kyoto

address: 54 Kawaharacho, Shogoin, Sakyoku

department: Gastroenterology and Hepatology

country: Japan

institute: Kyoto University Graduate School of Medicine

description: Gene expression data from organoids from biliary epithelia of mus musculus.

hyb_protocol: Approximately 5.5 μg of labeled DNA target was hybridized to the Affymetrix GeneChip Array at 45°C for 16 hours.

scan_protocol: Hybridized arrays were washed and stained on a GeneChip Fluidics Station 450 and scanned on a GCS3000 Scanner (Affymetrix).

data_processing: The probe cell intensity data computation and a CEL file generation was performed using Affymetrix® GeneChip Command Console® Software (AGCC).

label: biotin

source_name: Hnf1b-CreERT2; Pten flox/flox; Rosa26LSL-NotchIC

label_protocol: cDNA was synthesized using the GeneChip WT (Whole Transcript) Amplification kit as described by the manufacturer. The sense cDNA was then fragmented and biotin-labeled with TdT (terminal deoxynucleotidyl transferase) using the GeneChip WT Terminal labeling kit.

growth_protocol: Two weeks before the extraction of total RNA, cells were incubated with analysis medium (Ad-DMEM/F12 supplemented with B27 and N2, GlutaMAX, 10 mM HEPES, 1% penicillin-streptomycin, 1 mM N-acetylcysteine, 10 mM nicotinamide, 50 ng/mL EGF, 1 ug/mL Rspondin-1, 50 ng/mL Wnt3a, 100 ng/mL Noggin, 100 ng/mL FGF10, and 10uM Y-27632)

extract_protocol: RNA was prepared using the RNeasy Mini kit (QIAGEN, Valencia, CA) following the manufacturer's recommendations.   RNA was quantified using a NanoDrop-1000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

value: organoids from biliary epithelia


title: HK6

source_name: Hnf1b-CreERT2; KrasLSL-G12D


title: Pool113_RS2_Plate7-4-L15-G19


title: Pool113_RS2_Plate7-6-N17-I12


title: HK5


title: Pool113_RS2_Plate7-4-L15-F19


title: Pool113_RS2_Plate7-4-L15-F7


title: Pool113_RS2_Plate7-4-L15-F20


title: Bmal1 bHLH, 3 replicates (protein)

city: Philadelphia

first: Priyankara

middle: J

last: Wickramasinghe

state: PA

address: 3601 Spruce Street

department: Bioinformatics

institute: The Wistar Institute

library_source: transcriptomic single cell

data_processing:
Cellranger was executed with refdata-cellranger-mm10 transcriptome
Antibody capture hashtags are used to de-multiplex individual replicates in each sample
Assembly: mm10
Supplementary files format and content: standard cellranger output

molecule: polyA RNA

source_name: YUMM2.1 cell line

extract_protocol:
Single cell droplets were generated using the Chromium next gem single cell 3' kit v3.1 (10x Genomics)
cDNA synthesis and amplification, library preparation and indexing were done using the 10x Genomics Library Preparation kit (10x Genomics)
10x genomics single cell RNA-seq

tag: hashtags

tag: names

tag: antibodycapturebarcodes


title: Pool113_RS2_Plate7-4-L15-G7


title: Pool113_RS2_Plate7-4-L15-E8


title: Pool113_RS2_Plate7-4-L15-E7


title: Bmal1 bHLH, 3 replicates (GE)


title: C4


title: Bmal1 WT, 3 replicates (protein)


title: HN2

source_name: Hnf1b-CreERT2; Rosa26LSL-NotchIC


title: HPN2


title: Bmal1 WT, 3 replicates (GE)


title: HK4


title: C3


title: HN3


title: HPN1


title: HKN3


title: HKN2


title: Empty vector, 3 replicates (GE)


title: Pool113_RS2_Plate7-4-L15-D8


title: HN4


title: Pool113_RS2_Plate7-4-L15-C8


title: HKN1


title: Empty vector, 3 replicates (protein)


title: Pool113_RS2_Plate7-4-L15-E19


title: Pool of 3 vehicle and 3 ACSS2i treated samples (protein)

data_processing:
Cellranger was executed with refdata-cellranger-mm10 transcriptome
Demultiplexing is done using antibody capture barcodes (vehicle: U2-ACCCACCAGTAAGAC U3-CTTGCCGCATGTCAT U4CTTTGTCTTTGTGAG; ACSS2i: D0-GAGTCTGCCAGTATC D1-TATAGAACGCCAGGC D4-TGCCTATGAAACAAG )
Assembly: mm10
Supplementary files format and content: standard cellranger output

source_name: tumor

extract_protocol:
4,000-6,000 live cells from each sample were pooled to create one multiplexed single cell suspension; this was loaded onto one lane of a 10x Chromium Next GEM G Chip and partitioned into single cell droplets in a 10x Chromium Controller using the Chromium Next GEM Single Cell Gel Bead Kit.
Final libraries were made using both the Chromium Next GEM Single Cell 3’ Library Construction Kit and the 3’ Feature Barcode Library Kit (10x Genomics, Pleasanton, CA) as per manufactures protocol.
10x genomics single cell RNA-seq

tag: strain

value: NGS mouse

tag: treatment

value: vehicle and ACSS2i treated

value: tumor


title: Pool of 3 vehicle and 3 ACSS2i treated samples (GE)


title: Pool113_RS2_Plate7-4-L15-D19


title: Pool113_RS2_Plate7-4-L15-E20


title: Pool113_RS2_Plate7-6-N17-O12


title: Pool113_RS2_Plate7-4-L15-C20


title: Pool113_RS2_Plate7-4-L15-B8


title: CRC-MPS (Con-SWAT CM-1 Biol 1)

city: New Orleans

first: Suzana

last: Savkovic

state: LA

address: 1430 Tulane Ave

department: Pathology & Laboratory Medicine

institute: Tulane University

description:
HT29 (SWAT-Con-CM)-1
HT29_ASC-Con-CM_vs_HT29_SWAT-Con-CM.summary.genes p0.05.xlsx

data_processing:
Paired-end reads were aligned to hg38 genome using STAR(v.2.6.1d).  Abundance levels were calculated using Kallisto(v.0.46.0) and differential expression testing performed using DESeq2.
Assembly: human, hg38
Supplementary files format and content: Excel files with TPMs and results of differential expression testing from DESeq2

organism: Homo sapiens

extract_protocol:
Zymogen, Dnase Treated
High Output Paired End Read

tag: cell line

tag: cell type

value: Colon Cancer line

value: 24 hr treatment with CM from Adipose tissue


title: CM-ESC (Con-ASC CM-3 Biol 3)

description:
HT29 (ASC-Con-CM)-3
HT29_ASC-Con-CM_vs_HT29_SWAT-Con-CM.summary.genes p0.05.xlsx

value: 24 hr treatment with CM from Adiopose Stromal Cell Control


title: Pool113_RS2_Plate7-4-L15-C7


title: CRC-MPS (Con-SWAT CM-2 Biol 2)

description:
HT29 (SWAT-Con-CM)-2
HT29_ASC-Con-CM_vs_HT29_SWAT-Con-CM.summary.genes p0.05.xlsx


title: Pool113_RS2_Plate7-4-L15-B20


title: CRC-MPS (Con-SWAT CM-3 Biol 3)

description:
HT29 (SWAT-Con-CM)-3
HT29_ASC-Con-CM_vs_HT29_SWAT-Con-CM.summary.genes p0.05.xlsx


title: Pool113_RS2_Plate7-4-L15-B19


title: Pool113_RS2_Plate7-4-L15-B7


title: Con Biol 2

description:
HT29 (Con)-2
HT29_Con_vs_HT29_SWAT-Con-CM.summary.genes_p0.05.xlsx
HT29_ASC-Con-CM_vs_HT29_Con.summary.genes-P<0.05.xlsx

value: Cells were grown to 50% confluency on a 100mm dish in complete media, then serum starved for 24hrs, then collected for RNAseq


title: CM-ESC (Con-ASC CM-2 Biol 2)

description:
HT29 (ASC-Con-CM)-2
HT29_ASC-Con-CM_vs_HT29_SWAT-Con-CM.summary.genes p0.05.xlsx


title: CM-ESC (Con-ASC CM-1 Biol 1)

description:
HT29 (ASC-Con-CM)-1
HT29_ASC-Con-CM_vs_HT29_SWAT-Con-CM.summary.genes p0.05.xlsx


title: Pool113_RS2_Plate7-4-L15-A8

value: brain


title: Pool113_RS2_Plate7-4-L15-D20

value: ACA


title: Pool113_RS2_Plate7-4-L15-A20

value: PTLp


title: Con Biol 3

description:
HT29 (Con)-3
HT29_Con_vs_HT29_SWAT-Con-CM.summary.genes_p0.05.xlsx
HT29_ASC-Con-CM_vs_HT29_Con.summary.genes-P<0.05.xlsx


title: Pool113_RS2_Plate7-2-M10-P4


title: Pool113_RS2_Plate7-2-M10-P15

value: male


title: Con Biol 1

description:
HT29 (Con)-1
HT29_Con_vs_HT29_SWAT-Con-CM.summary.genes_p0.05.xlsx
HT29_ASC-Con-CM_vs_HT29_Con.summary.genes-P<0.05.xlsx


title: MUC5B T/TtdT/tdT laminin ALI

city: Boston

first: Feiya

last: Wang

state: MA

address: 670 Albany street, 2nd floor

institute: Center for Regenerative Medicine, Boston University

data_processing:
The sample was processed using the standard cellranger pipeline
Reads were mapped to GRCh38 with tdtomato sequence
Downstream analysis and QC done on Seurat
Differential expression using MAST models
Assembly: GRCh38
Supplementary files format and content: the processed files are the standard output from the cellranger pipeline:

source_name: MUC5B T/TtdT/tdT air-liquid interace airway epithelial cultures 21 days post-air phase transition

growth_protocol: Cultures were grown according to iBC-ALI culture technique cited in Hawkins et al. Cell Stem Cell 2021, except laminin was substituted as the growth matrix.  The culture media at time of sequencing was Pneumacult-ALI basal media

extract_protocol:
10X Chromium system
NextSeq2000

value: MUC5B T/TtdT/tdT


title: Pool113_RS2_Plate7-4-L15-A7


title: Pool113_RS2_Plate7-4-L15-A19


title: C1


title: Pool113_RS2_Plate7-2-M10-O3


title: Pool113_RS2_Plate7-2-M10-O16

value: female


title: Pool113_RS2_Plate7-2-M10-O15


title: Pool113_RS2_Plate7-2-M10-N4


title: HeLa, DMSO, 4sU 30 min, rep1

city: Göttingen

first: Hsu-Min

last: Sung

state: Niedersachsen

address: Humboldtallee 23

country: Germany

institute: Heart Centre Göttingen

data_processing:
Reads were mapped with STAR v2.5.3a (PMID: 23104886) the a reference of the human genome (hg38), providing the basic set of Gencode V27 for transcript annotation, allowing up to 10 mismatches for 150 nt long reads and 5 mismatches for 80 nt long reads.
To identify reads originating from mature RNA, only reads were retained that contain “N” in the CIGAR string. These reads were assigned to genes (Gencode V27) using featureCounts of the subread package v1.6.3 (PMID: 24227677). Their read IDs and matching annotations were extracted using the -R option of featureCounts.
Likewise, intronic reads were identified as alignments that are entirely contained within purely intronic regions.
The number of T-to-C transitions depending on the number of Ts in the reference was determined with an in-house developed perl script, separately for spliced and intronic reads.
The proportion of nascent reads, the probability of a T-to-C transition within nascent reads and the background probability of such transitions within non-nascent reads was estimated using a binomial mixture model (PMID: 29949974). The proportion of nascent reads within intronic or spliced reads was then used to reconstruct the proportion of intronic or spliced reads within nascent or pre-existing reads.
Assembly: hg38
Supplementary files format and content: Processed data files contain the number of T-to-C transitions separately according to the number of matching Ts in the reference sequence (e.g. the column of_20_1 shows the number of reads with 20 Ts in the reference and 1 T-to-C transition), one gene per line. The files ending in _intronic_counts.txt refer to intronic reads, files ending in _spliced_counts.txt refer to reads covering splice junctions.

source_name: HeLa

growth_protocol: HeLa cells were maintained in Dulbecco's modified Eagle's medium (DMEM, Gibco) supplemented with 10% fetal bovine serum (FBS, Gibco), 2 mM L-glutamine (PAN-Biotech), 100 U/ml penicillin (PAN-Biotech) and 0.1 mg/ml streptomycin (PAN-Biotech).

extract_protocol:
RNA was extracted with the GeneMatrix universal RNA purification kit (Roboklon).
Ribosomal RNA was depleted with the NEBNext rRNA Depletion Kit (NEB E6350L). To enhance the efficiency of 4sU-to-C conversion, RNA was fragmented to an average length of ~200 nt by alkaline hydrolysis at pH 10.0 for 7minutes at 95 °C. Conversion of 4sU to C was induced by treatment with 10 mM NaIO4 in 600 mM NH4Cl (pH 8.5) for 15 min at 40 °C as described previously for ribosome-protected fragments (PMID: 34480152). Sequencing libraries were prepared with the NEBnext Ultra II Directional RNA Library Prep Kit and sequenced single-end on a NextSeq550 device (Illumina). The 30 minute and 2 hour time-point libraries were sequenced to a length of 150 and 80 nt, respectively, to account for the lower 4sU incorporation rate after 30 min of 4sU treatment.

treatment_protocol: HeLa cells were incubated with 4sU (200 µM) for 2 hours in parallel to ANI treatment (0.1 µg/ml) or during the last 30 minutes of ANI treatment (or DMSO treatment as a control).

value: HeLa

value: DMSO (2 h) + 4sU (30 min)


title: HeLa, DMSO, 4sU 120 min, rep1

value: DMSO (2 h) + 4sU (120 min)


title: HeLa, DMSO, 4sU 120 min, rep2


title: Pool113_RS2_Plate7-2-M10-N15


title: HeLa, ANI, 4sU 120 min, rep2


title: HeLa, ANI, 4sU 120 min, rep1


title: HeLa, DMSO, ActD 2 h, rep2

data_processing:
Reads were mapped with STAR v2.5.3a (PMID: 23104886) to a reference of the human genome (hg38), providing the basic set of Gencode V27 for transcript annotation, allowing up to 2 mismatches and chimeric read detection with a minimum of 10 nt per segment (--chimSegmentMin 10).
Read counts were summarized at the gene level with the featureCounts function of the subread package v1.6.3 (PMID: 24227677), considering only reads that are completely contained within an exon.
Circular RNAs were detected with the CIRCexplorer2 v2.3.8 functions parse and annotate (PMID: 27365365).
For normalization, read counts per gene were divided by the sum of all reads spanning circRNA junctions in the respective sample.
Linear regression was performed on ln-transformed read counts. Half-lives (HL) were calculated from the slope of the regression line with the equation -ln(2)/slope. Only genes with a coefficient of determination > 0.5 in both conditions and replicates were included in the analysis.
Assembly: hg38
Supplementary files format and content: Comma separated values (csv) file with read counts and normalized read counts per sample, and half-life and coefficient of determination (R2) for each ActD time-course.

growth_protocol: HeLa cells were maintained in Dulbecco's modified Eagle's medium (DMEM, Gibco) supplemented with 10% fetal bovine serum (FBS, Gibco), 2 mM L-glutamine (PAN-Biotech), 100 U/ml penicillin (PAN-Biotech) and 0.1 mg/ml streptomycin (PAN-Biotech). Cells were seeded at a density of 1.8 × 10^6 per 10 cm dish on the evening before the experiment.

extract_protocol:
RNA was extracted with the GeneMatrix universal RNA purification kit (Roboklon).
Ribosomal RNA was depleted with the riboPOOL kit (Biozym, 27DP-K024). RNA-Seq libraries were prepared with the NEBnext Ultra II Directional RNA Library Prep Kit and sequenced single-end (81 nt) on a NextSeq550 device (Illumina).

treatment_protocol: After treatment with DMSO or Anisomycin (0.1 µg/ml; Sigma) for 2 hours, transcription was inhibited by adding 10 µg/ml actinomycin D (AppliChem, A1489,0005) for 0, 1, 2 and 4 hours.

value: DMSO

value: ActD 2 h


title: HeLa, DMSO, ActD 4 h, rep2

value: ActD 4 h


title: HeLa, ANI, 4sU 30 min, rep2

value: ANI (2 h) + 4sU (30 min)


title: Pool113_RS2_Plate7-2-M10-M16


title: HeLa, DMSO, ActD 1 h, rep2

value: ActD 1 h


title: Pool113_RS2_Plate7-2-M10-M3


title: Pool113_RS2_Plate7-2-M10-L4


title: Pool113_RS2_Plate7-2-M10-L16


title: HeLa, DMSO ActD 4 h, rep1


title: HeLa, DMSO, 4sU 30 min, rep2


title: Pool113_RS2_Plate7-2-M10-L15


title: HeLa, DMSO, ActD 0 h, rep2

value: ActD 0 h


title: Pool113_RS2_Plate7-2-M10-K4


title: Pool113_RS2_Plate7-2-M10-K3


title: Pool113_RS2_Plate7-2-M10-N16


title: HeLa, DMSO ActD 2 h, rep1


title: HeLa, ANI ActD 4 h, rep1

value: ANI


title: HeLa, DMSO, ActD 0 h, rep1


title: Pool113_RS2_Plate7-2-M10-K16


title: HeLa, DMSO ActD 1 h, rep1


title: HeLa, ANI, 4sU 30 min, rep1


title: HeLa, ANI, ActD 4 h, rep2


title: Pool113_RS2_Plate7-2-M10-I4


title: Pool113_RS2_Plate7-2-M10-K15


title: HeLa, ANI, ActD 1 h, rep2


title: HeLa, ANI, ActD 2 h, rep2


title: Pool113_RS2_Plate7-2-M10-J3


title: Pool113_RS2_Plate7-2-M10-J16


title: AML processed with GTAC

city: Oxford

first: Sven

last: Turkalj

address: John Radcliffe Hospital/Headley Way, Oxford OX3 9DS

department: Radcliffe Department of Medicine

country: United Kingdom

institute: WIMM

description: demultiplexed scATAC-seq data from a GTAC experiment

data_processing:
FASTQ files were trimmed and converted to BAM. BAM files were de-duplicated using Picard. De-duplicated BAM files were merged with Samtools and the provided fragment files were generated. Fragment files were used as input for analysis in ArchR.
Assembly: hg38
Supplementary files format and content: Fragment files from merged BAM files. Each fragment is linked to the single cell where it derives from.

source_name: bone marrow

extract_protocol:
NGS library preparation and purification
GTAC

value: bone marrow

value: primary sample


title: Pool113_RS2_Plate7-2-M10-I3

value: brain

value: ACA


title: Pool113_RS2_Plate7-2-M10-I15

value: PTLp

value: male


title: K562 processed by GTAC or ATAC only

source_name: haematopoietic

value: haematopoietic

value: cell line


title: Pool113_RS2_Plate7-2-M10-H3


title: Pool113_RS2_Plate7-2-M10-H16

value: female


title: Pool113_RS2_Plate7-2-M10-H15


title: HeLa, ANI ActD 2 h, rep1

value: HeLa


title: Pool113_RS2_Plate7-2-M10-J4


title: Pool113_RS2_Plate7-2-M10-G4


title: Pool113_RS2_Plate7-2-M10-G15


title: HeLa, ANI, ActD 0 h, rep1


title: HeLa, ANI, ActD 0 h, rep2


title: Pool113_RS2_Plate7-2-M10-F15


title: Pool113_RS2_Plate7-2-M10-F3


title: HeLa, ANI ActD 1 h, rep1


title: Pool113_RS2_Plate7-2-M10-F16


title: Pool113_RS2_Plate7-2-M10-E3


title: Pool113_RS2_Plate7-2-M10-E16


title: hESCs Control, tHENSM condition, Rep#2, MARS-seq

city: Rehovot

first: Orly

last: Reiner

address: 234, Herzl Street,

department: Molecular Genetics

country: Israel

institute: Weizmann Institute of Science

description: Biological replicate2

data_processing:
Fastq files were processed using UTAP pipeline. Sequenced reads were trimmed for adaptor sequence using Cutadapt and were aligned with STAR.
Raw counts were processed with qCount, and normalized reads were obtained by DESeq2.
Assembly: GRCh38/hg38
Supplementary files format and content: raw count quantification files

source_name: human embryonic stem cells

growth_protocol: Human ES cells were grown in tHENSM and NHSM conditions

extract_protocol:
Total RNA was extracted from cells, using the miRNAeasy kit (Qiagen) according to the manufacturer’s protocol.
RNA libraries were prepared for sequencing using bulk MARS-seq protocol [Jaitin, D. A. et al. Massively parallel single-cell RNA-seq for marker-free decomposition of tissues into cell types. Science 343, 776–9 (2014)].

tag: culture medium

value: tHENSM

value: Control


title: hESCs Control, NHSM condition, Rep#2, MARS-seq

description: Biological replicate2

value: NHSM


title: hESCs Control, NHSM condition, Rep#3, MARS-seq

description: Biological replicate3


title: hESCs Control, NHSM condition, Rep#4, MARS-seq

description: Biological replicate4


title: hESCs Control, tHENSM condition, Rep#3, MARS-seq

description: Biological replicate3


title: hESCs Control, tHENSM condition, Rep#4, MARS-seq

description: Biological replicate4


title: hESCs Control, NHSM condition, Rep#1, MARS-seq

description: Biological replicate1


title: hESCs LIS1 OE, tHENSM condition, Rep#3, MARS-seq

description: Biological replicate3

value: LIS1 overexpression (LIS1-GFP OE)


title: hESCs LIS1 OE, tHENSM condition, Rep#2, MARS-seq

description: Biological replicate2


title: hESCs LIS1 OE, tHENSM condition, Rep#1, MARS-seq

description: Biological replicate1


title: Pool113_RS2_Plate7-2-M10-E15


title: hESCs LIS1 OE, tHENSM condition, Rep#4, MARS-seq

description: Biological replicate4


title: hESCs Control, tHENSM condition, Rep#1, MARS-seq

description: Biological replicate1


title: hESCs LIS1 OE, NHSM condition, Rep#4, MARS-seq

description: Biological replicate4


title: Pool113_RS2_Plate7-2-M10-D15


title: hESCs LIS1 OE, NHSM condition, Rep#3, MARS-seq

description: Biological replicate3


title: Pool113_RS2_Plate7-2-M10-C4


title: Pool113_RS2_Plate7-2-M10-G16


title: hESCs LIS1 OE, NHSM condition, Rep#2, MARS-seq

description: Biological replicate2


title: Pool113_RS2_Plate7-2-M10-E4


title: Pool113_RS2_Plate7-2-M10-D16


title: Pool113_RS2_Plate7-2-M10-C15


title: hESCs LIS1 int6*/*, tHENSM condition, Rep#4, MARS-seq

description: Biological replicate4

value: LIS1-int6*/* (homozygous point mutation)


title: Pool113_RS2_Plate7-2-M10-B3


title: hESCs LIS1 int6*/*, tHENSM condition, Rep#3, MARS-seq

description: Biological replicate3


title: Pool113_RS2_Plate7-2-M10-B16


title: Pool113_RS2_Plate7-2-M10-C3


title: hESCs LIS1 OE, NHSM condition, Rep#1, MARS-seq

description: Biological replicate1


title: hESCs LIS1 int6*/*, tHENSM condition, Rep#2, MARS-seq

description: Biological replicate2


title: Pool113_RS2_Plate7-2-M10-D4


title: hESCs LIS1 int6*/*, NHSM condition, Rep#3, MARS-seq

description: Biological replicate3


title: hESCs LIS1 int6*/*, tHENSM condition, Rep#1, MARS-seq

description: Biological replicate1


title: hESCs LIS1 int6*/*, NHSM condition, Rep#2, MARS-seq

description: Biological replicate2


title: Pool113_RS2_Plate7-2-M10-B15


title: Pool113_RS2_Plate7-1-P22-P14


title: hESCs LIS1 int6*/*, NHSM condition, Rep#4, MARS-seq

description: Biological replicate4


title: hESCs LIS1 +/-, tHENSM condition, Rep#7, MARS-seq

description: Biological replicate3, isogenic coloneB


title: Pool113_RS2_Plate7-2-M10-A16


title: hESCs LIS1 +/-, tHENSM condition, Rep#8, MARS-seq

description: Biological replicate4, isogenic coloneB


title: Pool113_RS2_Plate7-1-P22-P2


title: hESCs LIS1 int6*/*, NHSM condition, Rep#1, MARS-seq

description: Biological replicate1


title: Pool113_RS2_Plate7-1-P22-P13


title: hESCs LIS1 +/-, tHENSM condition, Rep#6, MARS-seq

description: Biological replicate2, isogenic coloneB


title: Pool113_RS2_Plate7-1-P22-P1


title: hESCs LIS1 +/-, tHENSM condition, Rep#5, MARS-seq

description: Biological replicate1, isogenic coloneB


title: Pool113_RS2_Plate7-1-P22-O2


title: Pool113_RS2_Plate7-1-P22-O14


title: Pool113_RS2_Plate7-1-P22-O13


title: hESCs LIS1 +/-, NHSM condition, Rep#8, MARS-seq

description: Biological replicate4, isogenic coloneB


title: Pool113_RS2_Plate7-2-M10-A15


title: hESCs LIS1 +/-, NHSM condition, Rep#7, MARS-seq

description: Biological replicate3, isogenic coloneB


title: Pool113_RS2_Plate7-1-P22-O1


title: hESCs LIS1 +/-, NHSM condition, Rep#6, MARS-seq

description: Biological replicate2, isogenic coloneB


title: hESCs LIS1 +/-, tHENSM condition, Rep#4, MARS-seq

description: Biological replicate4, isogenic coloneA


title: hESCs LIS1 +/-, NHSM condition, Rep#5, MARS-seq

description: Biological replicate1, isogenic coloneB


title: hESCs LIS1 +/-, tHENSM condition, Rep#3, MARS-seq

description: Biological replicate3, isogenic coloneA


title: hESCs LIS1 +/-, tHENSM condition, Rep#2, MARS-seq

description: Biological replicate2, isogenic coloneA


title: Pool113_RS2_Plate7-1-P22-M2


title: Pool113_RS2_Plate7-1-P22-N1


title: Pool113_RS2_Plate7-1-P22-N13


title: Pool113_RS2_Plate7-1-P22-M13


title: Pool113_RS2_Plate7-1-P22-M14


title: hESCs LIS1 +/-, NHSM condition, Rep#4, MARS-seq

description: Biological replicate4, isogenic coloneA


title: hESCs LIS1 +/-, tHENSM condition, Rep#1, MARS-seq

description: Biological replicate1, isogenic coloneA


title: hESCs LIS1 +/-, NHSM condition, Rep#1, MARS-seq

description: Biological replicate1, isogenic coloneA


title: hESCs LIS1 +/-, NHSM condition, Rep#3, MARS-seq

description: Biological replicate3, isogenic coloneA


title: Pool113_RS2_Plate7-1-P22-L2


title: Pool113_RS2_Plate7-1-P22-M1


title: Pool113_RS2_Plate7-1-P22-L14


title: Pool113_RS2_Plate7-1-P22-K14


title: CP_3

city: Shanghai

first: mengjun

last: Hu

address: Shanghai Jiao Tong University，School of Agriculture & Biology, Dongchuan road 800

institute: Shanghai Jiao Tong University

description: S. Enteritidis, ΔphoP, ceftazidime, 8 h

data_processing:
Illumina Casava software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence to get clean reads,the clean reads was compared to reference genomic sequences using Bowti2 and RSeQC, and the genomic mapped ratio of each sample reached 98.42%.
The clean reads were mapped to the integral reference genes with Bowtie2 v2.2.5(Parameter: ：-q --phred64 --sensitive --dpad 0 --gbar 99999999 --mp 1,1 --np 1 --score-min L,0,-0.1 -I 1 -X 1000 --no-mixed --no-discordant -p 1 -k 200) and the gene expression level was calculated by RSEM v1.2.12(Parameter：--forward-prob=0.0)
The transcripts per kilobase per million mapped reads(TPM) incorporate normalization steps to ensure that expression levels for different genes and transcripts can be compared across runs. The DESeq2 method(parameter: abs log2(FoldChange) >= 1 && Adjusted Pvalue <= 0.05) was used to calculate the differentially expressed genes (DEG). Genes with fold change ≥ 2 and Bonferroni-corrected P value (Padj) ≤0.05 in at least one sample were determined to be DGEs.
Assembly: Salmonella enterica serovar Enteritidis SJTUF 12367 genome, the accession number is GCA_004323915.1
Supplementary files format and content: Excel files (NP/CP/NWT/CWT.xlsx) include Gene ID, Normalized TPM value of WT-Expression and ΔphoP-Expression under antibiotic stress, Padj Pvalue type , KEGG Orthology, GO Component, GO Function, GO Process, and Blast nr. Excel files of‘NP VS NWT.xlsx' and ‘CP VS CWT.xlsx' inclues the differentially expressed genes between ΔphoP and WT under nalidixic acid and ceftazidime respectively, the value of FC(NP/NWT), FC(CP/CWT), log2FoldChange(NP/NWT) and log2FoldChange(CP/CWT) that calculated with DESeq2 method,and Up-Down-Regulation.

organism: Salmonella enterica subsp. enterica serovar Enteritidis

source_name: SJTUF 12367

growth_protocol: S.Enteritidis wild-type and its derivate ΔphoP cells were cultured in Lysogeny broth (LB) broth with or without antibiotics at 37°C.

extract_protocol:
RNA was extracted using TRIzol Reagent (Invitrogen, CAS 15596026) according to the manual.RNA quality and integrity was verified by electrophoretic analysis and UV spectroscopy using NanoDrop and Agilent 2100 instruments. The RNA integrity number for all samples were between 7.3 and 9.3.
RNA libraries for RNA-seq were prepared using TruSeq™ Stranded Total RNA Library Prep Kit (Illumina) following manufacturer's protocols.

treatment_protocol:
The mid-log phase exponentially bacteria cultures that grown in LB at 37°C with shaking at 200 rpm, was harvest and equalized to an optical density at 600nm (OD600) value of 0.2. Volume of 160 μL exponentially growing cells were then added into 3.84 mL LB, to which had been preadded with subinhibitory concentrations of antibiotics to reach final concentrations of 32 mg/L (1/8 MIC) nalidixic acid and 2 mg/L (1/16 MIC) ceftazidime, respectively. The bacterial cultures were harvast after incubation at 8 h.
The ice-cold RNAlater solution (2/5 of the bacteria culture volume) was added in the 4 mL bacteria cultures immediately. The mixture was incubated on ice for 40 min, transferred to 2 mL RNase free ice-cold centrifuge tubes, and centrifuged at 3000 × g for 10 min at 4°C to pellet the bacteria. The cell pellets were then immediately frozen in liquid nitrogen and stored at -80°C.

value: SJTUF 12367

value: phoP deletion mutant

value: 2 ug /mL ceftazidime

tag: time

value: 8 h


title: CP_2

description: S. Enteritidis, ΔphoP, ceftazidime, 8 h


title: CP_1

description: S. Enteritidis, ΔphoP, ceftazidime, 8 h


title: CWT_2

description: S. Enteritidis, WT, ceftazidime, 8 h

value: wild type


title: CWT_3

description: S. Enteritidis, WT, ceftazidime, 8 h


title: Pool113_RS2_Plate7-1-P22-J14

value: brain

value: ACA


title: Pool113_RS2_Plate7-1-P22-J13

value: PTLp

value: male


title: Pool113_RS2_Plate7-1-P22-K1


title: Pool113_RS2_Plate7-1-P22-J1


title: CWT_1

description: S. Enteritidis, WT, ceftazidime, 8 h


title: NP_2

description: S. Enteritidis, ΔphoP, nalidixic acid, 8 h

value: 32 ug/mL nalidixic acid


title: NP_1


title: Pool113_RS2_Plate7-1-P22-I2

value: female


title: hESCs LIS1 +/-, NHSM condition, Rep#2, MARS-seq

description: Biological replicate2, isogenic coloneA


title: NWT_1

description: S. Enteritidis, WT, nalidixic acid, 8 h


title: Pool113_RS2_Plate7-1-P22-I1


title: Pool113_RS2_Plate7-1-P22-L1


title: Pool113_RS2_Plate7-1-P22-H13


title: Pool113_RS2_Plate7-1-P22-J2


title: Pool113_RS2_Plate7-1-P22-G13


title: Pool113_RS2_Plate7-1-P22-G1


title: Primary colon cancer, subject 761, sample ID 21

city: St. Louis

first: Christopher

last: Maher

state: Missouri

address: 1 Brookings Dr

institute: Washington University in St. Louis

data_processing:
STAR 2.7.3a for RNA-Seq alignment
CIRCexplorer2 2.3.8 for circRNA detection
featureCounts 1.6.0 for linear gene quantification
Assembly: Gene annotations were combined from Gencode v23, RefSeq downloaded from the UCSC Genome Browser, and the Broad long noncoding RNA (lncRNA) catalog (see supplementary file hg38_annotation.gtf.gz)
Supplementary files format and content: For patients, tab-delimited text files include 1) Raw counts for each sample for both linear genes and circRNAs; 2) TPM values for each sample for both linear genes and circRNAs; 3) backsplice-normalized exprfession values for each sample for circRNAs.
Supplementary files format and content: For cell lines, tab-delimited text files include 1) Raw counts for each sample for circRNAs; 2) TPM values for each sample for circRNAs.

source_name: Primary colon cancer

growth_protocol: For cell lines, HCT116 and HT29 cells were grown in McCoy’s medium (Invitrogen, Carlsbad, CA) supplemented with 10% fetal bovine serum and 1% penicillin/streptomycin. SW480 and SW620 cells were grown in DMEM (Invitrogen) supplemented with 10% fetal bovine serum (Sigma, St. Louis, MO) and 1% penicillin/streptomycin. LoVo cells were grown in DMEM/F12 (Invitrogen) supplemented with 10% fetal bovine serum, and 1% penicillin/streptomycin.

extract_protocol:
For patients, Input RNA quantity was 1μg except for Sample ID 15 (0.5μg) and 27 (0.24μg) due to low volume.  For cell lines, total RNA inputs of 1μg were used to generate libraries using the New England BioLabs NEB Ultra II Directional RNA Library Prep for Illumina with rRNA Depletion kits.
For patients, RNA-Seq libraries were constructed using the Illumina TruSeq Stranded Total RNA Library Prep kit with IDT xGen Dual Index UMI Adapters.  For cell lines, 200ng aliquots of each library were pooled and used as input for cDNA-Capture. The IDT xGen Exome Research Panel v2 including 415,115 exon probes was used for exome capture.
Total RNA-Seq for patient samples, cDNA-Cap RNA-Seq for cell lines.

value: Primary colon cancer


title: Primary colon cancer, subject 819, sample ID 8


title: Primary colon cancer, subject 722, sample ID 29


title: NP_3


title: Pool113_RS2_Plate7-1-P22-L13


title: Pool113_RS2_Plate7-1-P22-F13


title: Pool113_RS2_Plate7-1-P22-F1


title: Pool113_RS2_Plate7-1-P22-G14


title: NWT_3

description: S. Enteritidis, WT, nalidixic acid, 8 h


title: Pool113_RS2_Plate7-1-P22-E13


title: Primary colon cancer, subject 622, sample ID 23


title: Pool113_RS2_Plate7-1-P22-H1


title: Pool113_RS2_Plate7-1-P22-E2


title: Primary colon cancer, subject 655, sample ID 16


title: NWT_2

description: S. Enteritidis, WT, nalidixic acid, 8 h


title: Normal liver, subject 722, sample ID 31

source_name: Normal liver

value: Normal liver


title: Pool113_RS2_Plate7-1-P22-G2


title: Normal liver, subject 705, sample ID 28


title: Normal liver, subject 655, sample ID 19


title: Pool113_RS2_Plate7-1-P22-D14


title: Normal colon mucosa, subject 819, sample ID 7

source_name: Normal colon mucosa

value: Normal colon mucosa


title: Normal colon mucosa, subject 761, sample ID 22


title: Pool113_RS2_Plate7-1-P22-C13


title: Pool113_RS2_Plate7-1-P22-D1


title: Pool113_RS2_Plate7-1-P22-C1


title: Pool113_RS2_Plate7-1-P22-B2


title: Normal colon mucosa, subject 684, sample ID 6


title: Pool113_RS2_Plate7-1-P22-B14


title: Normal colon mucosa, subject 722, sample ID 30


title: Normal colon mucosa, subject 655, sample ID 17


title: Pool113_RS2_Plate7-1-P22-E1


title: Normal colon mucosa, subject 618, sample ID 14


title: Pool113_RS2_Plate7-1-P22-A2


title: Pool113_RS2_Plate7-1-P22-B13


title: Primary colon cancer, subject 684, sample ID 4


title: Pool113_RS2_Plate7-1-P22-A14


title: Liver metastasis, subject 722, sample ID 37

source_name: Liver metastasis

value: Liver metastasis


title: Liver metastasis, subject 684, sample ID 5


title: Liver metastasis, subject 705, sample ID 27


title: Liver metastasis, subject 663, sample ID 26


title: Pool113_RS2_Plate6-6-O1-O23

source_name: brain

value: AUD


title: Pool113_RS2_Plate6-6-O1-P11


title: Pool113_RS2_Plate6-6-O1-O11


title: Pool113_RS2_Plate6-6-O1-P23


title: Pool113_RS2_Plate6-6-O1-P12


title: Liver metastasis, subject 655, sample ID 18


title: Liver metastasis, subject 656, sample ID 20


title: Liver metastasis, subject 622, sample ID 25


title: Liver metastasis, subject 622, sample ID 24


title: Pool113_RS2_Plate6-6-O1-N23


title: Pool113_RS2_Plate6-6-O1-M24


title: Liver metastasis, subject 442, sample ID 2


title: Liver metastasis, subject 618, sample ID 15


title: Pool113_RS2_Plate6-6-O1-M23


title: Pool113_RS2_Plate6-6-O1-M12


title: Normal colon mucosa, subject 442, sample ID 3


title: Pool113_RS2_Plate6-6-O1-L24


title: Pool113_RS2_Plate6-6-O1-P24


title: Normal colon mucosa, subject 1144, sample ID 10


title: Liver metastasis, subject 1291, sample ID 12


title: Pool113_RS2_Plate6-6-O1-L23


title: Liver metastasis, subject 1231, sample ID 11


title: Pool113_RS2_Plate6-6-O1-L11


title: Liver metastasis, subject 1144, sample ID 9


title: SW620 cell line

description: cDNA-Capture RNA

value: human colon cancer cell line

value: Metastatic colon cancer


title: Pool113_RS2_Plate6-6-O1-K24


title: SW480 cell line

description: cDNA-Capture RNA


title: Pool113_RS2_Plate6-6-O1-N12


title: LoVo cell line

description: cDNA-Capture RNA

value: LoVo


title: HCT116 cell line

description: cDNA-Capture RNA


title: Pool113_RS2_Plate6-6-O1-J11


title: Pool113_RS2_Plate6-6-O1-I24


title: KFT, replicate 2, ATAC-seq 1

city: Stanford

first: Laura

middle: D

last: Attardi

address: 269 Campus Drive

institute: Stanford University

description:
ATAC-seq
AK2

data_processing:
ATAC-seq reads were trimmed of adapter sequences using Skewer (version 0.2.2, https://github.com/relipmoc/skewer), aligned to the mouse genome (mm10) using Bowtie2 (version 2.4.0, https://github.com/BenLangmead/bowtie2), and sorted based on genomic location and indexed using Samtools (version 1.3.1, https://github.com/samtools/samtools). Peak calling and differential peak analysis were performed using the ‘ChrAccR’ package in R (version 0.9.17, https://github.com/GreenleafLab/ChrAccR) with the sorted BAM file as input using the default parameters. The setConfigElement “doPeakCalling” was used with “annotationPeakGroupAgreePerc” at 1 to generate the conserved peaks list.
Assembly: mm10
Supplementary files format and content: raw counts for all peaks for all samples

source_name: lung

extract_protocol:
KT, KFT, and KPT mice were transduced with Ad5-SPC-Cre and harvested for cell sorting at 10 weeks post-transduction. Non-transduced lungs were used as a control. Briefly, lungs were perfused with 10 mL of ice-cold PBS and placed in a sterile dish on ice. Lungs were finely minced with sterile scissors and razor blades and resuspended in 6 mL digestion media (RPMI with 2.5 mg of Liberase TL (Sigma-Aldrich) and 25 µg/mL DNase (Sigma Aldrich)). Lungs were rotated for 45 minutes at 37ºC. Tubes were briefly cooled on ice, and then samples were passed through a 40 µM filter. 5 mL of FACS buffer (10% FBS, 2 mM EDTA, 25 µg/mL DNase in DPBS) was added and tubes were spun for 5 minutes at 300g. Cells were resuspended in ACK lysing buffer (Gibco), incubated for 1 minute on ice, and quenched with 8 mL of FACS buffer. Cells were washed 2x with FACS buffer, resuspended with biotinylated primary antibodies (CD45, BioLegend 103104 30-F11; CD31, BioLegend 102404 390; F4/80, BioLegend 123106 BM8; Ter119, BioLegend 116204 TER-119, 1:800 in FACS buffer) and incubated for 20 minutes on ice. After washing 2x, cells were resuspended in streptavidin-APC secondary antibody (BioLegend 405207, 1:800) for 20 minutes on ice. Cells were washed 2x and resuspended in FACS buffer with 1 µg/mL DAPI, filtered through a 40 µM filter, and sorted using a Sony SH800S cell sorter. Data were analyzed using the default Sony SH800S software and FCS Express (Version 7, De Novo Software).
ATAC-sequencing was performed as previously described. Two independent ATAC-sequencing experiments were performed, one with KT and KPT mice and the second with KT and KFT cells. Briefly, 5x10^5 cells were sorted and washed 2x in FACS buffer without DNase added. Nuclei were then isolated, lysed, and incubated with Tn5 transposase precisely as described. Transposed DNA was then isolated using the MinElute Reaction Cleanup Kit (Qiagen). Libraries were prepared by amplifying DNA for 5 cycles with NEBNext 2x MasterMix (NEB), after which qPCR was run on samples to determine the number of additional cycles needed. After any additional amplifications were performed, libraries were purified using the MinElute Reaction Cleanup Kit (Qiagen). Samples were sequenced on a NextSeq500 (Illumina) (KT vs. KFT experiment).

value: lung

value: KFT


title: Pool113_RS2_Plate6-6-O1-K12


title: KT, replicate 2, ATAC-seq 1

description:
ATAC-seq
AK4

value: KT


title: Pool113_RS2_Plate6-6-O1-I23

value: brain


title: Pool113_RS2_Plate6-6-O1-K23


title: Pool113_RS2_Plate6-6-O1-J23


title: KFT, replicate 1, ATAC-seq 1

description:
ATAC-seq
AK1


title: Pool113_RS2_Plate6-6-O1-H12


title: Pool113_RS2_Plate6-6-O1-H23


title: S1bko_4N_sorted_spermatocytes

city: Dresden

first: Rolf

last: Jessberger

state: Saxony

address: Fetscherstraße 74

department: Institut für Physiologische Chemie

institute: Technische Universität Dresden

data_processing:
bcl2fastq2 version 2.19.1 was used to generate fastq files.
Alignment of the reads to the mouse reference (mm10) was done with GSNAP (v2018-07-04), and Ensembl gene annotation version 92 was used to detect splice sites. Here, the standard GSNAP parameters were used for the alignment.
TPM values were generated with Kallisto (0.43.1) which only needs an index of the transcriptome. This index was created with the Ensembl gene annotation version 92 and the gtf_to_fasta script from the tophat package. All samples were collected into a single spreadsheet where each row is a gene and two columns show the TPM values in their respective samples. The other columns are annotation information from Ensembl
Assembly: mm10
Supplementary files format and content: bfx1258.tpm-quantification.xlsx: All samples were collected into a single spreadsheet where each row is a gene and two columns show the TPM values in their respective samples. The other columns are annotation information from Ensembl

source_name: testis

extract_protocol:
Total RNA was extracted from sorted spermatocytes and also from total testis with TRIzol  reagent (Invitrogen Inc.) according to the manufacturer’s guidelines. Total amount of RNA  was solubilized in RNAse free water and quantified using nanodrop for qPCR or  tapestation for RNA sequencing.
mRNA was isolated from DNAse treated total RNA using the NEBNext rRNA depletion Kit (human, mouse, rat) from New England Biolabs (NEB) according to the manufacturer’s instructions. Final elution was done in 5ul nuclease free water. Samples were then directly subjected to the workflow for strand specific RNA-Seq library preparation (NEBNext Ultra II Directional RNA Library Prep, NEB). For ligation custom adaptors were used (Adaptor-Oligo 1: 5'-ACA CTC TTT CCC TAC ACG ACG CTC TTC CGA TCT-3', Adaptor-Oligo 2: 5'-P-GAT CGG AAG AGC ACA CGT CTG AAC TCC AGT CAC-3'). After ligation adapters were depleted by a XP bead purification (Beckman Coulter) adding beads in a ratio of 1:0.9. Dual indexing was done during the following PCR enrichment (15 cycles, 65°C) using custom amplification primers carrying the index sequence indicated with ‘NNNNNNN’. (Primer1: AAT GAT ACG GCG ACC ACC GAG ATC TAC ACT CTT TCC CTA CAC GAC GCT CTT CCG ATC T, primer2: CAA GCA GAA GAC GGC ATA CGA GAT NNNNNNNN GTG ACT GGA GTT CAG ACG TGT GCT CTT CCG ATC T). After two more XP bead purifications (1:0.9) libraries were quantified using the Fragment Analyzer (Agilent). Libraries were equimolarly pooled before sequencing them with a length of 75bp in single end mode on an Illumina NextSeq500 system to a depth of at least 40 mio reads.

value: testis

value: primary cells

value: spermatocytes

value: SMC1beta knockout


title: KT, replicate 1, ATAC-seq 1

description:
ATAC-seq
AK3


title: s_1_1bko1a_4N

data_processing:
bcl2fastq2 version 2.19.1 was used to generate fastq files.
Alignment of the reads to the mouse reference (mm10) was done with GSNAP (v2018-07-04), and Ensembl gene annotation version 92 was used to detect splice sites. Here, the standard GSNAP parameters were used for the alignment.
TPM values were generated with Kallisto (0.43.1) which only needs an index of the transcriptome. This index was created with the Ensembl gene annotation version 92 and the gtf_to_fasta script from the tophat package. All samples were collected into a single spreadsheet where each row is a gene and two columns show the TPM values in their respective samples. The other columns are annotation information from Ensembl
Assembly: mm10
Supplementary files format and content: bfx1211.tpm-quantification.xlsx: All samples were collected into a single spreadsheet where each row is a gene and two columns show the TPM values in their respective samples. The other columns are annotation information from Ensembl

value: SMC1beta knockout overexpressing SMC1alpha


title: Pool113_RS2_Plate6-6-O1-H11

value: PTLp

value: male


title: Pool113_RS2_Plate6-6-O1-G24

value: female


title: WT_4N_spermatocytes_1D

data_processing:
bcl2fastq2 version 2.19.1 was used to generate fastq files.
The Nf-core/atacseq pipeline (software version from 28.05.2020) was run with --genome mm10 and default settings otherwise. The pipeline is very comprehensive and automatically runs all required steps, including raw read QC, adapter trimming, alignment, filtering, and the generation of normalized coverage tracks.
In addition, we run Macs2 to identify broad and narrow peaks of enriched ATAC-seq signal with the custom parameters -g mm -B -q 0.05 --nomodel --extsize 200 --shift -100 --nolamda --keep-dup -f BAM --call-summits (narrow peaks), and --broad respectively (broad peaks).
Assembly: mm10
Supplementary files format and content: bigWig (normalized coverage tracks)

extract_protocol:
Seminiferous tubules were isolated from the testes of mice after removal of tunica  albuginea. Single cell suspension were prepared by passing the cells through the 40 μm  strainer. Cells were collected in collected in PBS and washed one time. Then pellet was  resuspended in FACS incubation buffer (HBSS supplemented with 20 mM HEPES (pH  7.2), 1.2 mM MgSO4 , 1.3 mM CaCl 2 , 6.6 mM sodium pyruvate, 0.05% lactate, glutamine,  and 1% fetal calf serum) at a density of 2 million cells/ml. Then 5 μg/ml of Hoechst 33342  was added and cells were incubated for 1hr at 32°C in a water bath. Before the sorting 2  μg/ml of propidium iodide (PI) is added to exclude the dead cells. Meiocytes were sorted  with 85 μm in an ARIA II (BD Biosciences). PI and Hoechst were excited using lasers 488  nm and 355 nm respectively. 685 LP and 710/40 BP filter were used to detect PI signal.  Hoechst blue signal was detected using 600 LP and 620/10 BP filters in front of first  detector and Hoechst red was detected with 440/40 BP filter in front of the second  detector. Cells were collected in PBS and frozen at −80°C for subsequent RNA  sequencing, qPCR and protein extraction. For ATAC sequencing 5000 cells per genotype  were collected. FlowJo (Tree Star Inc.) and FACSDiva software were used for cell sorting  and data analysis.
Library preparation was prepared according to the 10x genomics guidelines. 5000 spematocytes were sorted into 30 µl PBS and transposition is carried in 10 µl of reaction buffer.  Following transposition DNA was purified either with bead based methods or with Qiagen MinElute Kit. Index PCR was performed in 25 µl of reaction buffer mixture to prepare the libraries. Libraries were purified twice with 1.3x volume of GE beads. Size distribution were analyzed with fragment analyzer. Library size distribution were analyzed by the Fragment Analyzer (company) and samples diluted in 1:3 ratio.

value: SMC1beta WT


title: Pool113_RS2_Plate6-6-O1-G12

data_processing:
Reads trimed with Cutadapt for adapters and low quality bases (Phred score >= 20)
The resulting files are mapped to in-silico bisulfite converted reference genome using Bismark.
The raw BAM file will be filtered using samtools to filter reads by MAPQ > 10 and use Picard to remove PCR duplicates
Tab-delimited files (ALLC files) describing the quantity of unmethylated and methylated cytosine base calls will be generated with in-house developing package using the filtered BAM files
Assembly: mm10
Supplementary files format and content: tab-delimited files (ALLC files) describing the quantity of unmethylated and methylated cytosine base calls. Columns are: 1. Chromosome, 2. Position, 3. Strand, 4. Cytosin Context, 5. methylated base call, 6. total mapped base call, 7. not used, place holder column
Library strategy: snmC-seq2 & 3

value: AUD


title: s_1_WT_4N


title: Pool113_RS2_Plate6-6-O1-G23


title: s1bko_4N_spermatocytes_tube__6


title: Pool113_RS2_Plate6-6-O1-F24


title: s1bko1a_4N_spermatocytes_tube__7


title: HT29 cell line

description: cDNA-Capture RNA

value: human colon cancer cell line

value: Primary colon cancer


title: Pool113_RS2_Plate6-6-O1-J12


title: WT_4N_spermatocytes_tube__8


title: Pool113_RS2_Plate6-6-O1-F12


title: Pool113_RS2_Plate6-6-O1-F11


title: H3K27ac.shMyh9.2

data_processing:
CHIP-seq data analysis was aligned using bowtie against mm10 genome version
HOMER was used for peak calling and generating bigwig files
Assembly: mm10
Supplementary files format and content: Prosessed files contain bigwig CHIP-seq signal

extract_protocol:
Chromatin was eluted from the antibody/protein G beads by incubating at 65 °C for 30 minutes with gentle vortex. To reverse cross-links, 6 uL of 5 M NaCl and 2 uL of Proteinase K were added into the cleared supernatant which contains eluted chromatin and incubated at 65 °C for 2 hours. And DNA from all samples was purified using spin columns and stored at -20 °C for qPCR and sequencing.
2.5ng of ChIP DNA was used to prepare libraries for Next Generation Sequencing using the NEBNext Ultra II DNA kit (New England Biolabs, Ipswich, MA), according to manufacturer's direction

value: YUMM2.1 cell line

tag: factor

value: EV

value: KD

tag: replicate


title: H3K27ac.shMyh9.1


title: H3K4me3.shMyh9.2


title: Pool113_RS2_Plate6-6-O1-D12

extract_protocol:
Approximately two weeks after the AAVretro injection, brains were extracted from the 56-63 day old INTACT mice, immediately submerged in ice-cold slicing buffer (2.5mM KCl, 0.5mM CaCl2, 7mM MgCl2, 1.25mM NaH2PO4, 110mM sucrose, 10mM glucose and 25mM NaHCO3) that was bubbled with carbogen, and sliced into 0.6 mm coronal sections starting from the frontal pole. From each AAVretro-injected brain, the slices were kept in the ice-cold dissection buffer from which selected brain regions (Supplementary Table 1) were manually dissected under a fluorescent dissecting microscope (Olympus SZX16), following the Allen Mouse Common Coordinate Framework (CCF), Reference Atlas, Version 3 (2015) (Extended Data Fig. 1). The dissected brain tissues were transferred to prelabeled microcentrifuge tubes, immediately frozen in dry ice, and subsequently stored at -80oC.   For each dissected brain region, samples from 2 males and 2 females were pooled separately as biological replicates for nuclei preparation. The 2-mL glass tissue dounce homogenizer and pestles (Sigma-Aldrich D8938-1SET) were pre-chilled on ice. Nuclei were prepared using a modified protocol as reported by Lacar et al., 201622. In summary, the frozen brain tissues were transferred to the dounce homogenizer with 1 mL ice-cold NIM buffer (0.25M sucrose, 25mM KCl, 5mM MgCl2, 10mM Tris-HCl (pH7.4), 1mM DTT (Sigma 646563), 10μl of protease inhibitor (Sigma P8340)), with 0.1% Triton X-100 and 5μM Hoechst 33342 (Invitrogen H3570), and gently homogenized on ice with the pestle 10-15 times. The homogenate was transferred to pre-chilled microcentrifuge tubes and centrifuged at 1000 rcf for 8 min at 4oC to pellet the nuclei. The pellet was resuspended in 1 mL ice-cold NIM buffer, and again centrifuged at 1000 rcf for 8 min at 4oC. The pellet was then resuspended in 450 μL of ice-cold NSB buffer (0.25M sucrose, 5mM MgCl2, 10mM Tris-HCl (pH7.4), 1mM DTT, 9ul of Protease inhibitor), and filtered through 40μM cell strainer. The filtered nuclei suspension was incubated on ice for at least 30 minutes with 50μl of nuclease-free BSA for at least 10 minutes, then incubated with GFP antibody, Alexa Fluor 488 (Invitrogen, A-21311) and anti-NeuN antibody (EMD Millipore MAB377) conjugated with Alexa Fluor 647 (Invitrogen A20173). GFP+/NeuN+ single nuclei were isolated using fluorescence-activated nuclei sorting (FANS) on a BD Influx sorter with 100μm nozzle, and sorted into 384-well plates preloaded with 2μl of digestion buffer for snmC-seq (20 mL digestion buffer consists of 10 mL M-digestion buffer (2×, Zymo D5021-9), 1 ml Proteinase K (20 mg, Zymo D3001-2-20), 9 mL water, and 10 µL unmethylated lambda DNA (100 pg/µL, Promega, D1521)). The collected plates were incubated at 50oC for 20 minutes then stored at -20 oC.
The bisulfite conversion and library preparation were performed following the detailed snmC-seq2 protocol as previously described (Luo, C. et al., Nat. Commun. 2018, 9(1):3824.) or snmC-seq3 protocol described in (Liu, H. et al., Biorxiv. 2023:2023-04.). The libraries were sequenced on Illumina Novaseq 6000 using the S4 flow cell 2 x 150 bp mode.


title: Control

city: Marseille

first: Romain

last: Fenouil

address: Parc Scientifique et Technologique de Luminy - Case 906

department: CIML

country: France

institute: CNRS

description: 3' mRNA library: read1 file contains cell barcode and UMI; read2 file contains transcript

data_processing:
FASTQ raw files were aligned to the mouse mm10 genome using Cell Ranger software (v2.0.0), which performs filtering, barcode counting, and unique molecular identifier (UMI) counting.
Quality control (QC) was performed to identify poor quality cells for downstream analyses. Cells with less than 200 or more than 4000 (potential doublets) detected genes, and cells with more than 10% mitochondrial gene expression (apoptotic cells) or less than 5% ribosomal genes were excluded from analyses.
Assembly: mm10
Supplementary files format and content: Cellranger output: barcodes.tsv is a list of filtered barcodes associated with count matrix
Supplementary files format and content: Cellranger output: genes.tsv is a list of filtered features associated with count matrix
Supplementary files format and content: Cellranger output: matrix.mtx is the (sparse) matrix containing feature counts across all selected barcodes

source_name: Peyer's patch (n=88)

extract_protocol:
Peyer's patches were digested for 40 min at room temperature in RPMI cell culture medium containing collagenase II/DNase I. All subsequent procedures were at 0–4°C. CD11c+ cells were enriched using anti-CD11c microbeads and an AutoMACS magnetic cell separator according to manufacturer’s instructions. CD11c+ cells were preincubated on ice for 10 min with 2.4G2 antibody to block Fc receptors and stained for the surface markers CD11c, MHCII, SIRPa, Bst2, CD4, CD11b, XCR1 and CD24. Cell viability was evaluated using LIVE/DEAD™ Fixable Blue Dead Cell Stain Kit (Life Technologies). Live cDC1s, cDC2s, LysoDC and macrophages were sorted using a FACSAria III and processed according to the ChromiumTM Single Cell 3’ Reagent Guidelines from 10X genomics.
RNA library was prepared using the Chromium Single Cell 3’ kit protocol from 10X genomics (California, USA)

treatment_protocol: Intraperitoneal injection of 10 µg of R848 or 125µg of CpG in 100 µL of sterile PBS for 9 hours

tag: mouse strain

value: Peyer's patch (n=88)

value: Phagocytes

tag: library type

value: mRNA

value: No treatment


title: Pool113_RS2_Plate6-6-O1-D11

tag: tissue

value: brain

tag: source


title: Pool113_RS2_Plate6-6-O1-C24

tag: target

tag: Sex


title: Pool113_RS2_Plate6-6-O1-D23


title: Pool113_RS2_Plate6-6-O1-F23


title: Pool113_RS2_Plate6-6-O1-C23


title: H3K27ac.shNC.2

source_name: YUMM2.1 cell line

value: WT


title: Pool113_RS2_Plate6-6-O1-C12


title: IgG.shMyh9.1

value: IgG


title: H3K27ac.shNC.1


title: Pool113_RS2_Plate6-6-O1-A24

value: PTLp


title: Pool113_RS2_Plate6-6-O1-B23

value: male


title: Pool113_RS2_Plate6-6-O1-B11


title: R848

source_name: Peyer's patch (n=90)

value: female

value: Peyer's patch (n=90)

value: intraperitoneal injection of 10 µg R848 for 9 hours


title: H3K4me3.shNC.1


title: IgG.shNC.2


title: Pool113_RS2_Plate6-6-O1-A23

value: AUD


title: IgG.shNC.1


title: Pool113_RS2_Plate6-6-O1-D24


title: Pool113_RS2_Plate6-6-O1-A12


title: Pool113_RS2_Plate6-6-O1-E24


title: CpG

source_name: Peyer's patch (n=85)

value: Peyer's patch (n=85)

value: intraperitoneal injection of 125 µg CpG for 9 hours


title: H3K4me3.shMyh9.1

value: YUMM2.1 cell line

value: EV


title: H3K27ac.bHLH.1

value: bHLH


title: IgG.bHLH.2 (H3K27ac control)


title: IgG.bHLH.1 (H3K27ac control)


title: Pool113_RS2_Plate6-5-E7-P9


title: Pool113_RS2_Plate6-6-O1-A11


title: Pool113_RS2_Plate6-5-E7-P21


title: Pool113_RS2_Plate6-5-E7-P10


title: Pool113_RS2_Plate6-5-E7-O10


title: H3K27ac.WT.2


title: H3K4me3.shNC.2


title: H3K27ac.WT.1


title: Pool113_RS2_Plate6-5-E7-N9


title: Pool113_RS2_Plate6-5-E7-N22


title: IgG.WT.2 (H3K27ac control)


title: IgG.shMyh9.2

value: KD


title: Pool113_RS2_Plate6-5-E7-N21


title: Pool113_RS2_Plate6-5-E7-N10


title: Pool113_RS2_Plate6-5-E7-M22


title: IgG.EV.2 (H3K27ac control)


title: IgG.WT.1 (H3K27ac control)


title: IgG.EV.1 (H3K27ac control)


title: H3K27me3.bHLH.2


title: Pool113_RS2_Plate6-5-E7-M21


title: H3K27ac.EV.2


title: H3K27ac.EV.1


title: Pool113_RS2_Plate6-5-E7-L9


title: H3K27ac.bHLH.2


title: Pool113_RS2_Plate6-5-E7-M10


title: Pool113_RS2_Plate6-5-E7-O22


title: Pool113_RS2_Plate6-5-E7-L22


title: H3K4me3.bHLH.1


title: H3K4me3.bHLH.2


title: IgG.bHLH.1


title: H3K27me3.WT.2


title: H3K27me3.bHLH.1


title: H3K27me3.WT.1


title: Pool113_RS2_Plate6-5-E7-K22


title: Pool113_RS2_Plate6-5-E7-L10


title: H3K4me3.WT.2


title: Pool113_RS2_Plate6-5-E7-K10


title: Pool113_RS2_Plate6-5-E7-K21


title: Pool113_RS2_Plate6-5-E7-J9


title: H3K4me3.WT.1


title: IgG.WT.2


title: Pool113_RS2_Plate6-5-E7-J22


title: IgG.WT.1


title: Pool113_RS2_Plate6-5-E7-J21


title: Pool113_RS2_Plate6-5-E7-I10


title: H3K27me3.EV.1


title: Pool113_RS2_Plate6-5-E7-H9


title: H3K27me3.EV.2


title: Pool113_RS2_Plate6-5-E7-I22


title: H3K4me3.EV.2


title: H3K4me3.EV.1


title: Pool113_RS2_Plate6-5-E7-L21


title: IgG.bHLH.2


title: IgG.EV.2


title: Pool113_RS2_Plate6-5-E7-H22


title: IgG.EV.1


title: Pool113_RS2_Plate6-5-E7-G21


title: Pool113_RS2_Plate6-5-E7-H10


title: Pool113_RS2_Plate6-5-E7-H21


title: Pool113_RS2_Plate6-5-E7-F22


title: Y21.dH.shM4.1

data_processing:
RNA-Seq data analysis was done with rsem (ver. 1.2.3) and mm10 genome with ensemble transcriptome information
DESeq2 was used for count normalization and differentail expression analysis
Assembly: mm10
Supplementary files format and content: Prosessed files contains the raw counts for each gene

extract_protocol:
All RNA samples were extracted with TRIzol Reagent (Invitrogen, Cat. #15596018) according to the manufacture's instruction and cleaned by DNA-free DNAase Treatment and Removal Reagents (Ambion, #AM1906) to get rid of DNA contamination before submission for RNA sequencing.
3' mrna-seq libraries were generated from 100ng of DNAseI treated total RNA using the quantSeq FWD Library Preparation Kit (Lexogen, Vienna, Austria)

tag: arntl

value: ctr

value: dH

tag: myh9 sirna


title: Pool113_RS2_Plate6-5-E7-F21

value: brain


title: Pool113_RS2_Plate6-5-E7-E22


title: Y21.dH.shM4.2


title: Y21.dH.shM2.1


title: Y21.dH.shNC.2

value: shNC


title: Pool113_RS2_Plate6-5-E7-F10


title: Y21.dH.shNC.1


title: Pool113_RS2_Plate6-5-E7-E21


title: Pool113_RS2_Plate6-5-E7-E10


title: Pool113_RS2_Plate6-5-E7-D9


title: Y21.WT.shM4.1

value: WT


title: Pool113_RS2_Plate6-5-E7-D22

value: PTLp


title: Y21.WT.shM2.2


title: Y21.WT.shM4.2


title: Pool113_RS2_Plate6-5-E7-D10


title: Y21.WT.shM2.1


title: Y21.EV.shM4.1


title: Pool113_RS2_Plate6-5-E7-F9

value: male


title: Y21.WT.shNC.2


title: Y21.EV.shM4.2


title: Y21.WT.shNC.1


title: Pool113_RS2_Plate6-5-E7-C22

value: female


title: Pool113_RS2_Plate6-5-E7-C21


title: Pool113_RS2_Plate6-5-E7-B9


title: Pool113_RS2_Plate6-5-E7-C10


title: Y21.EV.shM2.2


title: Y21.EV.shM2.1


title: Y21.EV.shNC.2


title: Y21.EV.shNC.1


title: Pool113_RS2_Plate6-5-E7-B21


title: Pool113_RS2_Plate6-5-E7-A22


title: Y21.dH.shM2.2


title: Pool113_RS2_Plate6-5-E7-B10


title: Y17.bH.2

source_name: YUMM1.7 cell line


title: Y17.bH.1


title: Pool113_RS2_Plate6-4-G16-O20


title: Pool113_RS2_Plate6-4-G16-O19


title: Y17.WT.1


title: Y17.WT.2


title: Pool113_RS2_Plate6-4-G16-N7


title: Pool113_RS2_Plate6-5-E7-A10


title: Y17.EV.2


title: Pool113_RS2_Plate6-4-G16-N19


title: Pool113_RS2_Plate6-4-G16-M20


title: Pool113_RS2_Plate6-4-G16-M19


title: Pool113_RS2_Plate6-4-G16-L8


title: Y21.KO.WT.2

value: KO


title: Y17.EV.1


title: Y21.KO.WT.1


title: Pool113_RS2_Plate6-4-G16-L7


title: Y21.KO.EV.2


title: Y21.KO.EV.1


title: Y21.bH.2


title: Pool113_RS2_Plate6-4-G16-K7


title: Pool113_RS2_Plate6-4-G16-O8


title: Y21.bH.1


title: Pool113_RS2_Plate6-4-G16-K8


title: Pool113_RS2_Plate6-4-G16-L19


title: Pool113_RS2_Plate6-4-G16-K20


title: Y21.WT.2


title: Y21.EV.2


title: Y21.WT.1


title: Pool113_RS2_Plate6-4-G16-J8


title: Pool113_RS2_Plate6-5-E7-D21


title: Pool113_RS2_Plate6-4-G16-J20


title: Pool113_RS2_Plate6-4-G16-J7


title: Y21.EV.1


title: B16.KO.2

source_name: B16 cell line


title: Pool113_RS2_Plate6-4-G16-J19


title: Pool113_RS2_Plate6-4-G16-I8


title: Pool113_RS2_Plate6-4-G16-I20


title: Pool113_RS2_Plate6-4-G16-H7


title: C57BI6.ACSS2i.4

source_name: tumor

extract_protocol:
Bulk tumor tissue was pulverized as indicated above and RNA was extracted using Trizol and purified using an RNeasy Plus kit (Qiagen).
200 ng of total RNA was used to prepare library for Illumina Sequencing using the Quant-Seq 3’mRNA-Seq Library Preparation Kit (Lexogen, Austria)

value: C57BI/6 mouse

value: tumor


title: B16.ctr.1


title: B16.ctr.2


title: C57BI6.ACSS2i.3


title: Pool113_RS2_Plate6-4-G16-I19

value: AUD


title: Pool113_RS2_Plate6-4-G16-H20


title: C57BI6.ACSS2i.2


title: C57BI6.ACSS2i.1


title: C57BI6.vehicle.4

value: vehicle


title: Pool113_RS2_Plate6-4-G16-K19


title: Pool113_RS2_Plate6-4-G16-G8


title: C57BI6.vehicle.2


title: C57BI6.vehicle.3


title: Pool113_RS2_Plate6-4-G16-F8


title: B16.KO.1


title: C57BI6.vehicle.1


title: Pool113_RS2_Plate6-4-G16-G19


title: NGS.ACSS2i.3

value: NGS mouse


title: NGS.ACSS2i.2


title: Pool113_RS2_Plate6-4-G16-F7


title: NGS.ACSS2i.1


title: Pool113_RS2_Plate6-4-G16-F20


title: Pool113_RS2_Plate6-4-G16-E8


title: Y21.KO.bH.2


title: NGS.vehicle.1


title: NGS.vehicle.3


title: NGS.vehicle.2


title: Pool113_RS2_Plate6-4-G16-E20


title: Pool113_RS2_Plate6-4-G16-D20


title: Hippocampus prion VU846 injected rep2

city: Bearsden

first: Pawel

last: Herzyk

address: Wolfson Wohl Cancer Research Centre, Garscube Estate

department: College of Medical, Veterinary and Life Sciences

institute: University of Glasgow

data_processing:
Fastq files were generated with bcl2fastq v.1.8.4 Illumina software
All downstream analysis was done using Galaxy bioinformatics data analysis platform (version 0.72)
The raw fastq files containing paired-end 2 x 75bp reads were pre-processed to trim the 3’ end adapter and to trim the low quality reads using Trimomatic (version 0.36.5) software using Q25 quality threshold.
The reads were then mapped to the “mouse-mm10” genome using HISAT2 tool (version 2.1.0) and gene-level expression quantification was performed with the StringTie tool (version 1.3.3.2).
Differential expression was then analysed with DESeq2 software (version 2.11.40.2).
Assembly: mouse-mm10
Supplementary files format and content: Tab delimited (.tsv) sample specific gene counts generated with SpringTie tool (version 1.3.3.2) within Galaxy platform (version 0.72)

source_name: Hippocampus

extract_protocol:
RNA from each hippocampus was extracted using the RNeasy Plus Mini Kit (Qiagen, Manchester), following the manufacturer’s instructions.
RNA libraries were prepared from totalRNA using TruSeq Stranded mRNA Library Prep kit and standard Illumina protocols

treatment_protocol: All the animal work and care done with the hemizygous MloxP Tg37 transgenic mice that overexpresses mouse cellular prion protein (PrPC) were carried out under a project license according to United Kingdom Home Office Regulations.

tag: genotype

value: Hemizygous Tg37

value: prion + VU846

tag: inoculation

value: post natal week 4

tag: injection period

value: post inoculation week 7 to 11


title: Hippocampus prion VU846 injected rep1

tag: treatment


title: Pool113_RS2_Plate6-4-G16-D19


title: Hippocampus prion VU846 injected rep3


title: Pool113_RS2_Plate6-4-G16-C8


title: Pool113_RS2_Plate6-5-E7-A21


title: Hippocampus prion Vehicle injected rep2

value: prion + vehicle


title: Hippocampus prion Vehicle injected rep1


title: Hippocampus prion Vehicle injected rep3


title: Hippocampus ctr VU846 injected rep3

value: control + VU846


title: Pool113_RS2_Plate6-4-G16-B8

value: brain


title: Pool113_RS2_Plate6-4-G16-C19


title: Pool113_RS2_Plate6-4-G16-B20


title: Pool113_RS2_Plate6-4-G16-D7


title: Pool113_RS2_Plate6-4-G16-D8


title: Hippocampus ctr VU846 injected rep1


title: Pool113_RS2_Plate6-4-G16-F19


title: Pool113_RS2_Plate6-4-G16-A20


title: brain, Tg2576, 11-month old female [zr2924_79]

first: Sangkyu

last: KIM

address: 1430 Tulane Ave.

department: Center for Aging, Medicine

institute: Tulane University Health Sciences Center

data_processing:
Data alignment and mapping were done using Bismark, and methylation calling was done using Bismark Methylation Extractor
Processed BAM files were analyzed using the R package methylKit
Assembly: mm10
Supplementary files format and content: methyRaw text files (tab-delimited) contain genomic locations of covered CpG sites and their numbers in 12 samples (numbered in the order of samples listed above).

source_name: a mixture of hipocampus and cortex brain

extract_protocol:
Mouse genomic DNA was prepared using Quick-DNA Microprep Plus Kit
DNA samples (≥ 500 ng) were subjected to Classic RRBS (Reduced representation bisulfite sequencing) by Zymo Research. The bisulfite sequencing service included bisulfite treatment, library construction and quality control, paired-end data generation (Illumina HiSeq 2000)

value: 11-month old


title: Hippocampus ctr VU846 injected rep2


title: Hippocampus ctr Vehicle injected rep2

value: control + vehicle


title: Pool113_RS2_Plate6-4-G16-B19

value: PTLp

value: male


title: Hippocampus ctr Vehicle injected rep1


title: Pool113_RS2_Plate6-4-G16-A19


title: Hippocampus ctr Vehicle injected rep3


title: brain, Tg2576, 11-month old female [zr2924_78]

value: a mixture of hipocampus and cortex brain

value: female


title: Pool113_RS2_Plate6-4-G16-C20


title: brain, Tg2576, 11-month old female [zr2924_77]


title: Pool113_RS2_Plate6-3-G18-P6


title: Pool113_RS2_Plate6-4-G16-B7


title: Kdney, Diabetes, ZT20, rep1

city: Zhengzhou

first: Xiao-Qian

last: Li

state: Henan

address: No. 1, East of Jianshe Street, Erqi District

department: Nephrology Hospital

institute: the First Affiliated Hospital of Zhengzhou University

description: DM-fpkm

data_processing:
The transcriptome sequencing and analysis were conducted by OE biotech Co., Ltd. (Shanghai, China). In brief, the libraries were sequenced on the Illumina sequencing platform (HiSeqTM 2500) and 125bp/150bp paired-end reads were generated. Raw data (raw reads) were processed using Trimmomatic. The reads containing ploy-N and the low quality reads were removed to obtain the clean reads.
Fragments per kilobase million (FPKM) value of each gene was calculated using cufflinks, and the read counts of each gene were obtained by htseq-count.
Supplementary files format and content: FPKM

source_name: renal cortex

extract_protocol:
The RNA isolation were conducted by OE biotech Co., Ltd. (Shanghai, China). Total RNA was isolated using the mirVana miRNA Isolation Kit (AM1561; Thermo Fisher Scientific, MA, USA) following the manufacturer’s protocol.
The library preparation were conducted by OE biotech Co., Ltd. (Shanghai, China). The libraries were constructed using TruSeq Stranded mRNA LTSample Prep Kit (Illumina, San Diego, CA, USA)

value: renal cortex

tag: zeitgeber time_(zt)

tag: strain

value: C57BLKS/J db/db

tag: group

value: Diabetes


title: Kdney, Diabetes, ZT20, rep2

description: DM-fpkm


title: Kdney, Diabetes, ZT20, rep3

description: DM-fpkm


title: Kdney, Diabetes, ZT16, rep3

description: DM-fpkm


title: Kdney, Diabetes, ZT16, rep2

description: DM-fpkm


title: Pool113_RS2_Plate6-4-G16-A8

first: Joseph

last: Ecker

address: 10010 North Torrey Pines Road

institute: HHMI-Salk-Institute

value: AUD


title: Kdney, Diabetes, ZT16, rep1

description: DM-fpkm


title: Kdney, Diabetes, ZT12, rep3

description: DM-fpkm


title: Pool113_RS2_Plate6-3-G18-P18


title: Kdney, Diabetes, ZT12, rep2

description: DM-fpkm


title: brain, Tg2576,11-month old male [zr2924_74]


title: Pool113_RS2_Plate6-3-G18-O6


title: Kdney, Diabetes, ZT8, rep2

description: DM-fpkm


title: Pool113_RS2_Plate6-3-G18-O18


title: brain, Tg2576,11-month old male [zr2924_73]


title: Kdney, Diabetes, ZT8, rep3

description: DM-fpkm


title: Pool113_RS2_Plate6-4-G16-H19


title: brain, Tg2576,11-month old male [zr2924_72]


title: Pool113_RS2_Plate6-3-G18-O17


title: Pool113_RS2_Plate6-3-G18-P5


title: brain, wild-type, 11-month old female [zr2924_76]

value: Wild type


title: Kdney, Diabetes, ZT4, rep1

description: DM-fpkm


title: brain, Tg2576,11-month old male [zr2924_70]


title: Kdney, Diabetes, ZT0, rep2

description: DM-fpkm


title: brain, wild-type, 11-month old female [zr2924_75]


title: Pool113_RS2_Plate6-3-G18-N5


title: Pool113_RS2_Plate6-3-G18-P17


title: Kdney, Diabetes, ZT0, rep3

description: DM-fpkm


title: Pool113_RS2_Plate6-3-G18-N6


title: brain, wild-type, 11-month old male [zr2924_68]


title: Kdney, Diabetes, ZT12, rep1

description: DM-fpkm


title: Kdney, Diabetes, ZT0, rep1

description: DM-fpkm


title: Kdney, Diabetes, ZT8, rep1

description: DM-fpkm


title: Kdney, Control, ZT20, rep2

description: Ctrl-fpkm

value: C57BLKS/J m/m

value: Control


title: Kdney, Control, ZT20, rep3

description: Ctrl-fpkm


title: Kdney, Diabetes, ZT4, rep3

description: DM-fpkm


title: Pool113_RS2_Plate6-3-G18-N18


title: brain, wild-type, 11-month old female [zr2924_65]


title: Kdney, Control, ZT16, rep3

description: Ctrl-fpkm


title: Kdney, Diabetes, ZT4, rep2

description: DM-fpkm


title: Kdney, Control, ZT20, rep1

description: Ctrl-fpkm


title: Kdney, Control, ZT16, rep1

description: Ctrl-fpkm


title: kidney papilla, KRP473

city: Saint Louis

first: Sanjay

last: Jain

state: MO

address: 660 S. Euclid Ave.

department: Division of Nephrology

institute: Washington University in Saint Louis

description: 10x Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v6.1.1 (first 3 samples) and v 7.1.0 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Doublets were identified and removed with DoubletDetection software (v2.4.0),  nuclei were clustered with pagoda2, and UMAP calculated with Seurat v4.
Standardized anatomical and cell type nomenclature was used to annotate cell types and subtypes, based on the collaborative KPMP and HuBMAP definitions
Papillary samples were selected, and cell types with less than 100 nuclei were excluced
Assembly: GRCh38-2020-A
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Papilla

extract_protocol:
7 sections (40um) of Human kidney sample were put into 1.5 ml tube on dry ice, then on wet ice, add 1 ml of ice cold NEB/PIC buffer with RNase inhibitor. After pipette sections up and down using a P1000 tip (cut the end off to increase pore size) to disperse and dissolve OCT, then using regular P1000 tip, pipette to further dissociate tissues into manageable sizes. Transfer solution to Dounce homogenizer, gently dounce tissue on ice: (with pestle A first, followed with pestle B). Transfer dounced solution to a 15 ml tube. Wash dounce with 1 ml of ice cold NEB/PIC buffer with RNase inhibitor, and then add this into the same tube. Incubate on ice for 10 min. Pass supernatant through 30 um CellTrics filter to a new 15 ml tube, bring up to 10 ml with PBSE/PIC with RNase inhibitor. Spin at 900xg for 10 min at 4 0C to pellet nuclei, then remove the supernatant, re-suspend the pellet in 20 ul of 1X Nuclei buffer. After count nuclei using hemocytometer, adjust the nuclei concentration to 3100-5000 nuclei/ul.
Library was performed according to the manufacter’s instructions (single cell 3’ v3 protocol, 10x Genomics). Briefly, GCs were resuspended in the master mix and loaded together with partitioning oil and gel beads into the chip to generate the gel bead-in-emulsion (GEM). The poly-A RNA from the cell lysate contained in every single GEM was retrotranscripted to cDNA, which contains an Ilumina R1 primer sequence, Unique Molecular Identifier (UMI) and the 10x Barcode. The pooled barcoded cDNA was then cleaned up with Silane DynaBeads, amplified by PCR and the apropiated sized fragments were selected with SPRIselect reagent for subsequent library construction. During the library construction Ilumina R2 primer sequence, paired-end constructs with P5 and P7 sequences and a sample index were added.
snRNA-seq

value: Papilla

tag: organ

value: kidney

value: Male

tag: age

tag: disease state

value: stone disease


title: Kdney, Control, ZT12, rep2

description: Ctrl-fpkm


title: Kdney, Control, ZT12, rep3

description: Ctrl-fpkm


title: Kdney, Control, ZT12, rep1

description: Ctrl-fpkm


title: Pool113_RS2_Plate6-3-G18-M18

city: La Jolla

value: brain


title: Pool113_RS2_Plate6-3-G18-M6


title: Pool113_RS2_Plate6-3-G18-M17


title: kidney papilla, K2200020

description: 10x Genomics

value: healthy control


title: kidney medulla, K2100202

description: 10x Genomics

source_name: Medulla

value: Inner Medulla, Outer Medulla


title: Kdney, Control, ZT8, rep2

description: Ctrl-fpkm

value: male


title: Kdney, Control, ZT4, rep3

description: Ctrl-fpkm


title: Kdney, Control, ZT8, rep3

description: Ctrl-fpkm


title: brain, Tg2576, 11-month old female [zr2924_67]

value: a mixture of hipocampus and cortex brain

value: 11-month old


title: Kdney, Control, ZT8, rep1

description: Ctrl-fpkm

value: renal cortex


title: kidney papilla, K2100055

description: 10x Genomics

value: Female


title: Pool113_RS2_Plate6-3-G18-L6

value: PTLp

value: female


title: Kdney, Control, ZT16, rep2

description: Ctrl-fpkm


title: Pool113_RS2_Plate6-3-G18-L17

value: AUD


title: Pool113_RS2_Plate6-3-G18-K6


title: PBMC, EYVC4, healthy, vaccinated, TCR

city: New Haven

first: Anis

last: Barmada

state: CT

address: 300 Cedar Street

department: Department of Immunobiology

institute: Yale University

description: 10x Genomics, TCR

data_processing:
The single-cell transcriptome sequencing data were aligned and processed using CellRanger v5.0.1.
Assembly: GRCh38 reference genome.
Supplementary files format and content: CellRanger output files: filtered feature-barcode matrices (filtered_feature_bc_matrix.h5) and BCR/TCR annotations (filtered_contig_annotations.csv).

source_name: Blood

extract_protocol:
PBMCs were first isolated by Ficoll-Paque PLUS (GE Healthcare) or Lymphoprep (STEMCELL Technologies) density gradient centrifugation. Cells were subsequently washed twice in phosphate buffered saline (PBS) and resuspended in complete RPMI 1640 (cRPMI) medium (Lonza) containing 10% fetal bovine serum (FBS), 2 mM glutamine, and 100 U/ml each of penicillin and streptomycin (Invitrogen). PBMCs were then stored at 10^6 cells/ml in 10% dimethyl sulfoxide (DMSO) in FBS and stored in -80 °C overnight before further storage in liquid nitrogen. Serum was isolated by centrifugation of serum tubes and saving the supernatant in aliquots, which were flash frozen in liquid nitrogen prior to cryopreservation in -80 °C. All patient PBMCs were processed and cryopreserved within 1-6 hours of blood draw. Cryopreserved PBMCs were thawed in a water bath at 37 °C for ~2 minutes and removed from the water bath when a tiny ice crystal remained. Cells were transferred to a 15 mL conical tube of pre-warmed growth medium. The cryovial was rinsed with additional growth medium (10% FBS in DMEM) to recover leftover cells, and the rinse medium was added to the 15 mL conical tube while gently shaking the tube. Thawed PBMCs were centrifuged at 400g for 8 minutes at RT, and the supernatant was removed without disrupting the cell pellet. The pellet was resuspended in 1X PBS with 2% FBS, and cells were filtered with a 30 μM cell strainer. Cellular concentration was adjusted to 1,000 cells/μL based on the cell count and cells were immediately loaded onto the 10x Chromium Next GEM Chip G, according to the manufacturer's user guide (Chromium Next GEM SingleCell V(D)J Reagent Kits v1.1). We aimed to obtain a yield of ~10,000 cells per lane.
cDNA libraries for gene expression and TCR/BCR sequencing were generated according to manufacturer’s instructions (Chromium Next GEM SingleCell V(D)J Reagent Kits v1.1). Each library was then sequenced on an Illumina NovaSeq 6000 platform.

value: Blood

tag: cell type

value: PBMC

tag: condition

value: Healthy, vaccinated


title: PBMC, EYVC3, healthy, vaccinated, TCR

description: 10x Genomics, TCR

tag: tissue


title: Kdney, Control, ZT0, rep3

description: Ctrl-fpkm

value: C57BLKS/J m/m

value: Control


title: Kdney, Control, ZT0, rep1

description: Ctrl-fpkm


title: Kdney, Control, ZT0, rep2

description: Ctrl-fpkm


title: Kdney, Control, ZT4, rep1

description: Ctrl-fpkm


title: kidney papilla, KRP429

description: 10x Genomics

value: Papilla

value: kidney

value: Male

value: stone disease


title: PBMC, EYVC2, healthy, vaccinated, TCR

description: 10x Genomics, TCR


title: Ribosome profiling in Nrde2 knockout mES cells_ replicate 2

city: Basel

first: Fabio

last: Mohn

address: Maulbeerstrasse 66

country: Switzerland

institute: Friedrich Miescher Institute for Biomedical Research

description:
Riboseq_cpm_per_gene.txt
Nrde2KO_Riboseq_r2

data_processing:
Library strategy: Ribo-seq
Samples were pooled and sequenced on an Illumina HiSeq 2500 instrument.
BCLIP-seq and Ribo-seq samples were demultiplexed using pyBarcodeFilter.py. RNA-seq demultiplexing and fastq conversion were performed with bcl2fastq2 v1.17.
BCLIP-seq preprocessed reads (collapsed and adaptor trimmed) were aligned (splicing-aware) to the mouse genome (mm10) including the transcriptome annotation of GENCODE release M23 using STAR version 2.7.0a (Dobin et al., 2013) with the parameters: --outFilterMultimapNmax 20 --outFilterMismatchNoverLmax 0.05
RNA-seq and Ribo-seq reads were mapped (splicing-aware) to the mouse genome (mm10) including the transcriptome annotation of GENCODE release M23 using STAR version 2.7.3a. with the parameters: --outFilterMultimapNmax 100 --outFilterMismatchNoverLmax 0.05 --outSAMmultNmax 1. Counts per million tables were generated using the featureCounts function from the Rsubread package with the parameters: useMetaFeatures=TRUE,allowMultiOverlap=FALSE, minOverlap=5, countMultiMappingReads=FALSE, fraction=FALSE, minMQS=255, strandSpecific=1 for Ribo and 2 for RNAseq.
Genome_build: mm10
Supplementary_files_format_and_content: bigWig files were generated by first using samtools to filter out only uniquely mapping reads, then per base coverage was calculated using bedtools, counts were normalized to 1 mio genome mapping reads and bigwigs were generated using bedGraphToBigWig (USCS tools). Bed files containing peak positions were generated from the .narrowPeak output file from MACS2. HiC allValidPairs files were generated by HiC-Pro 2.9.0. 4C wig files for replicates were generated from the filtered_reads output from peak_C by adding a wiggle file header.

source_name: embryonic stem (ES) cells

growth_protocol: Mouse embryonic stem cells were grown under standard conditions in medium containing serum, LIF and 2i.

extract_protocol:
Cells were lysed and digested with Benzonase. Ribosome footprints were isolated as a band migrating slightly slower than a 35 nt ssDNA oligo on a 15 % Novex TBE-Urea polyacrylamide gel. After ribosomal RNA depletion, ribosome footprints were polyadenylated and purified using SPRI beads. For details see Flemr et al, 2021.
RNA was reverse transcribed with SuperScript II (ThermoFisher 18064014) in the presence of a template-switching oligo. The resulting cDNA was purified with SPRI beads and libraries were amplified using NEBNext Ultra II Q5 master mix (NEB M0544L). For a detailed protocol, see Flemr et al, 2021.
BCLIP-seq

treatment_protocol: Mtrex-KO and Nrde2-KO cells were treated with 100 nM 4-hydroxytamoxifen for 3 and 4 days, respectively. Cells expressing proteins fused to FKBP12F36V degron were treated with 500 nM dTAG-13 for 24 hours. The indicated RNA-seq samples were treated with 0.1 mg/ml cycloheximide (CHX) for 4 hours.

value: embryonic stem (ES) cells

tag: genetic background

value: hybrid 129-C57BL/6

value: Nrde2 knockout


title: Pool113_RS2_Plate6-3-G18-K18

source_name: brain

value: brain

tag: source

tag: target

tag: Sex


title: Ribosome profiling in Nrde2 knockout mES cells_ replicate 1

description:
Riboseq_cpm_per_gene.txt
Nrde2KO_Riboseq_r1

tag: genotype


title: Ribosome profiling in wt mES cells_ replicate 2

description:
Riboseq_cpm_per_gene.txt
Nrde2WT_Riboseq_r2

value: wt


title: Pool113_RS2_Plate6-3-G18-K17

value: PTLp

value: male


title: Kdney, Control, ZT4, rep2

description: Ctrl-fpkm

value: renal cortex


title: PBMC, EYVC1, healthy, vaccinated, TCR

description: 10x Genomics, TCR

value: Blood


title: PBMC, EYVC3, healthy, vaccinated, BCR

description: 10x Genomics, BCR

value: PBMC


title: PBMC, EYVC4, healthy, vaccinated, BCR

description: 10x Genomics, BCR

value: Healthy, vaccinated


title: Pool113_RS2_Plate6-3-G18-J6

value: AUD

value: female


title: Pool113_RS2_Plate6-3-G18-J5


title: RNAseq in untreated Nrde2 knockout mES cells, replicate 1

description:
RNAseq_cpm_per_gene.txt
Nrde2KO_noCHX_RNAseq_r1

data_processing:
Samples were pooled and sequenced on an Illumina HiSeq 2500 instrument.
BCLIP-seq and Ribo-seq samples were demultiplexed using pyBarcodeFilter.py. RNA-seq demultiplexing and fastq conversion were performed with bcl2fastq2 v1.17.
BCLIP-seq preprocessed reads (collapsed and adaptor trimmed) were aligned (splicing-aware) to the mouse genome (mm10) including the transcriptome annotation of GENCODE release M23 using STAR version 2.7.0a (Dobin et al., 2013) with the parameters: --outFilterMultimapNmax 20 --outFilterMismatchNoverLmax 0.05
RNA-seq and Ribo-seq reads were mapped (splicing-aware) to the mouse genome (mm10) including the transcriptome annotation of GENCODE release M23 using STAR version 2.7.3a. with the parameters: --outFilterMultimapNmax 100 --outFilterMismatchNoverLmax 0.05 --outSAMmultNmax 1. Counts per million tables were generated using the featureCounts function from the Rsubread package with the parameters: useMetaFeatures=TRUE,allowMultiOverlap=FALSE, minOverlap=5, countMultiMappingReads=FALSE, fraction=FALSE, minMQS=255, strandSpecific=1 for Ribo and 2 for RNAseq.
Genome_build: mm10
Supplementary_files_format_and_content: bigWig files were generated by first using samtools to filter out only uniquely mapping reads, then per base coverage was calculated using bedtools, counts were normalized to 1 mio genome mapping reads and bigwigs were generated using bedGraphToBigWig (USCS tools). Bed files containing peak positions were generated from the .narrowPeak output file from MACS2. HiC allValidPairs files were generated by HiC-Pro 2.9.0. 4C wig files for replicates were generated from the filtered_reads output from peak_C by adding a wiggle file header.

extract_protocol:
Total RNA was extracted using the Absolutely RNA Miniprep kit (Agilent) with on-column DNase treatment
Libraries were prepared using the TruSeq Stranded Total RNA library prep kit (Illumina 20020597) according to manufacturers instructions.

value: untreated


title: RNAseq in untreated Nrde2 knockout mES cells, replicate 2

description:
RNAseq_cpm_per_gene.txt
Nrde2KO_noCHX_RNAseq_r2


title: Pool113_RS2_Plate6-3-G18-N17


title: RNAseq in CHX-treated Nrde2 knockout mES cells, replicate 2

description:
RNAseq_cpm_per_gene.txt
Nrde2KO_CHX_RNAseq_r2

value: CHX-treated


title: RNAseq in CHX-treated wt (conditional Nrde2 knockout) mES cells, replicate 1

description:
RNAseq_cpm_per_gene.txt
Nrde2WT_CHX_RNAseq_r1


title: RNAseq in CHX-treated wt (conditional Nrde2 knockout) mES cells, replicate 2

description:
RNAseq_cpm_per_gene.txt
Nrde2WT_CHX_RNAseq_r2


title: RNAseq in untreated wt (conditional Nrde2 knockout) mES cells, replicate 2

description:
RNAseq_cpm_per_gene.txt
Nrde2WT_noCHX_RNAseq_r2


title: PBMC, EYVC2, healthy, vaccinated, BCR

description: 10x Genomics, BCR


title: PBMC, EYVC1, healthy, vaccinated, BCR

description: 10x Genomics, BCR


title: PBMC, EYVC4, healthy, vaccinated, GEX

description: 10x Genomics, GEX


title: Pool113_RS2_Plate6-3-G18-I6


title: Pool113_RS2_Plate6-3-G18-J17


title: RNAseq in untreated wt (conditional Nrde2 knockout) mES cells, replicate 1

description:
RNAseq_cpm_per_gene.txt
Nrde2WT_noCHX_RNAseq_r1


title: Ribosome profiling in wt mES cells_ replicate 1

description:
Riboseq_cpm_per_gene.txt
Nrde2WT_Riboseq_r1


title: Pool113_RS2_Plate6-3-G18-K5


title: RNAseq in CHX-treated Ccdc174-depleted mES cells, replicate 2

description:
RNAseq_cpm_per_gene.txt
Ccdc174dTAG_CHX_RNAseq_r2


title: RNAseq in CHX-treated Nrde2 knockout mES cells, replicate 1

description:
RNAseq_cpm_per_gene.txt
Nrde2KO_CHX_RNAseq_r1


title: RNAseq in untreated Ccdc174-depleted mES cells, replicate 2

description:
RNAseq_cpm_per_gene.txt
Ccdc174dTAG_noCHX_RNAseq_r2


title: Pool113_RS2_Plate6-3-G18-H6


title: RNAseq in CHX-treated Ccdc174-depleted mES cells, replicate 1

description:
RNAseq_cpm_per_gene.txt
Ccdc174dTAG_CHX_RNAseq_r1


title: RNAseq in CHX-treated wt (Ccdc174-FKBP12F36V fusion) mES cells, replicate 2

description:
RNAseq_cpm_per_gene.txt
Ccdc174WT_CHX_RNAseq_r2


title: RNAseq in CHX-treated wt (Ccdc174-FKBP12F36V fusion) mES cells, replicate 1

description:
RNAseq_cpm_per_gene.txt
Ccdc174WT_CHX_RNAseq_r1


title: Pool113_RS2_Plate6-3-G18-H5


title: RNAseq in untreated Ccdc174-depleted mES cells, replicate 1

description:
RNAseq_cpm_per_gene.txt
Ccdc174dTAG_noCHX_RNAseq_r1


title: PBMC, EYVC1, healthy, vaccinated, GEX

description: 10x Genomics, GEX


title: RNAseq in untreated wt (Ccdc174-FKBP12F36V fusion) mES cells, replicate 1

description:
RNAseq_cpm_per_gene.txt
Ccdc174WT_noCHX_RNAseq_r1


title: PBMC, EYVC3, healthy, vaccinated, GEX

description: 10x Genomics, GEX


title: RNAseq in Mtrex knockout mES cells, replicate 1

description:
RNAseq_cpm_per_gene.txt
MtrexKO_RNAseq_r1

value: Mtrex knockout


title: RNAseq in wt (conditional Mtrex knockout) mES cells, replicate 2

description:
RNAseq_cpm_per_gene.txt
MtrexWT_RNAseq_r2


title: RNAseq in wt (conditional Mtrex knockout) mES cells, replicate 1

description:
RNAseq_cpm_per_gene.txt
MtrexWT_RNAseq_r1


title: PBMC, R-P1, myocarditis, recovered, TCR

description: 10x Genomics, TCR

value: Myocarditis, recovered


title: RNAseq in Nrde2D174R mES cells, replicate 2

description:
RNAseq_cpm_per_gene.txt
Nrde2D174R_RNAseq_r2

value: embryonic stem (ES) cells

value: Nrde2 D174R mutation


title: Pool113_RS2_Plate6-3-G18-G6


title: PBMC, R-P4, myocarditis, recovered, TCR

description: 10x Genomics, TCR


title: Pool113_RS2_Plate6-3-G18-G18


title: RNAseq in Nrde2D174R mES cells, replicate 1

description:
RNAseq_cpm_per_gene.txt
Nrde2D174R_RNAseq_r1

value: hybrid 129-C57BL/6


title: Pool113_RS2_Plate6-3-G18-F6

value: brain


title: RNAseq in Nrde2d200 mES cells, replicate 2

description:
RNAseq_cpm_per_gene.txt
Nrde2d200_RNAseq_r2

value: N-terminal 200 amino acid deletion of Nrde2


title: Pool113_RS2_Plate6-3-G18-G17

value: PTLp


title: RNAseq in Nrde2 knockout mES cells, replicate 2

description:
RNAseq_cpm_per_gene.txt
Nrde2KO_RNAseq_r2

value: Nrde2 knockout


title: Pool113_RS2_Plate6-3-G18-I17

value: male


title: PBMC, R-P4, myocarditis, recovered, BCR

description: 10x Genomics, BCR

value: Blood


title: PBMC, R-P3, myocarditis, recovered, BCR

description: 10x Genomics, BCR

value: PBMC


title: Pool113_RS2_Plate6-3-G18-F5


title: RNAseq in Nrde2 knockout mES cells, replicate 1

description:
RNAseq_cpm_per_gene.txt
Nrde2KO_RNAseq_r1


title: Pool113_RS2_Plate6-3-G18-H17


title: RNAseq in Mtrex knockout mES cells, replicate 2

description:
RNAseq_cpm_per_gene.txt
MtrexKO_RNAseq_r2


title: RNAseq in wt (conditional Nrde2 knockout) mES cells, replicate 2

description:
RNAseq_cpm_per_gene.txt
Nrde2WT_RNAseq_r2

value: wt


title: RNAseq in wt (conditional Nrde2 knockout) mES cells, replicate 1

description:
RNAseq_cpm_per_gene.txt
Nrde2WT_RNAseq_r1


title: Pool113_RS2_Plate6-3-G18-F17

value: AUD


title: RNAseq in untreated wt (Ccdc174-FKBP12F36V fusion) mES cells, replicate 2

description:
RNAseq_cpm_per_gene.txt
Ccdc174WT_noCHX_RNAseq_r2


title: PBMC, R-P1, myocarditis, recovered, BCR

description: 10x Genomics, BCR


title: PBMC, R-P4, myocarditis, recovered, GEX

description: 10x Genomics, GEX