title: s338_SerE4-L001-R1-001_ctrl_35_b


title: s339_SerE5-L001-R1-001_p01_acetophenone_35_b

status: Public on Oct 06 2024

type: SRA

city: Durham

first: Aashutosh

last: Vihani

state: NC

address: 264 CARL Building

country: USA

institute: Duke University

library_source: transcriptomic

data_processing:
Library strategy: pS6-IP-Seq
STAR alignment
RSEM read quantification
Genome_build: modified GENCODE M25
Supplementary_files_format_and_content: expected_count, TPM, FPKM

molecule: total RNA

organism: Mus musculus

source_name: Whole olfactory mucosa

extract_protocol:
Antibody: Cell Signaling D68F8
Qiagen RNeasy Mini Kit #74104
Library construction protocol: Illumina Nexterra XT DNA Library Preparation Kit #15032354

tag: strain

tag: group

value: experimental

tag: odor

value: acetophenone

tag: concentration

tag: differential expression number

tag: trial

value: b


title: s336_SerE2-L001-R1-001_p01_acetophenone_35_a

value: a


title: s332_SerD10_ctrl_34_c

value: control

value: c


title: s351_SerG2-L001-R1-001_p01_tmt_36_a

value: tmt


title: s333_SerD11_1p_ntmt_34_c

value: ntmt


title: s329_SerD07_ctrl_34_b


title: s322_SerC12-GTAGAGGA_100p_sbt_33_b

value: sbt


title: s324_SerD02_1p_sbt_33_c


title: s323_SerD01_ctrl_33_c


title: s321_SerC11-AAGAGGCA_1p_sbt_33_b


title: s320_SerC10-CGAGGCTG_ctrl_33_b


title: s327_SerD05_1p_ntmt_34_a


title: s335_SerE1-L001-R1-001_ctrl_35_a


title: s316_SerC6-TAGGCATG_100p_2m2t_32_c


title: s315_SerC5-GGACTCCT_1p_2m2t_32_c


title: s319_SerC9-GCTACGCT_100p_sbt_33_a


title: s314_SerC4-TCCTGAGC_ctrl_32_c


title: s312_SerC2-CGTACTAG_1p_2m2t_32_b


title: s310_SerB9-GCTACGCT_100p_2m2t_32_a


title: s309_SerB8-CAGAGAGG_1p_2m2t_32_a


title: s313_SerC3-AGGCAGAA_100p_2m2t_32_b


title: s330_SerD08_1p_ntmt_34_b


title: s326_SerD04_ctrl_34_a


title: s325_SerD03_100p_sbt_33_c


title: s307_SerB3-AGGCAGAA_100p_tmt_31_c


title: s311_SerC1-TAAGGCGA_ctrl_32_b


title: s306_SerB2-CGTACTAG_1p_tmt_31_c


title: s304_SerA12-GTAGAGGA_100p_tmt_31_b


title: s302_SerA10-CGAGGCTG_ctrl_31_b


title: s303_SerA11-AAGAGGCA_1p_tmt_31_b


title: s305_SerB1-TAAGGCGA_ctrl_31_c


title: s301_SerA9-GCTACGCT_100p_tmt_31_a


title: s308_SerB7-CTCTCTAC_ctrl_32_a


title: s299_SerA7-CTCTCTAC_ctrl_31_a


title: s298_SerB12-GTAGAGGA_100p_acetophenone_30_c


title: s300_SerA8-CAGAGAGG_1p_tmt_31_a


title: s317_SerC7-CTCTCTAC_ctrl_33_a


title: s296_SerB10-CGAGGCTG_ctrl_30_c


title: s295_SerB6-TAGGCATG_100p_acetophenone_30_b


title: s294_SerB5-GGACTCCT_1p_acetophenone_30_b


title: s292_SerA6-TAGGCATG_100p_acetophenone_30_a


title: s291_SerA5-GGACTCCT_1p_acetophenone_30_a


title: s288_29-2-Ci_1p_citral_29_c

value: citral


title: Donor_1_AAVS1_8_2

city: Baltimore

first: Josh

last: Weinstock

state: MD

address: 3100 Wyman Park Dr

institute: Johns Hopkins University

data_processing:
Adapters were trimmed from fastq files with cutadapt. Low-quality bases from reads were trimmed using the Phred algorithm implemented in seqtk. Reads were aligned with STAR and mapped to GRCh38. Gene counts from deduplicated reads were quantified using featureCounts.
Assembly: GRCh38
Supplementary files format and content: dedup_counts.txt stores gene counts from deduplicated reads

organism: Homo sapiens

source_name: CD4 T cells

growth_protocol: Primary CD25-CD4+ effector T cells were isolated from fresh Human Peripheral Blood Leukopaks (STEMCELL Technologies, #70500) from healthy donors, after institutional review board–approved informed written consent (STEMCELL Technologies). Peripheral blood mononuclear cells (PBMCs) were washed twice with a 1X volume of EasySep buffer (DPBS, 2% fetal Bovine Serum (FBS), 1mM pH 8.0 EDTA). The washed PBMCs were resuspended at 200E6 cells/mL in EasySep buffer and isolated with the EasySep™ Human CD4+CD127lowCD25+ Regulatory T Cell Isolation Kit (STEMCELL Technologies, #18063), according to the manufacturer’s protocol. Cells were seeded at 1x106 cells/mL in complete RPMI-1640 supplemented with 10% FCS, 2 mM L-Glutamine (Fisher Scientific #25030081), 10 mM HEPES (Sigma, #H0887-100ML), 1X MEM Non-essential Amino Acids (Fisher, #11140050), 1 mM Sodium Pyruvate (Fisher Scientific #11360070), 100 U/mL Penicillin-Streptomycin (Sigma, #P4333-100ML), and 50 U/mL IL-2 (Amerisource Bergen, #10101641) and stimulated with 6.25 uL/mL ImmunoCult™ Human CD3/CD28/CD2 T Cell Activator (STEMCELL Technologies, #10990). Following activation and electroporation, cells were split 1:2 every other day to maintain an approximate density of 1x106 cells/mL.

extract_protocol:
8 days after T cell isolation and activation, the cells were pelleted and resuspended at 1×106cells per 300 ul of RNA lysis buffer (Zymo, #R1060–1-100). Cells were pipette mixed and frozen at −80 until RNA isolation was performed. RNA was isolated using the Zymo-Quick RNA micro prep kit (#R1051) according to the manufacturer’s protocol with the following modifications: After thawing the samples, each tube was vortexed vigorously to ensure complete lysis prior to loading into the extraction columns. In lieu of the kit provided DNAse, RNA was eluted from the isolation column after the recommended washes and digested with Turbo-DNAse (Fisher Scientific, AM2238) at 37 C for 20 minutes. Following digestion, RNA was purified using the RNA Clean & Concentrator-5 kit (Zymo, #R1016) according to the manufacturer’s protocol. The resulting purified RNA was submitted to the UC Davis DNA Technologies and Expression Analysis Core to generate 3′ Tag-seq libraries with unique molecular indices (UMIs).
Barcoded sequencing libraries were prepared using the QuantSeq FWD kit (Lexogen) for multiplexed sequencing on an Hiseq 4000 (Illumina).

treatment_protocol: Custom crRNAs (Dharmacon) and Dharmacon Edit-R CRISPR-Cas9 Synthetic tracrRNA (Dharmacon, #U-002005-20) were resuspended in Nuclease Free Duplex Buffer (IDT, #11-01-03-01) at 160uM stock concentration. In a 96 well plate, each crRNA was combined with tracrRNA at a 1:1 molar ratio and incubated at 37°C for 30 minutes. Single-stranded donor oligonucleotides (ssODN; sequence: TTAGCTCTGTTTACGTCCCAGCGGGCATGAGAGTAACAAGAGGGTGTGGTAATATTACGGTACCGAGCACTATCGATACAATATGTGTCATACGGACACG, 100uM stock) was added to the complex at a 1:1 molar ratio and incubated at 37°C for 5 minutes. Finally, Cas9 protein (MacroLab, Berkeley, 40 µM stock) was added at a 1:2 molar ratio and incubated at 37°C for 15 minutes. The resulting RNPs were frozen at -80°C until the day of electroporation. 48 hours following effector T cell activation, the cells were pelleted at 100x g for 10 minutes and resuspended in room temperature Lonza P3 buffer (Lonza, catalog no. V4XP-3032) at 1.5x106 cells per 20 ul P3. The cells were combined with 5 ul aliquots of the thawed RNPs, transferred to a 96-well electroporation cuvette plate (Lonza, #VVPA-1002) and nucleofected with pulse code EH-115. Immediately following electroporation, the cells were gently resuspended in 90 ul warmed complete RPMI with IL-2 and incubated at 37 C for 15 minutes. After recovery, the cells were cultured in 96 well plates at 1x106 cells/mL for the duration of the experiment. To prevent edge effects, the guides were randomly distributed across each plate and the first and last column of each plate was excluded, being filled instead with PBS to prevent evaporation.

tag: cell type

value: CD4 T cells


title: s290_SerA4-TCCTGAGC_ctrl_30_a


title: s289_29-3-An_1p_anisaldehyde_29_c

value: anisaldehyde


title: s284_28-1-No_ctrl_29_b


title: s285_28-2-Ci_1p_citral_29_b


title: s287_29-1-No_ctrl_29_c


title: s286_28-3-An_1p_anisaldehyde_29_b


title: s293_SerB4-TCCTGAGC_ctrl_30_b


title: s275_25-1-No_ctrl_28_b


title: s281_27-1-No_ctrl_29_a


title: s278_26-1-No_ctrl_28_c


title: s274_24-3-Cy_p01_cyclopentanethiol_28_a

value: cyclopentanethiol


title: s277_25-3-Cy_p01_cyclopentanethiol_28_b


title: s283_27-3-An_1p_anisaldehyde_29_a


title: s272_24-1-No_ctrl_28_a


title: s273_24-2-Sk_p01_e2butene1thiol_28_a


title: s297_SerB11-AAGAGGCA_1p_acetophenone_30_c


title: s279_26-2-Sk_p01_e2butene1thiol_28_c


title: s271_mn12_1p_acetophenone_27_c


title: s270_mn11_1p_tbm_27_c

value: tbm


title: s269_mn10_ctrl_27_c


title: s318_SerC8-CAGAGAGG_1p_sbt_33_a


title: s268_mn9_1p_acetophenone_27_b


title: s266_mn7_ctrl_27_b


title: s280_26-3-Cy_p01_cyclopentanethiol_28_c


title: s263_mn4_ctrl_27_a


title: s264_mn5_1p_tbm_27_a


title: s276_25-2-Sk_p01_e2butene1thiol_28_b


title: s262_mn3_1p_2phenylethylalcohol_26_c


title: s282_27-2-Ci_1p_citral_29_a


title: s265_mn6_1p_acetophenone_27_a


title: s261_mn2_1p_2hexanone_26_c


title: s254_18-1-No_ctrl_26_a


title: s258_19-2-He_1p_2hexanone_26_b


title: s256_18-3-PEA_1p_2phenylethylalcohol_26_a


title: s255_18-2-He_1p_2hexanone_26_a


title: s259_19-3-PEA_1p_2phenylethylalcohol_26_b


title: s257_19-1-No_ctrl_26_b


title: s252_14-17mn11_1p_tbm_25_c


title: s246_14-17mn5_1p_tbm_25_a


title: s253_14-17mn12_1p_diacetyl_25_c

value: diacetyl


title: s247_14-17mn6_1p_diacetyl_25_a


title: s250_14-17mn9_1p_diacetyl_25_b


title: s243_10-13mn11_1p_butyricAcid_24_c

value: butyricAcid


title: s267_mn8_1p_tbm_27_b


title: s260_mn1_ctrl_26_c


title: s251_14-17mn10_ctrl_25_c


title: s248_14-17mn7_ctrl_25_b


title: s244_10-13mn12_1p_indole_24_c

value: indole


title: s245_14-17mn4_ctrl_25_a


title: s241_10-13mn9_1p_indole_24_b

value: experimental


title: s239_10-13mn7_ctrl_24_b


title: s240_10-13mn8_1p_butyricAcid_24_b


title: s238_10-13mn6_1p_indole_24_a


title: s249_14-17mn8_1p_tbm_25_b


title: s236_10-13mn4_ctrl_24_a


title: s237_10-13mn5_1p_butyricAcid_24_a


title: s234_10-13mn2_1p_paraCresol_23_c

value: paraCresol


title: s232_6-9mn12_1p_dimethyltrisulfide_23_b

value: dimethyltrisulfide

value: b


title: s231_6-9mn11_1p_paraCresol_23_b


title: s230_6-9mn10_ctrl_23_b

value: control


title: s228_6-9mn8_1p_paraCresol_23_a

value: a


title: s226_14-17mn3_1p_heptanal_21_c

value: heptanal

value: c


title: s225_14-17mn2_1p_3methyl1butanethiol_22_c


title: s220_1-5mn12_1p_3methyl1butanethiol_22_b


title: s242_10-13mn10_ctrl_24_c


title: s233_10-13mn1_ctrl_23_c


title: s227_6-9mn7_ctrl_23_a


title: s222_6-9mn2_1p_4methylAcetophenone_22_c


title: s215_1-5mn7_ctrl_22_a


title: s216_1-5mn8_1p_4methylAcetophenone_22_a


title: s213_6-9mn5_1p_2hac_21_c


title: s219_1-5mn11_1p_4methylAcetophenone_22_b


title: s218_1-5mn10_ctrl_22_b


title: s217_1-5mn9_1p_3methyl1butanethiol_22_a


title: s221_6-9mn1_ctrl_22_c


title: s229_6-9mn9_1p_dimethyltrisulfide_23_a


title: s235_10-13mn3_1p_dimethyltrisulfide_23_c


title: s212_6-9mn4_ctrl_21_c


title: s211_1-5mn6_1p_heptanal_21_b


title: s224_14-17mn1_ctrl_21a22_c


title: s210_1-5mn5_1p_2hac_21_b


title: s209_1-5mn4_ctrl_21_b


title: Mouse feces, WT_fostered_to_Plcb3_KO, DSS, rep4

city: La Jolla

first: Ikuo

last: Takazawa

state: CA

address: 9420 Athena Cir

institute: La Jolla Institute for Immunology

library_source: genomic

data_processing:
The library was sequenced using Illumina Miseq  with Miseq reagent kit v3 (600 cycles)
Generated FASTQ reads were processed with Illumina 16S metagenomics 1.0.1 pipeline (Illumina; basespace application)
The reads classified to the individual genus and species were divided by the total number of classified reads
to calculate the proportion
Assembly: Greengenes database
Supplementary files format and content: comma separated text files for taxonomy abundance of the samples
Supplementary files format and content: aggregated species' level counts in comma separated text file

molecule: genomic DNA

organism: feces metagenome

source_name: feces

extract_protocol:
Fecal pellets were collected from mice before and after DSS treatment. DNA was extracted from  approximately 20 mg of feces with QIAamp DNA Stool Mini Kit (QIAGEN) following manufacturer’s  protocol.
Libraries were prepared following 16S metagenomic sequencing library preparation guide  (Illunina)

tag: source

value: Mouse

tag: rna population

value: 16S rRNA

tag: tissue

value: feces

tag: treatment

value: DSS

tag: genotype


title: s208_1-5mn3_1p_heptanal_21_a


title: Mouse feces, WT_fostered_to_Plcb3_KO, DSS, rep2


title: Mouse feces, WT_fostered_to_Plcb3_KO, DSS, rep3


title: s207_1-5mn2_1p_2hac_21_a


title: Mouse feces, WT_fostered_to_Plcb3_KO, DSS, rep1


title: Mouse feces, WT_fostered_to_Plcb3_KO, H2O, rep4


title: s192_5000-S11_1p_2ethyl3methylPyrazine_19_c


title: s206_1-5mn1_ctrl_21_a


title: Mouse feces, WT_fostered_to_Plcb3_KO, H2O, rep3


title: s191_5000-S10_1p_hexylTiglate_19_c

value: hexylTiglate


title: Mouse feces, WT_fostered_to_Plcb3_KO, H2O, rep2


title: Mouse feces, WT_fostered_to_Plcb3_KO, H2O, rep1


title: s193_5000-S12_1p_isopropylTiglate_19_c

value: isopropylTiglate


title: s190_5000-S9_ctrl_19_c


title: Mouse feces, Plcb3_KO, DSS, rep5


title: Mouse feces, Plcb3_KO, DSS, rep3


title: Mouse feces, Plcb3_KO, DSS, rep2


title: s186_5000-S5_ctrl_19_b


title: s188_5000-S7_1p_2ethyl3methylPyrazine_19_b


title: s187_5000-S6_1p_hexylTiglate_19_b


title: Mouse feces, Plcb3_KO, DSS, rep4


title: Mouse feces, Plcb3_KO, DSS, rep1


title: s185_5000-S4_1p_isopropylTiglate_19_a


title: Mouse feces, WT, DSS, rep4

value: WT


title: s189_5000-S8_1p_isopropylTiglate_19_b


title: Mouse feces, WT, DSS, rep3


title: Mouse feces, WT, DSS, rep2


title: s183_5000-S2_1p_hexylTiglate_19_a


title: s181_4999-S12_1p_transCinnamaldehyde_18_c

value: transCinnamaldehyde


title: Mouse feces, WT, DSS, rep1


title: s178_4999-S9_ctrl_18_c


title: Mouse feces, Plcb3_KO, H2O, rep5


title: s177_4999-S8_1p_transCinnamaldehyde_18_b


title: s179_4999-S10_1p_2m2p_18_c


title: Mouse feces, Plcb3_KO, H2O, rep1


title: Mouse feces, Plcb3_KO, H2O, rep4


title: Mouse feces, WT, H2O, rep4


title: s174_4999-S5_ctrl_18_b


title: Mouse feces, Plcb3_KO, H2O, rep2


title: s175_4999-S6_1p_2m2p_18_b


title: Mouse feces, WT, H2O, rep2


title: s173_4999-S4_1p_transCinnamaldehyde_18_a


title: s171_4999-S2_1p_2m2p_18_a


title: Mouse feces, WT, H2O, rep3


title: Mouse feces, WT, H2O, rep1


title: s168_4761-S11_1p_aPinene_17_c

value: aPinene


title: s170_4999-S1_ctrl_18_a


title: s169_4761-S12_1p_bDamascone_17_c

value: experimental

value: bDamascone


title: s184_5000-S3_1p_2ethyl3methylPyrazine_19_a


title: s182_5000-S1_ctrl_19_a


title: Microlgia, Female 1 wk Control, sample 4

city: Rochester

first: Ania

middle: K.

last: Majewska

state: NY

address: 601 Elmwood Ave

department: Department of Neuroscience

institute: University of Rochester Medical Center

data_processing:
Raw reads generated from the Illumina basecalls were demultiplexed using bcl2fastq v2.19.1
Quality filtering and adapter removal was performed using FastP v.0.23.1.
Processed reads were then mapped to the mouse reference genome (GRCm39 + gencode-M31 annotation) using STAR_2.7.9a.
Read counts were quantified using both Subread-featureCounts v2.0.1 with “-s 0” indicating unstranded reads, and Salmon v1.5.2.
Assembly: GRCm39
Supplementary files format and content: tab delimited text file includes normalized counts for each sample.
Supplementary files format and content: The tximport package was used to import and summarize Salmon transcript-level abundance, estimated counts and transcript lengths into gene-level counts, which were then normalized.

source_name: Brain, cortex

extract_protocol:
Microglia were isolated using FACS. Total microglial RNA was extracted using the RNeasy Plus Micro Kit (Qiagen). RNA concentration was determined with the NanopDrop One spectrophotometer (NanoDrop) and RNA quality assessed with the Agilent Bioanalyzer 2100 (Agilent). 500 pg of total RNA was pre-amplified with the SMARTer Ultra Low Input kit v4 (Clontech) per manufacturer’s recommendations. The quantity and quality of the subsequent cDNA was determined using the Qubit Fluorometer 3.0 (Life Technnologies) and the Agilent Bioanalyzer 2100 (Agilent).
150pg of cDNA was used to generate Illumina compatible sequencing libraries with the NexteraXT library preparation kit (Illumina) per manufacturer’s protocols.

treatment_protocol: Mice were treated for 1 week prior to microglia isolation with PLX3397 or control chow.

value: Brain, cortex

value: Microglia

value: Female Control


title: Microlgia, Female 1 wk Control, sample 2


title: Microlgia, Female 1 wk Control, sample 3


title: s166_4761-S9_ctrl_17_c

value: control


title: s165_4761-S8_1p_bDamascone_17_b

value: b


title: Microlgia, Female 1 wk Control, sample 1


title: s164_4761-S7_1p_aPinene_17_b


title: Microglia, Female 1 wk PLX, sample 3

value: Female PLX


title: s163_4761-S6_p01_sbt_17_b

value: sbt


title: Microglia, Female 1 wk PLX, sample 1


title: s162_4761-S5_ctrl_17_b


title: s161_4761-S4_1p_bDamascone_17_a

value: a


title: s159_4761-S2_p01_sbt_17_a


title: Microlgia, Male 1 wk Control, sample 4

value: Male Control


title: s167_4761-S10_p01_sbt_17_c

value: c


title: s160_4761-S3_1p_aPinene_17_a


title: Microlgia, Male 1 wk Control, sample 3


title: s158_4761-S1_ctrl_17_a


title: Microlgia, Male 1 wk Control, sample 1


title: Microglia, Male 1 wk PLX, sample 4

value: Male PLX


title: Microlgia, Male 1 wk Control, sample 2


title: Microglia, Male 1 wk PLX, sample 3


title: Microglia, Male 1 wk PLX, sample 2


title: s153_4575-S2_77p_dhb_15_c

value: dhb


title: s151_4998-S7_10p_p2octanol_15_c


title: Microglia, Female 1 wk PLX, sample 4


title: s150_4575-S1_ctrl_15_c


title: Myc-CaP_Control_FVB

city: Ann Arbor

first: Arul

middle: M.

last: Chinnaiyan

state: MICHIGAN

address: 1500 E. Medical Center Dr

institute: University of Michigan

library_source: transcriptomic single cell

data_processing:
Per-sample FASTQ files were generated from the raw base call files using CellRanger mkfastq. The raw gene count matrices were generated from the FASTQ files using the CellRanger count command and the 10x supplied mm10 reference
Assembly: mm10
Supplementary files format and content: filtered gene by cell count matrix in h5 file

molecule: polyA RNA

source_name: Myc-CaP tumor

extract_protocol:
Tumor tissues were cut into small pieces and then digested PBS containing 2% FBS and 0.5 mg/ml collagenase D (Roche; #: COLLD-RO) and 0.25 mg/ml DNase I (Roche; #: 10104159001) for digestion at 37 ℃ for 30 minutes. The tissues were then filtered with 70 µm cell strainers, and then the cells were washed once with PBS. Next, the cells were stained with Zombie NIR™ (BioLegend; #: 423106) in PBS, blocked with anti-mouse CD16/32 (Biolegend; # 156604) in MACS, and stained with anti-CD45 (BD Biosciences; # 550994) in MACS for 12 minutes at room temperature. The live CD45+ cells were then sorted with a cell sorter (SONY SH800S). For pathway enrichment and identifying differently expressed genes (DEGs) in malignant cells, live CD45- cells were mixed 1:1 with live CD45+ cells, prior to subjection to scRNA-seq. The sequencing was performed using the Chromium Next GEM Single Cell 3' HT Kit v3.1 (Dual Index), a product from 10x Genomics, following the instructions from the manufacturer.
Chromium Next GEM Single Cell 3' HT Kit v3.1 (Dual Index), a product from 10x Genomics, was used following the instructions from the manufacturer.

value: FVB

value: Myc-CaP tumor

tag: cell line

value: Myc-CaP

value: Epithelial

value: WT


title: Myc-CaP_sgUba1_FVB


title: s147_4429-S10_10p_p2octanol_15_b

value: experimental


title: Myc-CaP_TAK243_FVB


title: Microglia, Male 1 wk PLX, sample 1

value: Brain, cortex

value: Microglia


title: Microglia, Female 1 wk PLX, sample 2


title: s146_4429-S9_ctrl_15_b

value: control


title: Mouse feces, Plcb3_KO, H2O, rep3

value: Mouse

value: 16S rRNA

value: feces


title: s148_4429-S11_10p_n2octanol_15_b

value: b


title: s145_4429-S8_77p_dhb_15_a

value: a


title: R3_PEBW

city: college station

first: Min

last: Feng

state: Texas

address: 200 Spence street

department: Chemical Engineering

institute: Texas A&M University

data_processing:
Adaptor sequences and low-quality reads were removed using Trimmomatic, The RNA-Seq reads were then mapped to the C. elegans genome using STAR 2.5.3a with default settings. Transcript abundance, measured as read counts per gene, was extracted using HTSeq. Differential gene expression analysis was performed using Featurecounts.
Assembly: c elegans ce11
Supplementary files format and content: DifferentialExpression_

organism: Caenorhabditis elegans

source_name: whole worms

growth_protocol: Worms were maintained on nematode growth media (NGM) at room temperature

extract_protocol:
Approximately 1000 worms per sample were collected and centrifuged to a final volume of 50 μl, then worms were washed three times with M9 buffer. Then 250 µl of TRIzol reagent (Invitrogen) was add to the worm pellet and worms were homogenized for 5 min. RNA was isolated by adding 50 µl of chloroform, followed by centrifugation to separate the aqueous phase. The aqueous phase was transferred to a new tube and mixed with isopropanol (125 µl) to precipitate RNA. The resulting RNA pellet was washed twice with 70% ethanol (250 µl). RNA pellets were air-dried and then re-suspended in RNase-free water. Any potential genomic DNA contamination was removed by DNaseI treatment using the TURBO DNA-free Kit (Invitrogen).
RNA libraries were prepared using TruSeq RNA library preparation kit following manufacture's protocol.

treatment_protocol: Synchronized L1 stage C. elegans worms were grown on NGM agar plates seeded with E. coli BW25113 bacteria. After reaching the desired developmental stage, worms were transferred to NGM agar plates with either wild-type E. coli BW25113 or the E. coli purE mutant. Following a 48-hour feeding period, worms underwent a 2-hour diet switch.

value: whole worms

value: wild-type N2

value: Fed E. coli purE mutant for 48 hours then swich to BW25113 diet for 2 hours


title: s141_4331-S12_100uM_MTMT_14_c

value: MTMT

value: c


title: R3_PE

value: Fed E. coli purE mutant for 48 hours then swich to E. coli purE mutant diet for 2 hours


title: Myc-CaP_Vehicle_FVB

value: FVB

value: Myc-CaP tumor

value: Myc-CaP

value: Epithelial

value: Vehicle


title: s142_4429-S5_ctrl_15_a

value: control


title: s143_4429-S6_10p_p2octanol_15_a

value: experimental


title: s152_4998-S8_10p_n2octanol_15_c


title: s139_4331-S10_100p_ebFarnesene_14_c

value: ebFarnesene


title: R3_BW

value: Fed BW25113 for 48 hours then swich to BW25113 diet for 2 hours


title: R3_BWPE

value: Fed BW25113 for 48 hours then swich to E. coli purE mutant diet for 2 hours


title: Myc-CaP_TAK243_T5 [SI_35012]

data_processing:
Transcripts were quantified by kallisto with mouse reference genome (mm10) and then summarized to obtain gene level counts and TPM.
Assembly: mm10
Supplementary files format and content: comma-delimited text file includes raw counts of each sample
Supplementary files format and content: comma-delimited text file includes normalized data in TPM of each sample

source_name: prostate tumor

extract_protocol:
RNA was extracted from Myc-CaP cells or Myc-CaP or B16-BL6 tumors using Qiagen RNA extraction kit. RNA quality was determined using a Bioanalyzer RNA Nano Chip
Poly-A selection was performed with Sera-Mag Oligo(dT)-Coated Magnetic Particles (38152103010150; GE Healthcare Life Sciences), and libraries were generated using a KAPA RNA HyperPrep kit (KK8541; Roche Sequencing Solutions).

value: prostate tumor

value: WT


title: s137_4331-S8_100uM_MTMT_14_b

value: b


title: R2_PEBW

value: whole worms

value: wild-type N2

value: Fed E. coli purE mutant for 48 hours then swich to BW25113 diet for 2 hours


title: s140_4331-S11_1p_25dmp_14_c

value: c


title: Myc-CaP_Uba1_OE_FVB

value: FVB


title: Myc-CaP_TAK243_T4 [SI_35011]


title: s144_4429-S7_10p_n2octanol_15_a

value: a


title: s136_4331-S7_1p_25dmp_14_b


title: s138_4331-S9_ctrl_14_c


title: s134_4331-S5_ctrl_14_b


title: R2_PE

value: Fed E. coli purE mutant for 48 hours then swich to E. coli purE mutant diet for 2 hours


title: R2_BWPE


title: Myc-CaP_TAK243_T3 [SI_35010]

value: Myc-CaP

value: Epithelial


title: s135_4331-S6_100p_ebFarnesene_14_b


title: Myc-CaP_TAK243_T2 [SI_35009]


title: R2_BW


title: Myc-CaP_EV_FVB

value: Myc-CaP tumor


title: Myc-CaP_TAK243_T1  [SI_35008]


title: s130_4331-S1_ctrl_14_a

value: control


title: s131_4331-S2_100p_ebFarnesene_14_a

value: experimental

value: ebFarnesene


title: s126_4269-S9_1M_nMenthol_12_c

value: nMenthol


title: s127_4269-S10_ctrl_13_c


title: s129_4269-S12_1p_pyridine_13_c

value: pyridine


title: R1_PEBW


title: s133_4331-S4_100uM_MTMT_14_a

value: MTMT


title: R1_PE


title: R1_BWPE

value: Fed BW25113 for 48 hours then swich to E. coli purE mutant diet for 2 hours


title: R1_BW

value: whole worms

value: Fed BW25113 for 48 hours then swich to BW25113 diet for 2 hours


title: s123_4269-S6_1M_nMenthol_12_b

value: b


title: Myc-CaP_Veh_T3 [SI_35004]

value: prostate tumor

value: WT

value: Vehicle


title: Myc-CaP_Veh_T5 [SI_35006]


title: s128_4269-S11_1p_2heptanone_13_c

value: c


title: s124_4269-S7_ctrl_12_c


title: Myc-CaP_Veh_T4 [SI_35005]

value: Myc-CaP


title: s121_4269-S4_ctrl_12_b


title: Myc-CaP_Veh_T2 [SI_35003]

value: Epithelial


title: s120_4269-S3_1M_nMenthol_12_a

value: a


title: s132_4331-S3_1p_25dmp_14_a


title: s122_4269-S5_1M_pMenthol_12_b

value: pMenthol


title: s125_4269-S8_1M_pMenthol_12_c

value: experimental


title: s119_4269-S2_1M_pMenthol_12_a


title: Myc-CaP_Veh_T1  [SI_35002]


title: s149_4429-S12_77p_dhb_15_b

value: dhb


title: s118_4269-S1_ctrl_12_a

value: control


title: Myc-CaP_Veh_T6 [SI_35007]


title: Sw.71, CVB4-JVB infected, biol rep3

city: Albany

first: Salima

last: Lalani

state: New York

address: 47 New Scotland Avenue

department: Department of Molecular & Cellular Physiology

institute: Albany Medical College

description: small RNA was used to perform sequencing

data_processing:
Samples 1-18, standard RNA-seq:  "The sequencing libraries were multiplexed and clustered on the seven lanes of a flowcell. The samples were sequenced using a 2x150 Pair-End (PE) configuration Raw sequence data (.bcl files) generated from Illumina NovaSeq was converted into fastq files and de-multiplexed using Illumina bcl2fastq program version 2.20. One mismatch was allowed for index sequence identification. Statistical analysis on lengths and counts of the filtered reads as well as data volume was performed as part of data quality control. The filtered reads were aligned to human reference genome, Genome Reference Consortium Human Build 38 with STAR 2.7.10b"
Samples 19-30, small RNA-seq: "The raw sequence reads were quality and adapter trimmed using CLC Genomics Server 10. The trimmed reads with a length of 15 to 31 bp were retained. These trimmed reads were compared and annotated using the small RNA database (miRbase 21). The annotated and unannotated sequences were separated from each other and analyzed separately. In both cases, hit counts for each small RNA were used as expression values and quantile normalization and log2- transformation were performed. For the known small RNAs exploratory data analysis using hierarchical clustering and Principal Component Analysis (PCA) were performed. Significantly differentially expressed annotated and unannotated small RNA were identified via empirical analysis using the Exact test in CLC Genomics Server 10. Small RNAs were selected as being statistically significantly differentially expressed if p < 0.05 and fold-change of normalized expression values > 2."
Assembly: "Reads were aligned to the human reference genome, Genome Reference Consortium Human Build 38 with STAR 2.7.10b"
Supplementary files format and content: Tab-delimited files, raw counts for RNA seq data
Supplementary files format and content: Tab-delimited files,expression profile for small RNA seq data

growth_protocol:
The immortalized pancreatic β cell line, EndoC-βH1 was grown in Matrigel-fibronectin coated plates in OPTIβ1 medium. Cells were passaged every 7 days. The immortalized human trophoblast cell line hTERT (Sw.71) were grown on dishes coated with Applied Cell Extracellular Matrix in PriGrow IV medium supplemented with 10% fetal bovine serum, 1% L-glutamine, 10 mM HEPES, 0.1 mM MEM non-essential amino acids, 1 mM sodium pyruvate and 1% penicillin-streptomycin.
Coxsackievirus (CVB) serotype 4 JVB (ATCC# VR-184) and CVB-E2 (diabetogenic strain) were propagated in LLC-MK2 derivative cells (ATCC# CCL-7.1).

extract_protocol:
Total RNA was extracted using RNeasy Plus Kit, Cat. #74136 per manufacturer's protocol. Small RNA was extracted using mirVana™ miRNA isolation kit (ThermoFisher Scientific, Cat. #AM1560) per manufacturer's protocol.
For standard RNA-seq: NEBNext Ultra II RNA Library Preparation Kit with QIAseq FastSelect for rRNA depletion
For small RNA-seq: NEB small RNA library preparation kit

treatment_protocol:
EndoC-βH1 cells were seeded overnight and then infected with CVB4 (CVB4-JVB or E2 strain) for 1 hour at a MOI=0.1. Infected cells were washed and pelleted for RNA extraction library preparation, and RNA-Seq.
Sw.71 cells were seeded overnight and then infected with CVB4-JVB strain for 24 hours at a multiplicity of infection (MOI) of 1. Infected cells were washed and pelleted for RNA extraction, library preparation, and small RNA-Seq.

value: Trophoblast cells

value: Wild type

value: CVB4-JVB infected


title: Sw.71, CVB4-JVB infected, biol rep1


title: s117_4259-S12_1p_ethylButyrate_11_c

value: ethylButyrate


title: s114_4259-S9_ctrl_11_c


title: Sw.71, Control, biol rep3, unifected

value: Control


title: s116_4259-S11_1p_linalool_11_c

value: linalool


title: B16-BL6_sgUba1_T3 [SI_34372]

source_name: skin/melanoma

value: skin/melanoma


title: B16-BL6_sgUba1_T4 [SI_34373]


title: s112_4259-S7_1p_linalool_11_b

value: b


title: Sw.71, Control, biol rep1, unifected


title: s113_4259-S8_1p_ethylButyrate_11_b


title: B16-BL6_sgUba1_T2 [SI_34371]


title: s111_4259-S6_1p_2heptanone_11_b


title: B16-BL6_sgUba1_T1 [SI_34370]


title: Sw.71, Control, biol rep2, unifected


title: EndoC-βH1, CVB4-JVB infected, biol rep2

value: Pancreatic beta cells


title: B16-BL6_sgNC_T4 [SI_34365]

value: WT


title: s108_4259-S3_1p_linalool_11_a


title: B16-BL6_sgNC_T2 [SI_34363]


title: EndoC-βH1, CVB4-JVB infected, biol rep3


title: Sw.71, CVB4-JVB infected, biol rep2


title: s104_4258-S11_1p_bCaryophyllene_10_c

value: bCaryophyllene

value: c


title: s107_4259-S2_1p_2heptanone_11_a

value: a


title: s110_4259-S5_ctrl_11_b


title: s109_4259-S4_1p_ethylButyrate_11_a


title: EndoC-βH1, CVB4-JVB infected, biol rep1


title: s103_4258-S10_1p_pyridine_10_c

value: pyridine


title: EndoC-βH1, CVB4-E2 infected, biol rep3

value: CVB4-E2 infected


title: s102_4258-S9_ctrl_10_c


title: B16-BL6_sgNC_T1 [SI_34362]

value: Epithelial


title: s101_4258-S8_1p_methylSalicylate_10_b

value: experimental

value: methylSalicylate


title: s99_4258-S6_1p_pyridine_10_b


title: EndoC-βH1, CVB4-E2 infected, biol rep2

value: Wild type


title: s98_4258-S5_ctrl_10_b

value: control


title: EndoC-βH1, CVB4-E2 infected, biol rep1


title: Myc-CaP_sgUba1_T6 [SI_34416]

value: prostate tumor

value: Myc-CaP


title: s106_4259-S1_ctrl_11_a


title: Myc-CaP_sgUba1_T5 [SI_34415]


title: EndoC-βH1, Control, biol rep2, unifected

value: Control


title: Myc-CaP_sgUba1_T4 [SI_34414]


title: EndoC-βH1, Control, biol rep1, unifected


title: s96_4258-S3_1p_bCaryophyllene_10_a


title: Myc-CaP_sgUba1_T3 [SI_34413]


title: s97_4258-S4_1p_ethylTiglate_10_a

value: ethylTiglate


title: s94_4258-S1_ctrl_10_a


title: Myc-CaP_sgUba1_T2 [SI_34412]


title: PLC124 Control R3

city: Solna

first: Irene

last: Stevens

address: Tomtebodavägen 23A (Gamma5)

department: Department of Microbiology, Tumor and Cell Biology

country: Sweden

institute: Karolinska Institutet

description: RNAseq

data_processing:
After quality control, raw data was mapped to SC5314 reference genome (ASM18296v3) using STAR version 2.7.9a aligner (paired-end), file formats were converted, sorted and indexed using samtools
Assembly: SC5314 reference genome (ASM18296v3)
Supplementary files format and content: Gene count file was generated using Subread featureCounts version 1.5.1 with the option ‘-t CDS’
Supplementary files format and content: tab delimited file containing gene level raw counts

organism: Candida albicans

source_name: Clinical isolate; fluconazole resistant

growth_protocol: C. albicans reference strain SC5314 and fluconazole resistant clinical isolate PLC124 were maintained on YPD (yeast extract 1%, peptone 2%, and glucose 2%). cultures were pre-grown overnight at 30 °C with constant shaking. The following day cultures were diluted to OD600 of 0.1.

extract_protocol:
Total RNA was extracted from frozen cell pellets using the RiboPure-Yeast RNA Isolation Kit (Thermo Fisher) and RNA concentrations were measured using a Nanodrop 2000c Spectrophotometer (Thermo Fisher Scientific).
Ribosomal RNA was depleted from ~1 µg of total RNA using riboPOOLs (siTOOLs Biotech) kit as recommended by the manufacturer. After depletion samples were precipitated using 2.5 volumes of 95% (vol/vol) ethanol, a 1/10 volume of 3M sodium acetate and 1 µL of glyucoblue, mixed and incubated overnight at -20 °C. Concentration was done by centrifugation at 14000 x g, 30 minutes at 4°C, the pellets were washed twice with 70% ethanol, dried and resuspended.
For library preparation, we used the NEBNext Ultra directional RNA Library Prep kit for Illumina (New England BioLabs) as recommended by the manufacturer for relatively low input,13 amplification cycles, and mean library size was around 350bp.

treatment_protocol: The starting culture was split into two tubes (2 mL per tube) and subsequently grown at 30 °C aerated until an OD600 of 1.5 – 2.2. One tube was treated with 2% DMSO (diluent control), while the second tube was treated for 30 minutes with 1 μg/ml (1x MIC (24)) fluconazole.

value: Clinical isolate; fluconazole resistant

value: 2% DMSO control


title: s92_3769a-S11_p1_isovalericAcid_9_c

value: isovalericAcid


title: s93_3769a-S12_3mM_androstenone_9_c

value: androstenone


title: s89_3769a-S8_3mM_androstenone_9_b

value: b


title: s91_3769b-S10_1p_isoamylAcetate_9_c

value: isoamylAcetate

value: c


title: s90_3769b-S9_ctrl_9_c


title: PLC124 Control R2

description: RNAseq


title: Myc-CaP_sgUba1_T7 [SI_34417]


title: s87_3769a-S6_1p_isoamylAcetate_9_b


title: s100_4258-S7_1p_bCaryophyllene_10_b

value: bCaryophyllene


title: EndoC-βH1, Control, biol rep3, unifected

value: Pancreatic beta cells


title: PLC124 Fluconazole R3

description: RNAseq

value: Fluconazole 1 ug/ml


title: usp,usp-GFP,unknown,Exp1,ChIP1

city: Seattle

first: Louis

last: Gevirtzman

state: WA

address: 3720 15th Ave NE

department: Genome Science

institute: University of Washington

data_processing:
alignment with BWA Version: 0.7.17-r1188
peak calling with SPP Version 1.15.5
Irreproducible Discovery Rate (IDR) Version 2.0.4.2
Signal tracks using macs2 version 2.2.4 for read pileup
Assembly: dm6
Supplementary files format and content: bigWig, narrowPeak, html

organism: Drosophila melanogaster

source_name: usp-GFP

extract_protocol:
Fly growth was performed as described previously for the modENCODE and modERN projects Kudron et al., 2018(PMID: 29284660). Transgenic flies were expanded in vials and bottles containing standard Drosophila media at ~22℃ and larvae, white pre-pupae(WPP) and adults were collected from these expansion vials. Pupae were obtained by collecting WPP and incubating for 1-2 days at ~22℃. For embryonic collections, 0-8 day old adult flies were moved to embryo cages capped with apple juice plates. After a 24 hour hours, apple juice plates were replaced at appropriate intervals, restricting the collected embryos to their desired developmental stages. For late embryonic stages, collection plates were removed and embryos were grown at room temperature until the desired stage was reached prior to chromatin collection.    Chromatin was collected and ChIP was performed using the goat anti-GFP as described previously Kudron et al., 2018 (PMID: 29284660).  However, later experiments were performed using Ab290 (Abcam) and denoted as such in Kudron et al., 2024;
Library preparation during the modENCODE and early stages of the modERN project were performed as previously described in Zhong et al. 2010 (PMID: 20174564); Niu et al. 2011 (PMID: 21177963); Kasper et al. 2014(PMID: 25373775); and Kudron et al., 2018(PMID: 29284660). More recently, chromatin has been prepared for sequencing using the following methods at the Yale Center for Genome Analysis (Kudron et al., 2024 Supplemental_File_S1). ChIP and input control samples (genomic DNA from the same sample) for two technical replicates for worm and three for fly were used for library construction using approximately 5-10ng of DNA after the samples were end-repaired, A-tailed, adapter ligated and PCR enriched (8 -10 cycles) (KAPA Biosystems, Part#KK8504).  Indexed libraries were quantified by qPCR (KAPA Biosystems, Part#KK4854) and inserts were distributed by size using the Caliper LabChip GX system.  Samples that had a concentration of ≥0.5 ng/ul were used for sequencing.  Samples were normalized to 10 nM and sequenced using 100bp paired-end sequencing on an Illumina HiSeq NovaSeq Sequencer achieving > 5 million reads passing filter clusters.  A positive control provided by Illumina is spiked into every lane at a concentration of 0.3% to monitor quality in real time. Sequencing data that passed internal quality controls at YCGA were transferred to the Waterston Lab for downstream processing.

value: usp-GFP

tag: genetic modification

value: stable transfection

tag: developmental stage

value: unknown

tag: chip antibody


title: usp,usp-GFP,unknown,Exp1,ChIP2


title: s86_3769a-S5_ctrl_9_b

value: control


title: Myc-CaP_sgNC_T2 [SI_34409]

value: prostate tumor

value: Myc-CaP

value: Epithelial

value: WT


title: s85_3769a-S4_3mM_androstenone_9_a

value: experimental

value: a


title: usp,usp-GFP,unknown,Exp1,Input1


title: PLC124 Fluconazole R2

description: RNAseq

value: Clinical isolate; fluconazole resistant


title: Myc-CaP_sgNC_T1  [SI_34408]


title: sc,yellow_cinnabar_brown_speck,embryonic,Exp2,ChIP2

value: embryonic

value: non-commercial scute modENCODE antibody 1(769c6b1e-6202-4207-858c-da42a83f6367)


title: s88_3769a-S7_p1_isovalericAcid_9_b

value: isovalericAcid

value: b


title: s84_3769a-S3_p1_isovalericAcid_9_a


title: s83_3769b-S2_1p_isoamylAcetate_9_a

value: isoamylAcetate


title: s82_3769a-S1_ctrl_9_a


title: PLC124 Fluconazole R1

description: RNAseq

value: Fluconazole 1 ug/ml


title: sc,yellow_cinnabar_brown_speck,embryonic,Exp2,Input1


title: sc,yellow_cinnabar_brown_speck,embryonic,Exp2,ChIP1


title: Myc-CaP_sgUba1_T1 [SI_34411]


title: Myc-CaP_Uba1_OE_T3 [SI_34406]


title: Myc-CaP_Uba1_OE_T4 [SI_34407]


title: usp,usp-GFP,unknown,Exp1,ChIP3

value: usp-GFP


title: SC5314 Control R2

description: RNAseq

source_name: Prototrophic wildtype

value: Prototrophic wildtype

value: 2% DMSO control


title: SC5314 Control R3

description: RNAseq


title: s80_3645-S11_1p_nCarvone_8_c

value: nCarvone

value: c


title: Myc-CaP_Uba1_OE_T1 [SI_34404]

value: prostate tumor

value: Myc-CaP


title: Myc-CaP_sgNC_T3 [SI_34410]

value: Epithelial

value: WT


title: prd,yellow_cinnabar_brown_speck,embryonic,Exp2,ChIP2

value: non-commercial prd modENCODE antibody 2(3daf8a7f-b87a-4718-a715-9ace22aedc47)


title: PLC124 Control R1

description: RNAseq

value: Clinical isolate; fluconazole resistant


title: SC5314 Control R1

description: RNAseq


title: Myc-CaP_EV_T3 [SI_34402]


title: s79_3645-S10_1p_pCarvone_8_c

value: experimental

value: pCarvone


title: SC5314 Fluconazole R3

description: RNAseq


title: prd,yellow_cinnabar_brown_speck,embryonic,Exp2,ChIP1

value: embryonic


title: Myc-CaP_EV_T2 [SI_34401]


title: SC5314 Fluconazole R2

description: RNAseq


title: prd,yellow_cinnabar_brown_speck,embryonic,Exp1,ChIP2

value: non-commercial prd modENCODE antibody 1(06f16dc9-a8a4-4c9c-a4ee-1275e8b2c19f)


title: Myc-CaP_EV_T1 [SI_34400]


title: prd,yellow_cinnabar_brown_speck,embryonic,Exp1,ChIP1


title: CG8478,yellow_cinnabar_brown_speck,prepupa,Exp1,ChIP1

value: prepupa

value: non-commercial CG8478 modENCODE antibody 1(c9739440-7ee4-41d7-8d26-c39179cadebf)


title: Myc-CaP_Uba1_OE_T2 [SI_34405]


title: CG8478,yellow_cinnabar_brown_speck,prepupa,Exp1,Input1


title: s74_3645-S5_ctrl_8_b

value: control

value: b


title: SC5314 Fluconazole R1

description: RNAseq

value: Prototrophic wildtype

value: Fluconazole 1 ug/ml


title: Myc-CaP_sgUba1_I_R2 [SI_35036]

value: IFN-γ


title: SC5314 YPD control 5P-Seq biol rep3

data_processing:
Base calls (BCL) were converted to fastq files and subsequently demultiplexed using the Illumina bcl2fastq v2.20.0.422 tool with option –barcode-mismatches 1. Sequencing adapter read trimming at 3’ end was applied using cutadapt V3.1 with Python 3.7.2 (https://cutadapt.readthedocs.io/en/v3.1/installation.html). The 5’ end 8-nt random barcodes were extracted and added as UMI to the header of fastq files using UMI-tools (27). Reads were mapped to the SC5314 reference genome (ASM18296v3) for    Candida albicans using STAR version 2.7.9a (28) with parameter --alignEndsType Extend5pOfRead1 to exclude 5’end soft-clipped bases. In addition, reads were mapped to mRNA, rRNA, tRNA, snRNA, snoRNA and ncRNA separately with corresponding indexes generated by STAR 2.7.9a to calculate RNA content composition (see Supplementary Table 1). Duplicated 5’ read ends introduced by PCR during library preparation were collapsed and removed based on random barcode sequences with UMI-tools (27). Low complexity samples (may478_fluc_rep01, may478_ut_rep01, plc124_ut_rep01) were removed from further analyses ( see Supplementary Table 12). To compare differences in 5P’ read coverage at gene level, reads per CDS were counted using Subread package (featureCounts) using the options -t CDS -g ID -s 0 -T 8  (29). Differential gene expression analysis was performed using DeSeq2 (11). The threshold for differentially expressed genes was defined as p-value < 0.05 and log2FoldChange > 0.5. We adjusted the alpha parameter to 0.5, corresponding to FDR threshold 50% to increase the number of Differentially Expressed Genes (DEG) to 61. Analysis of 5’ ends positions was done using a modified version of the Fivepseq package (30) that accounts for the CUG codon reassignment from Leucine to Serine in C. albicans (31). Briefly, the 5’ mRNA reads are summed in biological samples and normalized to reads per million (rpm). The relative position of 5’ reads with respect to all codons of all open reading frames (ORF) were summed at each position. Metagene plots are generated by plotting the summed reads within a window of each annotated start and termination site, or codon.
Assembly: SC5314 reference genome (ASM18296v3)
Supplementary files format and content: tab-delimited text files with transcript id, raw count, preferred frame, preferred frame raw count, percentage, frame protection index

growth_protocol: C. albicans reference strain SC5314 and fluconazole resistant clinical isolates PLC124, MAY7 and MAY478 were maintained on YPD (yeast extract 1%, peptone 2%, and glucose 2%).

extract_protocol:
Total RNA was extracted from frozen cell pellets using the RiboPure-Yeast RNA Isolation Kit (Thermo Fisher) and RNA concentrations were measured using a Nanodrop 2000c Spectrophotometer (Thermo Fisher Scientific).
HT-5’P sequencing library preparation was performed as described in PMID: 35474692 and PMID: 33870233

treatment_protocol: Fluconazole treatment: cultures were pre-grown overnight at 30 °C with constant shaking. The following day cultures were diluted to OD600 of 0.1. The starting culture was split into two tubes (2 mL per tube) and subsequently grown at 30 °C aerated until an OD600 of 1.5 – 2.2. One tube was treated with 2% DMSO (diluent control), while the second tube was treated for 30 minutes with 1 μg/ml (1x MIC (24)) fluconazole. Cells from three biological replicates were harvested by centrifugation and flash frozen in liquid nitrogen. Cycloheximide treatment: cultures were pre-grown as for fluconazole treatment. The following day cultures were used to inoculate two flasks (150 ml per flask) at an OD600 of 0.1. When the cultures reached an OD = 1, one culture was treated for 15 minutes with 1 mL cycloheximide working solution in ethanol (final 0.067 mg/ml concentration in media), whereas the control culture received 1 mL of 90% Ethanol. Cells from three biological replicates were harvested by centrifugation and flash frozen in liquid nitrogen.  Amino acid deprivation: strain SC5314 was pre-grown overnight in 3 mL YPD shaking at 30 °C. Cells were harvested by centrifugation and resuspended in either proline starvation media or replete media. Proline starvation media is YNB (Yeast Nitrogen Base without amino acids and ammonium sulfate; 0.17%) supplemented with 2% glucose and all amino acids (0.2 g/L) except Proline, Arginine and Ornithine.

value: YPD control


title: Myc-CaP_sgUba1_I_R1 [SI_35035]

value: prostate tumor

value: Myc-CaP


title: SC5314 YPD control 5P-Seq biol rep1


title: Myc-CaP_sgUba1_R2 [SI_35034]

value: Epithelial

value: PBS


title: SC5314 Proline Arginine Ornithine depletion R3

value: proline, arginine, ornithine depletion


title: s72_3645-S3_1p_nCarvone_8_a

value: experimental

value: nCarvone

value: a


title: Myc-CaP_sgUba1_R1 [SI_35033]


title: CG11902,CG11902-GFP,prepupa,Exp1,ChIP3

value: site-specific recombination


title: s71_3645-S2_1p_pCarvone_8_a

value: pCarvone


title: CG11902,CG11902-GFP,prepupa,Exp1,ChIP2

value: prepupa


title: SC5314 Proline Arginine Ornithine depletion R1


title: s78_3645-S9_ctrl_8_c

value: control

value: c


title: s70_3645-S1_ctrl_8_a


title: s76_3645-S7_1p_nCarvone_8_b

value: b


title: CG11902,CG11902-GFP,prepupa,Exp1,ChIP1


title: s75_3645-S6_1p_pCarvone_8_b


title: s69_3606a-S12_1p_guaiacol_7_c

value: guaiacol


title: Myc-CaP_NC_I_R1 [SI_35031]

value: WT

value: IFN-γ


title: CG11902,CG11902-GFP,prepupa,Exp1,Input1


title: SC5314 Cycloheximide 5P-Seq biol rep3

value: Prototrophic wildtype

value: cycloheximide


title: SC5314 Cycloheximide 5P-Seq biol rep1


title: prd,yellow_cinnabar_brown_speck,embryonic,Exp2,Input1

value: embryonic

value: non-commercial prd modENCODE antibody 2(3daf8a7f-b87a-4718-a715-9ace22aedc47)


title: s67_3606b-S10_ctrl_7_c


title: grh,grh-GFP,wanderingthirdinstarlarva,Exp1,ChIP2

source_name: grh-GFP

value: grh-GFP

value: wanderingthirdinstarlarva


title: MAY478 Control 5P-Seq biol rep2

value: Clinical isolate; fluconazole resistant

value: DMSO control


title: Myc-CaP_NC_R1 [SI_35029]

value: prostate tumor

value: Myc-CaP

value: Epithelial

value: PBS


title: Myc-CaP_50T+I_R2 [SI_34589]

value: 50 nM TAK-243 plus IFN-γ


title: MAY478 Fluconazole 5P-Seq biol rep3

value: fluconazole


title: Myc-CaP_NC_R2 [SI_35030]


title: MAY478 Control 5P-Seq biol rep3


title: MAY478 Fluconazole 5P-Seq biol rep2


title: grh,grh-GFP,wanderingthirdinstarlarva,Exp1,Input1

value: site-specific recombination


title: Myc-CaP_I_R2 [SI_34587]

value: WT


title: Myc-CaP_50T+I_R1 [SI_34588]


title: s64_3606b-S7_ctrl_7_b

value: control

value: b


title: ChIP-Seq_HeLa_YY1_siPHF8

city: Xiamen

first: Jiancheng

last: Ding

state: Fujian

address: School of Pharmaceutical Sciences, Xiamen University Xiang`an South Road

country: China

institute: Xiamen University

data_processing:
Basecalling was performed using CASAVA version 1.4
Reads were aligned to the hg19 genome assembly using Bowtie version 2.2.1 with the default options.
The bigwig files were generated by using HOMER, in which the total tags are normalized to 1.00e+07.
Peaks are called by using Homer findPeaks script
Genome_build: hg19
Supplementary_files_format_and_content: bigWig

source_name: cervical cancer

growth_protocol: HeLa cells were cultured in DMEM medium supplemented with 10% FBS.

extract_protocol:
For ChIP assays, cells were then fixed with 1% formaldehyde (Sigma) for 10 mins at room temperature (RT). Fixation was stopped by adding glycine (0.125 M) and incubated for 5 mins at RT, followed by washing with PBS twice. Chromatin DNA was sheared to 300~500 bp average in size through sonication. Resultant was immunoprecipitated with anti-PHF8 or anti-YY1 antibody overnight at 4 ℃, followed by incubation with protein G magnetic beads for an additional 2 hrs. After washing and elution, the protein-DNA complex was reversed by heating at 65 ℃ overnight. Immunoprecipitated DNA was purified by using QIAquick spin columns (Qiagen) and subjected to high throughput sequencing.
The libraries were constructed following NEB’s Chip-Seq Sample prep kit. Briefly, Chip DNA was end-blunted and added with an ‘A’ base so the adaptors from Illumina with a ‘T’ can ligate on the ends. Then 200–400 bp fragments are gel-isolated and purified. The library was amplified by 18 cycles of PCR.

treatment_protocol: HeLa cells were transfected with siCTL or siPHF8 RNA as indicated using Lipofectamine 2000 according to the manufacturer’s protocol.

value: HeLa

value: YY1 (Santa Cruz sc-7341)


title: Myc-CaP_NC_I_R2 [SI_35032]

value: IFN-γ


title: s65_3606a-S8_1p_citronellol_7_b

value: experimental

value: citronellol


title: MAY7 Control 5P-Seq biol rep3

value: Clinical isolate; fluconazole resistant


title: s66_3606b-S9_1p_guaiacol_7_b

value: guaiacol


title: Myc-CaP_I_R1 [SI_34586]

value: prostate tumor


title: ChIP-Seq_HeLa_YY1_siCTL

value: siCTL


title: s63_3606b-S6_1p_guaiacol_7_a

value: a


title: s62_3606a-S5_1p_citronellol_7_a


title: MAY7 Control 5P-Seq biol rep2

value: DMSO control


title: Myc-CaP_50T_R2 [SI_34585]

value: Myc-CaP

value: Epithelial


title: ChIP-Seq_HeLa_YY1


title: grh,grh-GFP,wanderingthirdinstarlarva,Exp1,ChIP1

value: grh-GFP

value: site-specific recombination

value: wanderingthirdinstarlarva


title: Myc-CaP_50T_R1 [SI_34584]

value: WT


title: ChIP-Seq_HeLa_PHF8

value: HeLa

value: PHF8 (Abcam ab36068)


title: s61_3606b-S4_ctrl_7_a

value: control


title: MAY7 Fluconazole 5P-Seq biol rep3

value: fluconazole


title: Myc-CaP_R2 [SI_34583]

value: Control


title: MAY7 Fluconazole 5P-Seq biol rep2

value: Clinical isolate; fluconazole resistant


title: 05_single cell_TKO_2

city: Boston

first: Rulin

last: Zhuang

state: MA

address: 77 Avenue Louis Pasteur NRB-742F

department: Department of Medicine, Cardiovascular Division

institute: Brigham and Women’s Hospital/Harvard Medical School

data_processing:
All samples were processed using an RNA-seq pipeline implemented by Genewiz (South Plainfield, NJ).
Sequence reads were trimmed to remove possible adapter sequences and nucleotides with poor quality using Trimmomatic v.0.36.
The trimmed reads were mapped to the Mus musculus GRCm38 reference genome available on ENSEMBL using the STAR aligner v.2.5.2b.
BAM files were generated as a result
Unique gene hit counts were calculated by using featureCounts from the Subread package v.1.5.2. Only unique reads that fell within exon regions were counted.
Assembly: GRCm38
Supplementary files format and content: barcodes, features, matrix

source_name: Non-stripped aorta digested for scRNAseq

extract_protocol:
Aortas were removed, fibrolaste were isolated from disgested aortas, flash frozen on dry ice, and RNA was harvested using Trizol reagent.
1) RNAseq: RNA libraries were prepared for sequencing using standard Illumina protocols; 2) ScRNA seq:The cells were processed using a 10X Genomics microfluidics chip to generate barcoded Gel Bead-In Emulsions according to manufacturer protocols. Indexed single-cell libraries were then created according to 10X Genomics specifications (Chromium Next GEM Single Cell 3ʹ v3.1-Dual Index Libraries). Samples were multiplexed and sequenced in pairs on an Illumina HiSeq 4000 device.

treatment_protocol: Mice were treated with Ang II for 28 days, or Ang II+IgG/IL9 mAb for 28days

tag: strain background

value: TKO

value: 28 days Ang II infusion


title: Myc-CaP_R1 [SI_34582]

value: prostate tumor


title: s58_3639-S6_1p_pDihydrocarveol_6_c

tag: strain

value: experimental

value: pDihydrocarveol

value: c


title: MAY7 Fluconazole 5P-Seq biol rep1


title: s57_3639-S5_ctrl_6_c

tag: group


title: 05_single cell_TKO_1


title: s55_3639-S3_1p_nDihydrocarveol_6_b

tag: odor

value: nDihydrocarveol

value: b


title: PLC124 Control 5P-Seq biol rep3

value: DMSO control


title: Muscle vdr 7wk rep 1

city: New Delhi

first: G Aneeshkumar

last: Arimbasseri

state: Delhi

address: Aruna Asaf Ali Marg

department: Molecular Genetics Laboratory

country: India

institute: National Institute of Immunology

data_processing:
Sequence reads were trimmed for adaptor sequence/low-quality sequence trimmomatic
Trimmed sequence reads were mapped to GRCM38/mm10 and the reads per gene were counted using STAR.
Normalization and differential expression analysi swere performed using DEseq2.
Assembly: mm10
Supplementary files format and content: tab-delimited text files include raw read counts for each Sample

source_name: Muscle

growth_protocol: WT (C57BL/6J) and VDR knockout (B6.129S4-Vdrtm1Mbd/J mice) were genotyped and weaned at 21 days and subjected to regular chow and water (ad libitum)

extract_protocol:
The frozen tissue samples were ground in liquid nitrogen, added 1 ml of RNAIsoPlus and allowed to thaw. The samples were extracted for 10 minutes at room temperature followed by addition of 200μl chloroform. After vortexing, the samples were centrifuged at maximum speed for 5 minutes. The aqueous layer was transferred to fresh tubes and precipitated with isopropanol.
RNA libraries for RNA-seq were prepared using TruSeq RNAseq library prep kit v2 following manufacturer's protocols.

treatment_protocol: Skeletal muscles from the hind limbs (QUAD) were dissected, transferred to 1 ml RNAIsoPlus (Takara) and flash frozen in liquid nitrogen.

value: Muscle

value: vdr-/-


title: Muscle vdr 7wk rep 2


title: 05_single cell_Cre_1

value: Cre


title: 05_single cell_Cre_2


title: PLC124 Control 5P-Seq biol rep2


title: Muscle WT 7wk rep 2

value: WT


title: 04_IL9_blocker_nonstripped_aorta_IL9-Blocker_2645

description:
04_IL9_blocker_nonstripped_aorta_annotation.csv
04_IL9_blocker_nonstripped_aorta_rawcount.cvs

data_processing:
All samples were processed using an RNA-seq pipeline implemented by Genewiz (South Plainfield, NJ).
Sequence reads were trimmed to remove possible adapter sequences and nucleotides with poor quality using Trimmomatic v.0.36.
The trimmed reads were mapped to the Mus musculus GRCm38 reference genome available on ENSEMBL using the STAR aligner v.2.5.2b.
BAM files were generated as a result
Unique gene hit counts were calculated by using featureCounts from the Subread package v.1.5.2. Only unique reads that fell within exon regions were counted.
Assembly: GRCm38

source_name: Non-stripped aorta

value: 28 days Ang II infusion+IL9mAb

tag: tissue/cell type

value: Non-stripped aorta


title: s54_3639-S2_1p_pDihydrocarveol_6_b

tag: concentration

tag: differential expression number


title: MAY7 Control 5P-Seq biol rep1

tag: cell type


title: PLC124 Control 5P-Seq biol rep1


title: s53_3639-S1_ctrl_6_b

value: control

tag: trial


title: Muscle WT 7wk rep 1


title: 04_IL9_blocker_nonstripped_aorta_IL9-Blocker_2642


title: PLC124 Fluconazole 5P-Seq biol rep3

value: Clinical isolate; fluconazole resistant

value: fluconazole


title: s59_3639-S7_1p_nDihydrocarveol_6_c


title: s51_3552-S9_1p_nDihydrocarveol_6_a

value: a


title: 04_IL9_blocker_nonstripped_aorta_IL9-Blocker_2634

value: TKO

value: 28 days Ang II infusion+IgG


title: CG8478,yellow_cinnabar_brown_speck,prepupa,Exp1,ChIP2

value: prepupa

value: non-commercial CG8478 modENCODE antibody 1(c9739440-7ee4-41d7-8d26-c39179cadebf)


title: PLC124 Fluconazole 5P-Seq biol rep2


title: s50_3552-S8_1p_pDihydrocarveol_6_a

value: experimental

value: pDihydrocarveol


title: 3T3_nuclear_RNA

city: Hefei

first: Ge

last: Shan

state: Anhui

address: 443 Huangshan Road

department: School of Life Sciences

institute: University of Science and Technology of China

description: RNA-seq

data_processing:
For circRNA identification, the clean reads not aligned to rDNA sequences filtered by bowtie2 (version 2.3.2) were mapped to the reference genome (human: hg38; muose: mm10) by bowtie2 followed by samtools (version 2.3.2) to generate sorted BAM files. The unmapped sequences were obtained by samtools and anchor sequences were extracted from both ends of the sequence. The circRNA were predicted by find_circ (v1.2) after anchor sequences were aligned to the genome.
Assembly: hg38, mm10
Supplementary files format and content: bed files include count values for each Sample

molecule: nuclear RNA

extract_protocol:
The isolated nuclei were lysed in TRizol (Life Technologies). RNA were extracted by using TRizol reagent according to the manufacturer’s instructions.
For RNA-seq, the RNA extracted from nuclei were digested by RNase R. The library construction was conducted as followed: First, RNAs were concentrated. Second, 100 ng of RNA was fragmented at high temperature, followed by the addition of a 5' adaptor. Subsequently, reverse transcription was performed using a 3' adaptor with random hexamers to obtain library cDNA. This was followed by PCR and fragment size selection. After quantification and quality control of the constructed library, sequencing was performed on the HiSeq X10 sequencing platform.


title: PLC124 Fluconazole 5P-Seq biol rep1


title: N2a_nuclear_RNA

description: RNA-seq


title: s49_3552-S7_ctrl_6_a


title: s47_3606b-S2_1p_octanal_5_c

value: octanal

value: c


title: SC5314 Control 5P-Seq biol rep3

value: Prototrophic wildtype

value: DMSO control


title: 04_IL9_blocker_nonstripped_aorta_IL9-Blocker_2631


title: 04_IL9_blocker_nonstripped_aorta_IL9-Blocker_2633


title: sma-4,CS692,L4larva,Exp1,ChIP2

data_processing:
alignment with BWA Version: 0.7.17-r1188
peak calling with SPP Version 1.15.5
Irreproducible Discovery Rate (IDR) Version 2.0.4.2
Signal tracks using macs2 version 2.2.4 for read pileup
Assembly: ce11
Supplementary files format and content: bigWig, narrowPeak, html

extract_protocol:
For the modENCODE and modERN project, worm growth and ChIP were conducted as previously described in Zhong et al. 2010 (PMID: 20174564); Niu et al. 2011 (PMID: 21177963); Kasper et al. 2014(PMID: 25373775); and Kudron et al., 2018(PMID: 29284660) with the following modifications. Embryonic stages were collected after bleaching and arresting in M9 at 20°C with shaking until the desired embryonic stage was visualized by DIC microscopy. Larval and the young adult stages were synchronized by bleaching and L1 starvation and then arrested L1s were plated on peptone-enriched plates seeded with OP50 bacteria and grown for 6 hrs at 20°C for L1 collection, or grown to the desired stage based on visual examination of their development (Brenner 1974 (PMID: 4366476). GFP fluorescent and DIC images were collected immediately before collection. Worm samples were then cross-linked with 2% formaldehyde for 28 min at room temperature and quenched with 1M Tris pH 7.5. The pelleted worms were rinsed with M9 buffer twice and then with 150 mM NaCl FA buffer (50mM HEPES/KOH pH7.5, 1mM EDTA, 1% Triton X-100, 0.1% sodium deoxycholate, 150mM NaCl) with one Roche Complete tablet (Catalog number 11697498001) before the pellet was flash frozen in liquid nitrogen and stored at -80°C. Worm pellets resuspended in 150 mM FA Buffer containing one Roche Complete tablet, 25 ul 1M DTT and 125 ul of 100 mM PMSF per 25 mL chilled FA were sonicated using a microtip to achieve mostly 200–800 bp DNA fragments. For a subset of factors (OP662, OP565, OP579, OP638, OP553, OP550, OP658, OP696, OP552, OP563, OP688, OP685, OP707, OR3349, and XIL99), an additional dounce step was added prior to sonication as described in Kudron MM et al., 2018 (PMID: 29284660).    Worm lysate was measured by Bradford assay and extract corresponding to 2.2 or 4.4 mg was resuspended in 150 mM FA Buffer with Complete protease inhibitors along with 20µl 20% N-lauroylsarcosine sodium salt and spun for 5 minutes at 13,000 g at 4℃ in a non-stick Eppendorf tube. Samples were transferred to a fresh tube and 10% of the lysate was removed as input. Input samples were stored at -20℃ until the following day. ChIP samples were immunoprecipitated using 7.5 μg anti-GFP antibodies (gifts of Tony Hyman and Kevin White) overnight at 4℃ with rotation.    The following day, input samples were thawed and 2μl of 10 mg/mL RNase A was added and samples were digested at room temperature for 2 hours. Then input samples were brought up to 300 μl using Elution Buffer (1% SDS in TE pH 8.0 with 250 mM NaCl), and 4 μl of 10 mg/mL Proteinase K (Roche 03115887001) was added and they were incubated at 55℃ for 4 hours.   In the meantime, the ChIP samples were incubated with protein G sepharose beads for 2 hours at 4℃ with rocking (GE Healthcare Cat. # 17-0618-01). Beads were first washed 4 times in 150 mM FA buffer. All subsequent spins were at 2500 x g for 2 minutes each. The beads were then washed 2 times with room temperature 150 mM FA buffer for 5 minutes and then 1 time with 1M NaCl FA (50mM HEPES/KOH pH7.5, 1mM EDTA, 1% Triton X-100, 0.1% sodium deoxycholate, 1M NaCl) for 5 minutes. Samples were then transferred to new tubes and washed one time with 500 mM NaCl FA (50mM HEPES/KOH pH7.5, 1mM EDTA, 1% Triton X-100, 0.1% sodium deoxycholate, 500mM NaCl) for 10 minutes, 1 time with TEL buffer (0.25M LiCl, 1% NP40, 1% sodium deoxycholate, 1mM EDTA, 10mM Tris-HCl, pH8.0) for 10 minutes and then 2 times with TE pH 8.0 for 5 minutes. To elute the immunocomplexes, the beads were incubated two times for 15 minutes each with 150 μl Elution Buffer with gentle vortexing every 5 minutes. The two elutions were pooled after spinning down and 1 ul of 20 mg/mL Proteinase K was added to each ChIP sample. Both the eluted ChIP samples and the input samples were incubated overnight at 65℃ to reverse crosslinks. All samples were purified using either a minElute PCR Purification Kit from Qiagen (Catalog number 28006) or in later stages of the modERN project a ChIP DNA Clean and concentrator kit from Zymo (ZD5205).
Library preparation during the modENCODE and early stages of the modERN project were performed as previously described in Zhong et al. 2010 (PMID: 20174564); Niu et al. 2011 (PMID: 21177963); Kasper et al. 2014(PMID: 25373775); and Kudron et al., 2018(PMID: 29284660). More recently, chromatin has been prepared for sequencing using the following methods at the Yale Center for Genome Analysis (Kudron et al., 2024 Supplemental_File_S1). ChIP and input control samples (genomic DNA from the same sample) for two technical replicates for worm and three for fly were used for library construction using approximately 5-10ng of DNA after the samples were end-repaired, A-tailed, adapter ligated and PCR enriched (8 -10 cycles) (KAPA Biosystems, Part#KK8504).  Indexed libraries were quantified by qPCR (KAPA Biosystems, Part#KK4854) and inserts were distributed by size using the Caliper LabChip GX system.  Samples that had a concentration of ≥0.5 ng/ul were used for sequencing.
Samples were normalized to 10 nM and sequenced using 100bp paired-end sequencing on an Illumina HiSeq NovaSeq Sequencer achieving > 5 million reads passing filter clusters.  A positive control provided by Illumina is spiked into every lane at a concentration of 0.3% to monitor quality in real time. Sequencing data that passed internal quality controls at YCGA were transferred to the Waterston Lab for downstream processing.

value: syb2546[EGFP::sma-4] III.

value: CRISPR


title: 03_Aotric_fibroblast_2447

description:
03_Aotric_fibroblast_annotation.cvs
03_Aotric_fibroblast_rawcount.csv

source_name: Isolated aortic fibroblasts

value: 28 days Ang II infusion

value: Isolated aortic fibroblasts


title: 03_Aotric_fibroblast_2445


title: SC5314 Control 5P-Seq biol rep2


title: sma-4,CS692,L4larva,Exp1,Input1


title: sma-4,CS692,L4larva,Exp1,ChIP1


title: 03_Aotric_fibroblast_2443


title: s46_3606a-S1_ctrl_5_c

data_processing:
Library strategy: pS6-IP-Seq
STAR alignment
RSEM read quantification
Genome_build: modified GENCODE M25
Supplementary_files_format_and_content: expected_count, TPM, FPKM

source_name: Whole olfactory mucosa

value: control


title: s43_3552-S4_ctrl_5_b

value: b


title: SC5314 Control 5P-Seq biol rep1


title: s44_3552-S5_1p_octanal_5_b


title: 03_Aotric_fibroblast_1465

value: Cre


title: sma-3,CS152,L4larva,Exp1,Input1

value: bombardment


title: SC5314 Fluconazole 5P-Seq biol rep2

value: fluconazole


title: 03_Aotric_fibroblast_1464


title: sma-3,CS152,L4larva,Exp1,ChIP2


title: SC5314 Fluconazole 5P-Seq biol rep1


title: s26_3284-S11_1p_benzaldehyde_3_c

value: benzaldehyde


title: 02_Nonstripped_aorta_A308

description:
02_Stripped_aorta_annotation.csv
02_Stripped_aorta_rawcount.csv

source_name: Stripped aorta

value: TKO

value: Stripped aorta


title: 03_Aotric_fibroblast_1463


title: sma-3,CS152,L4larva,Exp1,ChIP1


title: pop-1,JIM531,earlyembryonic,Exp1,Input1

value: earlyembryonic


title: pop-1,JIM531,earlyembryonic,Exp1,ChIP2


title: Injured Bronchoalveolar Lavage Fluid replicate 5

first: Piyush

last: Ranjan

state: Michigan

address: 1150 W Medical Center Dr

department: Internal Medicine - Pulmonary and Critical Care

data_processing:
A decoy index for Pseudomonas aeruginosa PAO1 was created with Salmon v 1.10.3 using cds as true reference and PAO1 genome as background.
Transcript quantification was performed using Salmon v 1.10.3 with flags --numBootstraps 100 --seqBias --gcBias --posBias --writeUnmappedNames along with other program defaults.
Assembly: GCF_000006765.1
Supplementary files format and content: Salmon quantification results in .tar.gz format

organism: Pseudomonas aeruginosa

growth_protocol: PAO1 was cultured at 37 degrees C shaking for 10 hours in the media conditions included in the title

extract_protocol:
Qiagen RNeasy Mini Kit
Ribodepletion and library construction with NEBNext kits

value: Pseudomonas aeruginosa PAO1

value: wildtype


title: Injured Bronchoalveolar Lavage Fluid replicate 6


title: s23_3134-S11_1p_benzaldehyde_3_b

extract_protocol:
Antibody: Cell Signaling D68F8
Qiagen RNeasy Mini Kit #74104
Library construction protocol: Illumina Nexterra XT DNA Library Preparation Kit #15032354

value: experimental


title: SC5314 Fluconazole 5P-Seq biol rep3

value: Prototrophic wildtype


title: 02_Nonstripped_aorta_A307


title: s25_3284-S10_ctrl_3_c

value: c


title: pop-1,JIM531,earlyembryonic,Exp1,ChIP1


title: 02_Nonstripped_aorta_A407


title: Injured Bronchoalveolar Lavage Fluid replicate 4


title: 02_Nonstripped_aorta_A406


title: s20_3134-S8_1p_benzaldehyde_3_a

value: a


title: Injured Bronchoalveolar Lavage Fluid replicate 3


title: s40_3552-S1_ctrl_5_a


title: mec-3,OP55,lateembryonic,Exp1,Input1

value: lateembryonic


title: Injured Bronchoalveolar Lavage Fluid replicate 2


title: s22_3134-S10_ctrl_3_b


title: mec-3,OP55,lateembryonic,Exp1,ChIP2


title: Injured Bronchoalveolar Lavage Fluid replicate 1


title: 02_Nonstripped_aorta_A401

value: 28 days Ang II infusion


title: 02_Nonstripped_aorta_A402


title: s17_3134-S2_10mM_MTMT_2_c

value: MTMT


title: fkh-7,PS9154,L1larva,Exp1,Input1


title: Healthy Bronchoalveolar Lavage Fluid replicate 6


title: Healthy Bronchoalveolar Lavage Fluid replicate 5


title: 01_Nonstripped_aorta_AO_8

description:
01_Nonstripped_aorta_annotation.csv
01_Nonstripped_aorta_rawcount.cvs

value: Non-stripped aorta


title: Healthy Bronchoalveolar Lavage Fluid replicate 3


title: s16_3134-S1_ctrl_2_c

value: control


title: s41_3552-S2_1p_octanal_5_a

value: octanal


title: fkh-7,PS9154,L1larva,Exp1,ChIP1

value: bombardment


title: fkh-7,PS9154,L1larva,Exp1,ChIP2


title: 01_Nonstripped_aorta_AO_7


title: s13_3046-S10_ctrl_2_b

value: b


title: s14_3046-S11_10mM_MTMT_2_b


title: ceh-5,PHX1592,lateembryonic,Exp1,Input1

value: CRISPR


title: s10_3046-S7_ctrl_2_a


title: 01_Nonstripped_aorta_AO_5

value: Cre


title: 01_Nonstripped_aorta_AO_3


title: mec-3,OP55,lateembryonic,Exp1,ChIP1


title: s11_3046-S8_10mM_MTMT_2_a


title: ceh-5,PHX1592,lateembryonic,Exp1,ChIP2


title: Healthy Bronchoalveolar Lavage Fluid replicate 2


title: ceh-5,PHX1592,lateembryonic,Exp1,ChIP1


title: Healthy Bronchoalveolar Lavage Fluid replicate 1


title: 01_Nonstripped_aorta_AO_2


title: s19_3134-S7_ctrl_3_a


title: s8_3134-S5_100mM_CPD_1_c

value: CPD


title: 01_Nonstripped_aorta_AO_10

value: TKO


title: Healthy Bronchoalveolar Lavage Fluid replicate 4

value: Pseudomonas aeruginosa PAO1

value: wildtype


title: ceh-51,PHX1551,midembryonic,Exp1,Input1

value: midembryonic


title: s7_3134-S4_ctrl_1_c

value: c


title: ceh-51,PHX1551,midembryonic,Exp1,ChIP2


title: Lennox Broth Positive Control replicate 5


title: s5_3046-S5_100mM_CPD_1_b

value: experimental


title: Lennox Broth Positive Control replicate 4


title: K. phaffii, N Starvation, rep2

city: Saint Petersburg

first: Anton

middle: V.

last: Sidorin

address: 7/9 Universitetskaya nab., St. Petersburg, Russia

department: Faculty of Biology

country: Russia

institute: St. Petersburg State University

data_processing:
Raw reads were filtered and trimmed by Trimmomatic program (Bolger, Lohse, and Usadel, 2014).
Trimmed sequence reads were mapped to ASM2700v1 genome using hisat-2 program (Kim et al., 2019).
Read count were performed using the featureCounts program (Liao, Smyth, and Shi, 2019).
Assembly: ASM2700v1 (GCF_000027005.1)
Supplementary files format and content: tab-delimited text file includes raw counts for e\ach Sample. The names of the samples correspond to the file names without the extension (Control_1, Control_2, Control_3, Starv_1, Starv_2, Starv_3)

organism: Komagataella phaffii

growth_protocol: K. phaffii X-33  cells were grown for 40 hours in 100 ml of BMG medium with glycerol as the only carbon source. Cells were then harvested by centrifugation and transferred into 100 ml volumes of medium with methanol - BMM+N (control with ammonium sulfate) and BMM-N (experimental samples without nitrogen source). The cells were cultured for 18 h.

extract_protocol:
RNA was harvested using YeaStar RNA Kit (Zymo Research, USA). 300 ng of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using the QuantSeq 3′ mRNA-Seq Library Prep Kit FWD for Illumina (Lexogen, Austria) following manufacturer's protocols.

value: WT

value: absence of nitrogen source

tag: time

value: Hour 18


title: Lennox Broth Positive Control replicate 3


title: K. phaffii, N Starvation, rep3


title: K. phaffii, N Starvation, rep1


title: s4_3046-S4_ctrl_1_b


title: ceh-37,OH16345,L1larva,Exp1,Input1


title: Lennox Broth Positive Control replicate 2


title: s2_3046-S2_100mM_CPD_1_a

value: a


title: ceh-37,OH16345,L1larva,Exp1,ChIP1


title: Lennox Broth Positive Control replicate 1


title: K. phaffii, Control, rep3

value: presence of nitrogen source


title: K. phaffii, Control, rep2


title: RIP-Input-R

status: Public on Oct 05 2024

city: Changsha

first: Xiaomin

last: Shang

state: Hunan Province

address: 172 Tongzipo Road

department: Department of Parasitology

institute: Central South University

data_processing:
Reads were trimmed by trim-galore.
The resulting data was aligned to the genome using Hisat2.
The Samtools was used to filter low mapping quality reads and transfer the mapping results from sam format to position sorted bam format.
The bam files were converted to bigwig files using bamCoverage from the deeptools.
Assembly: Pf 3D7 v45
Supplementary files format and content: Bw files for enrichment ratio

organism: Plasmodium falciparum

growth_protocol: Parasites were cultured in medium containing 0.5% Albumax I with O type fresh red blood cells, and a gas phase with 5% O2, 5 % CO2 at 37 °C.

extract_protocol:
The RNA was extracted by phenol-chloroform method.
Libraries were carried out by the KAPA mRNA Capture Beads (KAPA) and fragmentation to about 300–400 nucleotides (nt) in length according to the KAPA Stranded mRNA-Seq Kit (KK8421).

treatment_protocol: About 5 x 109 synchronized ring-stage parasites were collected and lysed by saponin. The resulting parasite pellet was lysed under non-denaturing condition (50 mM Tris-Cl pH7.4, 150 mM NaCl, 1 mM EDTA, 1 mM EGTA, 1% Triton X-100, 1% NP-40, 1 x Proteinase inhibitors, 0.2 U/μl RNase inhibitor) for 2 hours at 4 ℃ with rotation. The supernatant was collected and incubated with 10 μg mouse anti-ty1 antibodies for 3 hours, then incubated overnight with protein G magnetic beads at 4 ℃. The complex was washed twice with IPP500 (500 mM NaCl, 10 mM Tris-Cl pH 8.0, 0.05% NP-40, 1 x Proteinase inhibitor, 0.2 U/μl RNase inhibitor) and once with 1 x PBS, then RNA was eluted by TRIzol reagen.

value: ring

tag: rip antibody

tag: fraction

value: total RNA


title: Lennox Broth Positive Control replicate 6

tag: genotype


title: s1_3046-S1_ctrl_1_a

value: control


title: K. phaffii, Control, rep1

tag: treatment


title: ceh-37,OH16345,L1larva,Exp1,ChIP2

tag: genetic modification

value: CRISPR


title: NSUN1-S-GlcN(+)-rep2

data_processing:
RNA-seq reads were trimmed by trim-galore.
The resulting data was aligned to genome using Hisat2.
The Samtools was used to filter low mapping quality reads and transfer the mapping results from sam format to position sorted bam format.
Read counts  were obtained using FeatureCounts.
Assembly: Pf 3D7 v45
Supplementary files format and content: The raw counts were calculated by FeatureCounts. Then FPKM of each gene was calculated in RStudio.

extract_protocol:
Total RNA was extracted with the kit (Zymo Research) according to a standardized procedure.
Libraries were carried out by poly(A) selection with the KAPA mRNA Capture Beads (KAPA) and fragmentation to about 300–400 nucleotides (nt) in length according to the KAPA Stranded mRNA-Seq Kit (KK8421).

treatment_protocol: Pfnsun1-ty1-glmS parasites were tightly synchronized by percoll and sorbitol to a 5-hour window with or without 5 mM GlcN treatment. Samples were collected in TRIzol at ring (10-15 hpi), trophozoite (25-30 hpi) and schizont (40-45 hpi) stages of the next cycle, respectively.

tag: developmental stage

value: schizont

value: knockdown

value: GlcN(+)


title: NSUN1-T-GlcN(+)-rep2

value: trophozoite


title: RIP-NSUN1-R

value: PfNSUN1 binding RNA


title: s68_3606a-S11_1p_citronellol_7_c

value: citronellol


title: ceh-51,PHX1551,midembryonic,Exp1,ChIP1

value: midembryonic

tag: chip antibody


title: NSUN1-T-GlcN(-)-rep2

value: normal

value: GlcN(-)


title: NSUN1-R-GlcN(+)-rep2


title: NSUN1-R-GlcN(-)-rep2


title: NSUN1-S-GlcN(-)-rep1


title: NSUN1-T-GlcN(+)-rep1


title: NSUN1-S-GlcN(+)-rep1


title: NSUN1-T-GlcN(-)-rep1


title: NSUN1-R-GlcN(+)-rep1


title: Larvae, 30 hours post fertilization

city: DURHAM

first: Alejandro

last: Berrio

address: 124 Science Dr

department: Biology

description: 10X Genomics

data_processing:
Raw sequencing data was processed using the Cellranger 3.1.0  pipeline (10X Genomics) to generate FASTQ files.
FASTQ files were aligned to the reference genome (H. erythrogramma 1.0 Genome) and gene expression matrices were generated using Cell Ranger.
Quality control, normalization, and clustering were performed using Seurat (v4.0).
Differential expression analysis was conducted using the FindMarkers function in Seurat.
Assembly: GCA_025617745.1 (Davidson et al., 2022)
Supplementary files format and content: Processed data files are provided in TSV and MTX format, containing gene expression matrices. TSV files include  files with cell metadata and gene annotations.

organism: Heliocidaris erythrogramma

source_name: Larvae

extract_protocol:
Single-cell suspensions were prepared, to do this,  larvae were washed twice in calcium-free artificial seawater (CFASW) then resuspended in dissociation buffer [1.0 M glycine and 0.25 mM EDTA (pH 8.0)] at 4°C. The embryos were then dissociated by gentle trituration. Following dissociation, cells were resuspended in CFASW, and fixed at a final concentration of 80% methanol in CFASW for 1 h, at 4°C. Following fixation, cells were stored at −20°C and all cell libraries were processed within 1 month of dissociation.
Single-cell RNA-seq libraries were prepared using the Chromium Single Cell 3' Reagent Kits v3.1 (10X Genomics) according to the manufacturer's protocol. Briefly, single cells were encapsulated into Gel Bead-In-Emulsions (GEMs) using the Chromium Controller, followed by reverse transcription, cDNA amplification, and library construction.
Libraries were titered and pooled at Duke University’s Sequencing and Genomic Technologies Core Facility, then sequenced in one S1 flow cell on an Illumina NovaSeq 6000 with 28 x 8 x 91 bp.

tag: tissue

value: Larvae

tag: age

value: 30 hours post fertilization


title: Larvae, 20 hours post fertilization

description: 10X Genomics

value: 20 hours post fertilization


title: Larvae, 24 hours post fertilization

description: 10X Genomics

value: 24 hours post fertilization


title: NSUN1-S-GlcN(-)-rep2

tag: strain


title: Larvae, 16 hours post fertilization

description: 10X Genomics

value: 16 hours post fertilization


title: Larvae, 9 hours post fertilization

description: 10X Genomics

value: 9 hours post fertilization


title: Larvae, 6 hours post fertilization

description: 10X Genomics

value: 6 hours post fertilization


title: Larvae, 12 hours post fertilization

description: 10X Genomics

value: 12 hours post fertilization


title: 28Z CAR-T cells rest 2

city: Shanghai

first: Haochen

last: Yang

state: Shanghai

address: 320 Yue-yang Road

institute: Shanghai Institute of Biochemistry and Cell Biology

data_processing:
For deep sequencing analysis, we first conducted quality control and trimming using TrimGalore (0.6.0) to get Clean Data for downstream analysis.
For gene expression quantification, the transcript per million (TPM) values output from the RSEM analysis were used and transformed to log-space by taking the log10 (TPM). Gene counts were normalized by library size and differential expression analysis was performed using DESeq2 (V1.40.1)
Assembly: Reads were aligned to an assembly of Homo Sapiens (GRCh38) using STAR software (V2.4.2a).
Supplementary files format and content: A .csv table contains the count of each sample.

source_name: Blood

growth_protocol: CAR-T cells were cultured in X-VIVO 15 Serum-free Hematopoietic Cell Medium, supplemented with 1% antibiotics, 5% human serum, 10 mM N-Acetyl-L-cysteine, 10 nM human IL-7 and 10 nM human IL-15, in humidified atmosphere with 5% CO2 at 37°C.

extract_protocol:
Total RNA was isolated using the TRIzol Reagent (Invitrogen) from 0.5-1 million CAR-T cells after each round killing.
The sequencing libraries were generated and sequenced on NovaSeq 6000 platform (Illumina) by Novogene.

treatment_protocol: CAR-T cells and Raji cells were cocultured at the 1:1 ratio in the X-VIVO medium mentioned above. After 3 days, the coculture was thoroughly suspended and half of the cell suspension was sorted for GFP+ CAR-T cells. For a new round of tumor challenge, Raji cells were added to the remaining cell suspension at the same as CAR-T cells (The highest cell number among the experimental groups). This process was repeated for 6 rounds. The GFP+ CAR-T cells after 1st, 2nd, 3rd and 5th round tumor challenge were sorted for RNA-seq. The GFP+ CAR-T cells without tumor challenge were used as control.

value: Blood

value: PBMC

value: 28Z CAR

value: without tumor challenge


title: 28Z CAR-T cells rest 3


title: 28Z CAR-T cells 5th round 2

value: 5th round tumor challenge


title: 28Z CAR-T cells rest 1


title: 28Z CAR-T cells 5th round 1


title: 28Z CAR-T cells 3rd round 2

value: 3rd round tumor challenge


title: 28Z CAR-T cells 3rd round 3


title: NSUN1-R-GlcN(-)-rep1

value: ring


title: 28Z CAR-T cells 5th round 3


title: 28Z CAR-T cells 3rd round 1


title: 28Z CAR-T cells 2nd round 2

value: 2nd round tumor challenge


title: 28Z CAR-T cells 2nd round 1


title: ctrl-2

type: RNA

city: hang zhou

first: de yang

last: mu

address: 杭州医学院临安校区

institute: hang zhou medical college

description: Gene expression

hyb_protocol: 1. Add 500 μL of nuclease-free water to the vial containing lyophilized 10X Blocking Agent. Mix by gently vortexing.  2. Equilibrate water bath to 60°C.  3. For each microarray, add each of the components as indicated in the tables as below to a 1.5 mL nuclease-free microfuge tube:  For 1*244K array Amount  cyanine 3-labeled, linearly amplified cRNA 1.5ug  10X Blocking Agent 50ul  Nuclease-free water ×ul  25X Fragmentation Buffer 10ul  Total volume 250ul    For 2*105K array Amount  cyanine 3-labeled, linearly amplified cRNA 1. 5ug  10X Blocking Agent 25ul  Nuclease-free water ×ul  25X Fragmentation Buffer 5ul  Total volume 125ul    For 4*44K array Amount  cyanine 3-labeled, linearly amplified cRNA 1.65ug  10X Blocking Agent 11ul  Nuclease-free water ×ul  25X Fragmentation Buffer 2.2ul  Total volume 55ul    For 8*15K array Amount  cyanine 3-labeled, linearly amplified cRNA 0.6ug  10X Blocking Agent 5ul  Nuclease-free water ×ul  25X Fragmentation Buffer 1ul  Total volume 25ul    For 8*60K array Amount  cyanine 3-labeled, linearly amplified cRNA 0.6ug  10X Blocking Agent 5ul  Nuclease-free water ×ul  25X Fragmentation Buffer 1ul  Total volume 25ul      4. Mix well but gently on a vortex mixer.  5. Incubate at 60°C for exactly 30 minutes to fragment RNA.   6. Add 2x GEx Hybridization Buffer HI-RPM to the array to stop the fragmentation reaction.  Volumes per hybridization   Components 1*244K 2*105K 4*44K 8*15K 8*60k  cRNA from Fragmentation Mix 250ul 125ul 55ul 25ul 25ul  2* GEx Hybridization Buffer HI-RPM 250ul 125ul 55ul 25ul 25ul    7. Mix well by careful pipetting. Take care to avoid introducing bubbles. Do not mix on a vortex mixer; mixing on a vortex mixer introduces bubbles.  8. Spin for 1 minute at room temperature at 13,000 rpm in a microcentrifuge to drive the sample off the walls and lid and to aid in bubble reduction.  9. Place sample on ice and load onto the array as soon as possible.   10. Load a clean gasket slide into the Agilent SureHyb chamber base with the label facing up and aligned with the rectangular section of the chamber base. Ensure that the gasket slide is flush with the chamber base and is not ajar.  11. Slowly dispense the volume of hybridization sample onto the gasket well in a “drag and dispense” manner.  Volumes per hybridization   Components 1*244K 2*105K 4*44K 8*15K 8*60K  Volume Prepared 500ul 250ul 110ul 50ul 50ul  Hybridization Sample Volume 490ul 245ul 100ul 40ul 40ul    12. Slowly place an array “active side” down onto the SureHyb gasket slide, so that the “Agilent”-labeled barcode is facing down and the numeric barcode is facing up. Verify that the sandwich-pair is properly aligned.   13. Place the SureHyb chamber cover onto the sandwiched slides and slide the clamp assembly onto both pieces.  14. Hand-tighten the clamp onto the chamber.  15. Vertically rotate the assembled chamber to wet the gasket and assess the mobility of the bubbles.  16. Place assembled slide chamber in rotisserie in a hybridization oven set to 65°C. Set your hybridization rotator to rotate at 10 rpm.  17. Hybridize at 65°C for 17 hours.

scan_protocol: 1. Assemble the slides into an slide holder.   2. Place assembled slide holders into scanner carousel.  3. Verify scan settings for one-color scans.   Parameters  Scan region Scan Area (61 x 21.6 mm)  Scan resolution (μm) 5  5μm scanning mode Single Pass  eXtended Dynamic range (selected)  Dye channel Green  Green PMT   XDR Hi 100%   XDR Lo 10%  4. Click Scan Slot m-n on the Scan Control main window where the letter m represents the Start slot where the first slide is located and the letter n represents the End slot where the last slide is located.

data_processing: 1. Open the Agilent Feature Extraction (FE) software.  2. Add the images (.tif) to be extracted to the FE Project.  3. Set FE Project Properties.  4. Check the Extraction Set Configuration.  5. Save the FE Project (.fep) by selecting File > Save As and browse for desired location.  6. Select Project > Start Extracting and export data to txt.

label_protocol: 1. Add 1ug of total RNA to a 1.5-mL microcentrifuge tube.   2. Add 1.2 μL of T7 Promoter Primer.   3. Use nuclease-free water to bring the total reaction volume to 11.5 μL.  4. Denature the primer and the template by incubating the reaction at 65°C in a circulating water bath for 10 minutes.  5. Place the reactions on ice and incubate for 5 minutes.  6. Immediately prior to use, gently mix the components listed in the following table for the cDNA Master Mix by adding in the order indicated, and put on ice.   Volume(ul) per reaction  5×First Strand Buffer 4  0.1M DTT 2  10mM dNTP mix 1  MMLV-RT 1  RNaseOut 0.5  Total volume 8.5  7. Briefly spin each sample tube in a microcentrifuge to drive down the contents from the tube walls and the lid. Return the tubes to ice.  8. Add 8.5 μL of cDNA Master Mix to each sample tube and mix by pipetting up and down.  9. Incubate samples at 40°C in a circulating water bath for 2 hours.  10. Move samples to a 65°C circulating water bath and incubate for 15 minutes.  11. Move samples to ice. Incubate for 5 minutes.  12. Spin samples briefly in a microcentrifuge to drive down tube contents from the tube walls and lid.  13. Immediately prior to use, gently mix the components listed in the following table in the order indicated for the Transcription Master Mix by pipetting at room temperature.   Volume(ul) per reaction  Nuclease-free water 15.3  4X Transcription Buffer 20  0.1 M DTT 6  NTP mix 8  50% PEG 6.4  RNaseOUT 0.5  Inorganic pyrophosphatase 0.6  T7 RNA Polymerase 0.8  Cyanine-3-CTP 2.4  Total volume 60  14. Add 60 μL of Transcription Master Mix to each sample tube. Gently mix by pipetting.  15. Incubate samples in a circulating water bath at 40°C for 2 hours.

extract_protocol: 1. Mix the following in a microcentrifuge tube:  Redissolved RNA ≤85ul  10×Reaction buffer 10ul  Baseline-ZERO DNase 5ul  RNase-free water X ul  Total volume 100ul  2. Incubate at 37°C for 30 minutes.  3. Add 350 μl Buffer RLT, and mix well.  4. Add 250 μl ethanol (96–100%) to the diluted RNA, and mix well by pipetting. Do not centrifuge. Proceed immediately to step 5.  5. Transfer the sample (700 μl) to an RNeasy Mini spin column placed in a 2 ml collection tube. Close the lid gently, and centrifuge for 15 s at ≥8000 x g (≥10,000 rpm). Discard the flow-through.  6. Add 500 μl Buffer RPE to the RNeasy spin column. Close the lid gently, and centrifuge for 15 s at≥8000 x g (≥10,000 rpm) to wash the spin column membrane. Discard the flow-through.  7. Add 500 μl Buffer RPE to the RNeasy spin column. Close the lid gently, and centrifuge for 2 min at ≥8000 x g (≥10,000 rpm) to wash the spin column membrane.  8. Place the RNeasy spin column in a new 2 ml collection tube, and discard the old collection tube with the flow-through. Close the lid gently, and centrifuge at full speed for 1 min.  9. Place the RNeasy spin column in a new 1.5 ml collection tube. Add appropriate RNase-free water (please see report ”RNA-QC”) directly to the spin column membrane. Close the lid gently, and centrifuge for 1 min at ≥8000 x g (≥10,000 rpm) to elute the RNA.  10. RNA quantification and quality control(Passed-please see report ”RNA-QC”).

value: pancreatic paracellular tissue


title: exp-2

description: Gene expression

value: pancreatic  tissue


title: 28Z CAR-T cells 1st round 2

value: 1st round tumor challenge


title: 28Z CAR-T cells 1st round 3


title: 28Z CAR-T cells 2nd round 3


title: ctrl-3

description: Gene expression


title: E28Z CAR-T cells rest 2

value: E28Z CAR


title: E28Z CAR-T cells rest 3


title: 28Z CAR-T cells 1st round 1


title: exp-3

description: Gene expression


title: ctrl-1

description: Gene expression


title: Whole Blood from BAB12356

type: genomic

first: Jesse

last: Bengtsson

address: 720 Broadway

institute: Pacific Northwest Research Institute

hyb_protocol: Oligoarray control targets and hybridization buffer (Agilent In Situ Hybridization Kit Plus) were added, and samples were applied to microarrays enclosed in Agilent SureHyb-enabled hybridization chambers. After hybridization, slides were washed following the manufacturer’s protocol.

scan_protocol: Scanned on an Agilent G2600D scanner. Images were quantified using Agilent Feature Extraction Software (version 12.1.1.1)

data_processing: Agilent Feature Extraction Software (version 12.1.1.1) was used for background subtraction and normalization.

source_name: Whole Blood Extracted Genomic DNA from BAB12356

label_protocol: 1.2 ug of genomic patient and reference DNA were digested with AluI (5 U) and RsaI (5 U) (Promega, R6281 and R6371) for 2 hr at 37°C, 65°C for 20 minutes. Labeling reactions were performed according to the manufacturer’s instructions (BioPrime Array CGH Genomic Labeling Module,Invitrogen Corporation, #18095-012; Perkin-Elmer Las Inc. Cyanine Smart Pack dCTP,

extract_protocol: DNA was isolated from either peripheral blood or LCLs with a Puregene kit (Gentra Systems), following the manufacturer’s protocol

tag: sample type

value: Patient BAB12356

tag: Sex

value: Male

value: Whole Blood

source_name: Genomic DNA extracted from Male LCL BAB5319

value: Reference Sample

tag: cell ine


title: Whole Blood from BAB12343

source_name: Whole Blood Extracted Genomic DNA from BAB12343

value: Patient BAB12343


title: Whole Blood from BAB12480

source_name: Whole Blood Extracted Genomic DNA from BAB12480

value: Patient BAB12480


title: exp-1

description: Gene expression


title: E28Z CAR-T cells 5th round 3

value: Blood

value: PBMC


title: Whole Blood from BAB12400

source_name: Whole Blood Extracted Genomic DNA from BAB12400

value: Patient BAB12400


title: Whole Blood from BAB12526

source_name: Whole Blood Extracted Genomic DNA from BAB12526

value: Patient BAB12526


title: E28Z CAR-T cells rest 1

value: without tumor challenge


title: E28Z CAR-T cells 3rd round 2

value: 3rd round tumor challenge


title: E28Z CAR-T cells 2nd round 3

value: 2nd round tumor challenge


title: E28Z CAR-T cells 3rd round 3


title: E28Z CAR-T cells 2nd round 1


title: E28Z CAR-T cells 5th round 1

value: 5th round tumor challenge


title: E28Z CAR-T cells 1st round 2


title: E28Z CAR-T cells 1st round 1


title: EB6I28Z CAR-T cells rest 3

value: EB6I28Z CAR


title: EB6I28Z CAR-T cells rest 2


title: E28Z CAR-T cells 3rd round 1


title: EB6I28Z CAR-T cells 5th round 2


title: EB6I28Z CAR-T cells rest 1


title: EB6I28Z CAR-T cells 3rd round 3


title: EB6I28Z CAR-T cells 5th round 1


title: E28Z CAR-T cells 5th round 2


title: EB6I28Z CAR-T cells 3rd round 2


title: EB6I28Z CAR-T cells 2nd round 3


title: EB6I28Z CAR-T cells 3rd round 1


title: EB6I28Z CAR-T cells 1st round 3

value: 1st round tumor challenge


title: EB6I28Z CAR-T cells 1st round 2


title: E28Z CAR-T cells 1st round 3

value: E28Z CAR


title: EB6I28Z CAR-T cells 2nd round 2


title: EB6I28Z CAR-T cells 1st round 1


title: HCT116_ecMDM2_med

city: New York

first: Andrea

last: Ventura

department: Cancer Biology and Genetics

institute: Memorial Sloan Kettering Cancer Center

data_processing:
Reads were mapped to mm10 or hg19 using the Bowtie2 aligner. To calculate genome coverage and copy number changes we used the QDNAseq R package with 15kb bins.
Assembly: hg19 and mm10
Supplementary files format and content: bedgraph files with normalized coverage

source_name: HCT116 colorectal cancer cell line

growth_protocol: HCT116 cells were infected with AdCre, expanded and sorted baased on GFP expression.

extract_protocol:
Cells were lysed in a buffer containing 0.1M NaCl, 0.038M TrisHCl, 0.01M EDTA and 0.175M SDS. DNA was extracted using the phenol-chloroform method  followed by ethanol precipitation.
After PicoGreen quantification, 42-100 ng of genomic DNA were used for library construction using the KAPA Hyper Prep Kit (Kapa Biosystems KK8504) with 8 cycles of PCR.
Barcoded libraries were sequenced on the NovaSeq 6000, using the NovaSeq 6000 S2 or S4 Reagent Kit (200 or 300 Cycles) (Illumina) for PE100 reads. An average of 26M reads were generated per sample, corresponding to 0.7X coverage of the genome.

value: HCT116 colorectal cancer cell line

value: AdCre_sorted mediumGFP


title: HCT116_ecMDM2_low

value: AdCre_sorted lowGFP


title: HCT116_invMDM2_med


title: HCT116_ecMDM2_high

value: AdCre_sorted highGFP


title: EB6I28Z CAR-T cells 5th round 3


title: Whole Blood from BAB12190

source_name: Whole Blood Extracted Genomic DNA from BAB12190

value: Patient BAB12190

value: Male

value: Whole Blood

value: Reference Sample


title: MCF7, 2KR, 8h, Rep 2 [2R8B_S54]

first: Dan

last: Lu

address: 210 Longwood Avenue

department: Department of Systems Biology

institute: Harvard Medical School

data_processing:
Raw RNA-sequencing data was processed using the bcbio-nextgen toolkit (https://bcbio-nextgen). The bcbio-nextgen pipeline includes aligning reads to the human reference genome hg38 with STAR58 and quantifying transcripts with Salmon59. Genes with a mean average count < 10 across all samples or those with 0 counts in >90% of samples were removed from downstream analysis. For the remaining occasional missing values, a pseudocount was added and then the counts were normalized using DESeq260.
Assembly: hg38
Supplementary files format and content: tab-deliminated text file includes salmon_raw_counts for each Sample
Supplementary files format and content: tab-deliminated text file includes salmon_tpm values for each Sample

growth_protocol: RPMI, 10% FBS, 5% CO2, 37 degrees Celsius

extract_protocol:
Qiagen RNAeasy Kit (manufacturer's protocol) 500ng RNA were used for library preparation
Libraries were prepared using a SciClone G3 NGSx workstation (Perkin Elmer) using the Kapa mRNA HyperPrep kit (Roche Applied Science). Polyadenylated mRNAs were captured using oligo-dT-conjugated magnetic beads (Kapa mRNA HyperPrep kit, Roche Sequencing, KR1352 – v4.17) from 500 ng of total RNA on a Perkin Elmer SciClone G3 NGSx automated workstation. Poly-adenylated mRNA samples were immediately fragmented to 300-400bp using heat and magnesium. First-strand synthesis was completed using random priming followed by second-strand synthesis and A-tailing. dUTP was incorporated into the second strand to allow strand-specific sequencing of the library. Libraries were enriched and indexed using 9 cycles of amplification (Kapa mRNA HyperPrep kit, Roche Sequencing) with PCR primers, which included dual 8bp index sequences to allow for multiplexing (IDT for Illumina unique dual 8bp indexes). Excess PCR reagents were removed through magnetic bead-based cleanup using Kapa Pure magnetic beads on a SciClone G3 NGSx workstation (Perkin Elmer). The resulting libraries were assessed using a 4200 TapeStation (Agilent Technologies) and quantified by QPCR (Roche Sequencing). Libraries were pooled and sequenced on one lane of an Illumina NovaSeq S4 flow cell using paired-end, 100bp reads.

treatment_protocol: 10 Gy X-ray irradiation

tag: cell line

value: breast carcinoma

value: 10Gy X-ray Irradiation


title: HCT116_invMDM2_low

tag: cell type


title: MCF7, 2KR, 4h, Rep 2 [2R4B_S50]


title: MCF7, 2KR, 6h, Rep 2 [2R6B_S52]


title: E28Z CAR-T cells 2nd round 2

value: Blood

value: PBMC


title: MCF7, 2KR, 9h, Rep 2 [2R9B_S55]


title: MCF7, 2KR, 3h, Rep 2 [2R3B_S49]


title: MCF7, 2KR, 5h, Rep 2 [2R5B_S51]


title: EB6I28Z CAR-T cells 2nd round 1

value: 2nd round tumor challenge


title: MCF7, 2KR, 0h, Rep 2 [2R0B_S46]

value: Untreated


title: MCF7, WT, 8h, Rep 2 [WT8B_S24]

value: WT


title: MCF7, 2KR, 7h, Rep 2 [2R7B_S53]


title: MCF7, WT, 6h, Rep 2 [WT6B_S22]


title: MCF7, 2KR, 1h, Rep 2 [2R1B_S47]


title: MCF7, WT, 5h, Rep 2 [WT5B_S21]


title: MCF7, WT, 7h, Rep 2 [WT7B_S23]


title: MCF7, WT, 4h, Rep 2 [WT4B_S20]


title: MCF7, WT, 3h, Rep 2 [WT3B_S19]


title: MCF7, WT, 2h, Rep 2 [WT2B_S18]


title: HCT116_ecMDM2_DN

value: AdCre_sorted DN


title: HCT116_invMDM2_DN


title: Ctr-TA, scRNA-seq

first: Yi

last: Li

address: 320 Yueyang Road

institute: Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences

description: 10x Genomics

data_processing:
Each scRNA-seq data set was processed by CellRanger (v6.1.1) pipeline to perform the alignment against the modified mouse reference genome mm10, filter the alignment and count barcodes and UMIs.
Assembly: mm10
Supplementary files format and content: Tab-delimited text files contain barcodes, features and matrix.

source_name: descending thoracic aorta

extract_protocol:
The mice were perfused with 4℃ PBS, and then the tissues were collected, dissected in PBS to remove excess hair and blood. Then the aorta were finely minced and transferred to 5ml digestion mix (HBSS, 2U/µl Collagenase type I (17100017, Gibco), 2U/µl Collagenase type II (LS004177, Worthington)). The digestion mix included tissue were incubated at 37℃ for 15 minutes. The cell suspension was filtered through 40μm cell strainer and then pelleted by centrifugation at 500g for 5 minutes. Next the cells were incubated in red-blood-cell lysis buffer (1ml, eBioscience, 00-4333-57) at room temperature for 1 min. Add ten times the volume of cold PBS, centrifuged and resuspended with cold PBS. At last, the cells were pelleted by centrifugation at 300g for 5 minutes and resuspended with 100 µl cold PBS.
The cell suspense was loaded in 10x Chromium controller to generate GEMs, which were further processed into single cell 5ʹ gene expression libraries using Chromium Single Cell 5ʹ Library Kit (v2 Chemistry).

value: descending thoracic aorta

value: aortic cells

value: 16-20 weeks


title: MCF7, WT, 1h, Rep 2 [WT1B_S17]


title: MCF7, 2KR, 9h, Rep 1 [2R9A_S40]


title: Ctr-AA, scRNA-seq

description: 10x Genomics

source_name: aortic arch

value: aortic arch


title: MCF7, WT, 9h, Rep 2 [WT9B_S25]


title: MCF7, 2KR, 7h, Rep 1 [2R7A_S38]


title: MCF7, WT, 0h, Rep 2 [WT0B_S16]


title: MCF7, 2KR, 8h, Rep 1 [2R8A_S39]


title: MCF7, 2KR, 5h, Rep 1 [2R5A_S36]


title: CKO-TA, scRNA-seq

description: 10x Genomics


title: MCF7, 2KR, 4h, Rep 1 [2R4A_S35]