title: 25_2730_5_TimePoint5

description: Sequencing Run Id: 003560


title: Experiment2 Restraint Rep_1

status: Public on Mar 31 2021

type: RNA

city: Los Angeles

first: Donald

middle: M.

last: Lamkin

state: CA

address: 300 UCLA Medical Plaza, Room 3160

department: Semel Institute for Neuroscience

country: USA

institute: UCLA

description:
101036350051_C.AVG_Signal
Illumina MouseRef-8 v2.0 expression beadchip

hyb_protocol: Standard Illumina hybridization protocol (carried out by UCLA Neuroscience Genomics Core).

scan_protocol: Standard Illumina scan protocol for gene expression profiling (carried out by UCLA Neuroscience Genomics Core).

data_processing: Raw probe intensity values and quantile-normalized gene expression values were generated by Illumina GenomeStudio software using Gene Expression module 1.1.1.  All probe and gene values are provided, with no additional filtering.

label: biotin

molecule: total RNA

organism: Mus musculus

source_name: Sorted Femoral Bone Marrow Cells (Leukemia Negative)

label_protocol: Biotinylated cDNA was prepared with the NuGEN Encore Biotin Module following amplifcation with NuGEN Ovation PicoSL WTA System V2 (carried out by UCLA Neuroscience Genomics Core).

extract_protocol: Total RNA was extracted from sorted femoral bone marrow cell samples (leukemia cells gated out) lysed in RLT buffer following the protocol from a QIAGEN RNeasy mini kit on a QIACube instrument and included DNase I treatment.

tag: strain

value: SCID mice (CB17/Icr-Prkdcscid )

tag: Sex

value: male

tag: cell type

value: femoral bone marrow leukocytes

tag: age

value: 6-8 weeks

tag: experiment #

tag: experiment condition

value: restraint stress

tag: replicate #


title: Experiment2 Control Rep_5

description:
101036350051_B.AVG_Signal
Illumina MouseRef-8 v2.0 expression beadchip

value: home cage control


title: Meningioma M20

city: Nagoya

first: Atsushi

last: Natume

address: 65 Tsurumai-cho

country: Japan

institute: Nagoya University

hyb_protocol: Hybridized for 16 h at 32 C with rotary shake (250 rpm). Hybridization buffer and washing protocol was followed by the protocol supplied by TORAY Industries, Inc..

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

data_processing: The raw data of each spot was normalized by substitution with a mean intensity of the background signal determined by all blank spots’ signal intensities of 95% confidence intervals.

organism: Homo sapiens

source_name: urine

label_protocol: Extracted total RNA was labeled with Cy5 using the 3D-Gene miRNA labeling kit (Toray, Kamakura, Japan)

extract_protocol: RNA samples were extracted from urine using the SeraMir Exosome RNA Purification Kit (System Biosciences Inc.).

tag: disease

value: Meningioma

tag: gender

value: Female


title: Experiment2 Control Rep_2

description:
101036350048_G.AVG_Signal
Illumina MouseRef-8 v2.0 expression beadchip


title: Experiment2 Control Rep_4

description:
101036350051_A.AVG_Signal
Illumina MouseRef-8 v2.0 expression beadchip


title: Experiment2 Restraint Rep_2

description:
101036350051_D.AVG_Signal
Illumina MouseRef-8 v2.0 expression beadchip


title: Experiment2 Control Rep_3

description:
101036350048_H.AVG_Signal
Illumina MouseRef-8 v2.0 expression beadchip


title: Experiment2 Control Rep_1

description:
101036350048_F.AVG_Signal
Illumina MouseRef-8 v2.0 expression beadchip


title: 24_2730_4_TimePoint4

type: SRA

city: La Jolla

first: Ferran

last: soldevila

address: 9420 Athena Cir

institute: La Jolla Institute for Immunology

description: Sequencing Run Id: 003560

library_source: transcriptomic

data_processing:
Reads passing Illumina filters were further filtered for those mapping to tRNA, rRNA, adapters, and spike-in controls using Bowtie v1.0.0 (-S --fr)
Filtered reads were mapped against the mm9 reference using Tophat v1.4.1 (--library-type fr-firststrand)
Reads mapping to the reference genome are further filtered to remove low-complexity reads with PRINSEQ v0.20.3 (-lc_method "dust" -lc_threshold 4)
Sequencing read coverage per gene was counted using HTSeq-count v0.7.1 (-m union -s yes -t exon -i gene_id) and features with 0 counts across all samples were removed
Genome_build: GRCh37.p13.gencode.r19
Supplementary_files_format_and_content: read count matrix with rows as genes and columns as cells

molecule: polyA RNA

source_name: peripheral blood mononuclear cells

extract_protocol:
2x10^6 PBMC from each sample were transferred directly to Quiazol regent (QIAGEN), resuspended and immediately aliquoted and stored at -80ºC. RNA was extracted using the Qiagen miRNeasy Mini kit with on-column DNase treatment
500 ng of total RNA was used as input for library preparation using the Illumina TruSeq Stranded mRNA Library Prep Kit.
Libraries were sequenced on the HiSeq3000

tag: treatment

value: pertussis antigenic challenge

tag: primed

value: aP

tag: time

value: 7 days

value: PBMC


title: 23_2730_3_TimePoint3

description: Sequencing Run Id: 003560

value: 3 days


title: Meningioma M19


title: Meningioma M17


title: Meningioma M18


title: 27_2686_2_TimePoint2

description: Sequencing Run Id: 003560

value: wP

value: 1 days


title: Meningioma M16

value: Male


title: 22_2730_2_TimePoint2

description: Sequencing Run Id: 003560


title: Experiment1 Restraint+Propranolol Rep_1

description:
101036350048_C.AVG_Signal
Illumina MouseRef-8 v2.0 expression beadchip

value: restraint stress+propranolol


title: Experiment1 Restraint+Propranolol Rep_3

description:
101036350048_E.AVG_Signal
Illumina MouseRef-8 v2.0 expression beadchip

value: SCID mice (CB17/Icr-Prkdcscid )


title: 21_2730_1_TimePoint1

description: Sequencing Run Id: 003560

value: 0 days


title: Experiment1 Restraint Rep_5

description:
101036350048_B.AVG_Signal
Illumina MouseRef-8 v2.0 expression beadchip

value: male

value: femoral bone marrow leukocytes


title: Meningioma M14


title: Meningioma M15


title: 20_2728_5_TimePoint5

description: Sequencing Run Id: 003560

value: 14 days


title: Experiment1 Restraint Rep_3

description:
101036340010_H.AVG_Signal
Illumina MouseRef-8 v2.0 expression beadchip

value: 6-8 weeks

value: restraint stress


title: 180_2915_5_TimePoint5

description: Sequencing Run Id: 003560


title: 2_2685_2_TimePoint2

description: Sequencing Run Id: 003560


title: 19_2728_4_TimePoint4

description: Sequencing Run Id: 003560


title: 18_2728_3_TimePoint3

description: Sequencing Run Id: 003560


title: Experiment1 Restraint+Propranolol Rep_2

description:
101036350048_D.AVG_Signal
Illumina MouseRef-8 v2.0 expression beadchip


title: Meningioma M9

value: Meningioma

value: Female


title: 179_2915_4_TimePoint4

description: Sequencing Run Id: 003560

value: pertussis antigenic challenge

value: aP


title: Meningioma M12


title: 178_2915_3_TimePoint3

description: Sequencing Run Id: 003560

value: PBMC


title: Meningioma M13


title: Meningioma M10


title: 177_2915_2_TimePoint2

description: Sequencing Run Id: 003560


title: Meningioma M11


title: Experiment1 Control Rep_5

description:
101036340010_E.AVG_Signal
Illumina MouseRef-8 v2.0 expression beadchip

value: home cage control


title: Experiment1 Restraint Rep_1

description:
101036340010_F.AVG_Signal
Illumina MouseRef-8 v2.0 expression beadchip


title: Experiment1 Restraint Rep_4

description:
101036350048_A.AVG_Signal
Illumina MouseRef-8 v2.0 expression beadchip


title: 176_2915_1_TimePoint1

description: Sequencing Run Id: 003560


title: Experiment1 Restraint Rep_2

description:
101036340010_G.AVG_Signal
Illumina MouseRef-8 v2.0 expression beadchip


title: Meningioma M8


title: Meningioma M7


title: Experiment1 Control Rep_2

description:
101036340010_B.AVG_Signal
Illumina MouseRef-8 v2.0 expression beadchip


title: Experiment1 Control Rep_1

description:
101036340010_A.AVG_Signal
Illumina MouseRef-8 v2.0 expression beadchip


title: 175_2935_5_TimePoint5

description: Sequencing Run Id: 003560


title: Meningioma M6


title: 174_2935_4_TimePoint4

description: Sequencing Run Id: 003560

value: 7 days


title: Meningioma M4


title: Meningioma M5


title: 173_2935_3_TimePoint3

description: Sequencing Run Id: 003560

value: 3 days


title: Meningioma M3


title: 171_2935_1_TimePoint1

description: Sequencing Run Id: 003560


title: 172_2935_2_TimePoint2

description: Sequencing Run Id: 003560

value: 1 days


title: AL2 30°C 4

city: Amsterdam

first: Anne-Catherine

last: Ahn

address: Science Park 904

department: IBED

country: Netherlands

institute: University of Amsterdam

data_processing:
The software program kallisto (Bray et al., 2016) (v0.44.0) was used to create index files for the quantification from those references (Tv. versutus AL2T (NZ_MVAR00000000.1) and Tv. nitratis ALJ2 (NZ_ARKB00000000.1)).
Pseudo-alignments were generated in kallisto by mapping the reads from the fastq RNA-Seq files against the indexed reference and reads were quantified using 100 bootstrap samples
Differential expression analysis was performed with the software program sleuth (Pimentel et al., 2017) (0.30.0) using the Wald test.
Supplementary_files_format_and_content: Tab-delimited text files include TPM values of samples

organism: Thioalkalivibrio versutus AL 2

source_name: Bacterial cell

growth_protocol: Tv. versutus AL2T and Tv. nitratis ALJ2 were grown in continuous cultivation in 500 ml medium at 10°C and 30°C, and at a dilution rate of 0.010 ± 0.00027 h-1. The medium contained 17.5 g/l Na2CO3, 13.9 g/l NaHCO3, 6.1 g/l NaCl, 1 g/l K2HPO4, 0.2 g/l MgCl2, 20 mM Na2S2O3, 5 mM KNO3 and 1:1000 trace metals (Pfennig and Lippert, 1966). The final pH was adjusted for usage at 10°C and 30°C to 10. Dilution rate was regularly monitored by measuring the pump rate over time with a burette placed between the medium vessel and the peristaltic pump. The vessels were continuously aerated with compressed air at 0.5 l/min and magnetically stirred at 600 rpm. Full aeration was achieved by metallic baffles inside the reactor. All reactors were inoculated with 20 ml of batch culture and were grown in batch for two days at 30°C in order to obtain a dense culture. The 30°C-reactors were then switched to a continuous culture mode, whereas the 10°C-reactors were transferred to 10°C and then kept there for another four days to acclimatize before switching them to continuous culture mode. Cultures were run in two biological replicates and each reactor was run twice in time using around 100 ml from the previously culture as starting material, providing quadruplicate samples for each condition. The samples were collected at steady state after at least five volume changes of the reactor.

extract_protocol:
The frozen cell pellets were homogenized with a mortar and a pestle before being resuspended in QIAzol Lysis Reagent (Qiagen, Germany). Total RNA was extracted and purified with the RNeasy kit (Qiagen) following the manufacturer’s instructions. The purification step comprised a DNase treatment using the RNase-free DNase kit (Qiagen). The concentration was quantified with the NanoDrop ND2000 (Thermo Fisher Scientiﬁc, USA) and the integrity of the RNA was checked on the 2200 TapeStation with Agilent RNA ScreenTapes (Agilent Technologies, The Netherlands). Ribosomal RNA (rRNA) was removed by the Illumina Ribo-Zero rRNA Removal Kit (Bacteria) (Illumina, USA).
Bar-coded RNA libraries were prepared using the Ion Total RNA-Seq kit v2 and the Ion Xpress RNA-Seq barcoding kit according to the supplier’s instructions (Thermo Fisher Scientiﬁc).

tag: growth temperature (°c)


title: Meningioma M2


title: AL2 30°C 3


title: AL2 30°C 2


title: 17_2728_2_TimePoint2

description: Sequencing Run Id: 003560


title: AL2 10°C 4


title: AL2 30°C 1


title: AL2 10°C 3


title: Meningioma M1


title: Lower grade glioma LGG34

value: Lower grade glioma

value: Male


title: Experiment1 Control Rep_3

description:
101036340010_C.AVG_Signal
Illumina MouseRef-8 v2.0 expression beadchip

value: SCID mice (CB17/Icr-Prkdcscid )


title: 168_2928_3_TimePoint3

description: Sequencing Run Id: 003560


title: KO1_unstim

city: Rochester

first: Aditya

last: Bhagwate

state: MN

address: 200 1st Street SW

institute: Mayo Clinic

hyb_protocol: Microarray analysis was conducted according to manufacturer’s instructions for the Affymetrix WT Plus Reagent kit (Thermo Fisher Scientific, Waltham, MA).  Briefly, RNA quality was assessed by Agilent Bioanalyzer (Santa Clara, CA).  Single-stranded cDNA was generated, using primers with a T7 promoter sequence, from 100 ng of total RNA.  The single-stranded cDNA is converted into double-stranded cDNA using DNA polymerase.  The products were in vitro transcribed to generate cRNA, and then bead-purified (Thermo Fisher Scientific).  Complimentary RNA is then reverse transcribed  to single-stranded cDNA using 2nd cycle primers and  RNase H.  Samples are then bead purified and 5.5 ug of ss-cDNA was fragmented, and hybridized onto Affymetrix GeneChip™ Human Transcriptome Array 2.0 at 45º C for 16 hours.

scan_protocol: The arrays were washed and stained with streptavidin-phycoerythrin, then scanned in an Affymetrix GeneChip® Scanner 3000 (Thermo Fisher Scientific, Waltham, MA).  All Affy array experiments were carried out at the Mayo Clinic Genome Analysis Core.  Control parameters were confirmed to be within normal ranges before normalization and data reduction was initiated.

data_processing: The raw expression microarray data in .cel format (mouse MTA-1.0) were imported into the Transcriptome Analysis Console (TAC4.0, ThermoFisher Scientific). RMA algorithm was used to normalize and summarize gene level expression level.

label: SYBR

source_name: Splenic GFP+ cell (Treg)

label_protocol: PCRs were performed in 20 μL of total volume that contained primers and 10 μL of Express SYBR Green ER Quantitative PCR Supermaster Mix (Invitrogen).

growth_protocol: CD4+ cells were isolated from the spleens of 7-8-week-old mice using a Miltenyi magnet per manufacturer protocol. CD4+ T cells were then subjected to sorting for Foxp3 GFP+ cells using an Aria FACS sorter. The 15,000–40,000 cells collected were then stored in RNAprotect cell reagent (Qiagen, Cat#76526) and later processed using the RNAeasy Micro kit (Qiagen, cat#74004) for RNA isolation.

extract_protocol: Total RNA was isolated using the RNeasy Mini Kit (Qiagen, cat #74104) per manufacturer protocol. cDNA was synthesized from 0.5–1 μg of total RNA with random primers using the SuperScript® Kit III First-Strand (Invitrogen). 2 μL of reverse transcription products was used for each real-time PCR.

treatment_protocol: Cells were not treated prior.

tag: genotype

value: FOXP3-CRE (B6-Tg(Foxp3EGFP-cre)1cJbs/J x BMI1-flox C57BL/6


title: WT1_unstim

value: FOXP3-CRE (B6-Tg(Foxp3EGFP-cre)1cJbs/J x C57BL/6


title: KO2_unstim


title: WT3_unstim


title: Lower grade glioma LGG31


title: Experiment1 Control Rep_4

description:
101036340010_D.AVG_Signal
Illumina MouseRef-8 v2.0 expression beadchip

value: male

value: femoral bone marrow leukocytes


title: AL2 10°C 2


title: Lower grade glioma LGG32


title: Lower grade glioma LGG33


title: 166_2928_1_TimePoint1

description: Sequencing Run Id: 003560

value: 0 days


title: AL2 10°C 1


title: 170_2928_5_TimePoint5

description: Sequencing Run Id: 003560

value: 14 days


title: 165_2922_5_TimePoint5

description: Sequencing Run Id: 003560


title: 169_2928_4_TimePoint4

description: Sequencing Run Id: 003560


title: Lower grade glioma LGG30

value: Female


title: 164_2922_4_TimePoint4

description: Sequencing Run Id: 003560

value: pertussis antigenic challenge


title: EZH2KO BF-ATATC-35

library_source: genomic

data_processing:
Sequencing Reads were aligned to mm10 build of the mouse genome using Burrows-Wheeler Alignment (BWA)
Peaks were called using MACS2 software.
TDF files for visualization were generated using in-house scripts
Genome_build: mm10
Supplementary_files_format_and_content: TDF Files (visualization) and BED Files (Peak calls)

molecule: genomic DNA

source_name: Spleen

growth_protocol: Tregs isolated from mouse splenocytes - CD25 kit

extract_protocol:
ATAC-seq was performed from 50,000 Treg cells per a previously published protocol (Buenrostro, Nature Methods, 2013). Briefly, nuclei were prepared by washing cells with PBS, followed by lysis using cold lysis buffer. Nuclei were spun and the pellet was then resuspended in the transposase reaction mix for 30 min at 37 °C. The samples were then purified using a Qiagen Minelute kit.
Amplified libraries were purified, and the sizes of library DNA were determined by the Fragment Analyzer (Advanced Analytical Technologies, IA) using the High Sensitivity NGS Fragment Analysis Kit (Cat # DNF-486). The enrichment of accessible region was determined by the fold difference between positive and negative genomic loci using real-time PCR. The libraries were sequenced to 51 base pairs from both ends on an Illumina HiSeq 4000 instrument in the Mayo Clinic Center for Individualized Medicine Medical Genomics Facility.

tag: sample number

tag: mouse strain

value: FOXP3-CRE (B6-Tg(Foxp3EGFP-cre)1cJbs/J x EZH2-flox C57BL/6


title: BMI1KO BF-ATATC-34


title: Lower grade glioma LGG29


title: 163_2922_3_TimePoint3

description: Sequencing Run Id: 003560

value: aP

value: PBMC


title: Lower grade glioma LGG28


title: BMI1KO BF-ATATC-33


title: 162_2922_2_TimePoint2

description: Sequencing Run Id: 003560


title: Heads__3_5

city: Tel Aviv

first: Metsada

last: Pasmanik-Chor

address: Ramat Aviv

department: Biology

country: Israel

institute: Tel Aviv University

description:
Heads_3_5_ATAGCGTC_L004_R1_001
Heads_3_5_ATAGCGTC_L004_R1_002
Heads_3_5_ATAGCGTC_L005_R1_001
Heads_3_5_ATAGCGTC_L005_R1_002

data_processing:
Reads were trimmed using cutadapt and mapped to Drosophila melanogaster BDGP6 genome using STAR v2.4.2a.  Counting proceeded uaing htseq-count.
Differential expression analysis was performed using DESeq2, with the betaPrior, cooksCutoff and independentFiltering parameters set to False.
Raw P values were adjusted for multiple testing using the procedure of Benjamini and Hochberg
Pipeline was constructed using Snakemake (https://snakemake.readthedocs.io/en/v3.9.1/)
Gene lists were created by filtering the genes based on an absolute linear fold change ≥2, p ≤ 0.05, and reads ≥30. To view gene lists as a heat map, the Morpheos tool was used (https://software.broadinstitute.org/morpheus/)
Genome_build: Drosophila melanogaster BDGP6 genome.
Supplementary_files_format_and_content: Tab-delimited text file include RPKM values for each Sample.

organism: Drosophila melanogaster

source_name: heads

growth_protocol: 12-day-old flies

extract_protocol:
RNA was extracted from bodies and heads of 12-years-old drosophila. For each line (w1118, heterozygous insertion GBA1A, homozygous insertion GBA1A, heterozygous insertion GBA1B, homozygous insertion GBA1B), triplicates of fifty flies were used.
RNA libraries were prepared for sequencing using standard Illumina protocols.

value: isogenized w1118 background

value: homozygous insertion GBA1B


title: Lower grade glioma LGG27


title: Lower grade glioma LGG35


title: 167_2928_2_TimePoint2

description: Sequencing Run Id: 003560

value: 1 days


title: Heads__3_4

description:
Heads_3_4_TCGCCTTG_L004_R1_001
Heads_3_4_TCGCCTTG_L004_R1_002
Heads_3_4_TCGCCTTG_L005_R1_001
Heads_3_4_TCGCCTTG_L005_R1_002

value: heterozygous insertion GBA1B


title: Lower grade glioma LGG25

value: Lower grade glioma


title: Lower grade glioma LGG26

value: Male


title: 161_2922_1_TimePoint1

description: Sequencing Run Id: 003560


title: Heads__3_3

description:
Heads_3_3_CCTATGCC_L004_R1_001
Heads_3_3_CCTATGCC_L004_R1_002
Heads_3_3_CCTATGCC_L005_R1_001
Heads_3_3_CCTATGCC_L005_R1_002

value: homozygous insertion GBA1A


title: 160_2912_5_TimePoint5

description: Sequencing Run Id: 003560


title: Cont_CD11b_3

city: Minato-ku

first: Hideto

last: Koso

state: Tokyo

address: 4-6-1 Shirokanedai

institute: Institute of Medical Science, The University of Tokyo

description:
processed data file: count_normalized.txt
processed data file: FPKM.txt

data_processing:
bcl2fastq-v2.17.1.14 software was used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and mapped to the mouse genome assembly using Hisat2 (Hisat2-2.1.0) software.
Read count was obtained using featureCount software (subread-1.6.2).
Raw counts were processed using DESeq2 package (v1.20.0) to obtain normalized counts (median of ratio method).
Raw counts were processed using DESeq2 package (v1.20.0) to obtain FPKM values.
Genome_build: GRCm38.p6
Supplementary_files_format_and_content: count_normalized.txt: Tab-delimited text file includes normalized counts for each sample.
Supplementary_files_format_and_content: FPKM.txt: Tab-delimited text file includes FPKM values for each sample.

source_name: brain

extract_protocol:
RNA was harvested from cells using Sepazol reagent.
cDNA synthesis was performed using the SMARTer Universal Low Input RNA Kit (Clontech). RNA libraries were prepared for sequencing using the Nextera XT DNA Library Preparation Kit (Illumina).

tag: strain/background

tag: genotype/variation

value: CD11b+ phagocytes

tag: origin

value: cerebellum


title: WT BF-ATATC-31

description: WT

value: FOXP3-CRE (B6-Tg(Foxp3EGFP-cre)1cJbs/J x C57BL/6


title: Heads__3_2

description:
Heads_3_2_GACAGTAA_L004_R1_001
Heads_3_2_GACAGTAA_L004_R1_002
Heads_3_2_GACAGTAA_L004_R1_003
Heads_3_2_GACAGTAA_L005_R1_001
Heads_3_2_GACAGTAA_L005_R1_002
Heads_3_2_GACAGTAA_L005_R1_003

tag: strain

value: heterozygous insertion GBA1A


title: EZH2KO BF-ATATC-36


title: Cont_CD11b_2

tag: cell type


title: Lower grade glioma LGG24

tag: age


title: 159_2912_4_TimePoint4

description: Sequencing Run Id: 003560

value: 7 days


title: Heads__3_1

description:
Heads_3_1_AGGATCTA_L004_R1_001
Heads_3_1_AGGATCTA_L004_R1_002
Heads_3_1_AGGATCTA_L005_R1_001
Heads_3_1_AGGATCTA_L005_R1_002

value: wild-type (WT)


title: Lower grade glioma LGG23


title: 16_2728_1_TimePoint1

description: Sequencing Run Id: 003560

value: pertussis antigenic challenge

value: 0 days


title: Lower grade glioma LGG22

value: Female


title: Cont_CD11b_1


title: Lower grade glioma LGG21


title: Heads__2_5

description:
Heads_2_5_GAAGAAGT_L004_R1_001
Heads_2_5_GAAGAAGT_L004_R1_002
Heads_2_5_GAAGAAGT_L005_R1_001
Heads_2_5_GAAGAAGT_L005_R1_002


title: 157_2912_2_TimePoint2

description: Sequencing Run Id: 003560

value: aP

value: PBMC


title: WT BF-ATATC-32

description: WT


title: Lower grade glioma LGG20


title: Ras_CD11b_2

value: tumor


title: 155_2901_5_TimePoint5

description: Sequencing Run Id: 003560

value: 14 days


title: Ras_CD11b_1


title: 156_2912_1_TimePoint1

description: Sequencing Run Id: 003560


title: Heads__2_3

description:
Heads_2_3_CCTACCAT_L004_R1_001
Heads_2_3_CCTACCAT_L004_R1_002
Heads_2_3_CCTACCAT_L005_R1_001
Heads_2_3_CCTACCAT_L005_R1_002

value: isogenized w1118 background


title: Lower grade glioma LGG18

value: Lower grade glioma


title: Lower grade glioma LGG17

value: Male


title: Heads__2_1

description:
Heads_2_1_TGTCGGAT_L004_R1_001
Heads_2_1_TGTCGGAT_L004_R1_002
Heads_2_1_TGTCGGAT_L005_R1_001
Heads_2_1_TGTCGGAT_L005_R1_002


title: Cont_GFP_2

value: GFP+ cells


title: Cont_GFP_3


title: 154_2901_4_TimePoint4

description: Sequencing Run Id: 003560


title: Lower grade glioma LGG16


title: Cont_GFP_1


title: Heads__2_2

description:
Heads_2_2_ATTATGTT_L004_R1_001
Heads_2_2_ATTATGTT_L004_R1_002
Heads_2_2_ATTATGTT_L005_R1_001
Heads_2_2_ATTATGTT_L005_R1_002


title: 158_2912_3_TimePoint3

description: Sequencing Run Id: 003560

value: 3 days


title: Heads__1_4

description:
Heads_1_4_CATAGCGA_L004_R1_001
Heads_1_4_CATAGCGA_L004_R1_002
Heads_1_4_CATAGCGA_L005_R1_001
Heads_1_4_CATAGCGA_L005_R1_002

value: heterozygous insertion GBA1B


title: Heads__2_4

description:
Heads_2_4_TACTTAGC_L004_R1_001
Heads_2_4_TACTTAGC_L004_R1_002
Heads_2_4_TACTTAGC_L005_R1_001
Heads_2_4_TACTTAGC_L005_R1_002


title: Ras_GFP_3


title: Ras_CD11b_3

value: CD11b+ phagocytes


title: 152_2901_2_TimePoint2

description: Sequencing Run Id: 003560

value: 1 days


title: 153_2901_3_TimePoint3

description: Sequencing Run Id: 003560


title: Heads__1_3

description:
Heads_1_3_TCTGGCGA_L004_R1_001
Heads_1_3_TCTGGCGA_L004_R1_002
Heads_1_3_TCTGGCGA_L005_R1_001
Heads_1_3_TCTGGCGA_L005_R1_002

value: homozygous insertion GBA1A


title: Lower grade glioma LGG14


title: 151_2901_1_TimePoint1

description: Sequencing Run Id: 003560


title: Lower grade glioma LGG19


title: Ras_GFP_2


title: Heads__1_2

description:
Heads_1_2_GCACACGA_L004_R1_001
Heads_1_2_GCACACGA_L004_R1_002
Heads_1_2_GCACACGA_L005_R1_001
Heads_1_2_GCACACGA_L005_R1_002

value: heterozygous insertion GBA1A


title: Ras_GFP_1


title: Heads__1_1

description:
Heads_1_1_AAGGATGT_L004_R1_001
Heads_1_1_AAGGATGT_L004_R1_002
Heads_1_1_AAGGATGT_L005_R1_001
Heads_1_1_AAGGATGT_L005_R1_002

value: wild-type (WT)


title: Lower grade glioma LGG13


title: 15_2698_5_TimePoint5

description: Sequencing Run Id: 003560

value: pertussis antigenic challenge


title: Lower grade glioma LGG12


title: Heads__1_5

description:
Heads_1_5_CAGGAGCC_L004_R1_001
Heads_1_5_CAGGAGCC_L004_R1_002
Heads_1_5_CAGGAGCC_L004_R1_003
Heads_1_5_CAGGAGCC_L005_R1_001
Heads_1_5_CAGGAGCC_L005_R1_002
Heads_1_5_CAGGAGCC_L005_R1_003

value: homozygous insertion GBA1B


title: Brain_Old_LL_P21211

city: COLUMBIA

first: HAO

last: JI

state: SC

address: 715 SUMTER ST CLS RM 109

department: College of Pharmacy

institute: University of South Carolina

description:
S12
RNASeqCounts_LL.txt

data_processing:
Indexed sequences were checked by FastQC | version: 0.11.5.
Trimmed adapter by TrimGalore-0.4.5.
Reads were mapped to the P. maniculatus and P. leucopus reference genome using STAR | version 2.7.2b with default parameters (generation of sam files).
Convert .sam files to .bam files using samtools | version: 1.5 with parameters -bh -F 3840 -q 255.
Read counts over annotated genes Peromyscus_maniculatus_bairdii.HU_Pman_2.1.101.gtf and GCF_004664715.1_Pero_0.1_genomic.gtf were obtained using featureCount (subreads | version: 1.5.3) with parameters -p -T 10.
Genome_build: Peromyscus_maniculatus_bairdii.HU_Pman_2.1 and GCF_004664715.1_Pero_0.1_genomic
Supplementary_files_format_and_content: RNASeqCounts_*.txt: Tab-delimited text files include gene counts for each sample.

organism: Peromyscus leucopus

source_name: Brain

growth_protocol: Deer mice, P. maniculatus were obtained from the Peromyscus Genetic Stock Center (PGSC), University of South Carolina (USC), Columbia, SC (RRID:SCR_002769). P. maniculatus bairdii (BW Stock), was closed colony bred in captivity since 1948 and descended from 40 ancestors wild-caught near Ann Arbor, Michigan. P. leucopus (LL Stock) was derived from 38 wild ancestors captured between 1982 and 1985.

extract_protocol:
Total RNA was extracted from brain using the RNeasy Mini Kit (Qiagen).
Sequencing libraries were generated using the NEBNext Ultra II Directional RNA Library Prep Kit (NEB#E7490/NEB#E7760).

treatment_protocol: Brain tissues of 7-months-old and 2- to 3-years-old outbred deer mice P. maniculatus and P. leucopus were collected at sacrifice.

tag: stock

value: LL

tag: tissue

value: Brain

tag: age of animal at termination

value: 28 months


title: 149_2736_4_TimePoint4

description: Sequencing Run Id: 003560

value: aP

value: 7 days

value: PBMC


title: Brain_Old_LL_P20967

description:
S11
RNASeqCounts_LL.txt


title: Lower grade glioma LGG15

tag: disease

value: Lower grade glioma

tag: gender

value: Female


title: Brain_Old_LL_P21001

description:
S10
RNASeqCounts_LL.txt


title: Bodies__3_4

description:
Bodies_3_4_CACATCCT_L004_R1_001
Bodies_3_4_CACATCCT_L004_R1_002
Bodies_3_4_CACATCCT_L005_R1_001
Bodies_3_4_CACATCCT_L005_R1_002

source_name: bodies

value: isogenized w1118 background


title: Lower grade glioma LGG11


title: 148_2736_3_TimePoint3

description: Sequencing Run Id: 003560

tag: treatment

tag: primed

value: 3 days


title: Bodies__3_3

description:
Bodies_3_3_AACTTGAC_L004_R1_001
Bodies_3_3_AACTTGAC_L004_R1_002
Bodies_3_3_AACTTGAC_L005_R1_001
Bodies_3_3_AACTTGAC_L005_R1_002


title: 147_2736_2_TimePoint2

description: Sequencing Run Id: 003560

tag: time


title: Lower grade glioma LGG9

value: Male


title: Brain_Old_LL_P21069

description:
S08
RNASeqCounts_LL.txt


title: Brain_Old_LL_P21989

description:
S09
RNASeqCounts_LL.txt


title: 150_2736_5_TimePoint5

description: Sequencing Run Id: 003560

value: 14 days


title: Bodies__3_2

description:
Bodies_3_2_TTCGCTGA_L004_R1_001
Bodies_3_2_TTCGCTGA_L004_R1_002
Bodies_3_2_TTCGCTGA_L004_R1_003
Bodies_3_2_TTCGCTGA_L005_R1_001
Bodies_3_2_TTCGCTGA_L005_R1_002
Bodies_3_2_TTCGCTGA_L005_R1_003

tag: genotype


title: Bodies__3_1

description:
Bodies_3_1_GTATAACA_L004_R1_001
Bodies_3_1_GTATAACA_L004_R1_002
Bodies_3_1_GTATAACA_L005_R1_001
Bodies_3_1_GTATAACA_L005_R1_002


title: Lower grade glioma LGG7


title: 146_2736_1_TimePoint1

description: Sequencing Run Id: 003560

value: 0 days


title: 145_2900_5_TimePoint5

description: Sequencing Run Id: 003560


title: 144_2900_4_TimePoint4

description: Sequencing Run Id: 003560


title: Brain_Old_LL_P20980

description:
S07
RNASeqCounts_LL.txt


title: Brain_Young_LL_P22488

description:
S06
RNASeqCounts_LL.txt

value: 7 months


title: Bodies__2_5

description:
Bodies_2_5_GGTCCAGA_L004_R1_001
Bodies_2_5_GGTCCAGA_L004_R1_002
Bodies_2_5_GGTCCAGA_L005_R1_001
Bodies_2_5_GGTCCAGA_L005_R1_002


title: 143_2900_3_TimePoint3

description: Sequencing Run Id: 003560


title: Bodies__3_5

description:
Bodies_3_5_TCGGAATG_L004_R1_001
Bodies_3_5_TCGGAATG_L004_R1_002
Bodies_3_5_TCGGAATG_L005_R1_001
Bodies_3_5_TCGGAATG_L005_R1_002


title: Brain_Young_LL_P22547

description:
S05
RNASeqCounts_LL.txt


title: Lower grade glioma LGG5


title: Lower grade glioma LGG6


title: Lower grade glioma LGG10


title: 142_2900_2_TimePoint2

description: Sequencing Run Id: 003560

value: 1 days


title: 141_2900_1_TimePoint1

description: Sequencing Run Id: 003560

value: pertussis antigenic challenge


title: Lower grade glioma LGG4


title: Lower grade glioma LGG8


title: Brain_Young_LL_P22189

description:
S03
RNASeqCounts_LL.txt


title: Bodies__2_1

description:
Bodies_2_1_AGTTGCTT_L004_R1_001
Bodies_2_1_AGTTGCTT_L004_R1_002
Bodies_2_1_AGTTGCTT_L005_R1_001
Bodies_2_1_AGTTGCTT_L005_R1_002

value: wild-type (WT)


title: 140_2902_5_TimePoint5

description: Sequencing Run Id: 003560


title: Lower grade glioma LGG3


title: Bodies__1_4

description:
Bodies_1__4_TGCTCGAC_L004_R1_001
Bodies_1__4_TGCTCGAC_L004_R1_002
Bodies_1__4_TGCTCGAC_L005_R1_001
Bodies_1__4_TGCTCGAC_L005_R1_002

value: heterozygous insertion GBA1B


title: Lower grade glioma LGG2


title: Brain_Young_LL_P22186

description:
S01
RNASeqCounts_LL.txt

value: LL

value: Brain


title: 139_2902_4_TimePoint4

description: Sequencing Run Id: 003560

value: aP


title: Lower grade glioma LGG1


title: Glioblastoma GBM28

value: Glioblastoma


title: Bodies__1_3

description:
Bodies_1__3_GCACATCT_L004_R1_001
Bodies_1__3_GCACATCT_L004_R1_002
Bodies_1__3_GCACATCT_L004_R1_003
Bodies_1__3_GCACATCT_L005_R1_001
Bodies_1__3_GCACATCT_L005_R1_002
Bodies_1__3_GCACATCT_L005_R1_003

value: homozygous insertion GBA1A


title: Bodies__2_4

description:
Bodies_2_4_ACCAACTG_L004_R1_001
Bodies_2_4_ACCAACTG_L004_R1_002
Bodies_2_4_ACCAACTG_L005_R1_001
Bodies_2_4_ACCAACTG_L005_R1_002


title: Bodies__2_3

description:
Bodies_2_3_TTGAGCCT_L004_R1_001
Bodies_2_3_TTGAGCCT_L004_R1_002
Bodies_2_3_TTGAGCCT_L004_R1_003
Bodies_2_3_TTGAGCCT_L005_R1_001
Bodies_2_3_TTGAGCCT_L005_R1_002
Bodies_2_3_TTGAGCCT_L005_R1_003


title: 138_2902_3_TimePoint3

description: Sequencing Run Id: 003560

value: PBMC


title: Pt73_Tumor_CD8PlusCD28Plus

city: Madison

first: Jack

middle: M

last: Shireman

state: WI

address: 1500 Highland Ave

department: Neurological Surgery

institute: UW-Madison

data_processing:
Reds were mapped to HG38 using STAR using paramater --outSAMmapqUnique 60
The data was filtered using read count > 10 in more than three of the samples, normalized using TMM (trimmed mean of M values) method and subjected to differential expression analysis using R package edgeR
Functional analysis was performed on differential expression genes with false discovery rate cut-off less than 0.01 using DAVID.
Genome_build: HG38

source_name: Human Brain Tumor

growth_protocol: All tumor cells for this manuscript were not grown in culture but were freshly isolated from patients and then immediatelty isolated or purchased as frozen stocks and isolated in one batch upon arrival. Immune cells were isolated from patients according to standard procedures as descried in the manuscript

extract_protocol:
immune cells were extracted using standard protocols as detailed in the study methods and according to kit instructions for isolating from patient speciifc samples. Tissue samples were mechanically digested and DNA and RNA was isolated with an all-prep kit (Quiagen) according to protocol.
Library was constructed using Clontech SMART-Seq v4 ultra low input RNA kit according to manufactures protocol

treatment_protocol: no treatments were preformed on any of samples in this study

tag: sample type

value: Primary Human Cells

value: Brain Tumor

value: infiltrating T cells

tag: cell markers


title: Bodies__2_2

description:
Bodies_2_2_CCAGTTAG_L004_R1_001
Bodies_2_2_CCAGTTAG_L004_R1_002
Bodies_2_2_CCAGTTAG_L004_R1_003
Bodies_2_2_CCAGTTAG_L005_R1_001
Bodies_2_2_CCAGTTAG_L005_R1_002
Bodies_2_2_CCAGTTAG_L005_R1_003

value: isogenized w1118 background

value: heterozygous insertion GBA1A


title: Glioblastoma GBM27

value: Female


title: Brain_Young_LL_P22500

description:
S04
RNASeqCounts_LL.txt

value: 7 months


title: 137_2902_2_TimePoint2

description: Sequencing Run Id: 003560

value: 1 days


title: Pt73_Tumor _CD8PlusCD28Minus


title: Bodies__1_2

description:
Bodies_1__2_CATGCTTA_L004_R1_001
Bodies_1__2_CATGCTTA_L004_R1_002
Bodies_1__2_CATGCTTA_L004_R1_003
Bodies_1__2_CATGCTTA_L005_R1_001
Bodies_1__2_CATGCTTA_L005_R1_002
Bodies_1__2_CATGCTTA_L005_R1_003


title: Pt72_Tumor_CD8PlusCD28Plus


title: Glioblastoma GBM26

value: Male


title: Glioblastoma GBM25


title: Pt72_Tumor_CD8PlusCD28Minus


title: 136_2902_1_TimePoint1

description: Sequencing Run Id: 003560

value: pertussis antigenic challenge

value: 0 days


title: Bodies_1__1

description:
Bodies_1__1_CTACCAGG_L004_R1_001
Bodies_1__1_CTACCAGG_L004_R1_002
Bodies_1__1_CTACCAGG_L005_R1_001
Bodies_1__1_CTACCAGG_L005_R1_002

value: wild-type (WT)


title: 135_2890_5_TimePoint5

description: Sequencing Run Id: 003560

value: 14 days


title: 14_2698_4_TimePoint4

description: Sequencing Run Id: 003560

value: aP

value: 7 days


title: Pt63_Tumor_CD8PlusCD28Plus


title: 134_2890_4_TimePoint4

description: Sequencing Run Id: 003560


title: 133_2890_3_TimePoint3

description: Sequencing Run Id: 003560

value: 3 days


title: Pt63_Tumor_CD8PlusCD28Minus


title: Bodies__1_5

description:
Bodies_1__5_AGCAATTC_L004_R1_001
Bodies_1__5_AGCAATTC_L004_R1_002
Bodies_1__5_AGCAATTC_L004_R1_003
Bodies_1__5_AGCAATTC_L005_R1_001
Bodies_1__5_AGCAATTC_L005_R1_002
Bodies_1__5_AGCAATTC_L005_R1_003

value: homozygous insertion GBA1B


title: Qbar_3

city: Utrecht

first: Rik

last: Korswagen

address: Uppsalalaan 8

institute: Hubrecht Institute

data_processing:
We aligned the 50 base pair paired-end reads to the C. elegans references transcriptome, which was compiled from the C. elegans reference genome WS249 as described in (Ebbing et al. 2018).
Genome_build: C. elegans reference genome WS249
Supplementary_files_format_and_content: counts

organism: Caenorhabditis elegans

source_name: QR descendants

extract_protocol:
mRNA extraction, barcoding, reverse transcription and in vitro transcription were performed according to the CEL-seq protocol (Hashimshony et al., 2012) using the MessageAmp II kit (Ambion).
Illumina sequencing libraries were prepared according to the CEL-seq2 protocol (Hashimshony et al., 2016) using the SuperScript® II Double-Stranded cDNA Synthesis Kit (Thermofisher), Agencourt AMPure XP beads (Beckman Coulter), and randomhexRT for converting aRNA to cDNA using random priming.

tag: Stage

value: L1 larva fed for 7 hours after L1 arest

value: mab-5(gk670); huIs166; ayIs9; huIs179

tag: cell

value: QR descendants


title: 132_2890_2_TimePoint2

description: Sequencing Run Id: 003560

value: PBMC


title: Pt75_Blood_CD8PlusCD28Plus

source_name: Human Peripheral Blood

value: Primary Human Cells

value: Peripheral Blood

value: T cells


title: Glioblastoma GBM23

value: Glioblastoma


title: Glioblastoma GBM24

value: Female


title: Glioblastoma GBM22

value: Male


title: Qbar_2


title: 131_2890_1_TimePoint1

description: Sequencing Run Id: 003560

value: pertussis antigenic challenge

value: 0 days


title: Pt73_Blood_CD8PlusCD28Plus


title: Pt75_Blood_CD8PlusCD28Minus


title: Glioblastoma GBM21


title: 130_2886_5_TimePoint5

description: Sequencing Run Id: 003560

value: 14 days


title: Q_3

value: mab-5(gk670); huIs166; ayIs9


title: Qbar_1


title: Pt73_Blood_CD8PlusCD28Minus


title: Glioblastoma GBM19


title: Glioblastoma GBM20


title: FFPE Breast cancer 34298, luminal B, FBC+

type: genomic

city: Salamanca

first: Juan Luis

last: Garcia

state: Salamanca

address: Campus Miguel de Unamuno

country: Spain

institute: Centro de Investigación del Cáncer IBMCC-CIC

description: Sample name: 34298

hyb_protocol: DNA was restriction digested, PCR amplified, fragmented, labeled and hybridized to each array according to the manufacturer's instructions.

scan_protocol: The Arrays were then washed using Affymetrix fluidics stations, and scanned using the Gene Chip Scanner 3000.

data_processing: OncoScan console (v.1.3) from Affymetrix was used to assess genome wide copy number

source_name: FFPE breast cancer tissue

label_protocol: Labelling and hybridizations were performed according to protocols from Affymetrix

growth_protocol: Not applicable

extract_protocol: Genomic DNAs were extracted according to manufacturer's protocols.

treatment_protocol: Not applicable

tag: ki67 ihq

tag: p53 ihq

tag: histologic grade

tag: hormone receptor (hr)

tag: her2 ihq

tag: subtype

value: luminal B

tag: brca status

value: FBC+

value: FFPE breast cancer tissue


title: 13_2698_3_TimePoint3

description: Sequencing Run Id: 003560

value: aP

value: 3 days

tag: cell type


title: Glioblastoma GBM17

tag: disease

tag: gender

tag: age


title: Pt72_Blood_CD8PlusCD28Plus

tag: tissue


title: Glioblastoma GBM18


title: FFPE Breast cancer 34258, luminal B, FBC+

description: Sample name: 34258


title: Q_2

value: L1 larva fed for 7 hours after L1 arest

tag: genotype

value: QR descendants


title: 129_2886_4_TimePoint4

description: Sequencing Run Id: 003560

tag: treatment

tag: primed

tag: time

value: 7 days

value: PBMC


title: Pt72_Blood_CD8PlusCD28Minus

tag: sample type

value: Primary Human Cells

value: Peripheral Blood

value: T cells

tag: cell markers


title: Q_1

tag: Stage

tag: cell


title: Glioblastoma GBM16

value: Glioblastoma

value: Female


title: 127_2886_2_TimePoint2

description: Sequencing Run Id: 003560

value: pertussis antigenic challenge

value: 1 days


title: Pt63_Blood_CD8PlusCD28Plus


title: 128_2886_3_TimePoint3

description: Sequencing Run Id: 003560


title: Pt63_Blood_CD8PlusCD28Minus


title: Glioblastoma GBM14

value: Male


title: 126_2886_1_TimePoint1

description: Sequencing Run Id: 003560

value: 0 days


title: Ctrl4_AgeMatchBlood_CD8PlusCD28Plus


title: rnaseq_2017_YPGlya_tye7gal4a

city: San Francisco

first: Sheena

middle: D.

last: Singh-Babak

address: 600 16th Street

department: Microbiology & Immunology

institute: University of California San Francisco

description:
C. albicans / C. dubliniensis hybrid
Tetraploid gal4∆∆∆∆ tye7∆∆∆∆ leu2∆∆/++ his1∆∆/++ MTLa/alpha
DataS1.xlsx, DataS2.xlsx, DataS3.xlsx

data_processing:
Alignment using SOAP2 with custom flags.
Multimapped reads removed from analysis.
Read counts normalized using scaling factor derived from ratio of fragment counts-per-million of parental genomic DNA reads aligned to the same set of orthologous ORFs.
ASE quantified using binomial test, setting expectation to the total fraction of C. albicans:C. dubliniensis aligned reads & corrected for multiple tests.
Genome_build: Candida Genome Database C. albicans assembly 21-s02-m05-r02 and C. dubliniensis assembly CD36.
Supplementary_files_format_and_content: Excel - tables with raw read counts, normalized read counts, calculated significance for each gene.
Supplementary_files_format_and_content: DataS1.xlsx: Mapped read counts for allele-specific expression experiments.
Supplementary_files_format_and_content: DataS2.xlsx: Rank-sum test analysis for all GO categories tested for ASE experiments.
Supplementary_files_format_and_content: DataS3.xlsx: Sign test analysis for all GO categories tested for ASE experiments.
Supplementary_files_format_and_content: DataS4.xlsx: Mapped read counts for overexpression experiments.

organism: Candida albicans x Candida dubliniensis

source_name: Liquid culture extraction

growth_protocol: Grown in liquid culture with the specified media type overnight, backdiluted, then grown to mid log.

extract_protocol:
Ambion RiboPure RA Purification Kit for Yeast.
Illumina TruSeq v.2.

tag: strain

value: Tetraploid gal4<delta><delta><delta><delta> tye7<delta><delta><delta><delta> leu2<delta><delta>/++ his1<delta><delta>/++ MTLa/alpha

tag: growth media

value: YPGLY

tag: growth phase

value: mid-log


title: rnaseq_2017_YPGlyb_tye7gal4b


title: rnaseq_2017_YPDb_tye7gal4b

value: YPD


title: Ctrl4_AgeMatchBlood_CD8PlusCD28Minus


title: Brain_Young_LL_P22177

description:
S02
RNASeqCounts_LL.txt

tag: stock

value: LL

value: Brain

tag: age of animal at termination

value: 7 months


title: Glioblastoma GBM15

tag: disease


title: 124_2884_4_TimePoint4

description: Sequencing Run Id: 003560

value: wP

value: 7 days

tag: cell type

value: PBMC


title: Glioblastoma GBM13

tag: gender

tag: age


title: Ctrl3_AgeMatchBlood_CD8PlusCD28Minus

value: Primary Human Cells

tag: tissue

value: Peripheral Blood

value: T cells


title: rnaseq_2015_tye7B

description:
C. albicans / C. dubliniensis hybrid
Tetraploid C. albicans leu2∆::FRT/leu2∆::FRT mtl-alpha::FRT/MTLa C. dubliniensis his1Δ::FRT/his1Δ::FRT mtlA::FRT/MTL alpha
DataS1.xlsx, DataS2.xlsx, DataS3.xlsx

tag: genotype

value: Tetraploid C. albicans leu2<delta>::FRT/leu2<delta>::FRT mtl-alpha::FRT/MTLa C. dubliniensis his1<delta>::FRT/his1<delta>::FRT mtlA::FRT/MTL alpha


title: 122_2884_2_TimePoint2

description: Sequencing Run Id: 003560

tag: treatment

value: pertussis antigenic challenge

tag: primed

value: 1 days


title: Ctrl1_AgeMatchBlood_CD8PlusCD28Plus

tag: sample type


title: 123_2884_3_TimePoint3

description: Sequencing Run Id: 003560

tag: time

value: 3 days


title: Glioblastoma GBM11

value: Glioblastoma

value: Male


title: Glioblastoma GBM9


title: Glioblastoma GBM10


title: 120_1687_5_TimePoint5

description: Sequencing Run Id: 003560

value: 14 days


title: Ctrl1_AgeMatchBlood_CD8PlusCD28Minus

tag: cell markers


title: 125_2884_5_TimePoint5

description: Sequencing Run Id: 003560


title: rnaseq_2015_gal4A

value: YPD

value: mid-log


title: rnaseq_2015_gal4B


title: FFPE Breast cancer 34251, luminal A, FBC+

description: Sample name: 34251

tag: ki67 ihq

tag: p53 ihq

tag: histologic grade

value: nd

tag: hormone receptor (hr)

tag: her2 ihq

tag: subtype

value: luminal A

tag: brca status

value: FBC+

value: FFPE breast cancer tissue


title: 12_2698_2_TimePoint2

description: Sequencing Run Id: 003560

value: aP

tag: cell type

value: PBMC


title: rnaseq_2014_YPGLYb

tag: strain

tag: growth media

value: YPGLY

tag: growth phase


title: Glioblastoma GBM8

tag: disease

tag: gender

tag: age


title: Ctrl3_AgeMatchBlood_CD8PlusCD28Plus

tag: sample type

value: Primary Human Cells

tag: tissue

value: Peripheral Blood

value: T cells


title: 667_YoungBlood_CD28plus

tag: cell markers


title: 667_YoungBlood_CD28minus


title: rnaseq_2014_YPGLYa

tag: genotype

value: Tetraploid C. albicans leu2<delta>::FRT/leu2<delta>::FRT mtl-alpha::FRT/MTLa C. dubliniensis his1<delta>::FRT/his1<delta>::FRT mtlA::FRT/MTL alpha


title: Glioblastoma GBM7


title: Glioblastoma GBM6

value: Female


title: 544_YoungBlood_CD28plus


title: rnaseq_2015_tye7A


title: 119_1687_4_TimePoint4

description: Sequencing Run Id: 003560

tag: treatment

value: pertussis antigenic challenge

tag: primed

value: wP

tag: time

value: 7 days


title: 118_1687_3_TimePoint3

description: Sequencing Run Id: 003560

value: 3 days


title: rnaseq_2014_YPRAFFb

value: YPRAFF

value: mid-log


title: 544_YoungBlood_CD28minus


title: 121_2884_1_TimePoint1

description: Sequencing Run Id: 003560

value: 0 days


title: rnaseq_2014_YPRAFFa


title: 117_1687_2_TimePoint2

description: Sequencing Run Id: 003560

value: 1 days


title: rnaseq_2014_YPGALb

value: YPGAL


title: 116_1687_1_TimePoint1

description: Sequencing Run Id: 003560


title: Glioblastoma GBM4

value: Glioblastoma


title: rnaseq_2014_YPGALa


title: 529_YoungBlood_CD28minus


title: 115_2738_5_TimePoint5

description: Sequencing Run Id: 003560

value: 14 days

value: PBMC


title: 114_2738_4_TimePoint4

description: Sequencing Run Id: 003560


title: rnaseq_2014_YPDb

value: YPD


title: 113_2738_3_TimePoint3

description: Sequencing Run Id: 003560


title: 112_2738_2_TimePoint2

description: Sequencing Run Id: 003560


title: rnaseq_2014_YPDa


title: HM_mix_100k_scRNA(+ADT)-seq

first: Chun

middle: Jimmie

last: Ye

address: 513 Parnassus Ave

department: IHG

institute: UCSF

data_processing:
Library strategy: SCITO-seq
Alignment performed using Cell Ranger v3.0 to generate compressed h5 files containing barcode/UMI count matrix
We first removed RBC and Platelets and removed cells with more than 15% of mitochondrial gene related reads. We further removed genes with less than 1 counts across all cells.
(python scanpy) log1p transformed from raw counts and scaled (z-scored)
(python scanpy) Leiden clustering and UMAP generation
Genome_build: GRCh38/hg20 (for human mix experiment), hg19+mm10 (for human mouse mix experiment)
Supplementary_files_format_and_content: h5 (barcode/UMI count matrix)

organism:
Homo sapiens
Mus musculus

source_name: cervix/mammary gland

growth_protocol: HeLa and 4T1 cells were cultured in complete DMEM (10% FBS  and 1% penicillin-streptomycin) in a 37°C incubator with 5% CO2 on 10 cm culture dishes

extract_protocol:
Prior to staining, cells were trypsinized at 37°C for 5 minutes using 1 ml Trypsin-EDTA and were quenched with 10 ml complete DMEM. Cells were harvested and centrifuged at 300xg for 5 minutes.
Libraries were prepared according to 10x Genomics's instructions (Chromium Single Cell 3ʹ Reagent Kits v3 with Feature Barcode technology for Cell Surface Protein, CG000185 • Rev D).

value: HeLa and 4T1 epithelial cells

tag: molecule subtype

value: RNA/ADT (antibody derived tags)


title: Glioblastoma GBM3

value: Male


title: Glioblastoma GBM5

value: Female


title: Glioblastoma GBM2


title: Glioblastoma GBM1


title: 111_2738_1_TimePoint1

description: Sequencing Run Id: 003560

value: pertussis antigenic challenge


title: HEK293T-125ng-DMSO-rep1

city: Beijing

first: Meiling

last: Piao

address: Shuangqing Road 30

department: Life Science

country: China

institute: Tsinghua University

data_processing:
Library strategy: smartSHAPE
Calculate smartSHAPE score from smartSHAPE sequencing data:
1) The 3’ adaptor is removed with Cutadapt
2) Duplicated reads were collapsed with custom script;
3) The first 10nt were removed using trimmomatic
4) Clean reads were mapped to human rRNA with Bowtie2
5) Un-mapped reads were mapped to the human (hg38) or mouse (mm10) genome using STAR
6) Sam files were convert into .tab files using icSHAPE-pipe sam2tab;
7) The smartSHAPE score was calculated using icSHAPE-pipe calcSHAPENoCont
For uvCLAP data:
Raw reads were trimmed by Cutadapt and collapsed to remove duplicated reads. The clean reads were mapped to mouse rRNA by Bowtie2, and the remaining un-mapped reads were re-mapped to mouse genome (mm10) by STAR. Peaks were called out by Piranha with Reg1 group as response sample and GFP group as covariate sample. The bin size was set to 50 with -z 50.
For RNA-Seq data:
Raw reads were trimmed by Cutadapt. The trimmed reads were mapped to mouse rRNA by bowtie2, and the remaining un-mapped reads were re-mapped to mouse genome (mm10) by STAR. We set parameter --quantMode TranscriptomeSAM GeneCounts to generate the read count file. The RNA-Seq differentail expression analysis is carried by DESeq2.
Genome_build: hg38 and mm10
Supplementary_files_format_and_content: .shape format: tab-seperated file, each row represent a transcript. The meaning of each column: transcript_id, length, a star symbol, reactivity score for each base

source_name: HEK293T cell line

growth_protocol: HEK293T cells, iBMDM and Raw264.7 cells were cultured were maintained in DMEM (Gibco) medium with high glucose, supplemented with 10% FBS and 1% Penicillin-Streptomycin at 37°C with 5% CO2.

extract_protocol:
For smartSHAPE and RNA-Seq, RNAs were isolated with Trizol reagents.
For smartSHAPE, cells were treated with NAI-N3 or DMSO and RNAs were isolated with Trizol followed by rRNA removal. RNAs were reverse transcribed with random primers, and RNase I digestion was performed at 37 °C for 30 min. Enrichment was performed using MyOne C1 beads. After elution, cDNAs were ligated with biotinylated 3’ adaptor using CircLigase and immobilized with MyOne C1 beads. Second strand synthesis and 5’ligation was performed on the beads. smartSHAPE libraries were generated by amplification of ligation products. RNA seq libraries of Reg1 KO and WT iBMDMs were generated with KAPA RNA Hyper Prep kit. uvCLAP libraries were generated as published protocol (PMID: 29559621).

treatment_protocol: For structure probing, cells were treated with NAI-N3 or DMSO at 37°C for 5min and quenched by adding 500 µl Trizol. For RNA seq, cells were treated with 100 ng/ml LPS for 0 h or 3 h before RNA isolation. For uvCLAP, cells were maintained in media supplied with 50 µM biotin overnight and treated with 100 ng/mL LPS for 3 h.

tag: cell line


title: rnaseq_2019_GLK1OE_B

organism: Candida dubliniensis


title: HEK293T-125ng-DMSO-rep2


title: 110_2383_5_TimePoint5

description: Sequencing Run Id: 003560

value: wP


title: HEK293T-25ng-DMSO-rep2


title: rnaseq_2019_Empty_A


title: Glioblastoma GBM12


title: rnaseq_2019_GLK1OE_A


title: HEK293T-5ng-DMSO-rep2


title: 11_2698_1_TimePoint1

description: Sequencing Run Id: 003560

value: aP


title: 529_YoungBlood_CD28plus

value: Primary Human Cells

value: Peripheral Blood

value: T cells


title: HEK293T-25ng-DMSO-rep1


title: rnaseq_2019_GAL4OE_B

value: mid-log


title: 109_2383_4_TimePoint4

description: Sequencing Run Id: 003560

value: 7 days


title: HEK293T-5ng-DMSO-rep1


title: HEK293T-1ng-DMSO-rep2


title: rnaseq_2019_GAL4OE_A


title: 108_2383_3_TimePoint3

description: Sequencing Run Id: 003560

value: 3 days


title: rnaseq_2019_Empty_B


title: rnaseq_2019_TYE7OE_B


title: 107_2383_2_TimePoint2

description: Sequencing Run Id: 003560

value: 1 days


title: HEK293T-1ng-DMSO-rep1


title: 106_2383_1_TimePoint1

description: Sequencing Run Id: 003560

value: 0 days


title: ALJ2 30°C 4

organism: Thioalkalivibrio nitratis

tag: growth temperature (°c)


title: rnaseq_2019_TYE7OE_A


title: 105_2732_5_TimePoint5

description: Sequencing Run Id: 003560

value: 14 days

tag: cell type

value: PBMC


title: ALJ2 30°C 2

tag: strain


title: HEK293T-125ng-NAIN3-rep1


title: BM_AgaC2 GEX

city: Philadelphia

first: James

last: Garifallou

state: Pennsylvania

address: 3615 Civic Center Boulevard, ARC1014

department: Neonatology

institute: Children's Hospital of Philadelphia

description:
mRNA and protein (ADT)
BM_AgaC2_barcodes.tsv.gz
BM_AgaC2_features.tsv.gz
BM_AgaC2_matrix.mtx.gz

data_processing:
Next-generation sequencing libraries were prepared using the 10x Genomics Chromium Single Cell 5’ Library and Gel Bead kit v1 with Feature Barcoding technology for Cell Surface Protein per manufacturer’s “Chromium Single Cell V(D)J Reagent Kits” protocol. Libraries were uniquely indexed using the Single Index Kit N set A and sequenced on the Illumina NovaSeq 6000 sequencer (v1.5 chemistry) in a paired-end, single indexing run. Sequencing for each library targeted either 20,000 mean reads per cell for the 5’ chemistry gene expression libraries or 5,000 read pairs per cell for the cell surface/feature barcoding libraries. Data was processed using the cellranger count pipeline (10x genomics, v.3.1) for demultiplexing, alignment of sequencing reads to the transcriptome (10x genomics, human GRCh38) or antibody barcodes for the antibody capture feature barcode libraries, and creation of feature-barcode matrices. Individual  single cell RNAseq libraries were aggregated using the cellranger aggr pipeline. Libraries were normalized for  sequencing depth across all libraries during aggregation. Secondary analysis on the feature barcode matrices was performed using the Seurat package (v.4.0) within the R computing environment. Count matrices for CITE-Seq expression were adjusted based on isotype specific control expression on a per cell basis (Supplemental table XX). Briefly, Raw UMI counts of the isotype control surface marker were subtracted from the UMI count of each ADT surface expressed marker within a given cell. These altered count matrices were then read into the R computing environment and normalized via the CLR method in Seurat. Variable features, normalization, data scaling, and principal components were determined for each assay separately (ADT and RNA) followed by hierarchical clustering and visualization using UMAP. Differentially expressed genes between groups were determined using a wilcoxon rank sum test. P-value adjustment was performed using a bonferonni correction based on total number of genes/ADT surface expressed markers.
Genome_build: GRCh38
Supplementary_files_format_and_content: Processed data files for each sample consist of a barcode ID file, feature ID file, and count matrix file as produced from the Cellranger Pipeline (10x Genomics). An additional processed data file set includes the resulting barcode, feature, and matrix files from the aggregation of the two samples, listed as "AgaC2_HD2253_aggr_norm_mapped_*"

source_name: Bone marrow cells from agammaglobulineia patient

extract_protocol:
Mononuclear cells were extracted from bone marrow aspirates using Ficoll-Paque density gradient centrifugation
scRNA-seq and paired ADT-seq

value: diseased


title: 104_2732_4_TimePoint4

description: Sequencing Run Id: 003560


title: ALJ2 30°C 3


title: HEK293T-125ng-NAIN3-rep2


title: BM_AgaC2 CITE-Seq


title: BM_HD_2253 GEX

description:
mRNA and protein (ADT)
BM_HD_2253_barcodes.tsv.gz
BM_HD_2253_features.tsv.gz
BM_HD_2253_matrix.mtx.gz

source_name: Bone marrow cells from healthy donor

value: healthy


title: 103_2732_3_TimePoint3

description: Sequencing Run Id: 003560

source_name: peripheral blood mononuclear cells


title: BM_HD_2253 CITE-Seq


title: ALJ2 30°C 1

source_name: Bacterial cell


title: Hi-C_Bypass_inverted

city: Göttingen

first: Argyris

last: Papantonis

address: Robert-Koch-Straße 40

department: Institute of Pathology

country: Germany

institute: University Medical Centre Göttingen

data_processing:
Two mates of paired-end reads were aligned individually using the Bowtie~2 software version 2.3.4.1 with the parameter “--reorder –local”.
Reads were automatically filtered out and matrices were built with HiCExplorer version 3.2 with default parameters.
Hi-C interaction counts were normalized to be within the range 0-1 and then balanced with the Knight-Ruiz matrix balancing algorithm (KR) using HiCExplorer.
A/B compartments were called based on the signal of the first principal component of the Pearson's Hi-C contact matrices using HiCExplorer. The compartment associated with higher H3K27ac signals was defined as A compartment.
TADs were called with hitad 0.4.2-r1
Loops were called using HiCExplorer with default parameters. Loops containing convergent CTCF motifs were kept as valid CTCF loops.
Genome_build: hg19
Supplementary_files_format_and_content: cool: contact matrix

source_name: “Bypass” HBECs

growth_protocol: HBEC-CDC6 Tet-ON cells were maintained in Keratinocyte-Serum-Free Medium (#17005-075, Invitrogen) supplemented with 50μg/ml Bovine Pituitary Extract and 5ng/ml hEGF (#17005-075, Invitrogen) at 37οC and 5% CO2 [Komseli et al., 2018]. CDC6 induction was conducted by treatment of the cell culture with 1 μg/ml doxycycline (DOX) (Applichem) [Komseli et al., 2018].

extract_protocol:
In situ Hi-C on HBECs of different states and genotypes was performed and controlled for quality using the Arima Hi-C kit as per manufacturer’s instructions. All resulting libraries that met the QC criteria set by the manufacturer were paired-end sequenced on a NovoSeq6000 platform (Illumina) to at least 0.5 billion reads.
Standard Hi-C library construction on the basis of the Mate-pair kit (Illumina)
100-bp paired-end sequencing

treatment_protocol: "Bypass" cells are under constant doxycycline treatment to overexpress the CDC6 transgene. "OFF" cells are untreated.

value: human bronchial epithelial cells

value: Bypass


title: 102_2732_2_TimePoint2

description: Sequencing Run Id: 003560

value: pertussis antigenic challenge


title: HEK293T-25ng-NAIN3-rep1


title: HEK293T-5ng-NAIN3-rep2


title: Hi-C_OFF_inverted

source_name: “OFF” HBECs

value: OFF


title: HH_PBMC_mix_200k_scRNA(+ADT)-seq

source_name: PBMC

extract_protocol:
PBMCs were collected from anonymized healthy donors and were isolated from apheresis residuals by Ficoll gradient. Cells were frozen in 10% DMSO in FBS and stored in a freezing container at -80°C for one day before long term storage in liquid nitrogen. Cells from two donors were quickly thawed in a 37°C water bath before being slowly diluted with complete RPMI1640 before centrifugation at 300xg for 5 minutes at room temperature
Libraries were prepared according to 10x Genomics's instructions (Chromium Single Cell 3ʹ Reagent Kits v3 with Feature Barcode technology for Cell Surface Protein, CG000185 • Rev D).

value: RNA/ADT (antibody derived tags)


title: ALJ2 10°C 3


title: ALJ2 10°C 4


title: 101_2732_1_TimePoint1

description: Sequencing Run Id: 003560

value: wP


title: 100_2726_5_TimePoint5

description: Sequencing Run Id: 003560


title: HEK293T-1ng-NAIN3-rep2


title: HH_TB_mix_200k_scRNA(+ADT)-seq

extract_protocol:
PBMCs were collected from anonymized healthy donors and were isolated from apheresis residuals by Ficoll gradient. Cells were frozen in 10% DMSO in FBS and stored in a freezing container at -80°C for one day before long term storage in liquid nitrogen. Cells from two donors were quickly thawed in a 37°C water bath before being slowly diluted with complete RPMI1640 before centrifugation at 300xg for 5 minutes at room temperature. Cells were resuspended in EasySep Buffer at a concentration of 5x107cells/ml before being subject to CD4 and CD20 negative isolation.
Libraries were prepared according to 10x Genomics's instructions (Chromium Single Cell 3ʹ Reagent Kits v3 with Feature Barcode technology for Cell Surface Protein, CG000185 • Rev D).

value: T cells and B cells


title: 10_2689_5_TimePoint5

description: Sequencing Run Id: 003560

extract_protocol:
2x10^6 PBMC from each sample were transferred directly to Quiazol regent (QIAGEN), resuspended and immediately aliquoted and stored at -80ºC. RNA was extracted using the Qiagen miRNeasy Mini kit with on-column DNase treatment
500 ng of total RNA was used as input for library preparation using the Illumina TruSeq Stranded mRNA Library Prep Kit.
Libraries were sequenced on the HiSeq3000

value: aP


title: HEK293T-25ng-NAIN3-rep2


title: HH_TB_mix_100k_scRNA(+ADT)-seq


title: 1_2685_1_TimePoint1

description: Sequencing Run Id: 003560


title: HEK293T-1ng-NAIN3-rep1


title: DMSO_INFECTED_D6_rep3

status: Public on Mar 30 2021

city: New York

first: Sook Yuin Jessica

last: Ho

state: New York

address: 1468 Madison Avenue

department: Microbiology

institute: Icahn School of Medicine at Mount Sinai

data_processing:
After adaptor removal with cutadapt (Martin, 2011) and base-quality trimming to remove 3′read sequences if more than 20 bases with Q <20 were present, paired-end reads were mapped to the SARS-CoV-2 and hamster (MesAur1.0, reference genomes with STAR . Gene-count summaries were generated with featureCounts (Liao et al., 2014). A numeric matrix of raw read counts was generated, with genes in rows and samples in columns, and used for differential gene expression analysis with the Bioconductor Limma package.
Genome_build: MesAur1.0  ; Sars_cov_2.ASM985889v3
Supplementary_files_format_and_content: tab delimited table of raw counts for each sample

organism: Mesocricetus auratus

source_name: Lung

extract_protocol:
Infected hamsters that were treated with TPT or vehicle control were euthanized at days 4 and 6 post infection. Uninfected hamsters were used as controls. After euthanasia, lung left inferior lobe from hamsters were cut into pieces and lysed with RA1 lysis buffer provided with the NucleoSpin® RNA Plus kit (Macherey-nagel), RNA extraction was performed according the manufacturer’s recommendations, including an on-column genomic DNA digestion step.
RNA sequencing library preparation and sequencing were then performed by BGI Genomics

treatment_protocol: Female Golden Syrian hamster, aged 6-8 week old (~70-100g), were obtained from Laboratory Animal Unit, University of Hong Kong (HKU). All experiments were performed in a Biosafety Level-3 animal facility, LKS Facility of Medicine, HKU. The study has been approved by the Committee on the Use of Live Animals in Teaching and Research, HKU.  Virus stock was diluted with Phosphate-buffered saline (PBS) to 2 x 104 PFU/ml.  Hamsters were anesthetized with ketamine (150mg/kg) and xylazine (10 mg/mg) and then intranasally inoculation with 50 ul of diluted viruses containing 103 PFU of viruses. For drug treatments, 10mg/kg TPT resuspended in vehicle [5% DMSO + 5% corn oil in PBS] or vehicle alone was administered intraperitoneally to animals on the indicated days post infection.

tag: infection

value: Infected

value: DMSO

tag: time point

value: Day 6


title: TPT_INFECTED_D6_rep1

value: TPT


title: TPT_INFECTED_D4_rep3

value: Day 4


title: ALJ2 10°C 1

extract_protocol:
The frozen cell pellets were homogenized with a mortar and a pestle before being resuspended in QIAzol Lysis Reagent (Qiagen, Germany). Total RNA was extracted and purified with the RNeasy kit (Qiagen) following the manufacturer’s instructions. The purification step comprised a DNase treatment using the RNase-free DNase kit (Qiagen). The concentration was quantified with the NanoDrop ND2000 (Thermo Fisher Scientiﬁc, USA) and the integrity of the RNA was checked on the 2200 TapeStation with Agilent RNA ScreenTapes (Agilent Technologies, The Netherlands). Ribosomal RNA (rRNA) was removed by the Illumina Ribo-Zero rRNA Removal Kit (Bacteria) (Illumina, USA).
Bar-coded RNA libraries were prepared using the Ion Total RNA-Seq kit v2 and the Ion Xpress RNA-Seq barcoding kit according to the supplier’s instructions (Thermo Fisher Scientiﬁc).


title: DMSO_INFECTED_D6_rep2


title: TPT_INFECTED_D4_rep1


title: DMSO_INFECTED_D4_rep3


title: DMSO_INFECTED_D4_rep1


title: TPT_INFECTED_D6_rep3


title: MOCK_UNINFECTED_D4_rep2

value: Uninfected

value: No treatment


title: TPT_INFECTED_D6_rep2


title: HEK293T-5ng-NAIN3-rep1


title: DMSO_INFECTED_D6_rep1


title: TPT_INFECTED_D4_rep2


title: MOCK_UNINFECTED_D4_rep1


title: MOCK_UNINFECTED_D4_rep3


title: ALJ2 10°C 2


title: DMSO_INFECTED_D4_rep2


title: 1000 cell_Cyt

city: Birmingham

first: Sanjana

last: Pillay

address: Edgbaston

department: School of Biosciences

country: United Kingdom

institute: University of Birmingham

description: Total RNA (Poly A+ and Poly A-)

data_processing:
RNA-seq reads were trimmed using the Trimmomatic v0.27 and then mapped to the Zv9 genome using STAR v2.6.0a with parameters -p8
Transcript per million (TPM) was calculated using the Stringtie and Ballgown program
Genome_build: Zv9
Supplementary_files_format_and_content: tab delimited TPM files for all stages

organism: Danio rerio

source_name: 1000Cell stage embryo

growth_protocol: Wild-type male and female zebrafish (AB-strain) were set up in breeding tanks overnight and the eggs were collected the next day as soon as (~10 min) they were laid (important to get synchronised embryos). About 100-500 (depending upon the stage) embryos were collected for each developmental stage (64 cell, 256 cell, 1000 cell, shield, 24hpf, 50hpf). The embryos were treated with Pronase (protease from Streptomyces griseus, Sigma-Aldrich) to remove the chorion, 1mL of Pronase working solution (1mg/mL) was added to 2-3 ml of fish water containing embryos.

extract_protocol:
RNA was extracted using the Rneasy mini kit
Sequencing libraries were prepared using the TruSeq Stranded Total RNA library Prep kit with the Illumina Ribo-Zero rRNA removal kit (Human-Mouse-Rat).

treatment_protocol: Dechorionated embryos were then washed twice with 1 X PBS (Phosphate buffer solution, ThermoFisher). RLN buffer was added to the tube containing embryos and the yolk sac disrupted releasing the cells in the buffer. This was then incubated on ice for 5 mins and centrifuged. The resulting supernatant was collected and labelled as the cytosolic fraction. The pellet was washed twice with 200 µL of RLN buffer and finally, collected and labelled as the nuclear fraction.

value: zebrafish embryos

tag: developmental stage

value: 1000 cell

tag: fraction

value: Cytosolic


title: Shield_Nuc

description: Total RNA (Poly A+ and Poly A-)

source_name: Shield stage embryo

value: Shield

value: Nuclear


title: Dome_Cyt

description: Total RNA (Poly A+ and Poly A-)

source_name: Dome stage embryo

value: Dome


title: Dome_Nuc

description: Total RNA (Poly A+ and Poly A-)


title: 1000 cell_Nuc

description: Total RNA (Poly A+ and Poly A-)


title: 256 cell_Cyt

description: Total RNA (Poly A+ and Poly A-)

source_name: 256Cell stage embryo

value: 256 cell


title: Normal_urothelium_03

city: Kyoto

first: Takashi

last: Kobayashi

address: 54 Shogoinkawahara-cho, Sakyo-ku

department: Urology

institute: Kyoto University Graduate School of Medicine

description:
Gene expression of normal bladder
Wt_03
Wt_03

hyb_protocol: 1.5 ug of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 250 ml containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 250 ml of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Whole Human Genome Oligo Microarrays (G4112A) for 17 hours at 65Â°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37Â°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (Agilent Technologies Scanner G2505C US45102837) using one color scan setting for 1x44k array slides (Scan Area 61x21.6 mm, Scan resolution 3um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing:
The scanned images were analyzed with Feature Extraction Software 9.1 (Agilent) using default parameters (protocol GE1_1105_Oct12 and Grid: 074809_D_F_20150624) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.
Text files produced by Feature Extraction were processed using "limma" R package in Bioconductor Control spots were removed and replicate probes that mapped to the same transcript were replaced with their average. Signal intensities were quantile-normalized and log2 transformed.

source_name: Bladder, NO BBN treatment

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.5 ug RNA using the One-Color Low RNA Input Linear Amplification PLUS kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

extract_protocol: Total RNA was extracted using an RNeasy Mini kit (QIAGEN, Hilden, Germany) from whole bladders and reverse-transcribed into complementary DNA using a ReverTra Ace qPCR RT Kit (TOYOBO, Osaka, Japan).

treatment_protocol: Mice were given BBN in drinking water for 24 weeks (From 2m to 8m of the age)

value: normal bladder urothelium

tag: gender

value: female

tag: age

value: wild type

value: NO tamoxifen, NO BBN


title: Normal_urothelium_02

description:
Gene expression of normal bladder
Wt_02
Wt_02

tag: tissue


title: Krt5_Trp53+/R172H_03

description:
Gene expression of BBN-induced bladder tumor
p53_02_Ck5_03
20160328_05

source_name: Bladder, BBN treatment for 24 weeks

value: bladder tumor

value: male

value: Krt5-CreERT2; LSL-RFP; Trp53R172H/+

value: tamoxifen, BBN


title: Upk2_Trp53+/R270H_02

description:
Gene expression of BBN-induced bladder tumor
p53_01_Upk2_02
20151023_05

value: Upk2-CreERT2; LSL-RFP; Trp53R270H/+


title: Krt5_Trp53+/R172H_01

description:
Gene expression of BBN-induced bladder tumor
p53_02_Ck5_01
20150608_12


title: Upk2_Trp53+/R172H_01

description:
Gene expression of BBN-induced bladder tumor
p53_02_Upk2_01
20150608_13

value: Upk2-CreERT2; LSL-RFP; Trp53R172H/+


title: Upk2_02

description:
Gene expression of BBN-induced bladder tumor
Upk2_02
20151118_03

value: Upk2-CreERT2; LSL-RFP


title: Trp53+/-_03

description:
Gene expression of BBN-induced bladder tumor
p53hetero_03
20150824_09

value: NO tamoxifen, BBN


title: 256 cell_Nuc

description: Total RNA (Poly A+ and Poly A-)

value: zebrafish embryos


title: Normal_urothelium_01

description:
Gene expression of normal bladder
Wt_01
Wt_01


title: Upk2_Trp53+/R270H_01

description:
Gene expression of BBN-induced bladder tumor
p53_01_Upk2_01
20150810_02


title: Krt5_Trp53+/R270H_01

description:
Gene expression of BBN-induced bladder tumor
p53_01_Ck5_01
20150824_07

value: Krt5-CreERT2; LSL-RFP; Trp53R270H/+


title: Krt5_Trp53+/R172H_04

description:
Gene expression of BBN-induced bladder tumor
p53_02_Ck5_04
20160328_06


title: Krt5_Trp53+/R270H_02

description:
Gene expression of BBN-induced bladder tumor
p53_01_Ck5_02
20151118_06


title: 64 cell_Nuc

description: Total RNA (Poly A+ and Poly A-)

source_name: 64Cell stage embryo

value: 64 cell

value: Nuclear


title: hda6/ldl1/2 [H3K4me2]

city: Taipei

first: Fu-Yu

last: Hung

address: Institute of Plant Biology, National Taiwan University

country: Taiwan

institute: NTU, IPB

data_processing:
The raw sequence data were processed using the Illumina sequence data analysis pipeline GAPipeline 1.3.2. Bowtie was then employed to map the reads to the Arabidopsis genome (TAIR10).
To determine the correlation between biological repeats, Pearson correlation was computed using R statistical software on normalized signal intensity for ChIP binding peaks. The alignments were first converted to Wiggle (WIG) files using MACS. The data were then imported into the Integrated Genome Viewer (IGV) for visualization. The program SICER was used to identify ChIP-enriched domains (peaks).
Genome_build: TAIR 10
Supplementary_files_format_and_content: bigwig files

organism: Arabidopsis thaliana

source_name: 14 days old plants

growth_protocol: The transgenic Arabidopsis seedlings were grown under Long-day conditions at 22°C and harvested after 14 days.

extract_protocol:
5 ng of DNA from at least 5 ChIPs was pooled to ensure that there are enough starting DNA for library construction. Two biological replicates were prepared and sequenced for each ChIP-seq experiment. The ChIP DNA was first tested by qRT-PCR and then used to prepare ChIP-seq libraries.
End repair, adaptor ligation, and amplification were carried out using the Illumina Genomic DNA Sample Prep kit according to the manufacturer's protocol.

tag: ecotype

tag: genotype/variation

tag: antibody

value: anti-H3K4me2 antibody (diagenode; C15410035)


title: WT [H3K4me2]

value: WT


title: hda6 [H3K4me2]


title: Krt5_02

description:
Gene expression of BBN-induced bladder tumor
Ck5_02
20150824_03

value: female

tag: genotype

value: Krt5-CreERT2; LSL-RFP

tag: treatment


title: Trp53+/-_02

description:
Gene expression of BBN-induced bladder tumor
p53hetero_02
20150824_08


title: Krt5_Trp53+/R172H_02

description:
Gene expression of BBN-induced bladder tumor
p53_02_Ck5_02
20160127_10


title: Upk2_Trp53+/R172H_03

description:
Gene expression of BBN-induced bladder tumor
p53_02_Upk2_03
20160217_03


title: Krt5_01

description:
Gene expression of BBN-induced bladder tumor
CK5_01
20150824_02


title: 64 cell_Cyt

description: Total RNA (Poly A+ and Poly A-)

value: Cytosolic


title: ldl1/2 [H3K4me2]


title: hda6/ldl1/2 RNA-seq

data_processing:
The raw sequence data were processed using the Illumina sequence data analysis pipeline GAPipeline 1.3.2. Bowtie was then employed to map the reads to the Arabidopsis genome (TAIR10).
To determine the correlation between biological repeats, Pearson correlation was computed using CLC software on normalized signal intensity. The DEGs were caculated by CLC.
The DEGs were caculated by CLC genome work banch.
Genome_build: TAIR 10
Supplementary_files_format_and_content: excel files

growth_protocol: The Arabidopsis seedlings were grown under Long-day conditions at 22°C and harvested after 14 days.

extract_protocol:
RNA was harvested using RNA extration kit. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols


title: ldl1/2 RNA-seq


title: hda6 RNA-seq


title: WT RNA-seq

description:
hda6-WT
ldl12-WT
hda6ldl12-WT

value: wild type


title: Krt5_Trp53+/R270H_03

description:
Gene expression of BBN-induced bladder tumor
p53_01_Ck5_03
20151118_07

value: bladder tumor

value: male


title: Upk2_01

description:
Gene expression of BBN-induced bladder tumor
Upk2_01
20151118_03

value: tamoxifen, BBN


title: Upk2_Trp53+/R172H_02

description:
Gene expression of BBN-induced bladder tumor
p53_02_Upk2_02
20151023_03


title: ldl1/2

value: anti-H3K9K14Ac (Millipore; 06-599)


title: Trp53+/-_01

description:
Gene expression of BBN-induced bladder tumor
p53hetero_01
20150824_08


title: hda6/ldl1/2


title: hda6


title: daf-22 with ascarosides - replicate 3

city: Pasadena

first: Sarah

last: Cohen

address: 257 S. Hudson Ave, Unit 108

department: Biology and Bioengineering

institute: California Institute of Technology

data_processing:
ShortRead to assess sequence quality, as used in Anders et al 2013
TopHat2 to align sequences to reference genome, as used in Anders et al 2013
Bowtie, Samtools, HTSeq-Count to count reads, as used in Anders et al 2013
DESeq and EdgeR to analyze differential expression, as used in Anders et al 2013
Genome_build: WBcel235
Supplementary_files_format_and_content: csv or xlsx files containing normalized abundance output from DESeq

source_name: late L1 stage worms

growth_protocol: Worms were grown synchronously in liquid cultures at a density of approximately 1 worm per uL at 20C and 220 RPM.

extract_protocol:
Three hours after initial ascaroside exposure, worms were spun down. The supernatant was disposed of and the worm pellet was processed using an RNeasy kit.
Libraries were prepared using standard Ilumina protocols.

treatment_protocol: Six-hours post-hatch cultures were split into six - three were given ascaroside treatment and three were left as control. Ascaroside treatment was a 5uM total ascaroside cocktail made of equal parts synthetic ascr#2, ascr#3, and ascr#8.

value: Late L1


title: daf-22 with ascarosides - replicate 2


title: daf-22 with ascarosides - replicate 1


title: daf-22 without ascarosides - repliacate 2


title: N2 without ascarosides - replicate 3


title: N2 without ascarosides - replicate 2


title: N2 without ascarosides - replicate 1


title: N2 with ascarosides - replicate 3


title: HDA6pro::HDA6:GFP_2

data_processing:
The raw sequence data were processed using the Illumina sequence data analysis pipeline GAPipeline 1.3.2. Bowtie was then employed to map the reads to the Arabidopsis genome (TAIR10).
To determine the correlation between biological repeats, Pearson correlation was computed using R statistical software on normalized signal intensity for ChIP binding peaks. The alignments were first converted to Wiggle (WIG) files using MACS. The data were then imported into the Integrated Genome Viewer (IGV) for visualization. The program SICER was used to identify ChIP-enriched domains (peaks).
The binding correlation analysis was completed by Expasy ChIP-Seq tools (http://ccg.vital-it.ch/chipseq/chip_cor.php).
Genome_build: TAIR 10
Supplementary_files_format_and_content: Bed files

extract_protocol:
10 ng of DNA from at least 5 ChIPs was pooled to ensure that there are enough starting DNA for library construction. Two biological replicates were prepared and sequenced for each ChIP-seq experiment. The ChIP DNA was first tested by qRT-PCR and then used to prepare ChIP-seq libraries.
End repair, adaptor ligation, and amplification were carried out using the Illumina Genomic DNA Sample Prep kit according to the manufacturer's protocol.

tag: eco-type

value: anti-GFP antibody (ab290; ABCAM)


title: HDA6pro::HDA6:GFP_input


title: N2 with ascarosides - replicate 2


title: daf-22 without ascarosides - repliacate 1


title: PMH1065_YPD

city: Durham

first: John

middle: R.

last: Perfect

state: North Carolina

address: 303 Research Drive, Rm.337

department: Division of Infectious Diseases

institute: Duke University School of Medicine

data_processing:
The quality filtering and adaptor trimming were performed using Cutadapt (v 1.12).
Paired-read alignment for RNA-seq data was carried out against the gene set for C. neoformans var. grubii H99 (CNA3) excluding non-coding RNAs and mitochondria genes, using STAR (v 2.5.3a).
The expected count, TPM, and FPKM for each gene were estimated with RSEM (v1.2.31).
Genome_build: CNA3 (GCA_000149245.3)
Supplementary_files_format_and_content: Tab-delimited text files include length, Effective length, Expected count, TPM, and FPKM For each gene.

organism: Cryptococcus neoformans

source_name: yeast cell

growth_protocol: (1) aCSF: yeast cells incubated in aCSF at 37oC for 24 hours. Cells were harvested by centrifugation at 3000 RPM and stored at -800C. (2) rCSF: yeast cells were inoculated intracisternally into 2-3 kg New Zealand White rabbits receiving daily cortisone acetate. Each yeast strain was inoculated into three separate rabbits. Rabbit CSF was withdrawn (1-2ml) after 24 and 96 hours in the rabbit subarachnoid space.  rCSF containing the same strain were pooled, centrifuged to pellet the cells and the cell pellets were stored at -800C. (3) YPD / CAP:  yeast cells were grown for 24 hours in yeast peptone dextrose broth (YPD) or capsule-inducing media (CAP), centrifuged to collect the cell pellet, and store at -800C. (4) Human CSF (hCSF): yeasts per ml of CSF (1-5mls) was directly withdrawn under a lumbar puncture as standard of care, centrifuged to pellet and stored at -80C until RNA isolation was performed.

extract_protocol:
These lyophilized samples were treated with Trizol and total RNA was extracted using the Qiagen RNeasy Mini Kit according to the manufacturer's instructions.
Library preparation was prepared by shearing the RNA and adapted for Illumina sequencing using the TruSeq RNA Library Preparation Kit (Illumina, San Diego, CA) for YPD and CAP conditions or the Tag-Seq Protocol (Shishkin et al Nat Methods 2015) for the in vivo CSF and aCSF samples.

tag: isolate

value: VNI

tag: condition

value: YPD

tag: day

tag: repeat


title: Control2

city: Chongqing

first: Jintao

last: Zou

state: China

address: Gaotanyanstreet

institute: Army Medical University

data_processing:
use Cutadapt (v1.16) software to filter the sequencing data to get high quality sequence(Clean Data)for further analysis
Reference genome index was built by  Bowtie2(2.2.6) and the filtered reads were mapping to the reference genome using  Tophat2(2.0.14), the default mismatch was no more than 2
use HTSeq(0.9.1) statistics to compare the Read Count values on each gene as the original expression of the gene, and then used FPKM to standardize the expression
use DESeq (1.30.0)to analyze the genes of difference expression with screened conditions as follows: expression difference multiple |log2FoldChange| > 1, significant P-value < 0.05.
Genome_build: GRCm38
Supplementary_files_format_and_content: Matrix table with raw gene counts and FPKM for every gene and every sample

source_name: lung

growth_protocol: BALB/c mice were raised in SPF(specific pathogen free) environment

extract_protocol:
48h post infetion,lung were removed, flash frozen on dry ice, and RNA was harvested using Trizol reagent. VAHTS mRNA-seq V3 Library Prep Kit for  Illumina was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: intratracheally instillation of PBS or Klebsiella pneumoniae(5×10^6 CFUs) for 48h

tag: strain

value: BALB/c

value: lung

tag: sampling time

value: 48h post mock infection


title: Infection2

value: 48h post infection (Klebsiella pneumoniae clinical strain YBQ)


title: Control3


title: Infection1


title: Infection3


title: WT

value: WT


title: PMH1062_YPD

value: VNBI


title: Control1


title: PMH1063_YPD

value: VNBII


title: daf-22 without ascarosides - repliacate 3

tag: developmental stage


title: MT864_STAT1KO_repeat_2

city: Montréal

first: Claudia

middle: L

last: Kleinman

state: Québec

address: 3999 Côte Ste-Catherine Road

department: Human Genetics

country: Canada

institute: Lady Davis Institute for Medical Research

data_processing:
Raw reads are trimmed using Trimmomatic v0.32. First, adaptors and other Illumina-specific sequences from each read are removed using palindrome mode. Then, a four-nucleotide sliding window removes the bases once the average quality within the window falls below 30. Next, the first four bases at the start of each read are removed. Finally, reads shorter than 30 base pairs are dropped.
Cleaned reads are aligned to the mouse reference genome build mm10 using STAR v2.3.0e with default settings. Reads mapping to more than 10 locations in the genome (MAPQ < 1) were discarded.
Gene expression levels are estimated by quantifying uniquely mapped reads to exonic regions (the maximal genomic locus of each gene and its known isoforms) using featureCounts v1.4.4 and the Ensembl gene annotation set
Genome_build: mm10
Supplementary_files_format_and_content: Raw exonic counts for each sample using the mm10 Ensembl annotation set.

source_name: Mammary tumor cell line

growth_protocol: MT4788, MT864, and their STAT1 -/- counterparts  were generated with CRISPR/Cas9, as previously described (Ahn et al. Nat Comm, 2017. ). They were grown in DMEM media, 2.5 % FBS, mammary epithelial growth supplement (MEGS: 5 mg/ml insulin, 3 ng/ml human epidermal growth factor, 0.5 mg/ml hydrocortisone  and 0.4% v/v bovine pituitary extract) and penicillin/streptomycin and gentamycin. All cell lines were grown in 37 decree Celcius, 5% CO2

extract_protocol:
Total RNA was extracted using RNeasy Midi Kit (QIAGEN).
total RNA samples submitted to Genome Quebec facility for quality control assessment and library preparation. Illumina HiSeq 2500 with mRNA stranded library has been used.

treatment_protocol: After adherence, these cell lines were treated for 24 hours with recombinant mouse interferon gamma (IFNG) resuspended in PBS. Final concentration of IFNG was 1ng/ml.

tag: cell type

value: tumor cell line derived from MMTV/MT mammary tumor

value: STAT1 KO

value: 1ng/ml IFNG


title: MT864_STAT1KO_repeat_3


title: PMH1058_YPD


title: MT864_repeat_3

value: STAT1 WT


title: N2 with ascarosides - replicate 1


title: MT864_repeat_2


title: MT864_STAT1KO_repeat_1


title: MT4788_STAT1KO_repeat_3


title: PMH1055_YPD


title: HDA6pro::HDA6:GFP_1


title: PMH1051_YPD


title: PMH1040_YPD


title: PMH1054_YPD


title: PMH1034_YPD


title: PMH1049_YPD


title: MT4788_STAT1KO_repeat_2


title: MT864_repeat_1


title: MT4788_STAT1KO_repeat_1


title: PMH1056_YPD


title: PMH1032_YPD


title: NRH5063_YPD


title: PMH1026B_YPD


title: NRH5056_YPD


title: MT4788_repeat_2


title: MT4788_repeat_3


title: MT4788_repeat_1


title: PMH1014_YPD


title: NRH5057_YPD


title: NRH5031_YPD


title: NRH5030_YPD


title: NRH5045_YPD


title: NRH5028_YPD


title: NRH5064_YPD


title: NRH5061_YPD


title: NRH5027_YPD


title: NRH5021_YPD


title: NRH5044_YPD


title: NRH5015_YPD


title: NRH5020_YPD


title: PMH1065_hCSF

value: Human CSF


title: PMH1033_YPD


title: PMH1062_hCSF


title: PMH1055_hCSF


title: PMH1058_hCSF


title: PMH1051_hCSF


title: PMH1063_hCSF


title: PMH1040_hCSF


title: PMH1049_hCSF


title: PMH1034_hCSF


title: PMH1033_hCSF


title: PMH1026B_hCSF


title: PMH1014_hCSF


title: NRH5063_hCSF


title: NRH5061_hCSF


title: NRH5064_hCSF


title: NRH5057_hCSF


title: NRH5030_hCSF


title: NRH5027_hCSF


title: NRH5056_hCSF


title: NRH5044_hCSF


title: NRH5028_hCSF


title: PMH1056_hCSF


title: NRH5021_hCSF


title: PMH1063_CAP

value: CAP


title: PMH1054_hCSF


title: PMH1055_CAP


title: PMH1062_CAP


title: PMH1065_CAP


title: PMH1049_CAP


title: NRH5020_hCSF


title: NRH5015_hCSF


title: PMH1058_CAP


title: PMH1040_CAP


title: PMH1033_CAP


title: PMH1032_CAP


title: PMH1034_CAP


title: Shield_Cyt

description: Total RNA (Poly A+ and Poly A-)

value: zebrafish embryos

value: Shield

tag: fraction

value: Cytosolic


title: NRH5010_hCSF

value: VNI


title: PMH1032_hCSF


title: PMH1026B_CAP


title: NRH5045_hCSF


title: PMH1054_CAP


title: NRH5064_CAP


title: NRH5061_CAP


title: PMH1014_CAP


title: NRH5031_hCSF


title: NRH5057_CAP


title: NRH5045_CAP


title: PMH1056_CAP


title: PMH1051_CAP


title: NRH5044_CAP


title: NRH5031_CAP


title: NRH5030_CAP


title: NRH5027_CAP


title: NRH5028_CAP


title: NRH5021_CAP


title: NRH5063_CAP


title: NRH5020_CAP


title: SNRPA1-IP rep2

first: Hani

last: Goodarzi

department: Biochemistry and Biophysics

data_processing:
FASTQ reads were processed using cutadapt (v2.3) to extract the target RNA sequence from every read
Every target RNA species was then counted in each sample and normalized to total (count per million)
The enrichment of every RNA sequence over input was then calculated by averaging the IP replicates and dividing by input.
Genome_build: N/A
Supplementary_files_format_and_content: count files

organism: synthetic construct

source_name: synthetic RNA

extract_protocol:
Input and SNRPA1-bound RNA was isolated by acid phenol chloroform extraction
The input and SNRPA1-bound RNA was prepared for sequencing using the Takara SMARTer smRNA-Seq kit for Illumina (635030).

tag: rep

tag: rip antibody

value: Anti-SNRPA1, 1ug/ul (Bethyl A303-948A)


title: SNRPA1-IP rep1


title: NRH5056_CAP


title: Input RNA

value: none (input)


title: H9-dCas9-VP64-gRNA (HML-2) Day 41 tech rep 4

city: Freising

first: Hengyuan

last: Liu

state: Bavaria

address: Maximus-von-Imhof Forum 3

department: TUM School of Life Sciences

institute: Technical University of Munich

data_processing:
Quality control and preprocessing of RNA-seq data using fastp with default parameters
Pair-end reads were mapped to the human reference genome (GRCh38) using the STAR package with all default parameters. The STAR reference was built with primary assembly sequence regions contained in the GENCODE database version 27 (Harrow et al., 2012).
The reads mapped to genes were counted using the featureCounts software (Liao, Smyth, & Shi, 2014). Only read pairs that successfully aligned to the same chromosome were retained (command line options -B, -C, -p set). Multi-mapped read pairs were discarded (option -M not specified).
Genome_build: GRCh38
Supplementary_files_format_and_content: Matrix table with raw gene counts for protein coding genes of every sample

source_name: Human embryonic stem cell

growth_protocol: Human pluripotent stem cells (hPSCs) and H9 derivatives (H9-CRISPRa-control, H9-CRISPRa-HERV-K(HML-2)) were maintained with Essential 8 Flex media (#A28558501, Thermo Fisher Scientific) in feeder-free conditions on vitronectin (VTN-N) substrate (#A14700, Thermo Fisher Scientific). hPSCs were passaged as clumps with 0.5M EDTA (0.5M EDTA+ 5M NaCl+ 1X PBS).

extract_protocol:
Total RNA from hPSCs as well as cortical neurons, at different time points, was isolated using TRIzoL (#15596-026, Invitrogen) following manufacturer’s protocol. RNA extraction was performed using chloroform. RNA was precipitated in isopropanol and resuspended in nuclease free ddH2O. For RNAseq the RNA integrity number (RIN) was measured using the Agilent 2100 Bioanalyzer system.  RNA with a RIN value higher then 8 were sent for whole genome RNA sequencing. The TruSeq RNA Sample Preparation kit (Illumina) was used synthesizing the cDNA libraries and sequenced in paired-end-reads with the HiSeq4000 sequencer (Illumina).
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: The human pluripotent stem cells (hPSCs) H9 derivatives (H9-CRISPRa-control, H9-CRISPRa-HERV-K(HML-2) were differentiated into cortical neurons (Maroof et al., 2013; Qi et al., 2017) following optimized versions of previously published protocols (Kriks et al., 2011; Qi et al., 2017). Briefly, hESCs were dissociated into single cells using Accutase, and plated at high density on Matrigel (#354234, Corning) or Geltrex (#A14133-02, Thermo Fisher Scientific) coated wells. For cortical neuron patterning, cells were cultured in Essential 6 medium (E6, #A1516401, Thermo Fisher Scientific) in the presence of LDN193189 (#72142, Stem Cell Technologies), SB431542 (#1614, Tocris) and XAV939 (#3748, Tocris) (until day 5). From day 5 to 10, cells were cultured in the presence of TGFβ and BMP inhibitors (LDN193189, #72142, Stem Cell Technologies; SB431542, #1614, Tocris) to trigger cortical precursors for cortical neuron differentiation. Afterwards cells were maintained in mDA differentiation media (Neurobasal media (#21103-049, Thermo Fisher Scientific), 1% Pen/Strep (#15140-122, Thermo Fisher Scientific), L-Glutamine (#25030-024, Thermo Fisher Scientific), B27-Vitamin A (#12587010, Thermo Fisher Scientific)) supplemented with DAPT (#2634, Tocris), BDNF (#450-10, PreproTech), GDNF (#248-BD-025, R&D biosystems), cAMP (#D0627, Sigma) and AA (#4034-100, Sigma) as described previously (Kim et al., 2021; Kriks et al., 2011; Qi et al., 2017). Cortical neurons were cultured on polyornithine (PO)/laminin (L)/fibronectin (FN) coated wells.

tag: cell line

value: CRISPRa with HML-2 gRNA

tag: time

value: Day 41 of cortical differentiation


title: H9-dCas9-VP64-gRNA (HML-2) Day 60 tech rep 5

value: Day 60 of cortical differentiation


title: H9-dCas9-VP64-gRNA (HML-2) Day 27 tech rep 4

value: Day 27 of cortical differentiation


title: H9-dCas9-VP64-gRNA (HML-2) Day 41 tech rep 2


title: H9-dCas9-VP64-gRNA (HML-2) Day 27 tech rep 2


title: H9-dCas9-VP64-gRNA (HML-2) Day 27 tech rep 3


title: H9-dCas9-VP64-gRNA (HML-2) Day 41 tech rep 3


title: H9-dCas9-VP64-gRNA (HML-2) Day 60 tech rep 4


title: H9-dCas9-VP64-gRNA (HML-2) Day 41 tech rep 5


title: H9-dCas9-VP64-gRNA (HML-2) Day 60 tech rep 2


title: H9-dCas9-VP64-gRNA (HML-2) Day 41 tech rep 1


title: H9-dCas9-VP64-gRNA (HML-2) Day 60 tech rep 1


title: H9-dCas9-VP64-gRNA (HML-2) Day 27 tech rep 5


title: H9-dCas9-VP64-gRNA (HML-2) Day 60 tech rep 3


title: H9-dCas9-VP64-gRNA (HML-2) Day 10 tech rep 5

value: Day 10 of cortical differentiation


title: H9-dCas9-VP64-gRNA (HML-2) Day 27 tech rep 1


title: H9-dCas9-VP64-gRNA (HML-2) Day 10 tech rep 4


title: H9-dCas9-VP64-gRNA (HML-2) Day 10 tech rep 2


title: H9-dCas9-VP64-gRNA (HML-2) Day 10 tech rep 1


title: H9-dCas9-VP64-gRNA (HML-2) Day 0 tech rep 2

value: Day 0 of cortical differentiation


title: H9-dCas9-VP64-gRNA (HML-2) Day 0 tech rep 3


title: NRH5015_CAP


title: H9-dCas9-VP64-gRNA (HML-2) Day 0 tech rep 5


title: H9-dCas9-VP64-gRNA (HML-2) Day 0 tech rep 4


title: H9-dCas9-VP64-gRNA (HML-2) Day 0 tech rep 1


title: H9-dCas9-VP64-gRNA (Control) Day 60 tech rep 5

value: CRISPRa with Control gRNA


title: H9-dCas9-VP64-gRNA (Control) Day 60 tech rep 4


title: H9-dCas9-VP64-gRNA (Control) Day 60 tech rep 3


title: H9-dCas9-VP64-gRNA (Control) Day 60 tech rep 2


title: H9-dCas9-VP64-gRNA (Control) Day 60 tech rep 1


title: H9-dCas9-VP64-gRNA (Control) Day 41 tech rep 2


title: H9-dCas9-VP64-gRNA (Control) Day 27 tech rep 5


title: H9-dCas9-VP64-gRNA (Control) Day 41 tech rep 1


title: H9-dCas9-VP64-gRNA (HML-2) Day 10 tech rep 3


title: H9-dCas9-VP64-gRNA (Control) Day 27 tech rep 3


title: H9-dCas9-VP64-gRNA (Control) Day 10 tech rep 3


title: H9-dCas9-VP64-gRNA (Control) Day 27 tech rep 4


title: H9-dCas9-VP64-gRNA (Control) Day 27 tech rep 2


title: H9-dCas9-VP64-gRNA (Control) Day 10 tech rep 5


title: H9-dCas9-VP64-gRNA (Control) Day 10 tech rep 4


title: H9-dCas9-VP64-gRNA (Control) Day 10 tech rep 1


title: H9-dCas9-VP64-gRNA (Control) Day 0 tech rep 5


title: H9-dCas9-VP64-gRNA (Control) Day 10 tech rep 2


title: H9-dCas9-VP64-gRNA (Control) Day 27 tech rep 1


title: H9-dCas9-VP64-gRNA (Control) Day 0 tech rep 4


title: H9-dCas9-VP64-gRNA (Control) Day 0 tech rep 3


title: H9-dCas9-VP64-gRNA (Control) Day 0 tech rep 2


title: H9-dCas9-VP64-gRNA (Control) Day 0 tech rep 1


title: Infected_siTOP1_rep3

description:
RNAseq
J18_S18_CAT.genes.both.count

data_processing:
After adaptor removal with cutadapt (Martin, 2011) and base-quality trimming to remove 3′read sequences if more than 20 bases with Q <20 were present, paired-end reads were mapped to the SARS-CoV-2 and human (hg38) reference genomes with STAR . Gene-count summaries were generated with featureCounts (Liao et al., 2014). A numeric matrix of raw read counts was generated, with genes in rows and samples in columns, and used for differential gene expression analysis with the Bioconductor Limma package.
Genome_build: Hg38 and Sars_cov_2.ASM985889v3
Supplementary_files_format_and_content: tab delimited table of raw counts for each sample

growth_protocol: Generation of A549-ACE2 cells was performed as previously described (Blanco-Melo et al., 2020; Daniloski et al., 2020). Briefly, A549 cells were transduced with lentiviral vector pHR-PGK expressing human ACE2 coding sequence. A549 cells were then transduced with the lentivirus in the presence of polybrene (8 μg/ml). Cells were used for downstream assays after 48h post transduction.

extract_protocol:
RNA extracted using the Purelink RNA Minikit (Invitrogen) with DNAseI treatment, according to the manufacturer’s recommendations. RNA quality was determined using the RNA 6000 Nano kit and the Eukaryote Total RNA Nano assay on the Agilent 2100 Bioanalyzer System. RNA quantity was determined by Qubit™ RNA HS Assay Kit.
To  prepare RNA-sequencing libraries, 300 ng of RNA was depleted of ribosomal RNA using NEBNext® rRNA Depletion Kit (Human/Mouse/Rat), according to the manusfacturer’s instructions. Libraries were then prepared from rRNA depleted RNA using the NEBNext® Ultra™ II Directional RNA Library Prep Kit for Illumina®, following the manufacturer’s instructions. Final libraries were quantified and sizing was determined using the High Sensitivity DNA Assay reagents and chip in the Agilent 2100 Bioanalyzer System and the Qubit 1X dsDNA HS Assay Kit respectively. Individual libraries were then pooled and sequenced using 75bp paired end on the NextSeq 550 using the NextSeq 500/550 High Output Kit

treatment_protocol: 7.5E4 A549-ACE2 cells were plated in a 24 well dishes. 16 hours post plating, cells were transfected with control, scrambled (siSCR), Top1-targeting (siTOP1) or no siRNA (no siRNA) using Lipofectamine RNAiMax to a final concentration of 50nM. 48hours post transfection, the media was replaced, and fresh media was added to each well. Cells were then mock infected (PBS only) or infected with SARS-CoV-2 at MOI 0.5. 24 hours post infection, media was removed, and cells were lysed in 250ul of Trizol reagent (Thermo Scientific).

tag: infection

value: Infected

tag: sirna

value: TOP1 siRNA


title: Infected_siTOP1_rep2

description:
RNAseq
J17_S17_CAT.genes.both.count


title: Mock_siTOP1_rep3

description:
RNAseq
J15_S15_CAT.genes.both.count

value: Uninfected


title: Mock_siTOP1_rep2

description:
RNAseq
J14_S14_CAT.genes.both.count


title: Mock_siTOP1_rep1

description:
RNAseq
J13_S13_CAT.genes.both.count


title: Infected_siSCR_rep3

description:
RNAseq
J12_S12_CAT.genes.both.count

value: Scrambled siRNA


title: H9-dCas9-VP64-gRNA (Control) Day 41 tech rep 3

tag: treatment


title: H9-dCas9-VP64-gRNA (Control) Day 41 tech rep 4


title: H9-dCas9-VP64-gRNA (Control) Day 41 tech rep 5


title: Infected_siSCR_rep2

description:
RNAseq
J11_S11_CAT.genes.both.count


title: Infected_siSCR_rep1

description:
RNAseq
J10_S10_CAT.genes.both.count


title: Mock_siSCR_rep2

description:
RNAseq
J8_S8_CAT.genes.both.count


title: Mock_siSCR_rep1

description:
RNAseq
J7_S7_CAT.genes.both.count


title: Infected_no_siRNA_rep2

description:
RNAseq
J5_S5_CAT.genes.both.count


title: Mock_no_siRNA_rep1

description:
RNAseq
J1_S1_CAT.genes.both.count


title: Infected_no_siRNA_rep1

description:
RNAseq
J4_S4_CAT.genes.both.count


title: Mock_no_siRNA_rep2

description:
RNAseq
J2_S2_CAT.genes.both.count