title: COVID_69_77y_female_NonICU

description:
C69
genes.ec.tsv
genes.tpm.tsv

value: female

tag: ventilator-free days

tag: dm

tag: hospital-free days post 45 day followup (days)

tag: ferritin (ng/ml)

tag: crp (mg/l)

tag: ddimer (mg/l_feu)

tag: procalcitonin (ng/ml)

tag: lactate (mmol/l)

tag: tissue of origin


title: COVID_79_27y_male_NonICU

status: Public on Aug 29 2020

type: SRA

city: Albany

first: Adolfo

middle: Ariel

last: Jaitovich

state: NY

address: 47 New Scotland Av

department: Molecular and Cellular Physiology

country: USA

institute: Albany Medical Center

description:
C79
genes.ec.tsv
genes.tpm.tsv

library_source: transcriptomic

data_processing:
Basecalling via the standard Illumina Pipeline, version 1.8.2.
Trimming/Filtering for adapters and low quality via custom algorithm
Expression estimates via RSEM v1.3.0 under Python 2.7.15, using bowtie2-2.3.4.1. Executed command: rsem-calculate-expression --no-qualities --bowtie2 --bowtie2-k 200 --bowtie2-sensitivity-level sensitive --seed-length 20 --keep-intermediate-files --no-bam-output --paired-end [r1.fa.gz] [r2.fa.gz] [hg38 bowtie reference]
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited expression estimates, including non-normalized Expected Counts (EC), and normalized Transcripts Per Million (TPM)

molecule: total RNA

organism: Homo sapiens

source_name: Leukocytes from whole blood

extract_protocol:
10mL of whole blood collected from patients was filtered and RNA was isolated using LeukoLOCK Total RNA Isolation System.
TruSeq Stranded mRNA Library prep. Libraries were standardized to 2nM. Paired-end 2x50bp sequencing, using standard SBS chemistry (v3) on an Illumina NovaSeq6000 sequencer.

tag: disease state

tag: age (years)

tag: Sex

value: male

tag: icu

value: no

tag: apacheii

value: unknown

tag: charlson score

tag: mechanical ventilation

tag: fibrinogen

tag: sofa

tag: associated controlled-vocabulary terms

tag: cell type

value: leukocyte

value: whole blood

tag: sample type

value: primary cells


title: 8-week mouse kidney snATAC-seq sample 1

city: Philadelphia

first: Katalin

last: Susztak

state: Pennsylvania

address: 3400 Civic Center Boulevard, 12th floor

institute: University of Pennsylvania

description:
snATAC_cell_by_peak_matrix.txt
snATAC_peak_list.csv
snATAC_UMAP_coordinates.csv
snATAC_metadata.csv

library_source: genomic

data_processing:
snATAC raw fastq files were aligned to the mm10 (GRCm38) reference genome and quantified using Cell Ranger ATAC (v. 1.1.0). We only kept valid barcodes with number of fragments ranging from 1,000 to 40,000, mitochondria ratio less than 10%, and promoter ratio more than 20%. clustering was conducted using snapATAC.
snATAC peak calling was conducted for each cell type separately using MACS2 with parameters “--nomodel --keep-dup all --shift 100 --ext 200 --qval 1e-2 -B --SPMR --call-summits”.
Bulk ATAC-seq raw fastq files were processed using the end-to-end tool ENCODE ATAC-seq pipeline
scRNA raw fastq files were aligned to the mm10 (Ensembl GRCm38.93) reference genome and quantified using CellRanger v3.1.0. Seurat R package v3.0 was used for data quality control, preprocessing and dimensional reduction analysis. After gene-cell data matrix generation of both P0 and adult datasets, matrices were merged and poor-quality cells with <200 or >3,000 expressed genes and mitochondrial gene percentages >50 were excluded
Genome_build: mm10

molecule: genomic DNA

organism: Mus musculus

source_name: 8-week mouse kidney

extract_protocol:
3-week-old and 8-week-old mice were euthanized and perfused with chilled 1x PBS via left ventricle. Kidneys (0.25 g) were harvested, minced and lysed in 5 mL lysis buffer (10 mM Tris HCl pH 7.4, 10 mM NaCl, 3 mM MgCl2, and 0.1% NonidetTM P40 Substitute in nuclease-free water) for 15 min. 1-day-old mice were decapitated with surgical scissors, and both kidneys were harvested. Kidneys were minced and lysed in 2 mL lysis buffer for 15 min. Tissue lysis reaction was then blocked by adding 10 mL 1x PBS into each tube, and solution was passed through a 40 μm cell strainer. Cell debris and cytoplasmic contaminants were removed by Nuclei PURE Prep Nuclei Isolation Kit (Sigma, NUC-201) after centrifugation at 13,000 RPM for 45 min. Nuclei concentration was calculated with Countess AutoCounter (Invitrogen, C10227). Diluted nuclei suspension was loaded and incubated in transposition mix from Chromium Single Cell ATAC Library & Gel Bead Kit (10X Genomics, PN-1000110) by targeting 10,000 nuclei recovery. GEMs were then captured on the Chromium Chip E (10x Genomics, PN-1000082) in the Chromium Controller according to the manufacturer’s protocol (10X Genomics, CG000168).
Libraries were generated using the Chromium Single Cell ATAC Library & Gel Bead Kit and Chromium i7 Multiplex Kit N (10X Genomics, PN-1000084) according to the manufacturer’s manual. Quality control for constructed library was perform by Agilent Bioanalyzer High Sensitivity DNA kit.

tag: developmental stages


title: COVID_67_57y_male_ICU

description:
C67
genes.ec.tsv
genes.tpm.tsv

value: yes

tag: ventilator-free days

tag: dm

tag: hospital-free days post 45 day followup (days)

tag: ferritin (ng/ml)

tag: crp (mg/l)

tag: ddimer (mg/l_feu)


title: COVID_78_80y_male_NonICU

description:
C78
genes.ec.tsv
genes.tpm.tsv

tag: disease state

tag: age (years)

tag: Sex

tag: procalcitonin (ng/ml)

tag: lactate (mmol/l)

tag: tissue of origin


title: 2018-424/24

city: Bergen

first: Kai

middle: Kristoffer

last: Lie

state: Hordaland

address: Pobox 2029 Nordnes

department: Feed Safety

country: Norway

institute: Institute of Marine research

description:
24-2018-424-24_S25
24.bam

data_processing:
Adaptor removing and quality trimming was conducted using the TrimGalore 0.4.2 wrapper tool and default parameters. Library quality was investigated using fastQC imbedded in the TrimGalore wrapper (https://github.com/FelixKrueger/TrimGalore)
Mapping was counducted using HiSat2 software.
Read counts were generated using FeatureCounts
Read counst were filtered and normalized using the DESeq2 software.
Genome_build: Gene annotation files and assembly were downloaded from illumina Igenome (http://emea.support.illumina.com/sequencing/sequencing_software/igenome.html?langsel=/no/) containing the mus musculus Ensembl release 66 (NCBIM37).
Supplementary_files_format_and_content: Normalized read counts (FPKM) from all samples

extract_protocol:
Total RNA was extracted and treated BioRobot® EZ1 and RNA Tissue Mini Kit (Qiagen, Hilden, Germany). RNA quality and integrity were validated using a NanoDrop ND-1000 UV–vis Spectrophotometer (NanoDrop Technologies, Wilmington, USA) and Agilent 2100 Bioanalyzer and RNA 6000 Nano LabChip kit (Agilent Technologies, Palo Alto, USA) respectively.
DNA libraries were prepared as using 90 ng total RNA input to the TruSeq Stranded mRNA Library Prep Kit (Illumina) according to the manufacturers instrucitons. For multiplexing, standard Illumina adaptors were used.
One library was made for each individual RNA sample. The libraries were sequenced using the NextSeq Illumina platform according to manufacturer instructions, generating single end 75bp read libraries with an average library size of 25 ± 6 million reads.

tag: strain

value: BALB/c

tag: treatment

tag: tissue

value: hippocampus


title: COVID_68_79y_male_ICU

description:
C68
genes.ec.tsv
genes.tpm.tsv

tag: icu

tag: apacheii

tag: charlson score

tag: mechanical ventilation

tag: fibrinogen

tag: sofa

tag: associated controlled-vocabulary terms

tag: cell type

tag: sample type


title: 2018-424/23

description:
23-2018-424-23_S22
23.bam


title: COVID_64_65y_male_ICU

description:
C64
genes.ec.tsv
genes.tpm.tsv

tag: disease state

tag: age (years)

tag: ventilator-free days

tag: dm

tag: hospital-free days post 45 day followup (days)

tag: ferritin (ng/ml)

tag: crp (mg/l)

tag: ddimer (mg/l_feu)


title: COVID_66_66y_female_NonICU

description:
C66
genes.ec.tsv
genes.tpm.tsv

tag: Sex

tag: icu

tag: procalcitonin (ng/ml)

tag: lactate (mmol/l)

tag: tissue of origin


title: COVID_63_39y_female_ICU

description:
C63
genes.ec.tsv
genes.tpm.tsv

tag: apacheii

tag: charlson score

tag: mechanical ventilation

tag: fibrinogen

tag: sofa


title: 3-week mouse kidney snATAC-seq sample 1

source_name: 3-week mouse kidney

tag: developmental stages


title: 2018-424/2

description:
2-2018-424-2_S4
2.bam

tag: strain

tag: treatment

value: LD

tag: tissue


title: P0 mouse kidney snATAC-seq sample 2

source_name: P0 mouse kidney


title: 2018-424/22

description:
22-2018-424-22_S18
22.bam


title: 2018-424/21

description:
21-2018-424-21_S14
21.bam

value: HD


title: COVID_61_54y_female_NonICU

description:
C61
genes.ec.tsv
genes.tpm.tsv

tag: disease state

tag: age (years)

tag: ventilator-free days

tag: dm

tag: hospital-free days post 45 day followup (days)

tag: ferritin (ng/ml)

tag: associated controlled-vocabulary terms

tag: cell type

tag: sample type


title: COVID_60_49y_male_NonICU

description:
C60
genes.ec.tsv
genes.tpm.tsv

tag: Sex

tag: icu

tag: apacheii

tag: charlson score

tag: crp (mg/l)

tag: ddimer (mg/l_feu)

tag: procalcitonin (ng/ml)

tag: lactate (mmol/l)

tag: tissue of origin


title: P0 mouse kidney snATAC-seq sample 1

tag: developmental stages


title: COVID_59_55y_male_NonICU

description:
C59
genes.ec.tsv
genes.tpm.tsv

tag: disease state

tag: age (years)

tag: mechanical ventilation

tag: ventilator-free days

tag: fibrinogen

tag: sofa


title: COVID_58_62y_male_NonICU

description:
C58
genes.ec.tsv
genes.tpm.tsv

tag: dm

tag: hospital-free days post 45 day followup (days)

tag: ferritin (ng/ml)

tag: associated controlled-vocabulary terms

tag: cell type

tag: sample type


title: Ncas_WT_input_6

city: Cambridge

first: Carl

middle: G

last: de Boer

state: MA

address: 415 Main St

institute: The Broad Institute

data_processing:
Reads were mapped to their respective genomes using Bowtie2
Convert SAM files to big wig read coverage files
calculate the ratio of each ChIP to input signal (both antiSfp1-ChIP in WT and antiSfp1-ChIP in deltaSfp1)
Calculate the log ratio of these ratios (ChIP_WT/input_WT)/(ChIP_dSfp1/input_dSfp1).
Extract the ratios for various genomic elements (promoters, gene bodies); identify those that are significantly bound compared to the background.
Genome_build: S288C R64 for S. cerevisiae, YGOB v7 Aug 2012 for K. lactis and N. castellii, and Scannell et al. for S. paradoxus (Scannell et al., 2011)
Supplementary_files_format_and_content: Processed data files include both raw signal tracks (.unique.bw), log ratios relative to both input and to sfp1 mutants.

organism: Naumovozyma castellii

source_name: Log-phase culture in BMW

growth_protocol: Log-phase culture in rich media

extract_protocol:
The ChIP protocol was performed as described by Lefrancois et al. in The Guide to Yeast Genetics (Weissman, Jonathan F., Guthrie, 2010). Polyclonal antibodies were created (Bethyl, Inc) to bind a peptide from the conserved c-terminal portion of Sfp1 (NH2-Cys-GKRYKNLNGLKYHRGHSTH-COOH), designated, αSfp1-1, while αSfp1-3 was raised to recognize was raised to bind specifically to the N. castellii Sfp1pl (using NH2-Cys-QLKKNSTASSSHQNSNNQTH-COOH). In all cases, the antibody used for ChIP was αSfp1-1, with the exception of those N. castellii IP3 samples, which used αSfp1-3.
DNA was quantified using Qubit dsDNA HS Assay Kit (ThermoFisher Scientific). Input samples were diluted to the same concentration of ChIP samples. End Repair was carried out with the End-It DNA repair Kit (Epicenter). An AMPure Spri XP bead (Agencourt) clean-up was performed after end repair. A-base addition was carried out with 5 ul of NEB reagents Klenow Buffer (NEB Buffer #2), 10 ul of 1mM dATP (NEB) and 1 ul of Klenow exo (3’ to 5’ exo -; NEB) to each sample. An AMPure Spri XP bead clean-up was performed after A-base addition. Adaptor ligation was completed using 15 ul of 2x Quick DNA ligase buffer (NEB),1 ul of custom indexed adapters at uM, and 1 ul of Quick T4 DNA ligase (NEB) to each sample. An AMPure Spri XP bead clean-up was performed after adapter ligation. PCR was carried out using 1 ul of the PFU enzyme (Agilent), 5 ul of Pfu Buffer (Agilent), 0.5 ul of 100 uM dNTPs, and 2.5 ul of nuclease free water. An AMPure Spri XP bead clean up and samples were eluted in 15 ul of 10 mM Tris-Cl, pH 8.5. Samples were pooled in an equal molar ratio prior to sequencing.

tag: genotype

value: wild type

tag: replicate

tag: chip antibody

value: input


title: 2018-424/20

description:
20-2018-424-20_S10
20.bam

tag: strain

tag: Sex

tag: treatment

tag: tissue


title: 2018-424/19

description:
19-2018-424-19_S6
19.bam

value: Ctr


title: COVID_57_30y_female_NonICU

description:
C57
genes.ec.tsv
genes.tpm.tsv

tag: disease state

tag: age (years)

tag: icu

tag: apacheii

tag: charlson score

tag: mechanical ventilation

tag: crp (mg/l)

tag: ddimer (mg/l_feu)

tag: procalcitonin (ng/ml)

tag: lactate (mmol/l)

tag: tissue of origin


title: Ncas_WT_input_5

tag: genotype

tag: replicate


title: 2018-424/9

description:
9-2018-424-9_S30
9.bam

tag: strain


title: COVID_56_33y_female_NonICU

description:
C56
genes.ec.tsv
genes.tpm.tsv

tag: Sex

tag: ventilator-free days

tag: dm

tag: hospital-free days post 45 day followup (days)

tag: ferritin (ng/ml)

tag: fibrinogen

tag: sofa

tag: associated controlled-vocabulary terms

tag: cell type

tag: sample type


title: COVID_65_84y_male_NonICU

description:
C65
genes.ec.tsv
genes.tpm.tsv

tag: disease state

tag: age (years)

tag: icu

tag: apacheii

tag: charlson score

tag: mechanical ventilation

tag: crp (mg/l)

tag: ddimer (mg/l_feu)


title: COVID_53_35y_female_NonICU

description:
C53
genes.ec.tsv
genes.tpm.tsv

tag: Sex

tag: ventilator-free days

tag: procalcitonin (ng/ml)

tag: lactate (mmol/l)

tag: tissue of origin


title: COVID_55_62y_female_ICU

description:
C55
genes.ec.tsv
genes.tpm.tsv

tag: dm

tag: hospital-free days post 45 day followup (days)

tag: ferritin (ng/ml)

tag: fibrinogen

tag: sofa


title: 2018-424/18

description:
18-2018-424-18_S2
18.bam

tag: strain

tag: treatment

tag: tissue


title: COVID_62_78y_female_ICU

description:
C62
genes.ec.tsv
genes.tpm.tsv

tag: disease state

tag: age (years)

tag: icu

tag: apacheii

tag: charlson score

tag: associated controlled-vocabulary terms

tag: cell type

tag: sample type


title: Ncas_WT_input_4

tag: genotype

tag: replicate

tag: chip antibody


title: COVID_50_37y_male_ICU

description:
C50
genes.ec.tsv
genes.tpm.tsv

tag: Sex

tag: mechanical ventilation

tag: ventilator-free days

tag: dm

tag: hospital-free days post 45 day followup (days)

tag: ferritin (ng/ml)

tag: crp (mg/l)

tag: ddimer (mg/l_feu)

tag: procalcitonin (ng/ml)

tag: lactate (mmol/l)

tag: tissue of origin


title: COVID_51_58y_female_NonICU

description:
C51
genes.ec.tsv
genes.tpm.tsv

tag: disease state

tag: age (years)

tag: icu

tag: apacheii

tag: charlson score

tag: fibrinogen

tag: sofa

tag: associated controlled-vocabulary terms


title: 2018-424/16

description:
16-2018-424-16_S24
16.bam

tag: strain

tag: Sex

tag: treatment

tag: tissue


title: COVID_49_73y_male_ICU

description:
C49
genes.ec.tsv
genes.tpm.tsv

tag: mechanical ventilation

tag: ventilator-free days

tag: dm

tag: hospital-free days post 45 day followup (days)

tag: ferritin (ng/ml)

tag: crp (mg/l)

tag: cell type

tag: sample type


title: Ncas_WT_input_1

tag: genotype

tag: replicate

tag: chip antibody


title: COVID_47_78y_male_ICU

description:
C47
genes.ec.tsv
genes.tpm.tsv

tag: disease state

tag: age (years)

tag: icu

tag: apacheii

tag: charlson score

tag: ddimer (mg/l_feu)

tag: procalcitonin (ng/ml)

tag: lactate (mmol/l)

tag: fibrinogen

tag: sofa

tag: tissue of origin


title: Ncas_WT_IP3_3

value: αSfp1-3 custom polyclonal antibody (Bethyl)


title: COVID_48_72y_female_ICU

description:
C48
genes.ec.tsv
genes.tpm.tsv

tag: Sex

tag: mechanical ventilation

tag: ventilator-free days

tag: dm

tag: hospital-free days post 45 day followup (days)

tag: ferritin (ng/ml)

tag: crp (mg/l)

tag: associated controlled-vocabulary terms


title: COVID_46_62y_male_ICU

description:
C46
genes.ec.tsv
genes.tpm.tsv

tag: disease state

tag: age (years)

tag: icu

tag: cell type

tag: sample type


title: 2018-424/14

description:
14-2018-424-14_S17
14.bam

tag: strain

tag: treatment

tag: tissue


title: Ncas_WT_IP3_2

tag: genotype

tag: replicate

tag: chip antibody


title: COVID_42_21y_female_ICU

description:
C42
genes.ec.tsv
genes.tpm.tsv

tag: Sex

tag: apacheii

tag: charlson score

tag: mechanical ventilation

tag: ventilator-free days

tag: ddimer (mg/l_feu)

tag: procalcitonin (ng/ml)

tag: lactate (mmol/l)

tag: fibrinogen

tag: sofa

tag: tissue of origin


title: 2018-424/12

description:
12-2018-424-12_S9
12.bam

tag: strain


title: Ncas_WT_input_3


title: COVID_43_83y_female_ICU

description:
C43
genes.ec.tsv
genes.tpm.tsv

tag: disease state

tag: age (years)

tag: icu

tag: dm

tag: hospital-free days post 45 day followup (days)

tag: ferritin (ng/ml)

tag: crp (mg/l)

tag: associated controlled-vocabulary terms

tag: cell type

tag: sample type


title: Ncas_WT_IP3_1

tag: genotype

tag: replicate

tag: chip antibody


title: 2018-424/13

description:
13-2018-424-13_S13
13.bam

tag: Sex

tag: treatment

tag: tissue


title: COVID_52_71y_male_NonICU

description:
C52
genes.ec.tsv
genes.tpm.tsv

tag: apacheii

tag: charlson score

tag: mechanical ventilation

tag: ventilator-free days

tag: ddimer (mg/l_feu)

tag: procalcitonin (ng/ml)

tag: lactate (mmol/l)

tag: fibrinogen

tag: sofa

tag: tissue of origin


title: COVID_44_46y_male_ICU

description:
C44
genes.ec.tsv
genes.tpm.tsv

tag: disease state

tag: age (years)

tag: icu

tag: dm

tag: hospital-free days post 45 day followup (days)

tag: ferritin (ng/ml)

tag: crp (mg/l)

tag: associated controlled-vocabulary terms

tag: cell type

tag: sample type


title: COVID_41_74y_male_ICU

description:
C41
genes.ec.tsv
genes.tpm.tsv

tag: Sex

tag: apacheii

tag: charlson score

tag: mechanical ventilation

tag: ventilator-free days


title: COVID_39_80y_female_ICU

description:
C39
genes.ec.tsv
genes.tpm.tsv

tag: ddimer (mg/l_feu)

tag: procalcitonin (ng/ml)

tag: lactate (mmol/l)

tag: fibrinogen

tag: sofa


title: 2018-424/17

description:
17-2018-424-17_S27
17.bam

tag: strain

tag: treatment

tag: tissue


title: 2018-424/1

description:
1-2018-424-1_S29
1.bam


title: COVID_40_66y_male_ICU

description:
C40
genes.ec.tsv
genes.tpm.tsv

tag: disease state

tag: age (years)

tag: icu

tag: dm

tag: hospital-free days post 45 day followup (days)

tag: ferritin (ng/ml)

tag: crp (mg/l)

tag: tissue of origin


title: Ncas_WT_IP1_3

tag: genotype

tag: replicate

tag: chip antibody

value: αSfp1-1 custom polyclonal antibody (Bethyl)


title: 2018-424/15

description:
15-2018-424-15_S21
15.bam

tag: Sex


title: Ncas_WT_IP1_2


title: Ncas_WT_input_2


title: Ncas_WT_IP1_1


title: COVID_35_58y_female_NonICU

description:
C35
genes.ec.tsv
genes.tpm.tsv

value: female

tag: apacheii

tag: charlson score

tag: mechanical ventilation

tag: ventilator-free days

tag: ddimer (mg/l_feu)

tag: procalcitonin (ng/ml)

tag: lactate (mmol/l)

tag: fibrinogen

tag: associated controlled-vocabulary terms

tag: cell type

tag: sample type


title: COVID_37_87y_male_NonICU

description:
C37
genes.ec.tsv
genes.tpm.tsv

tag: disease state

tag: age (years)

value: male

tag: icu

tag: dm

tag: hospital-free days post 45 day followup (days)

tag: ferritin (ng/ml)

tag: crp (mg/l)

tag: sofa


title: COVID_36_68y_male_NonICU

description:
C36
genes.ec.tsv
genes.tpm.tsv

tag: Sex

value: no

tag: apacheii

tag: charlson score

tag: mechanical ventilation

tag: tissue of origin


title: 2018-424/10

description:
10-2018-424-10_S1
10.bam

tag: strain

tag: treatment

tag: tissue


title: COVID_45_62y_female_ICU

description:
C45
genes.ec.tsv
genes.tpm.tsv

tag: ventilator-free days

tag: ddimer (mg/l_feu)

tag: procalcitonin (ng/ml)

tag: lactate (mmol/l)

tag: fibrinogen

tag: associated controlled-vocabulary terms

tag: cell type

tag: sample type


title: Ncas_719_input_3

tag: genotype

value: delta Scas719.24

tag: replicate

tag: chip antibody


title: COVID_33_81y_male_NonICU

description:
C33
genes.ec.tsv
genes.tpm.tsv

tag: disease state

tag: age (years)

tag: Sex

tag: icu

tag: apacheii

value: unknown

tag: charlson score

tag: dm

tag: hospital-free days post 45 day followup (days)

tag: ferritin (ng/ml)

tag: crp (mg/l)

tag: sofa

value: leukocyte


title: COVID_34_64y_female_NonICU

description:
C34
genes.ec.tsv
genes.tpm.tsv

tag: mechanical ventilation

tag: ventilator-free days

tag: ddimer (mg/l_feu)

tag: procalcitonin (ng/ml)

tag: lactate (mmol/l)

tag: fibrinogen

tag: associated controlled-vocabulary terms

tag: tissue of origin

value: whole blood

value: primary cells


title: Ncas_719_input_1

tag: genotype

tag: replicate

tag: chip antibody


title: COVID_30_54y_male_ICU

description:
C30
genes.ec.tsv
genes.tpm.tsv

tag: disease state

tag: age (years)

tag: Sex

tag: icu

value: yes

tag: apacheii

tag: charlson score

tag: cell type

tag: sample type


title: Klac_WT_input_2

organism: Kluyveromyces lactis


title: COVID_29_63y_female_ICU

description:
C29
genes.ec.tsv
genes.tpm.tsv

tag: mechanical ventilation

tag: ventilator-free days

tag: dm

tag: hospital-free days post 45 day followup (days)

tag: ferritin (ng/ml)

tag: crp (mg/l)

tag: ddimer (mg/l_feu)

tag: sofa


title: Klac_WT_input_1

tag: genotype

tag: replicate

tag: chip antibody


title: Ncas_719_input_2


title: Klac_WT_input_3


title: COVID_28_63y_male_ICU

description:
C28
genes.ec.tsv
genes.tpm.tsv

tag: disease state

tag: age (years)

tag: Sex

tag: procalcitonin (ng/ml)

tag: lactate (mmol/l)

tag: fibrinogen

tag: associated controlled-vocabulary terms

tag: tissue of origin


title: Ncas_719_IP1_2


title: Klac_WT_IP1_3


title: Ncas_719_IP1_3


title: COVID_38_68y_male_ICU

description:
C38
genes.ec.tsv
genes.tpm.tsv

tag: icu

tag: apacheii

tag: charlson score

tag: mechanical ventilation

tag: ventilator-free days

tag: dm

tag: cell type

tag: sample type


title: Spar_WT_input_3

organism: Saccharomyces paradoxus

tag: genotype

tag: replicate

tag: chip antibody


title: 2018-424/11

description:
11-2018-424-11_S5
11.bam

tag: strain

value: BALB/c

tag: Sex

tag: treatment

tag: tissue

value: hippocampus


title: Klac_WT_IP1_2


title: Ncas_719_IP1_1


title: COVID_26_41y_female_ICU

description:
C26
genes.ec.tsv
genes.tpm.tsv

tag: disease state

tag: age (years)

tag: hospital-free days post 45 day followup (days)

tag: ferritin (ng/ml)

tag: crp (mg/l)

tag: ddimer (mg/l_feu)

tag: procalcitonin (ng/ml)

tag: lactate (mmol/l)

tag: fibrinogen

tag: sofa

tag: associated controlled-vocabulary terms


title: Spar_WT_input_2

tag: genotype

tag: replicate


title: COVID_24_55y_male_ICU

description:
C24
genes.ec.tsv
genes.tpm.tsv

tag: icu

tag: apacheii

tag: charlson score

tag: mechanical ventilation

tag: ventilator-free days

tag: dm

tag: cell type

tag: tissue of origin

tag: sample type


title: Spar_WT_input_1

tag: chip antibody


title: Klac_Sfp1d_input_3

value: delta sfp1


title: Klac_WT_IP1_1

value: wild type


title: Spar_WT_IP1_3


title: Ncas_551_input_6

value: delta Scas551.1

value: input


title: COVID_32_72y_male_ICU

description:
C32
genes.ec.tsv
genes.tpm.tsv

tag: disease state

tag: age (years)

tag: Sex

tag: hospital-free days post 45 day followup (days)

tag: ferritin (ng/ml)

tag: crp (mg/l)

tag: ddimer (mg/l_feu)

tag: procalcitonin (ng/ml)


title: COVID_31_50y_male_ICU

description:
C31
genes.ec.tsv
genes.tpm.tsv

tag: icu

tag: apacheii

tag: lactate (mmol/l)

tag: fibrinogen

tag: sofa

tag: associated controlled-vocabulary terms


title: Klac_Sfp1d_input_1

tag: genotype

tag: replicate


title: COVID_23_76y_male_ICU

description:
C23
genes.ec.tsv
genes.tpm.tsv

tag: charlson score

tag: mechanical ventilation

tag: ventilator-free days

tag: dm

tag: cell type

tag: tissue of origin

tag: sample type


title: COVID_22_43y_male_ICU

description:
C22
genes.ec.tsv
genes.tpm.tsv

tag: disease state

tag: age (years)

tag: Sex

tag: hospital-free days post 45 day followup (days)

tag: ferritin (ng/ml)

tag: crp (mg/l)

tag: ddimer (mg/l_feu)


title: Spar_WT_IP1_2

tag: chip antibody


title: COVID_27_71y_female_ICU

description:
C27
genes.ec.tsv
genes.tpm.tsv

tag: icu

tag: apacheii

tag: procalcitonin (ng/ml)

tag: lactate (mmol/l)

tag: fibrinogen

tag: sofa

tag: associated controlled-vocabulary terms


title: Ncas_551_input_3

tag: genotype

tag: replicate


title: Ncas_551_input_4


title: COVID_21_66y_male_ICU

description:
C21
genes.ec.tsv
genes.tpm.tsv

tag: disease state

tag: charlson score

tag: mechanical ventilation

tag: ventilator-free days

tag: dm

tag: cell type

tag: tissue of origin

tag: sample type


title: Ncas_551_input_2

tag: chip antibody


title: Spar_WT_IP1_1


title: Klac_Sfp1d_IP1_2


title: COVID_20_62y_male_ICU

description:
C20
genes.ec.tsv
genes.tpm.tsv

tag: age (years)

tag: Sex

tag: icu

tag: apacheii

tag: hospital-free days post 45 day followup (days)

tag: ferritin (ng/ml)

tag: crp (mg/l)

tag: ddimer (mg/l_feu)


title: Ncas_551_input_1

tag: genotype

tag: replicate


title: Ncas_551_input_5


title: Klac_Sfp1d_IP1_1


title: COVID_25_55y_male_ICU

description:
C25
genes.ec.tsv
genes.tpm.tsv

tag: disease state

tag: charlson score

tag: mechanical ventilation

tag: procalcitonin (ng/ml)

tag: lactate (mmol/l)

tag: fibrinogen

tag: sofa

tag: associated controlled-vocabulary terms


title: Spar_Sfp1d_input_1

tag: chip antibody


title: COVID_19_51y_male_NonICU

description:
C19
genes.ec.tsv
genes.tpm.tsv

tag: age (years)

tag: Sex

tag: icu

tag: ventilator-free days

tag: dm

tag: cell type

tag: tissue of origin

tag: sample type


title: Spar_Sfp1d_input_2

tag: genotype

tag: replicate


title: Ncas_551_IP3_1

value: αSfp1-3 custom polyclonal antibody (Bethyl)


title: COVID_18_70y_female_NonICU

description:
C18
genes.ec.tsv
genes.tpm.tsv

tag: disease state

tag: apacheii

tag: charlson score

tag: mechanical ventilation

tag: hospital-free days post 45 day followup (days)

tag: ferritin (ng/ml)

tag: crp (mg/l)

tag: ddimer (mg/l_feu)


title: SCAS WT_C

description:
Ncas.OG.logFC.txt.gz
Ncas.Gene.logFC.txt.gz
RNA-seq for wild type Naumovozyma castellii in Yeast culture (BMW) - log phase (log), replicateC. Used to generate column Ncas_551_Log and Ncas_719_Log in Ncas.Gene.logFC.txt.gz
Other columns derived from microarrays (microarray submission in-process).

data_processing:
Reads were mapped using RSEM (Li and Dewey, 2011) (version 1.2.11) utilizing Bowtie (Langmead, 2010) (version 1)
RSEM counts for the duplicated chromosome 2 in S. cerevisiae and S. paradoxus were similarly corrected by dividing the counts for genes on chromosome 2 by the median log fold change difference between genes on chromosome 2 and other genes between the WT and SFP1D mutant strains
We then used the edgeR package for R (Robinson, McCarthy and Smyth, 2010; McCarthy, Chen and Smyth, 2012) to TMM normalize the data and calculate the log fold changes and p-values of the gene expression differences between WT and SFP1D mutant strains.
Genome_build: The assembly (including transcriptome annotation information) from Scannell, et al. (Scannell et al., 2011) was used for S. paradoxus, and the r64 release of the S288C genome from the Saccharomyces Genome Database (Cherry et al., 2012) for S. cerevisiae. For C. glabrata, N. castellii, and K. lactis the genome and assembly and annotations were obtained from YGOB (v7 Aug 2012) and the S. pombe ASM294v2 genome assembly information was obtained from ENSEMBL (Vilella et al., 2009).
Supplementary_files_format_and_content: Files named "*.Gene.logFC.txt.gz" contain the gene-level (i.e. that species' genes) log-fold change (relative to WT) expression values for each species. Files names  "*.OG.logFC.txt.gz" contain orthogroup-level logFC values for each species. orthology_melted_aliases.txt.gz contains the orthogroup mappings for each species. Note that because gene expression was measured using both microarrays and RNA-seq, this processed data includes the data from both. The gene expression microarrays that are part of this study and described in their own GEO entry (TBD). OG_to_Scer-GNs.txt.gz contains the orthogroup to S. cerevisiae systematic name mappings.  Also included are raw counts (from RSEM) in files ending in ".counts.txt.gz" and copy-number-normalized TMM-normalized CPM values in files ending in ".TMM.txt.gz".

molecule: polyA RNA

source_name: Yeast culture (BMW) - log phase

growth_protocol: For log phase samples, cells were collected between O.D 0.6-0.8 Lag phase samples were collected at 30 mns and 60 mins post glucose repletion.

extract_protocol:
RNA extraction Total RNA was isolated using the RNeasyMidi or Mini Kit (Qiagen) and instructions were followed for mechanical lysis.
Library construction was completed as previously described (Engreitz et al., 2013; Schwartz et al., 2013).
Rna-seq libraries were pooled and Paired-end 25 base pair reads were performed on Illumina’s Hiseq2000.

value: C

tag: growth phase

value: log


title: SCAS WT_B

description:
Ncas.OG.logFC.txt.gz
Ncas.Gene.logFC.txt.gz
RNA-seq for wild type Naumovozyma castellii in Yeast culture (BMW) - log phase (log), replicateB. Used to generate column Ncas_551_Log and Ncas_719_Log in Ncas.Gene.logFC.txt.gz
Other columns derived from microarrays (microarray submission in-process).

value: B


title: Spar_Sfp1d_IP1_3

tag: chip antibody

value: αSfp1-1 custom polyclonal antibody (Bethyl)


title: Klac_Sfp1d_input_2


title: Ncas_551_IP1_1


title: Klac_Sfp1d_IP1_3


title: Ncas_551_IP1_2


title: SCAS WT_A

description:
Ncas.OG.logFC.txt.gz
Ncas.Gene.logFC.txt.gz
RNA-seq for wild type Naumovozyma castellii in Yeast culture (BMW) - log phase (log), replicateA. Used to generate column Ncas_551_Log and Ncas_719_Log in Ncas.Gene.logFC.txt.gz
Other columns derived from microarrays (microarray submission in-process).

value: A


title: SCAS 719_C

description:
Ncas.OG.logFC.txt.gz
Ncas.Gene.logFC.txt.gz
RNA-seq for delta Scas719.24 Naumovozyma castellii in Yeast culture (BMW) - log phase (log), replicateC. Used to generate column Ncas_719_Log in Ncas.Gene.logFC.txt.gz
Other columns derived from microarrays (microarray submission in-process).

value: delta Scas719.24


title: COVID_15_68y_male_ICU

description:
C15
genes.ec.tsv
genes.tpm.tsv

tag: age (years)

tag: Sex

value: male

tag: icu

tag: ventilator-free days

tag: procalcitonin (ng/ml)

tag: lactate (mmol/l)

tag: fibrinogen

tag: sofa

tag: associated controlled-vocabulary terms

value: leukocyte


title: pombe sfp1 ko_C

description:
Spom.OG.logFC.txt.gz
Spom.Gene.logFC.txt.gz
RNA-seq for delta sfp1 Schizosaccharomyces pombe in Yeast culture (BMW) - log phase (log), replicateC. Used to generate column Spom_KO_Log in Spom.Gene.logFC.txt.gz
Other columns derived from microarrays (microarray submission in-process).

organism: Schizosaccharomyces pombe

tag: genotype

tag: replicate


title: COVID_14_55y_male_ICU

description:
C14
genes.ec.tsv
genes.tpm.tsv

tag: disease state

tag: apacheii

tag: charlson score

tag: mechanical ventilation

tag: dm

tag: hospital-free days post 45 day followup (days)

tag: cell type

tag: tissue of origin

value: whole blood

tag: sample type

value: primary cells


title: bESC_r1_CutRun_H3K27me3

city: Fort Collins

first: Michelle

middle: M

last: Halstead

state: CO

address: 200 West Lake Street

department: Biomedical Sciences

institute: Colorado State University

data_processing:
Library strategy: Cut&Run
Raw sequencing reads were trimmed with Trim_Galore, a wrapper around Cutadapt (v1.18), to remove residual Illumina adapter sequences and low quality (q<20) ends, keeping unpaired reads and reads 10 bp or longer after trimming.
Trimmed reads were aligned to the genome using BWA mem (v0.7.17-r1188).
PCR duplicates were removed with PicardTools (v2.8.1), and low-quality alignments (q<5) were removed with SAMtools (v1.7).
Processed alignments were converted to bigWig format using bamCoverage from the DeepTools suite (v3.4.3), which binned the genome into 50 bp windows and calculated normalized signal (reads per kilobase million; RPKM) in each window.
Peaks were called with Epic2 (v0.0.41) with an effective genome fraction of 0.7 and an e-value of 500. For H3K4me3, peaks were called using the option -g 1. For H3K27me3, peaks were called using the option -g 5.
Genome_build: ARS-UCD1.2
Supplementary_files_format_and_content: BigWig files show genome-wide normalized signal.
Supplementary_files_format_and_content: BED files show regions of enrichment (peaks).

organism: Bos taurus

source_name: Embryonic stem cells

growth_protocol: Bovine embryonic stem cells (bESC) were derived from a single female in vitro fertilized day 7 blastocyst. This blastocyst was plated on a 0.1% gelatin-coated 48-well dish which contained a monolayer of mouse embryonic fibroblasts (MEF) at 37°C, 5% CO2. The culture media consisted of a mixture of 1:1 DMEM/F12 medium and Neurobasal medium, 0.5% v/v N-2 Supplement , 1% v/v B-27 Supplement, 2 mM MEM Non-essential Amino Acid Solution, 1% v/v GlutaMAX Supplement, 100 U/mL Penicillin and 100 μg/mL Streptomycin, 0.1 mM 2-mercaptoethanol, 20 ng/mL human FGF2, 2.5 μM IWR-1 and 1% v/v low fatty acid Bovine Serum Albumin. Media was supplemented with Roxi at blastocyst seeding or cell passage. Cells were passed using Tryple Express. After 4 passages, the cell line was established.

extract_protocol:
Cut&Run was performed following the published protocol with some modifications. To obtain pure bESC, MEF were depleted using feeder removal microbeads (MACs Miltenyi Biotec, 130-095-531). Approximately 5×104 bESC per sample were washed twice with 1 mL washing buffer (20 mM HEPES at pH 7.5, 150 mM NaCl, 0.5 mM Spermidine, and 1× Roche complete protease inhibitor) and resuspended in 60 µL washing buffer. Concanavalin-coated magnetic beads (Bangs Laboratories, BP531), 20 μL per sample, were washed and resuspended in binding buffer (20 mM HEPES-KOH at pH 7.9, 10 mM KCl, 1 mM CaCl2, 1 mM MnCl2), and added to the samples. Then, the samples were incubated at 24°C for 10 min on Thermomixer at 400 rpm. The sample tubes were placed on the magnetic stand to remove all the liquid. For each sample, 50 µL antibody buffer (washing buffer, 0.1% digitonin, 2 mM EDTA at pH 8.0) with H3K4me3 (1:100 dilution, Diagenode, C15410003) or H3K27me3 (1:100 dilution, Diagenode, C15410195) was added to the sample tube, and incubated overnight at 4°C on Thermomixer at 400 rpm. After antibody incubation, the tubes were placed on the magnetic stand to remove the liquid. After washing twice with digitonin buffer (washing buffer plus 0.1% digitonin), the samples were resuspended in 50 μL digitonin buffer containing pAG-MNase (dilution 1:20, EpiCypher, 15-1016), and incubated for 10 min at room temperature. After washing the samples twice with digitonin buffer, the samples were resuspended with 100 µL cold digitonin buffer and balanced on ice for 3 min. Targeted digestion was conducted by adding 2 μL CaCl2 (100 mM) on ice for 30 min, and the digestion was stopped by adding 100 µL 2× stop buffer (340 mM NaCl, 4 mM EGTA at pH 8.0, 20 mM EDTA at pH 8.0, 0.1% digitonin, 100 μg/mL glycogen, 50 μg/mL RNase A). After incubation at 37°C for 30 min, the samples were digested by adding 1.5 μL proteinase K (20 mg/ml), 2 μL 10% SDS and 10 ng carrier RNA (Qiagen, 1068337), and then incubated at 65°C for 30 min. DNA fragments were purified with phenol-chloroform-isoamyl alcohol and washed by ethanol, then dissolved in 25 µL ddH2O.
Library construction was carried out using NEBNext Ultra II DNA Library Prep Kit for Illumina (NEB, E7645L) according to the manufacturer’s instructions. Briefly, after end-repair/A-tailing, ligation, U-excision and post-ligation cleanup with 1.3× AMPure XP beads (Beckman, A63881), the first round of PCR was performed with KAPA HiFi HotStart Ready Mix (KAPA biosystems, KM2602), universal primer (NEB, E6861AA) and index primer (NEBNext multiplex Oligos kit) with PCR program of 98°C for 45 sec, (98°C for 15 sec and 60°C for 10 sec) with 8 cycles and 72°C for 1 min. PCR products were purified with 1.3× AMPure XP beads, and the purified products were subjected to the second round of PCR which was performed using KAPA HiFi HotStart Ready Mix with the same PCR program for 8 cycles. The final libraries were purified by 1.3× AMPure XP beads and submitted for sequencing.

value: Embryonic stem cells

tag: histone mark


title: bESC_r2_CutRun_H3K27me3


title: SCAS 719_A

description:
Ncas.OG.logFC.txt.gz
Ncas.Gene.logFC.txt.gz
RNA-seq for delta Scas719.24 Naumovozyma castellii in Yeast culture (BMW) - log phase (log), replicateA. Used to generate column Ncas_719_Log in Ncas.Gene.logFC.txt.gz
Other columns derived from microarrays (microarray submission in-process).

tag: growth phase


title: Ncas_551_IP1_3

tag: chip antibody


title: pombe sfp1 ko_B

description:
Spom.OG.logFC.txt.gz
Spom.Gene.logFC.txt.gz
RNA-seq for delta sfp1 Schizosaccharomyces pombe in Yeast culture (BMW) - log phase (log), replicateB. Used to generate column Spom_KO_Log in Spom.Gene.logFC.txt.gz
Other columns derived from microarrays (microarray submission in-process).


title: COVID_13_37y_male_NonICU

description:
C13
genes.ec.tsv
genes.tpm.tsv

tag: age (years)

tag: Sex

tag: icu

value: no

value: unknown

tag: ventilator-free days

tag: ferritin (ng/ml)

tag: crp (mg/l)

tag: ddimer (mg/l_feu)

tag: procalcitonin (ng/ml)

tag: lactate (mmol/l)

tag: fibrinogen


title: COVID_17_54y_male_NonICU

description:
C17
genes.ec.tsv
genes.tpm.tsv

tag: disease state

tag: apacheii

tag: charlson score

tag: mechanical ventilation

tag: dm

tag: hospital-free days post 45 day followup (days)

tag: sofa

tag: associated controlled-vocabulary terms


title: pombe sfp1 ko_A

description:
Spom.OG.logFC.txt.gz
Spom.Gene.logFC.txt.gz
RNA-seq for delta sfp1 Schizosaccharomyces pombe in Yeast culture (BMW) - log phase (log), replicateA. Used to generate column Spom_KO_Log in Spom.Gene.logFC.txt.gz
Other columns derived from microarrays (microarray submission in-process).

tag: genotype

value: delta sfp1

tag: replicate

tag: growth phase


title: COVID_12_50y_male_ICU

description:
C12
genes.ec.tsv
genes.tpm.tsv

tag: age (years)

tag: Sex

tag: icu

value: yes

tag: ventilator-free days

tag: ferritin (ng/ml)

tag: cell type

tag: tissue of origin

tag: sample type


title: SCAS 551_C

description:
Ncas.OG.logFC.txt.gz
Ncas.Gene.logFC.txt.gz
RNA-seq for delta Scas551.1  Naumovozyma castellii in Yeast culture (BMW) - log phase (log), replicateC. Used to generate column Ncas_551_Log in Ncas.Gene.logFC.txt.gz
Other columns derived from microarrays (microarray submission in-process).

value: delta Scas551.1


title: SCAS 551_B

description:
Ncas.OG.logFC.txt.gz
Ncas.Gene.logFC.txt.gz
RNA-seq for delta Scas551.1  Naumovozyma castellii in Yeast culture (BMW) - log phase (log), replicateB. Used to generate column Ncas_551_Log in Ncas.Gene.logFC.txt.gz
Other columns derived from microarrays (microarray submission in-process).


title: pombe wt_C

description:
Spom.OG.logFC.txt.gz
Spom.Gene.logFC.txt.gz
RNA-seq for wild type Schizosaccharomyces pombe in Yeast culture (BMW) - log phase (log), replicateC. Used to generate column Spom_KO_Log in Spom.Gene.logFC.txt.gz
Other columns derived from microarrays (microarray submission in-process).

value: wild type


title: COVID_11_52y_female_NonICU

description:
C11
genes.ec.tsv
genes.tpm.tsv

tag: disease state

value: female

tag: apacheii

tag: charlson score

tag: crp (mg/l)

tag: ddimer (mg/l_feu)

tag: procalcitonin (ng/ml)

tag: lactate (mmol/l)

tag: fibrinogen


title: pombe wt_B

description:
Spom.OG.logFC.txt.gz
Spom.Gene.logFC.txt.gz
RNA-seq for wild type Schizosaccharomyces pombe in Yeast culture (BMW) - log phase (log), replicateB. Used to generate column Spom_KO_Log in Spom.Gene.logFC.txt.gz
Other columns derived from microarrays (microarray submission in-process).

tag: genotype

tag: replicate

tag: growth phase

value: log


title: Spar_Sfp1d_IP1_2

tag: chip antibody


title: Spar_Sfp1d_IP1_1


title: COVID_16_48y_male_NonICU

description:
C16
genes.ec.tsv
genes.tpm.tsv

tag: age (years)

tag: Sex

tag: icu

tag: mechanical ventilation

tag: ventilator-free days

tag: dm

tag: hospital-free days post 45 day followup (days)

tag: sofa

tag: associated controlled-vocabulary terms


title: Spar_Sfp1d_input_3

value: input


title: pombe wt_A

description:
Spom.OG.logFC.txt.gz
Spom.Gene.logFC.txt.gz
RNA-seq for wild type Schizosaccharomyces pombe in Yeast culture (BMW) - log phase (log), replicateA. Used to generate column Spom_KO_Log in Spom.Gene.logFC.txt.gz
Other columns derived from microarrays (microarray submission in-process).


title: COVID_10_62y_male_ICU

description:
C10
genes.ec.tsv
genes.tpm.tsv

tag: disease state

tag: apacheii

tag: charlson score

tag: ferritin (ng/ml)

tag: crp (mg/l)

tag: ddimer (mg/l_feu)

tag: cell type

tag: tissue of origin

tag: sample type


title: SCAS 551_A

description:
Ncas.OG.logFC.txt.gz
Ncas.Gene.logFC.txt.gz
RNA-seq for delta Scas551.1  Naumovozyma castellii in Yeast culture (BMW) - log phase (log), replicateA. Used to generate column Ncas_551_Log in Ncas.Gene.logFC.txt.gz
Other columns derived from microarrays (microarray submission in-process).

tag: genotype

tag: replicate

tag: growth phase


title: COVID_09_64y_female_ICU

description:
C9
genes.ec.tsv
genes.tpm.tsv

tag: age (years)

tag: Sex

tag: icu

tag: mechanical ventilation

tag: ventilator-free days

tag: procalcitonin (ng/ml)

tag: lactate (mmol/l)

tag: fibrinogen


title: MNH4

city: Madison

first: Laura

middle: Catherine

last: Swanson

state: WI

address: 2631 University Avenue Apt 6

department: Medical Genetics

institute: University of Wisconsin-Madison

description:
mRNA
rsem_GENE.csv
rsem_ISOFORM.csv
edgeRglm_GENE_CNH-MNH.csv
edgeRglm_GENE_MNH-MH.csv
edgeRglm_ISOFORM_CNH-MNH.csv
edgeRglm_ISOFORM_MNH-MH.csv

data_processing:
Illumina Casava software used for basecalling.
Sequenced reads were adapter and quality trimmed using the Skewer trimming program (v0.1.118).
Quality reads were aligned to Drosophila melanogaster using the STAR aligner (v2.4.2a).
Quantification of expression for each gene were calculated by RSEM (v1.2.22).
Expected read counts from RSEM were filtered for low/empty values and used for differential gene expression analysis using EdgeR (v3.10.5).
Genome_build: dm6 (Release 6 plus ISO1 MT)
Supplementary_files_format_and_content: Gene read counts inferred by RSEM, and differential gene expression analysis performed with edgeR.

organism: Drosophila melanogaster

source_name: whole male flies

growth_protocol: Flies were maintained on molasses food at 25°C.

extract_protocol:
Whole fly RNA was harvested using Qiagen RNeasy plus mini kit (#74134) and Qiagen QIAshredder kit (#79654) according to manufacturer's instructions.
Illumina TruSeq RNA Sample Prep Kit (Cat#RS 200-0012 ) 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: 1-7 day flies were collected, and treated with our standard TBI protocol and placed on food for 4 hours, or collected without uninjured, and stored at -80°C until RNA extraction.

tag: line

value: Reldel/Reldel, yw

tag: age

value: 1-7 days

tag: injury status

value: uninjured

tag: tissue type

value: whole flies


title: scer_WT_60

description:
Spar.OG.logFC.txt.gz
Spar.Gene.logFC.txt.gz
RNA-seq for wild type Saccharomyces cerevisiae in Yeast culture (BMW) - lag phase (lag_60mins), replicateA. Unused.
Other columns derived from microarrays (microarray submission in-process).

organism: Saccharomyces cerevisiae

source_name: Yeast culture (BMW) - lag phase

value: A


title: MNH3

value: male


title: Cultured cortical neurons, Z2 (array)

type: genomic

city: Shenyang

first: JIE

last: LU

state: Liaoning

address: 77 Puhe Road, Shenbei Xiqu

department: Human Anatomy

country: China

institute: China Medical University

description: SAMPLE 2

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium 850k Human MethylationEPIC BeadChip using standard Illumina protocol

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

data_processing: BeadStudio software v3.2

label: Cy5 and Cy3

source_name: Cultured cortical neuron

label_protocol: Standard Illumina Protocol

growth_protocol: Lentivirus Infected cells were cultured in Neurobasal+2%B27 for 4 days

extract_protocol: The genomic DNA of each sample was extracted from the lentivirus infected, early differentiated HNPs with ZsGreen (n=3) or DNMT3L (n=3) overexpression. The DNA was isolated and cleaned by following the manufacturer’s protocol with DNA purification kit (Qiagen, MD, USA).

treatment_protocol: 1st passage of human neuroprogenitors were infected with letivirus carrying ZsGreen or DNMT3L gene

tag: cell type

value: neurons differentiated from 1st passage of neuroprogenitors from fetal frontal cortex

tag: developmental stage

value: 21 week of gestational age

tag: karyotype

tag: treatment

value: 1st passage neuroprogenitors infected with lentivirus carrying ZsGreen gene and cultured for 4 days

value: CON


title: COVID_08_78y_male_ICU

description:
C8
genes.ec.tsv
genes.tpm.tsv

tag: disease state

tag: apacheii

tag: charlson score

tag: dm

tag: hospital-free days post 45 day followup (days)

tag: ferritin (ng/ml)

tag: crp (mg/l)

tag: ddimer (mg/l_feu)

tag: sofa

tag: associated controlled-vocabulary terms

value: leukocyte

tag: tissue of origin

value: whole blood

tag: sample type

value: primary cells


title: bESC_r2_CutRun_H3K4me3

value: Embryonic stem cells

tag: histone mark


title: MNH2

tag: line

tag: Sex

tag: age

tag: injury status

tag: tissue type


title: bESC_r1_CutRun_H3K4me3

tag: cell type


title: scer wt_B

description:
Scer.OG.logFC.txt.gz
Scer.Gene.logFC.txt.gz
RNA-seq for wild type Saccharomyces cerevisiae in Yeast culture (BMW) - log phase (log), replicateB. Used to generate column Scer_KO_Log and Scer_HA_Log in Scer.Gene.logFC.txt.gz
Other columns derived from microarrays (microarray submission in-process).

tag: genotype

value: wild type

tag: replicate

value: B

tag: growth phase


title: scer wt_C

description:
Scer.OG.logFC.txt.gz
Scer.Gene.logFC.txt.gz
RNA-seq for wild type Saccharomyces cerevisiae in Yeast culture (BMW) - log phase (log), replicateC. Used to generate column Scer_KO_Log and Scer_HA_Log in Scer.Gene.logFC.txt.gz
Other columns derived from microarrays (microarray submission in-process).

value: C

value: log


title: COVID_07_38y_female_NonICU

description:
C7
genes.ec.tsv
genes.tpm.tsv

tag: disease state

tag: age (years)

value: female

tag: icu

value: no

tag: apacheii

value: unknown

tag: charlson score

tag: mechanical ventilation

tag: ventilator-free days

tag: dm

tag: hospital-free days post 45 day followup (days)

tag: ferritin (ng/ml)

tag: procalcitonin (ng/ml)

tag: lactate (mmol/l)

tag: fibrinogen


title: scer wt_A

description:
Scer.OG.logFC.txt.gz
Scer.Gene.logFC.txt.gz
RNA-seq for wild type Saccharomyces cerevisiae in Yeast culture (BMW) - log phase (log), replicateA. Used to generate column Scer_KO_Log and Scer_HA_Log in Scer.Gene.logFC.txt.gz
Other columns derived from microarrays (microarray submission in-process).

value: A


title: MH4

description:
mRNA
rsem_GENE.csv
rsem_ISOFORM.csv
edgeRglm_GENE_CH-MH.csv
edgeRglm_GENE_MNH-MH.csv
edgeRglm_ISOFORM_CH-MH.csv
edgeRglm_ISOFORM_MNH-MH.csv

tag: line

value: Reldel/Reldel, yw

tag: Sex

value: male

tag: age

value: 1-7 days

tag: injury status

value: injured

tag: tissue type

value: whole flies


title: MNH1

value: uninjured


title: scer sfp1 ko_C

description:
Scer.OG.logFC.txt.gz
Scer.Gene.logFC.txt.gz
RNA-seq for delta sfp1 Saccharomyces cerevisiae in Yeast culture (BMW) - log phase (log), replicateC. Used to generate column Scer_KO_Log in Scer.Gene.logFC.txt.gz
Other columns derived from microarrays (microarray submission in-process).

tag: genotype

value: delta sfp1

tag: replicate

tag: growth phase


title: MH3


title: COVID_04_49y_male_NonICU

description:
C4
genes.ec.tsv
genes.tpm.tsv

tag: disease state

tag: age (years)

tag: icu

tag: apacheii

tag: charlson score

tag: crp (mg/l)

tag: ddimer (mg/l_feu)

tag: sofa

tag: associated controlled-vocabulary terms

tag: cell type

value: leukocyte

tag: tissue of origin

value: whole blood

tag: sample type

value: primary cells


title: SCAS 719_B

description:
Ncas.OG.logFC.txt.gz
Ncas.Gene.logFC.txt.gz
RNA-seq for delta Scas719.24 Naumovozyma castellii in Yeast culture (BMW) - log phase (log), replicateB. Used to generate column Ncas_719_Log in Ncas.Gene.logFC.txt.gz
Other columns derived from microarrays (microarray submission in-process).

value: delta Scas719.24

value: B


title: MH2

tag: line

tag: Sex

tag: age

tag: injury status


title: scer_sfp1 ko_A

description:
Scer.OG.logFC.txt.gz
Scer.Gene.logFC.txt.gz
RNA-seq for delta sfp1 Saccharomyces cerevisiae in Yeast culture (BMW) - log phase (log), replicateA. Used to generate column Scer_KO_Log in Scer.Gene.logFC.txt.gz
Other columns derived from microarrays (microarray submission in-process).

tag: genotype

tag: replicate

tag: growth phase

value: log


title: COVID_03_33y_male_NonICU

description:
C3
genes.ec.tsv
genes.tpm.tsv

tag: disease state

tag: age (years)

tag: icu

tag: mechanical ventilation

tag: ventilator-free days

tag: dm

tag: hospital-free days post 45 day followup (days)

tag: ferritin (ng/ml)

tag: procalcitonin (ng/ml)

tag: lactate (mmol/l)

tag: fibrinogen


title: MH1

tag: line

tag: Sex

tag: tissue type


title: COVID_02_63y_male_NonICU

description:
C2
genes.ec.tsv
genes.tpm.tsv

tag: apacheii

tag: charlson score

tag: crp (mg/l)

tag: ddimer (mg/l_feu)

tag: sofa

tag: associated controlled-vocabulary terms

tag: cell type

tag: tissue of origin

tag: sample type


title: COVID_01_39y_male_NonICU

description:
C1
genes.ec.tsv
genes.tpm.tsv

tag: disease state

tag: age (years)

tag: icu

tag: mechanical ventilation

value: yes

tag: ventilator-free days

tag: dm

tag: hospital-free days post 45 day followup (days)


title: scer ha_B

description:
Scer.OG.logFC.txt.gz
Scer.Gene.logFC.txt.gz
RNA-seq for HA tagged Sfp1 Saccharomyces cerevisiae in Yeast culture (BMW) - log phase (log), replicateB. Used to generate column Scer_HA_Log in Scer.Gene.logFC.txt.gz
Other columns derived from microarrays (microarray submission in-process).

tag: genotype

value: HA tagged Sfp1

tag: replicate

tag: growth phase


title: HeNH4

description:
mRNA
rsem_GENE.csv
rsem_ISOFORM.csv
edgeRglm_GENE_CNH-HeNH.csv
edgeRglm_GENE_HeNH-HeH.csv
edgeRglm_ISOFORM_CNH-HeNH.csv
edgeRglm_ISOFORM_HeNH-HeH.csv

tag: line

value: +/Reldel, yw

tag: Sex

tag: age

tag: injury status

tag: tissue type


title: scer ha_C

description:
Scer.OG.logFC.txt.gz
Scer.Gene.logFC.txt.gz
RNA-seq for HA tagged Sfp1 Saccharomyces cerevisiae in Yeast culture (BMW) - log phase (log), replicateC. Used to generate column Scer_HA_Log in Scer.Gene.logFC.txt.gz
Other columns derived from microarrays (microarray submission in-process).

value: C


title: HeNH3


title: COVID_06_:y_male_NonICU

description:
C6
genes.ec.tsv
genes.tpm.tsv

value: no

tag: apacheii

value: unknown

tag: charlson score

tag: ferritin (ng/ml)

tag: crp (mg/l)

tag: ddimer (mg/l_feu)

tag: procalcitonin (ng/ml)

tag: lactate (mmol/l)

tag: fibrinogen

tag: sofa

tag: associated controlled-vocabulary terms

tag: cell type

tag: tissue of origin


title: scer ha_A

description:
Scer.OG.logFC.txt.gz
Scer.Gene.logFC.txt.gz
RNA-seq for HA tagged Sfp1 Saccharomyces cerevisiae in Yeast culture (BMW) - log phase (log), replicateA. Used to generate column Scer_HA_Log in Scer.Gene.logFC.txt.gz
Other columns derived from microarrays (microarray submission in-process).

tag: genotype

tag: replicate

value: A

tag: growth phase


title: si-SERINC2_repeat3

city: Guangzhou

first: Wen-Tao

last: Wang

state: Guangdong

address: No. 135, Xingang Xi Road

department: School of Life Sciences

institute: sun yat sen university

data_processing:
The raw sequencing reads from RNA-seq were aligned to human reference genome (Ensembl GRCh38, hg38) using Bowtie 2.
Raw read counts was calculated by featureCounts software based on Ensembl human gene annotation(version 91), and were further normalized to TPM.
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited text file include TPM values for each Sample …

source_name: Leukemia cell line

growth_protocol: The  Leukemia cell  was established by dissociating patient-derived xenograft and further cultured in IMEM supplemented with 10% fetal bovine serum and 1% NEAA for over 20 culture passages.

extract_protocol:
Total RNA was extracted from bone marrow and cell samples using an Invitrogen™ TRIzol™ Kit (Thermo Fisher, USA) according to the manufacturer’s instructions.
Libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: Leukemia cells were transfected with si-SEELA1, si-SERINC2 or control siRNA and cultured for 48h.

tag: cell line

value: Leukemia cell line MV4;11

tag: transfection


title: HeNH2

tag: line

tag: Sex

value: male

tag: age

value: 1-7 days

tag: injury status

tag: tissue type

value: whole flies


title: COVID_05_49y_male_NonICU

description:
C5
genes.ec.tsv
genes.tpm.tsv

tag: disease state

tag: age (years)

tag: icu

tag: apacheii

tag: charlson score

tag: mechanical ventilation

tag: ventilator-free days

tag: dm

tag: hospital-free days post 45 day followup (days)

tag: ferritin (ng/ml)

tag: crp (mg/l)

tag: ddimer (mg/l_feu)

tag: procalcitonin (ng/ml)

value: leukocyte

tag: sample type


title: si-SERINC2_repeat1

tag: cell line

tag: transfection


title: si-SERINC2_repeat2


title: HeNH1

tag: line

tag: Sex

tag: age

tag: injury status

value: uninjured

tag: tissue type


title: Cultured cortical neurons, D2 (RNA-seq)

data_processing:
Bcl2fastq (v2.17.1.14) software was used for base-calling
To remove technical sequences, including adapters, polymerase chain reaction (PCR) primers, or fragments thereof, and quality of bases lower than 20, pass filter data of fastq format were processed by Cutadapt (V1.9.1) to be high quality clean data.
Reference genome sequences and gene model annotation files of relative species were downloaded from genome website, such as UCSC, NCBI, ENSEMBL. Hisat2 (v2.0.1) was used to index reference genome sequence. Finally, clean data were aligned to reference genome via software Hisat2 (v2.0.1).
In the beginning transcripts in fasta format were converted from known gff annotation file and indexed properly. Then, with the file as a reference gene file, HTSeq (v0.6.1) estimated gene and isoform expression levels from the pair-end clean data.
QC,Cutadapt (V1.9.1); QC assessment, FastQC (V0.10.1); Alignment, HISAT2 (v2.0.1); Gene Expression, HTSEQ (v0.6.1); Assembly, Stringtie (V1.3.3b); Different expression gene analysis, DESeq2(V1.6.3), DESeq (v1.18.0), EdgeR (V3.4.6), Cuffdiff (v2.2.1)
Genome_build: GRCh37.91/hg19
Supplementary_files_format_and_content: xls file includes FPKM values for each sample

extract_protocol:
The total RNA of each sample was extracted from the cells by using TRIzol reagent (Life Technologies, USA)/RNeasy Mini Kit (Qiagen, USA) following the manufacturer’s protocol. Total RNA of each sample was quantified and qualified by Agilent 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA, USA), NanoDrop (Thermo Fisher Scientific Inc.) and 1% agrose gel. 1 μg total RNA with RIN value above 6.5 was used for following library preparation.
Next generation sequencing library preparations were constructed according to the manufacturer’s protocol. The poly(A) mRNA isolation was performed using Poly(A) mRNA Magnetic Isolation Module or rRNA removal Kit. The mRNA fragmentation and priming was performed using First Strand Synthesis Reaction Buffer and Random Primers. First strand cDNA was synthesized using ProtoScript II Reverse Transcriptase and the second-strand cDNA was synthesized using Second Strand Synthesis Enzyme Mix. The purified double- stranded cDNA by beads was then treated with End Prep Enzyme Mix to repair both ends and add a dA- tailing in one reaction, followed by a T-A ligation to add adaptors to both ends. Size selection of Adaptor- ligated DNA was then performed using beads, and fragments of ~420 bp (with the approximate insert size of 300 bp) were recovered. Each sample was then amplified by PCR for 13 cycles using P5 and P7 primers, with both primers carrying sequences which can anneal with flow cell to perform bridge PCR and P7 primer carrying a six-base index allowing for multiplexing. The PCR products were cleaned up using beads, validated using an Qsep100 (Bioptic,Taiwan, China), and quantified by Qubit3.0 Fluorometer (Invitrogen, Carlsbad, CA, USA).

tag: cell type

value: neurons differentiated from 1st passage of neuroprogenitors from fetal frontal cortex

tag: developmental stage

value: 21 week of gestational age

tag: karyotype

tag: treatment

value: 1st passage neuroprogenitors infected with lentivirus carrying DNMT3L-ZsGreen gene and cultured for 4 days

tag: genotype

value: DNMT3L overexpression


title: si-SEELA1_repeat3


title: Cultured cortical neurons, D1 (RNA-seq)


title: HeH4

description:
mRNA
rsem_GENE.csv
rsem_ISOFORM.csv
edgeRglm_GENE_CH-HeH.csv
edgeRglm_GENE_HeNH-HeH.csv
edgeRglm_ISOFORM_CH-HeH.csv
edgeRglm_ISOFORM_HeNH-HeH.csv

value: injured


title: Cultured cortical neurons, D3 (RNA-seq)


title: si-SEELA1_repeat1


title: Cultured cortical neurons, Z3 (RNA-seq)

value: 1st passage neuroprogenitors infected with lentivirus carrying ZsGreen gene and cultured for 4 days

value: CON


title: scer sfp1 ko_B

description:
Scer.OG.logFC.txt.gz
Scer.Gene.logFC.txt.gz
RNA-seq for delta sfp1 Saccharomyces cerevisiae in Yeast culture (BMW) - log phase (log), replicateB. Used to generate column Scer_KO_Log in Scer.Gene.logFC.txt.gz
Other columns derived from microarrays (microarray submission in-process).

value: delta sfp1

tag: replicate

value: B

tag: growth phase

value: log


title: HeH2

value: +/Reldel, yw


title: si-SEELA1_repeat2

value: Leukemia cell line MV4;11


title: HeH1

value: male


title: si-NC_repeat3

value: si-NC


title: Cultured cortical neurons, Z1 (RNA-seq)


title: Cultured cortical neurons, Z2 (RNA-seq)


title: si-NC_repeat2


title: CNH4

description:
mRNA
rsem_GENE.csv
rsem_ISOFORM.csv
edgeRglm_GENE_CNH-HeNH.csv
edgeRglm_GENE_CNH-CH.csv
edgeRglm_GENE_CNH-MNH.csv
edgeRglm_ISOFORM_CNH-HeNH.csv
edgeRglm_ISOFORM_CNH-CH.csv
edgeRglm_ISOFORM_CNH-MNH.csv

value: wild-type, yw

value: 1-7 days

value: whole flies


title: si-NC_repeat1


title: lactis sfp1 k o_B

description:
Klac.OG.logFC.txt.gz
Klac.Gene.logFC.txt.gz
RNA-seq for delta sfp1 Kluyveromyces lactis in Yeast culture (BMW) - log phase (log), replicateB. Used to generate column Klac_delta_Log in Klac.Gene.logFC.txt.gz
Other columns derived from microarrays (microarray submission in-process).


title: CNH3

value: uninjured


title: HeH3


title: CNH2


title: CNH1


title: lactis sfp1 k o_A

description:
Klac.OG.logFC.txt.gz
Klac.Gene.logFC.txt.gz
RNA-seq for delta sfp1 Kluyveromyces lactis in Yeast culture (BMW) - log phase (log), replicateA. Used to generate column Klac_delta_Log in Klac.Gene.logFC.txt.gz
Other columns derived from microarrays (microarray submission in-process).

value: A


title: klac wt_C

description:
Klac.OG.logFC.txt.gz
Klac.Gene.logFC.txt.gz
RNA-seq for wild type Kluyveromyces lactis in Yeast culture (BMW) - log phase (log), replicateC. Used to generate column Klac_delta_Log in Klac.Gene.logFC.txt.gz
Other columns derived from microarrays (microarray submission in-process).

value: wild type

value: C


title: Runx1_MMV2

type: protein

city: Durham

first: Raluca

last: Gordan

state: NC

address: 101 Science Dr, CIEMAS 2179

department: Center for Genomic and Computational Biology

institute: Duke University

hyb_protocol: Single-stranded DNA libraries containing transcription factor binding site sequences and all possible single base variants were commercially synthesized on microarray chips (Agilent). Double-stranded DNA was generated on the chip by hybridization with the wild-type reverse complement oligonucleotides in solution (variant complements were absent from the hybridization solution). For each wild-type sequence, the solution contained ~2.5 μM (large excess) unlabeled HPLC-purified oligonucleotides and ~0.25 μM FAM/Cy3-labelled HPLC-purified oligonucleotides (Integrated DNA Technologies). The reaction buffer mixture for the hybridization step was 100 μl 10x reaction buffer (260 mM Tris-HCl, pH 9.5, 65 mM MgCl2) in a total volume of 1000 μl, similarly to 20. The chip was incubated with reaction mixture in a hybridization oven using a pre-warmed stainless-steel chamber and gasket cover slip. After a 5-hour incubation (85 °C for 10 min, 75 °C for 10 min, 65 °C for 60 min, 60 °C for 120 min, and 55 °C for 100 min), the hybridization chamber was disassembled in a glass staining dish in 500 ml phosphate buffered saline (PBS) / 0.01% Triton X-100 at 37°C. The chip was transferred to a second staining dish, washed for 10 min in PBS / 0.01% Triton X-100 at 37°C, washed once more for 3 min in PBS at room temperature, similarly to 20. The fluorescent signal (Cy3/FAM) of hybridized oligonucleotides was measured using a GenePix 4400A microarray scanner to confirm that the hybridization was successful and reproducible, and that no significant cross-hybridization occurred. Protein binding and antibody steps were performed similarly to protein-binding microarray (PBM) assays (Berger et al, Nature Biotechnology 2006). The fluorescent signal of bound transcription factor for each DNA spot was measured using a GenePix 4400A microarray scanner.

scan_protocol: Protein-bound arrays were scanned to detect Alexa-488-conjugated or Alexa-647-conjugated (detected at 635nm wavelength) antibody using at least three different laser power settings to best capture a broad range of signal intensities and ensure signal intensities below saturation for all spots of interest. Microarray TIF images were analyzed using GenePix Pro version 6.0 software (Molecular Devices).

data_processing: To correct for any possible non-uniformities in protein binding, we adjusted the fluorescent signals according to their positions on the microarray. We calculated the median normalized intensity of the 15 x 15 block centered on each spot and divided the spot's signal by the ratio of the median within the block to the median over the entire chamber. For each unique sequence represented on the array, we then calculated the median over replicate spots.

label: Alexa 647

molecule: protein

organism: synthetic construct

source_name: Human Runx1

label_protocol: Cell growth, protein extraction, and protein labelling protocols are described in detail in the manucript, for each tested protein.

tag: transcription factor

tag: protein concentration


title: Stat3_MMV4

source_name: Human Stat3

growth_protocol: Cell growth, protein extraction, and protein labelling protocols are described in detail in the manucript, for each tested protein.


title: RelA_MMV4

source_name: Human RelA

extract_protocol: Cell growth, protein extraction, and protein labelling protocols are described in detail in the manucript, for each tested protein.

value: RelA


title: TBP_MMV4

source_name: Human TBP

value: TBP


title: CTCF_MMV2

source_name: Human CTCF

value: CTCF


title: CH3

description:
mRNA
rsem_GENE.csv
rsem_ISOFORM.csv
edgeRglm_GENE_CH-HeH.csv
edgeRglm_GENE_CNH-CH.csv
edgeRglm_GENE_CH-MH.csv
edgeRglm_ISOFORM_CH-HeH.csv
edgeRglm_ISOFORM_CNH-CH.csv
edgeRglm_ISOFORM_CH-MH.csv

value: injured


title: CH4


title: klac wt_B

description:
Klac.OG.logFC.txt.gz
Klac.Gene.logFC.txt.gz
RNA-seq for wild type Kluyveromyces lactis in Yeast culture (BMW) - log phase (log), replicateB. Used to generate column Klac_delta_Log in Klac.Gene.logFC.txt.gz
Other columns derived from microarrays (microarray submission in-process).

value: B


title: lactis sfp1 k o_C

description:
Klac.OG.logFC.txt.gz
Klac.Gene.logFC.txt.gz
RNA-seq for delta sfp1 Kluyveromyces lactis in Yeast culture (BMW) - log phase (log), replicateC. Used to generate column Klac_delta_Log in Klac.Gene.logFC.txt.gz
Other columns derived from microarrays (microarray submission in-process).

value: delta sfp1

value: log


title: CH2


title: klac wt_A

description:
Klac.OG.logFC.txt.gz
Klac.Gene.logFC.txt.gz
RNA-seq for wild type Kluyveromyces lactis in Yeast culture (BMW) - log phase (log), replicateA. Used to generate column Klac_delta_Log in Klac.Gene.logFC.txt.gz
Other columns derived from microarrays (microarray submission in-process).


title: CH1


title: Egr1_MMV2

source_name: Human Egr1


title: E2f1_MMV2

source_name: Human E2f1


title: Crem_MMV3

source_name: Human Crem

value: Crem


title: p53_MMV3

source_name: Human p53


title: Creb1_MMV2

source_name: Human Creb1


title: Elk1_MMV3

source_name: Human Elk1


title: Myc_MMV2

source_name: Human Myc

value: Myc


title: Ets1_MMV2

source_name: Human Ets1


title: Six6_MMV3

source_name: Human Six6


title: GR_MMV5

source_name: Human Glucocorticoid receptor

value: GR


title: Ap2a_MMV3

source_name: Human Ap2a


title: NetrinG1 KO-3-Rep1

status: Public on Aug 28 2020

city: philadelphia

first: suraj

last: peri

state: PA

address: 333 cottman ave

department: biostatistics and bioinformatics

institute: Fox chase cancer center

data_processing:
Single end reads at 50bp were generated by using Hiseq rapid SR cluster kit V2 (Illumina, Cat# GD-402-4002) and HiSeq rapid SBS kit v2 50 cycles (Illumina, Cat# FC-402-4022). Fastq files were obtained at Illumina base space (https://basespace.illumina.com) and aligned to Hg38 using Tophat2 and resulting BAM files were used to estimate the gene counts using HT-Seq.
Genome_build: Hg38
Supplementary_files_format_and_content: Counts file

source_name: PDAC stroma

growth_protocol: Control and NetrinG1 KO cancer associated fibroblasts were grown on gelatin coated plates in the presence DMEM containing 15% FBS, 4 mM glutamine, 1% penicillin/streptomycin, and 50 µg/mL L-ascorbic acid for 5-7 days, which generates a 3D culturing environment. The total RNA of these cells was extracted and subjected to RNAseq.

extract_protocol:
Cells were lysed in Trizol reagent and RNA was subsequently isolated.
1000ng total RNAs from each sample were used to make library according to the product guide of Truseq stranded mRNA library kit (Illumina, Cat# 20020595). In short, mRNAs were enriched twice via poly-T based RNA purification beads, and subjected to fragmentation at 94 degree for 8 minutes via divalent cation method. The 1st strand cDNA was synthesized by Superscript II reverse transcriptase (ThermoFisher, Cat# 18064014) and random primers at 42 degree for 15 minutes, followed by 2nd strand synthesis at 16 degree for 1hour.  During second strand synthesis, the dUTP was used to replace dTTP, thereby the second strand was quenched during amplification. A single ‘A’ nucleotide is added to the 3’ ends of the blunt fragments at 37 degree for 30 minutes.  Adapters with illuminaP5, P7 sequences as well as indices were ligated to the cDNA fragment at 30 degree for 10 minutes.  After SPRIselect beads (Beckman Coulter, Cat# B23318) purification, a 15-cycle PCR reaction was used to enrich the fragments. PCR was set at 98 degree for 10 sec, 60 degree for 30 sec and extended at 72 degree for 30 sec.  Libraries were again purified using SPRIselect beads, had a quality check on Agilent 2100 bioanalyzer (serial # DE34903146) using Agilent high sensitivity DNA kit (Cat# 5067-4626), and quantified with Qubit 3.0 flurometer (ThermoFisher Scientific, Cat#Q33216) using Qubit 1x dsDNA HS assay kit (Cat#Q33230). Sample libraries were subsequently pooled and loaded to the Hiseq 2500 (Illumina, serial number SN930).

value: Netrin-G1 Knockout

tag: tissue

value: Pancreas


title: NetrinG1 KO-1-Rep1


title: NetrinG1 KO-3-Rep2


title: Control Rep2

value: eGFP KO control (Wild-type)


title: NetrinG1 KO-1-Rep2


title: Control Rep1


title: NetrinG1 KO-2-Rep2


title: NetrinG1 KO-2-Rep1


title: Expt_HPC_AKP_Expt1

city: Hyderabad

first: Anil

middle: Kumar

last: Pasupulati

state: Telangana

address: CRRAO road Gachibowli

department: Department of Biochemistry

country: India

institute: University of Hyderabad

data_processing:
Raw data fastq files inspected into quality check using fastQC tool, data trimming and smoothening was performed with trimmomatic for all replicates.
trimmed reads were used to align with human reference genome assembly hg19 using tophat2 software.
The gene expression levels were quantified using cufflinks software and derived FPKM values for genome.
Read counts were calculated for each gene using HTSeq tool and derived differentially expressed genes.
To derive the pathways and functional annotations for differentially expressed genes between hormone treated and control podocytes we used DAVID KEGG database.
Genome_build: hg19
Supplementary_files_format_and_content: processed data files are in xlsx format

growth_protocol: Human podocytes were cultured in 10% FBS containing RPMI 1640 medium in growth permissive conditions at 33 degrees and 5% CO2. After achieving 80% confluency, then cells were moved to non growth permissive conditions at 37 degrees for deifferentiation. Cells were maintained for  six days in 37 degrees for diffrentiation.

extract_protocol:
Cells were rinsed briefly with ice cold PBS and total RNA was extracted using trizol method. Quality of RNA was determined using Agilent Bio-anlyzer
1µg of total RNA was used as template to make cDNA and libraries were constructed according to the manufacturers protocol.

treatment_protocol: Differentiated podocytes were starved for 12 hours in 0% FBS RPMI medium and treated with human growth hormone for 30 minutes.

tag: cell line

value: human podocyte cell line (HPC)

value: Differentiated podocytes

value: human growth hormone for 30 min


title: Expt_HPC_AKP_Expt2


title: HPC_Control_AKP_C1


title: Patient 4095 TIL scRNAseq: 10-72

city: Bethesda

first: Li

last: Jia

state: MD

address: 10 Clinic center

institute: NCI/NIH

description: single-cell RNA-Seq

data_processing:
Fastq files were generated by Illumina HiSeq2500 sequencer
Genome_build: hg19

source_name: KRAS-10mer tetramer(+) T cells from TILs

extract_protocol:
TILs were thawed and cultured overnight. TILs were then stained by tetramers and sorted by FACS.
RNA-seq libraries were prepared for sequencing using the single-cell mRNA-Seq protocol provided by Fluidigm. Clontech SMART-Seq v4 kit for Fluidigm C1 and Illumina Nextera XT DNA Library Preparation kit were used.

tag: patient id

tag: diagnosis

value: metastatic colorectal cancer

value: Tumor infiltrating lymphocytes (TILs)

tag: genotype/variation

value: KRAS-10mer tetramer-enriched T cells

tag: description

value: transcriptome on gene expression


title: Control_HPC_AKP_C2


title: Patient 4095 TIL scRNAseq: 10-70

description: single-cell RNA-Seq


title: Patient 4095 TIL scRNAseq: 10-69

description: single-cell RNA-Seq


title: Patient 4095 TIL scRNAseq: 10-68

description: single-cell RNA-Seq


title: Patient 4095 TIL scRNAseq: 10-71

description: single-cell RNA-Seq


title: Patient 4095 TIL scRNAseq: 10-67

description: single-cell RNA-Seq


title: Patient 4095 TIL scRNAseq: 10-66

description: single-cell RNA-Seq


title: Patient 4095 TIL scRNAseq: 10-65

description: single-cell RNA-Seq


title: Patient 4095 TIL scRNAseq: 10-64

description: single-cell RNA-Seq


title: Patient 4095 TIL scRNAseq: 10-63

description: single-cell RNA-Seq


title: Patient 4095 TIL scRNAseq: 10-62

description: single-cell RNA-Seq


title: Patient 4095 TIL scRNAseq: 10-61

description: single-cell RNA-Seq


title: Patient 4095 TIL scRNAseq: 10-59

description: single-cell RNA-Seq


title: Patient 4095 TIL scRNAseq: 10-56

description: single-cell RNA-Seq


title: Patient 4095 TIL scRNAseq: 10-57

description: single-cell RNA-Seq


title: Patient 4095 TIL scRNAseq: 10-55

description: single-cell RNA-Seq


title: Patient 4095 TIL scRNAseq: 10-60

description: single-cell RNA-Seq


title: Patient 4095 TIL scRNAseq: 10-58

description: single-cell RNA-Seq


title: Patient 4095 TIL scRNAseq: 10-52

description: single-cell RNA-Seq


title: Patient 4095 TIL scRNAseq: 10-53

description: single-cell RNA-Seq


title: Patient 4095 TIL scRNAseq: 10-54

description: single-cell RNA-Seq


title: Patient 4095 TIL scRNAseq: 10-51

description: single-cell RNA-Seq


title: Patient 4095 TIL scRNAseq: 10-49

description: single-cell RNA-Seq


title: Patient 4095 TIL scRNAseq: 10-45

description: single-cell RNA-Seq


title: Patient 4095 TIL scRNAseq: 10-50

description: single-cell RNA-Seq


title: Patient 4095 TIL scRNAseq: 10-46

description: single-cell RNA-Seq


title: Patient 4095 TIL scRNAseq: 10-48

description: single-cell RNA-Seq


title: Patient 4095 TIL scRNAseq: 10-42

description: single-cell RNA-Seq


title: Patient 4095 TIL scRNAseq: 10-41

description: single-cell RNA-Seq


title: Patient 4095 TIL scRNAseq: 10-47

description: single-cell RNA-Seq


title: Patient 4095 TIL scRNAseq: 10-40

description: single-cell RNA-Seq


title: Patient 4095 TIL scRNAseq: 10-44

description: single-cell RNA-Seq


title: Patient 4095 TIL scRNAseq: 10-39

description: single-cell RNA-Seq


title: Patient 4095 TIL scRNAseq: 10-43

description: single-cell RNA-Seq


title: Patient 4095 TIL scRNAseq: 10-37

description: single-cell RNA-Seq


title: Patient 4095 TIL scRNAseq: 10-38

description: single-cell RNA-Seq


title: Patient 4095 TIL scRNAseq: 10-36

description: single-cell RNA-Seq


title: Patient 4095 TIL scRNAseq: 10-35

description: single-cell RNA-Seq


title: Patient 4095 TIL scRNAseq: 10-34

description: single-cell RNA-Seq


title: Patient 4095 TIL scRNAseq: 10-33

description: single-cell RNA-Seq


title: Patient 4095 TIL scRNAseq: 10-32

description: single-cell RNA-Seq


title: Atf1_MMV3

source_name: Human Atf1


title: Patient 4095 TIL scRNAseq: 10-30

description: single-cell RNA-Seq


title: Patient 4095 TIL scRNAseq: 10-27

description: single-cell RNA-Seq


title: Patient 4095 TIL scRNAseq: 10-29

description: single-cell RNA-Seq


title: Patient 4095 TIL scRNAseq: 10-31

description: single-cell RNA-Seq


title: Patient 4095 TIL scRNAseq: 10-19

description: single-cell RNA-Seq


title: Patient 4095 TIL scRNAseq: 10-20

description: single-cell RNA-Seq


title: Patient 4095 TIL scRNAseq: 10-28

description: single-cell RNA-Seq


title: Patient 4095 TIL scRNAseq: 10-26

description: single-cell RNA-Seq


title: Patient 4095 TIL scRNAseq: 10-18

description: single-cell RNA-Seq


title: Patient 4095 TIL scRNAseq: 10-23

description: single-cell RNA-Seq


title: Patient 4095 TIL scRNAseq: 10-24

description: single-cell RNA-Seq


title: Patient 4095 TIL scRNAseq: 10-22

description: single-cell RNA-Seq


title: Patient 4095 TIL scRNAseq: 10-25

description: single-cell RNA-Seq


title: Patient 4095 TIL scRNAseq: 10-21

description: single-cell RNA-Seq


title: Patient 4095 TIL scRNAseq: 10-16

description: single-cell RNA-Seq


title: Patient 4095 TIL scRNAseq: 10-17

description: single-cell RNA-Seq


title: Patient 4095 TIL scRNAseq: 10-14

description: single-cell RNA-Seq


title: Patient 4095 TIL scRNAseq: 10-12

description: single-cell RNA-Seq


title: Patient 4095 TIL scRNAseq: 10-15

description: single-cell RNA-Seq


title: Patient 4095 TIL scRNAseq: 10-13

description: single-cell RNA-Seq


title: Patient 4095 TIL scRNAseq: 10-11

description: single-cell RNA-Seq


title: Patient 4095 TIL scRNAseq: 10-10

description: single-cell RNA-Seq


title: Patient 4095 TIL scRNAseq: 10-6

description: single-cell RNA-Seq


title: Patient 4095 TIL scRNAseq: 10-7

description: single-cell RNA-Seq


title: Patient 4095 TIL scRNAseq: 10-9

description: single-cell RNA-Seq


title: Patient 4095 TIL scRNAseq: 10-4

description: single-cell RNA-Seq


title: Patient 4095 TIL scRNAseq: 10-3

description: single-cell RNA-Seq


title: Patient 4095 TIL scRNAseq: 10-2

description: single-cell RNA-Seq


title: Patient 4095 TIL scRNAseq: 10-1

description: single-cell RNA-Seq


title: Patient 4095 TIL scRNAseq: 9.2-42

description: single-cell RNA-Seq

source_name: KRAS-9mer tetramer(+) T cells from TILs

value: KRAS-9mer tetramer-enriched T cells


title: Patient 4095 TIL scRNAseq: 9.2-41

description: single-cell RNA-Seq


title: Patient 4095 TIL scRNAseq: 9.2-40

description: single-cell RNA-Seq


title: Patient 4095 TIL scRNAseq: 9.2-34

description: single-cell RNA-Seq


title: Patient 4095 TIL scRNAseq: 9.2-39

description: single-cell RNA-Seq


title: Patient 4095 TIL scRNAseq: 9.2-33

description: single-cell RNA-Seq


title: Patient 4095 TIL scRNAseq: 9.2-31

description: single-cell RNA-Seq


title: Patient 4095 TIL scRNAseq: 9.2-36

description: single-cell RNA-Seq


title: Patient 4095 TIL scRNAseq: 9.2-37

description: single-cell RNA-Seq


title: Patient 4095 TIL scRNAseq: 9.2-35

description: single-cell RNA-Seq


title: Patient 4095 TIL scRNAseq: 9.2-38

description: single-cell RNA-Seq


title: Patient 4095 TIL scRNAseq: 9.2-29

description: single-cell RNA-Seq


title: Patient 4095 TIL scRNAseq: 9.2-30

description: single-cell RNA-Seq


title: Patient 4095 TIL scRNAseq: 9.2-28

description: single-cell RNA-Seq


title: Patient 4095 TIL scRNAseq: 9.2-27

description: single-cell RNA-Seq


title: Patient 4095 TIL scRNAseq: 9.2-26

description: single-cell RNA-Seq


title: Patient 4095 TIL scRNAseq: 10-8

description: single-cell RNA-Seq


title: Patient 4095 TIL scRNAseq: 9.2-24

description: single-cell RNA-Seq


title: Patient 4095 TIL scRNAseq: 9.2-23

description: single-cell RNA-Seq


title: Patient 4095 TIL scRNAseq: 9.2-25

description: single-cell RNA-Seq


title: Patient 4095 TIL scRNAseq: 9.2-22

description: single-cell RNA-Seq


title: Patient 4095 TIL scRNAseq: 10-5

description: single-cell RNA-Seq


title: Patient 4095 TIL scRNAseq: 9.2-19

description: single-cell RNA-Seq


title: Patient 4095 TIL scRNAseq: 9.2-18

description: single-cell RNA-Seq


title: Patient 4095 TIL scRNAseq: 9.2-20

description: single-cell RNA-Seq


title: Patient 4095 TIL scRNAseq: 9.2-21

description: single-cell RNA-Seq


title: Patient 4095 TIL scRNAseq: 9.2-16

description: single-cell RNA-Seq


title: Patient 4095 TIL scRNAseq: 9.2-15

description: single-cell RNA-Seq


title: Patient 4095 TIL scRNAseq: 9.2-32

description: single-cell RNA-Seq


title: Patient 4095 TIL scRNAseq: 9.2-14

description: single-cell RNA-Seq


title: Patient 4095 TIL scRNAseq: 9.2-12

description: single-cell RNA-Seq


title: Patient 4095 TIL scRNAseq: 9.2-10

description: single-cell RNA-Seq


title: Patient 4095 TIL scRNAseq: 9.2-9

description: single-cell RNA-Seq


title: Patient 4095 TIL scRNAseq: 9.2-5

description: single-cell RNA-Seq


title: Patient 4095 TIL scRNAseq: 9.2-2

description: single-cell RNA-Seq


title: Patient 4095 TIL scRNAseq: 9.2-1

description: single-cell RNA-Seq


title: Patient 4095 TIL scRNAseq: 9.2-6

description: single-cell RNA-Seq


title: Patient 4095 TIL scRNAseq: 9.1-123

description: single-cell RNA-Seq


title: Patient 4095 TIL scRNAseq: 9.1-122

description: single-cell RNA-Seq


title: Patient 4095 TIL scRNAseq: 9.1-120

description: single-cell RNA-Seq


title: Patient 4095 TIL scRNAseq: 9.2-3

description: single-cell RNA-Seq


title: Patient 4095 TIL scRNAseq: 9.1-121

description: single-cell RNA-Seq


title: Patient 4095 TIL scRNAseq: 9.2-7

description: single-cell RNA-Seq


title: Patient 4095 TIL scRNAseq: 9.1-119

description: single-cell RNA-Seq


title: Patient 4095 TIL scRNAseq: 9.1-116

description: single-cell RNA-Seq


title: Patient 4095 TIL scRNAseq: 9.1-115

description: single-cell RNA-Seq


title: Patient 4095 TIL scRNAseq: 9.2-17

description: single-cell RNA-Seq


title: Patient 4095 TIL scRNAseq: 9.1-112

description: single-cell RNA-Seq


title: Patient 4095 TIL scRNAseq: 9.1-113

description: single-cell RNA-Seq


title: Patient 4095 TIL scRNAseq: 9.1-114

description: single-cell RNA-Seq


title: Patient 4095 TIL scRNAseq: 9.2-13

description: single-cell RNA-Seq


title: Patient 4095 TIL scRNAseq: 9.1-111

description: single-cell RNA-Seq


title: Patient 4095 TIL scRNAseq: 9.1-110

description: single-cell RNA-Seq


title: Patient 4095 TIL scRNAseq: 9.1-109

description: single-cell RNA-Seq


title: Patient 4095 TIL scRNAseq: 9.2-11

description: single-cell RNA-Seq


title: Patient 4095 TIL scRNAseq: 9.2-8

description: single-cell RNA-Seq


title: Patient 4095 TIL scRNAseq: 9.2-4

description: single-cell RNA-Seq


title: Patient 4095 TIL scRNAseq: 9.1-108

description: single-cell RNA-Seq


title: Patient 4095 TIL scRNAseq: 9.1-107

description: single-cell RNA-Seq


title: Patient 4095 TIL scRNAseq: 9.1-102

description: single-cell RNA-Seq


title: Patient 4095 TIL scRNAseq: 9.1-105

description: single-cell RNA-Seq


title: Patient 4095 TIL scRNAseq: 9.1-101

description: single-cell RNA-Seq


title: Patient 4095 TIL scRNAseq: 9.1-104

description: single-cell RNA-Seq


title: Patient 4095 TIL scRNAseq: 9.1-106

description: single-cell RNA-Seq


title: Patient 4095 TIL scRNAseq: 9.1-117

description: single-cell RNA-Seq


title: Patient 4095 TIL scRNAseq: 9.1-98

description: single-cell RNA-Seq


title: Patient 4095 TIL scRNAseq: 9.1-96

description: single-cell RNA-Seq


title: Patient 4095 TIL scRNAseq: 9.1-95

description: single-cell RNA-Seq


title: Patient 4095 TIL scRNAseq: 9.1-99

description: single-cell RNA-Seq


title: Patient 4095 TIL scRNAseq: 9.1-97

description: single-cell RNA-Seq


title: Patient 4095 TIL scRNAseq: 9.1-93

description: single-cell RNA-Seq


title: Patient 4095 TIL scRNAseq: 9.1-94

description: single-cell RNA-Seq


title: Patient 4095 TIL scRNAseq: 9.1-91

description: single-cell RNA-Seq


title: Patient 4095 TIL scRNAseq: 9.1-103

description: single-cell RNA-Seq


title: Patient 4095 TIL scRNAseq: 9.1-90

description: single-cell RNA-Seq


title: Patient 4095 TIL scRNAseq: 9.1-89

description: single-cell RNA-Seq


title: Patient 4095 TIL scRNAseq: 9.1-118

description: single-cell RNA-Seq


title: Patient 4095 TIL scRNAseq: 9.1-87

description: single-cell RNA-Seq


title: Patient 4095 TIL scRNAseq: 9.1-86

description: single-cell RNA-Seq


title: Patient 4095 TIL scRNAseq: 9.1-83

description: single-cell RNA-Seq


title: Patient 4095 TIL scRNAseq: 9.1-84

description: single-cell RNA-Seq


title: Patient 4095 TIL scRNAseq: 9.1-82

description: single-cell RNA-Seq


title: Patient 4095 TIL scRNAseq: 9.1-100

description: single-cell RNA-Seq


title: Patient 4095 TIL scRNAseq: 9.1-76

description: single-cell RNA-Seq


title: Patient 4095 TIL scRNAseq: 9.1-77

description: single-cell RNA-Seq


title: Patient 4095 TIL scRNAseq: 9.1-74

description: single-cell RNA-Seq


title: Patient 4095 TIL scRNAseq: 9.1-81

description: single-cell RNA-Seq


title: Patient 4095 TIL scRNAseq: 9.1-79

description: single-cell RNA-Seq


title: Patient 4095 TIL scRNAseq: 9.1-78

description: single-cell RNA-Seq


title: Patient 4095 TIL scRNAseq: 9.1-92

description: single-cell RNA-Seq


title: Patient 4095 TIL scRNAseq: 9.1-72

description: single-cell RNA-Seq


title: Patient 4095 TIL scRNAseq: 9.1-69

description: single-cell RNA-Seq


title: Patient 4095 TIL scRNAseq: 9.1-71

description: single-cell RNA-Seq


title: Patient 4095 TIL scRNAseq: 9.1-70

description: single-cell RNA-Seq


title: Patient 4095 TIL scRNAseq: 9.1-68

description: single-cell RNA-Seq


title: Patient 4095 TIL scRNAseq: 9.1-67

description: single-cell RNA-Seq


title: Patient 4095 TIL scRNAseq: 9.1-65

description: single-cell RNA-Seq


title: Patient 4095 TIL scRNAseq: 9.1-75

description: single-cell RNA-Seq


title: Patient 4095 TIL scRNAseq: 9.1-80

description: single-cell RNA-Seq


title: Patient 4095 TIL scRNAseq: 9.1-66

description: single-cell RNA-Seq


title: Patient 4095 TIL scRNAseq: 9.1-64

description: single-cell RNA-Seq


title: Patient 4095 TIL scRNAseq: 9.1-60

description: single-cell RNA-Seq


title: Patient 4095 TIL scRNAseq: 9.1-62

description: single-cell RNA-Seq


title: Patient 4095 TIL scRNAseq: 9.1-73

description: single-cell RNA-Seq


title: Patient 4095 TIL scRNAseq: 9.1-88

description: single-cell RNA-Seq


title: Patient 4095 TIL scRNAseq: 9.1-59

description: single-cell RNA-Seq


title: Patient 4095 TIL scRNAseq: 9.1-58

description: single-cell RNA-Seq


title: Patient 4095 TIL scRNAseq: 9.1-57

description: single-cell RNA-Seq


title: Patient 4095 TIL scRNAseq: 9.1-56

description: single-cell RNA-Seq


title: Patient 4095 TIL scRNAseq: 9.1-85

description: single-cell RNA-Seq


title: Patient 4095 TIL scRNAseq: 9.1-55

description: single-cell RNA-Seq


title: Patient 4095 TIL scRNAseq: 9.1-54

description: single-cell RNA-Seq


title: Patient 4095 TIL scRNAseq: 9.1-51

description: single-cell RNA-Seq


title: Patient 4095 TIL scRNAseq: 9.1-48

description: single-cell RNA-Seq


title: Patient 4095 TIL scRNAseq: 9.1-63

description: single-cell RNA-Seq


title: Patient 4095 TIL scRNAseq: 9.1-46

description: single-cell RNA-Seq


title: Patient 4095 TIL scRNAseq: 9.1-44

description: single-cell RNA-Seq


title: Patient 4095 TIL scRNAseq: 9.1-45

description: single-cell RNA-Seq


title: Patient 4095 TIL scRNAseq: 9.1-61

description: single-cell RNA-Seq


title: Patient 4095 TIL scRNAseq: 9.1-43

description: single-cell RNA-Seq


title: Patient 4095 TIL scRNAseq: 9.1-42

description: single-cell RNA-Seq


title: Patient 4095 TIL scRNAseq: 9.1-39

description: single-cell RNA-Seq


title: Patient 4095 TIL scRNAseq: 9.1-41

description: single-cell RNA-Seq


title: Patient 4095 TIL scRNAseq: 9.1-37

description: single-cell RNA-Seq


title: Patient 4095 TIL scRNAseq: 9.1-38

description: single-cell RNA-Seq


title: Patient 4095 TIL scRNAseq: 9.1-36

description: single-cell RNA-Seq


title: Patient 4095 TIL scRNAseq: 9.1-34

description: single-cell RNA-Seq


title: Patient 4095 TIL scRNAseq: 9.1-33

description: single-cell RNA-Seq


title: Patient 4095 TIL scRNAseq: 9.1-32

description: single-cell RNA-Seq


title: Patient 4095 TIL scRNAseq: 9.1-28

description: single-cell RNA-Seq


title: Patient 4095 TIL scRNAseq: 9.1-29

description: single-cell RNA-Seq


title: Patient 4095 TIL scRNAseq: 9.1-30

description: single-cell RNA-Seq


title: Patient 4095 TIL scRNAseq: 9.1-27

description: single-cell RNA-Seq


title: Patient 4095 TIL scRNAseq: 9.1-31

description: single-cell RNA-Seq


title: Patient 4095 TIL scRNAseq: 9.1-53

description: single-cell RNA-Seq


title: Patient 4095 TIL scRNAseq: 9.1-50

description: single-cell RNA-Seq


title: Patient 4095 TIL scRNAseq: 9.1-52

description: single-cell RNA-Seq


title: Patient 4095 TIL scRNAseq: 9.1-26

description: single-cell RNA-Seq


title: Patient 4095 TIL scRNAseq: 9.1-47

description: single-cell RNA-Seq


title: Patient 4095 TIL scRNAseq: 9.1-24

description: single-cell RNA-Seq


title: Patient 4095 TIL scRNAseq: 9.1-25

description: single-cell RNA-Seq


title: Patient 4095 TIL scRNAseq: 9.1-49

description: single-cell RNA-Seq


title: Patient 4095 TIL scRNAseq: 9.1-23

description: single-cell RNA-Seq


title: Patient 4095 TIL scRNAseq: 9.1-40

description: single-cell RNA-Seq


title: Patient 4095 TIL scRNAseq: 9.1-20

description: single-cell RNA-Seq


title: Patient 4095 TIL scRNAseq: 9.1-35

description: single-cell RNA-Seq


title: Patient 4095 TIL scRNAseq: 9.1-17

description: single-cell RNA-Seq


title: Patient 4095 TIL scRNAseq: 9.1-18

description: single-cell RNA-Seq


title: Patient 4095 TIL scRNAseq: 9.1-15

description: single-cell RNA-Seq


title: Patient 4095 TIL scRNAseq: 9.1-14

description: single-cell RNA-Seq


title: Patient 4095 TIL scRNAseq: 9.1-19

description: single-cell RNA-Seq


title: Patient 4095 TIL scRNAseq: 9.1-10

description: single-cell RNA-Seq


title: Patient 4095 TIL scRNAseq: 9.1-12

description: single-cell RNA-Seq


title: Patient 4095 TIL scRNAseq: 9.1-11

description: single-cell RNA-Seq


title: Patient 4095 TIL scRNAseq: 9.1-7

description: single-cell RNA-Seq


title: Patient 4095 TIL scRNAseq: 9.1-4

description: single-cell RNA-Seq


title: Patient 4095 TIL scRNAseq: 9.1-6

description: single-cell RNA-Seq


title: Patient 4095 TIL scRNAseq: 9.1-3

description: single-cell RNA-Seq


title: Patient 4095 TIL scRNAseq: 9.1-5

description: single-cell RNA-Seq


title: Patient 4095 TIL scRNAseq: 9.1-8

description: single-cell RNA-Seq


title: Patient 4095 TIL scRNAseq: 9.1-1

description: single-cell RNA-Seq


title: Patient 4095 TIL scRNAseq: 9.1-9

description: single-cell RNA-Seq


title: Patient 4095 TIL scRNAseq: 9.1-22

description: single-cell RNA-Seq


title: Patient 4095 TIL scRNAseq: 9.1-21

description: single-cell RNA-Seq


title: Patient 4095 TIL scRNAseq: 9.1-2

description: single-cell RNA-Seq


title: Sci_03

city: ChangChun

first: Yuxin

last: Chang

address: 218 Ziqiang Street

institute: Jilin university

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm8 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: mm8
Supplementary_files_format_and_content: the junction read number, logCPM of each sample.

organism: Rattus norvegicus

source_name: SCI_Spinal cord

extract_protocol:
spinal cord were removed, flash frozen on dry ice, and RNA was harvested using Trizol reagent. 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 librarie were prepared for sequencing using standard llumina protcols.

tag: strain background

value: Wistar

value: spinal cord injury (SCI) rat

tag: age

value: 8 weeks

value: spinal cord


title: Sham_01

source_name: sham_Spinal cord

value: sham control


title: Sham_03


title: Sci_02


title: Sham_02


title: Sci_01


title: Patient 4095 TIL scRNAseq: 9.1-16

description: single-cell RNA-Seq


title: P9.t

type: RNA

hyb_protocol: according to standard Agilent protocol

scan_protocol: Agilent Technologies Scanner G2505B US22502680

data_processing: RNA was isolated from two sets of patient matched tumor adjacent fibroblasts and tumor associated fibroblasts (CAFs) at the end of CDM production (see above), which were generated in two technical repetitions. The RNA was processed by the Genomics Facility at Fox Chase Cancer Center to render differentially expressed genes between the two sets of matching tumor adjacent fibroblasts and CAFs. Briefly, an Agilent Technologies Gene Chip (~44,000 genes) was used and RNA was hybridized to the chip and run through the Agilent Technologies Instrument (S/N: US22502680). Raw data were processed using the Agilent Feature Extraction 9.5.1.1 Software, outputting processed data into excel spreadsheets. Quantile normalization was applied to microarray data.

source_name: Pancreas

label_protocol: Agilent labeling kit

extract_protocol: TRIzol

value: tumor


title: P9.n

value: normal


title: P7.ti

value: tumor immortalized


title: P7.ni

value: normal immortalized


title: RNA sequencing of eWAT 3

city: New York

first: Sean

last: O'Connor

address: 1230 York Ave

department: Laboratory of Molecular Metabolism

institute: Rockefeller University

data_processing:
Raw counts per transcript were determined by pseudo alignment tool Kallisto (version: 0.45.0) to mouse index GRCm38 (version: 10)
Per gene abundance measurements were calculated for each sample in R (version: 3.6.1) using package TxImport (version: 1.14.2)
Normalized abundance and log2FoldChange measurements were calculated using DESeq2 output, method "apelgm" (version: 1.26.0)
Genome_build: mm10
Supplementary_files_format_and_content: DEseq normalized counts of miRNA seq.csv
Supplementary_files_format_and_content: DEseq normalized counts of mRNA seq.csv

source_name: Mouse whole adipose tissue depot

growth_protocol: For miRNAseq, total RNA was extracted from fat pads of 13-week old C57BL/6J male mice housed at room temperature and from inguinal fat pads of 13-week old mice housed at 4° C for 1 week prior to sacrifice. For mRNAseq, iBAT and eWAT tissue was dissected from 15-week old C57BL/6J male mice and immediately flash frozen in liquid nitrogen

extract_protocol:
RNA was extracted from tissues and cells using a TRIzol (Invitrogen)/chloroform extraction, followed by purification with RNeasy mini kits (Qiagen). To retain small RNAs during RNA purification, 1.5X volumes of 100% ethanol was used to precipitate RNA prior to column loading and RW1 buffer was substituted with RWT (Qiagen).
For miRNA, The TruSeq Small RNA Library Prep Kit (Illumina) was used to prepare libraries for sequencing, which was performed by LC Sciences. For mRNA, the library was prepared using the Illumina TruSeq Stranded Total RNA Library Prep Kit, and sequencing was performed on an Illumina NextSeq 500 sequencer.

treatment_protocol: No treatment applied to adipose tissue depots

tag: strain

value: eWAT


title: RNA sequencing of eWAT 1


title: RNA sequencing of eWAT 2


title: RNA sequencing of iBAT 4

value: iBAT


title: Patient 4095 TIL scRNAseq: 9.1-13

description: single-cell RNA-Seq


title: RNA sequencing of iBAT 3


title: RNA sequencing of iBAT 2


title: RNA sequencing of iBAT 1


title: KPC PDA tumour 2 CD105neg CAFs

city: MANCHESTER

first: Alexander

last: Kononov

address: Oglesby Building, 555 Wilmslow Rd,

country: United Kingdom

institute: Cancer Research UK Manchester Institute

data_processing:
Sequencing reads (76bp, paired-end) were aligned to the mouse reference genome GRCm38.mm10 using STAR aligner version 2.5.1b
Gene annotation was taken from Ensembl build 92
Read counts were determined by using the featureCounts function from Bioconductor package Rsubread version 1.28.1
Expression of a gene was calculated as Transcipts Per Kilobase Million (TPM) using standard calculation
Genome_build: mm10
Supplementary_files_format_and_content: Matrix table with TPM values for every gene and every sample

source_name: KPC GEMM mouse Pdx1-Cre; KrasLSL-G12D/+; Trp53LSL-R172H/+ (KPC)

extract_protocol:
FACS isolated CAFs were centrifuged at 400g for 5 min, carefully aspirated and cells lysed in RLT buffer. Lysis and subsequent RNA isolation was conudcted as per instructions ffor the Qiagen RNeasy micro kits
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Spontaneous pancreatic tumours

tag: cell type


title: KPC PDA tumour 6 CD105neg CAFs


title: KPC PDA tumour 1 CD105neg CAFs


title: KPC PDA tumour 6 CD105pos CAFs


title: KPC PDA tumour 4 CD105neg CAFs


title: KPC PDA tumour 5 CD105neg CAFs


title: KPC PDA tumour 3 CD105neg CAFs


title: KPC PDA tumour 5 CD105pos CAFs


title: KPC PDA tumour 3 CD105pos CAFs


title: KPC PDA tumour 4 CD105pos CAFs


title: KPC PDA tumour 1 CD105pos CAFs


title: RNA sequencing of eWAT 4


title: uterine NK cell sorted from E6.5 surrogate mouse_Control_rep3 [NCR1_Control_m2]

city: Rehovot

first: Ron

last: Hadas

address: 234 Herzl st.

department: Department of Biological Regulation

country: Israel

institute: Weizmann Institute of Science

data_processing:
Bcl files were converted into fastq by bcl2fastq. Demultiplexing is done using the sample barcode found on R2, the UMI found on R2 is inserted in the read name (in R1 fastq).  R1 Fastq data submitted.
MARS-seq analysis was done using the UTAP transcriptome analysis pipeline (Kohen et al., 2019). Reads were trimmed using Cutadapt (parameters: -a AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC -a “A{10}” –times 2 -u 3 -u -3 -q 20 -m 25) and mapped to the Mus_musculus genome using STAR v2.4.2a (parameters: –alignEndsType EndToEnd, –outFilterMismatchNoverLmax 0.05, –twopassMode Basic, –alignSoftClipAtReferenceEnds No).
The pipeline quantifies the 3’ of Gencode annotated genes (The 3’ region contains 1,000 bases upstream of the 3’ end and 100 bases downstream). Counting was done using htseq-count (union mode). Genes having minimum 5 UMI-corrected reads in at least one sample, were considered. Normalization of the counts and differential expression analysis was performed using DESeq2 package. Differentially expressed genes were defined as genes that had a significant adjusted p value of less than 0.05 and at least 2-fold change.
Genome_build: mm10
Supplementary_files_format_and_content: Raw counts, normalized abundance measurements and DESeq2 analysis

source_name: E6.5 decidua

growth_protocol: Uterine NK cells sorted from E6.5 deciduae

extract_protocol:
NCR1+ cells were sorted into 40µl of lysis/binding buffer, from which, mRNA was captured with 12 ml of Dynabeads oligo(dT) (Dynabeads™ mRNA DIRECT™ Purification Kit, NY, USA), washed, and eluted at 85C with 10 ml of 10 mM Tris-Cl (pH 7.5) and processed according to protocol previously developed for single-cell RNA-seq (Jaitin et al., 2014).
A variation of MARS-seq was used as described (Jaitin et al., 2014), developed for single-cell RNA-seq to produce expression libraries.

value: control

value: uterine NK cell


title: perhpheral NK cells sorted from the circulation of preganant mice [NCR1_blood]

source_name: peripheral blood

value: perhpheral NK cells


title: uterine NK cell sorted from E6.5 surrogate mouse_Hyaluronidase 2_Over-expression_rep4 [NCR1_OEx_m3]

value: Hyaluronidase2 overexpression


title: uterine NK cell sorted from E6.5 surrogate mouse_Hyaluronidase 2_Over-expression_rep2 [NCR1_OEx_m1]


title: uterine NK cell sorted from E6.5 surrogate mouse_Hyaluronidase 2_Over-expression_rep3 [NCR1_OEx_m2]


title: uterine NK cell sorted from E6.5 surrogate mouse_Control_rep2 [NCR1_Control_m1]


title: uterine NK cell sorted from E6.5 surrogate mouse_Control_rep1 [NCR1_Control_high]