title: C4_ROI_12_well_D06

first: Liang

last: Zhang

state: Washington

address: 530 Fairview Ave N

institute: NanoString

description: Sample name: DSP-1004440003841-B-D06

data_processing:
Library strategy: GeoMx Seq
Samples were pooled during library preparation and split across lanes. Individual FASTQ files were generated for each lane, forward & reverse primers. The Fastq files contain the same identifier as the sample name for aggregation.
save-interim-files = false
quality-trim-score = 20
2color-trimming = True
adapter1 = AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC
adapter2 = AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT
adapter-trim-match-length = 10
adapter-trim-max-mismatch = 3
barcode-max-mismatch = 1
stitching-max-mismatch = 2
dedup-hd = 1
threads = 4
Genome_build: N/A, sequencing of synthetic tags and alignment to whitelist of RTS_IDs (probe barcodes) found in the config.ini output from the GeoMx DSP platform, see attached PKC file (TAP_H_WTA_v1.0.pkc)
Supplementary_files_format_and_content: Digital Count Conversion (DCC) file format outputted from GeoMx NGS Pipeline, contains software versions, scan attributes, GeoMx NGS pipeline parameters and output metrics, Q30 scores, and list of deduplicated counts per RTS_ID (probe barcode)
Supplementary_files_format_and_content: Values represented in "Collapsed Target Counts.txt" are the geometric mean of the probes for a given target--in the case that multiple probes were used-- and excludes any targets flagged as outliers.  "Analyzed Counts.txt" represents the upper quartile normalized collapsed counts across the study after removing QC flagged segments and features.

molecule: other

source_name: skin

extract_protocol:
Samples were incubated with DNA-oligo barcoded RNA-ISH probes which were conjugated with a UV-photocleavable linker following standard ISH protocols, along with fluorescently labeled antibodies for visualization of morphological structures. Regions of interest within the tissue were illuminated with UV light and oligo barcodes were physically aspirated from the tissue and collected into microtiter plates by the GeoMx® Digital Spatial Profiler (DSP) platform. For more information about DSP protocols please see Merritt et al. Nature Biotech 2020 (doi: 10.1038/s41598-020-63539-x)
Each collection of oligo tags from one well (representing an ROI from the tissue section) was indexed with i7xi5 unique dual indexes using GeoMx SeqCode primers with 18 cycles of PCR.  After PCR, indexed AOIs were pooled and purified in two rounds of AMPure XP PCR purification using 1.2x bead:sample ratio.

tag: slide id

tag: roi number

tag: segment type

value: Epidermis

value: SLE

tag: area

tag: roi x coordinate

tag: roi y coordinate

tag: rawreads

tag: alignedreads

tag: deduplicatedreads

tag: trimmedreads

tag: stitchedreads

tag: sequencingsaturation


title: thymus_TBI_day0_rep1

status: Public on Oct 01 2021

type: RNA

city: Seattle

first: Kirsten

last: Cooper

state: WA

address: 1100 Fairview Ave. N, Rm S3-208

country: USA

institute: Fred Hutchinson Cancer Research Center

description: Gene expression from CD45- thymic stromal cells

hyb_protocol: 10 ug of cDNA was hybridized for 16 hr to the Affymetrix array as described in the Expression Analysis Technical Manual. GeneChips were washed and stained in the Affymetrix Fluidics Station FS450.

scan_protocol: Affymetrix GeneArray scanner 7G

data_processing: Feature intensity was extracted by Affymetrix GeneChip Command Console as CEL files. Used Bioconductor Affy for normalization (GC-RMA) and gene annotation

label: Biotin

molecule: total RNA

organism: Mus musculus

source_name: Untreated mouse thymus

label_protocol: 500 ng total RNA converted to cRNA using Affymetrix GeneChip®3' IVT Kit and in vitro transcription resulting into biotin-labeled cRNA, fragmented prior to hybridization (Affymetrix Expression Analysis Technical Manual, as described).

extract_protocol: RNA extraction plus kit was used to isolate RNA, and cDNA was made with Invitrogen Superscriptase.

treatment_protocol: Cells were first isolated using CD45 MACS cell depletion, then endothelial cells were FACS purified (CD45- EpCAM- VE-Cad+). To obtain sufficient RNA for every timepoint, thymic ECs of several mice were pooled.

tag: strain

tag: age

tag: gender

value: female

tag: treatment

value: untreated

tag: tissue

value: thymus

tag: cell type

value: thymic endothelial cells


title: 1026_T1

type: SRA

city: Gainesville

first: VIJAYENDRAN

last: CHANDRAN

state: FL

address: Assistant Professor, Department of Pediatrics,  University of Florida, School of Medicine, 1600 SW Archer Road, Box 100296

institute: University of Florida

library_source: transcriptomic

data_processing:
Bluebee’s genomics analysis platform
Sequencing targeted mean three million 65-nt single-stranded reads per sample, which were mapped to the human transcriptome and quantified as transcripts per million mapped reads using the STAR aligner. Briefly, all sequencing data were uploaded to Illumina’s BaseSpace in real-time for downstream analysis of quality control. Raw Illumina (fastq.gz) sequencing files were downloaded from BaseSpace, and uploaded to Bluebee’s genomics analysis platform (https://www.bluebee.com) to align reads against the human genome and to obtain raw read counts.
Supplementary_files_format_and_content: Three csv file contains: (1) raw read counts, (2) normalized read counts with batch correction, and (3) normalized read counts with batch correction and cell type correction for every gene and every sample.

organism: Homo sapiens

source_name: T1 (baseline)_whole blood

extract_protocol:
The human blood samples collected into PAXgene Blood RNA Tubes were removed from the -80°C freezer and incubated overnight at room temperature before RNA extraction. RNA was harvested using the RNeasy Tissue Mini Kit (Qiagen), according to manufacturer’s instructions. RNA was reverse transcribed to complementary DNA (Lexogen QuantSeq 3′ FWD), and sequenced on a HiSeq 4000 instrument (Illumina).
RNA libraries were prepared for sequencing using  manufacturer’s instructions  (Lexogen QuantSeq 3′ FWD)

tag: Sex

value: Male

value: T1 (baseline)

value: Whole Blood


title: D8_MO

city: Houston

first: Noah

last: Shroyer

state: Texas

address: One Baylor Plaza, Room N710

department: Medicine Section of Gastroenterology and Hepatology

institute: Baylor College of Medicine

description:
Duodenal Enteroids Mock Infected
Line - D8

data_processing:
Pseudosalignment was performed using Kallisto (https://pachterlab.github.io/kallisto/) and raw gene counts were output as tsv files
Genome_build: hg38
Supplementary_files_format_and_content: Tab-delimited files with raw gene counts for every gene and every sample

source_name: Intestine

growth_protocol: Enteroids were mainted in IntestiCult Proliferation and differentiated in IntestiCult Differentiation

extract_protocol:
Total RNA was extracted using a Qiagen RNeasy kit
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Enteroids were treated with vehicle or BCM 16-16 norovirus in IntestiCult Differentiation

tag: segment

value: Duodenum

tag: format

value: Monolayer

tag: substrate

value: Collagen IV


title: 1026_T2

source_name: T2 (before meditation)_whole blood

value: T2 (before meditation)


title: 1025_T4

source_name: T4 (three months after meditation)_whole blood

value: T4 (three months after meditation)


title: C4_ROI_11_well_D05

description: Sample name: DSP-1004440003841-B-D05

value: skin

tag: slide id

tag: roi number

tag: segment type

tag: disease state

value: DLE

tag: area

tag: roi x coordinate

tag: roi y coordinate


title: desmoplastic malignant mesothelioma tumor tissue NCC-DMM1-T1-1

type: protein

city: Tokyo

first: Rei

last: Noguchi

state: Tokyo

department: Division of Rare Cancer Research

country: Japan

institute: National Cancer Center Research Institute

description: kinase activity profile data from desmoplastic malignant mesothelioma tumor tissue

hyb_protocol: Fully automated in a PamStation12 40 minutes at room temperature using 2 cycles per minute.

scan_protocol: Fully automated in the camera module of the PamStation12.

data_processing: Each combination of genotype and ligand was tested using three arrays and thus resulted in three binding values for each peptide. Each combination of genotype and ligand was tested using three arrays and thus resulted in three binding values for each peptide. These triplicates were used to calculate a mean binding and log10-fold change of binding (modulation Index, MI) vs. WT apo (unliganded) ERα (control), and to determine the significance of this modulation by Student’s t-Test with post-hoc false discovery rate correction.

label: FITC

molecule: protein

source_name: desmoplastic malignant mesoyhelioma

label_protocol: Binding was detected using fluorescently labeled secundary antibody and quantified as arbitrary unit’s fluorescence using Bionavigator Software (PamGene).

extract_protocol: Frozen cells were lysed using  lysis buffer containing protease inhibitor cocktail, centrifuged and the soluble fraction was collected. Crude lysate was incubated on a PamChip array.

tag: sample type

value: originated tumor tissue


title: desmoplastic malignant mesothelioma tumor tissue NCC-DMM1-T1-2


title: desmoplastic malignant mesothelioma cell line NCC-DMM1-C1-1

description: kinase activity profile data from desmoplastic malignant mesothelioma cell lines

tag: cell line

value: patient-derived cell line


title: thymus_TBI_day4_rep2

description: Gene expression from CD45- thymic stromal cells; SL-TBI was given at a dose of 550 cGy from a cesium source mouse irradiator with no hematopoietic rescue

source_name: Mouse thymus harvested 4 days post SL-TBI

tag: strain

tag: age

tag: gender

value: a sublethal dose of total body irradiation (SL-TBI, 550cGy)

tag: time

value: at day 4 post-treatment

value: CD45- thymic stromal cells


title: C4_ROI_10_well_D04

description: Sample name: DSP-1004440003841-B-D04

tag: tissue

value: Epidermis

tag: rawreads

tag: alignedreads

tag: deduplicatedreads

tag: trimmedreads

tag: stitchedreads

tag: sequencingsaturation


title: 1025_T3

source_name: T3 (after meditation) _whole blood

tag: Sex

tag: treatment

value: T3 (after meditation)


title: C4_ROI_8_well_D02

description: Sample name: DSP-1004440003841-B-D02

tag: slide id

tag: roi number

tag: segment type

tag: disease state

tag: area

tag: roi x coordinate


title: C4_ROI_7_well_C12

description: Sample name: DSP-1004440003841-B-C12

tag: roi y coordinate


title: thymus_TBI_day4_rep1

tag: strain

tag: age

tag: gender

value: female

tag: time

value: thymus

tag: cell type


title: C4_ROI_9_well_D03

description: Sample name: DSP-1004440003841-B-D03

tag: tissue

tag: rawreads

tag: alignedreads

tag: deduplicatedreads

tag: trimmedreads


title: C4_ROI_8_well_D01

description: Sample name: DSP-1004440003841-B-D01

tag: slide id

tag: stitchedreads

tag: sequencingsaturation


title: 1026_T3

tag: Sex

value: Male

tag: treatment

value: Whole Blood


title: HD44_TDF

city: Cleveland

first: Mark

last: Cameron

state: OH

address: 10900 Euclid Ave

department: Population and Quantitative Health Sciences

institute: Case Western Reserve University

description:
rawCounts.csv
normalizedCounts.csv

data_processing:
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence using skewer v0.2.2, then mapped to GRCh38 whole genome using Hisat2 v2.0.5
Read summarization was performed by the program featureCounts v1.5.0-p2 as part of the SubRead package.
Counts Per Million (CPM) values were generated through the edgeR Library v3.16.5 in R
Genome_build: GRCh38
Supplementary_files_format_and_content: rawCounts.csv: counts as generated by featureCounts, rows are gene features, columns are samples
Supplementary_files_format_and_content: normalizedCounts.csv: remove counts that were all zeroes (across the full set); Perform TMM normalization ; export log2(n+3) CPM

source_name: monocyte-derived macrophage

growth_protocol: For differentiation of monocyte-derived macrophages (MDMs), PBMCs (2 x 106/mL) were cultured in Teflon wells (Savillex) for 5 days in RPMI 1640 supplemented with 20% autologous serum. On day 5, cells were removed from Teflon and MDMs (3 x 105/mL) were purified by adherence to plastic for 3 h.

extract_protocol:
Total monocyte-derived macrophage RNA was extracted using RNeasy Plus Mini Kit (Qiagen).
RNA libraries were prepared for sequencing using the Illumina TruSeq Stranded Total RNA - Globin kit.

treatment_protocol: Cells isolated from HIV- donors were exposed to FTC (1 uM) or TDF (1 uM) for the 5 day differentiation process.

tag: drug

value: TDF

tag: donor


title: desmoplastic malignant mesothelioma cell line NCC-DMM1-C1-2

tag: cell line

tag: sample type


title: 1025_T2

tag: age


title: C4_ROI_7_well_C11

description: Sample name: DSP-1004440003841-B-C11

tag: roi number

tag: segment type

tag: disease state

tag: area

tag: roi x coordinate

tag: roi y coordinate


title: HD44_FTC

description:
rawCounts.csv
normalizedCounts.csv

value: FTC


title: C4_ROI_6_well_C10

description: Sample name: DSP-1004440003841-B-C10

tag: tissue

value: SMA+

tag: rawreads

tag: alignedreads

tag: deduplicatedreads

tag: trimmedreads


title: 1025_T1

tag: Sex

tag: treatment

value: T1 (baseline)


title: 1024_T2

value: T2 (before meditation)


title: C4_ROI_3_well_C07

description: Sample name: DSP-1004440003841-B-C07

value: skin

tag: slide id

value: SLE

tag: stitchedreads

tag: sequencingsaturation


title: HD33_TDF

description:
rawCounts.csv
normalizedCounts.csv

tag: drug

tag: donor


title: C4_ROI_4_well_C08

description: Sample name: DSP-1004440003841-B-C08

tag: roi number

tag: segment type


title: C4_ROI_5_well_C09

description: Sample name: DSP-1004440003841-B-C09

tag: disease state

tag: area


title: HD44_No_Drug

description:
rawCounts.csv
normalizedCounts.csv

value: No Drug


title: 1024_T1

tag: age


title: HD33_No_Drug

description:
rawCounts.csv
normalizedCounts.csv


title: C4_ROI_3_well_C06

description: Sample name: DSP-1004440003841-B-C06

tag: tissue

tag: roi x coordinate

tag: roi y coordinate


title: HD33_FTC

description:
rawCounts.csv
normalizedCounts.csv


title: 1024_T3


title: HD25_TDF

description:
rawCounts.csv
normalizedCounts.csv


title: C4_ROI_2_well_C05

description: Sample name: DSP-1004440003841-B-C05

value: healthy

tag: rawreads

tag: alignedreads

tag: deduplicatedreads


title: HD25_FTC

description:
rawCounts.csv
normalizedCounts.csv


title: 1023_T1

tag: Sex

tag: treatment


title: 1023_T2


title: C4_ROI_1_well_C04

description: Sample name: DSP-1004440003841-B-C04

tag: slide id

tag: trimmedreads

tag: stitchedreads


title: 1023_T3


title: B4_ROI_7_well_C03

description: Sample name: DSP-1004440003841-B-C03

value: DLE

tag: sequencingsaturation


title: HD25_No_Drug

description:
rawCounts.csv
normalizedCounts.csv

tag: drug

tag: donor


title: 1020_T4

value: T4 (three months after meditation)


title: HD16_TDF

description:
rawCounts.csv
normalizedCounts.csv


title: B4_ROI_6_well_C02

description: Sample name: DSP-1004440003841-B-C02

tag: roi number

tag: segment type

tag: disease state


title: 1020_T3

tag: age

tag: tissue


title: HD16_FTC

description:
rawCounts.csv
normalizedCounts.csv


title: 1020_T2


title: HD16_No_Drug

description:
rawCounts.csv
normalizedCounts.csv


title: B4_ROI_6_well_C01

description: Sample name: DSP-1004440003841-B-C01

tag: area

tag: roi x coordinate

tag: roi y coordinate


title: 1020_T1


title: HD2_TDF

description:
rawCounts.csv
normalizedCounts.csv


title: B4_ROI_4_well_B11

description: Sample name: DSP-1004440003841-B-B11

tag: rawreads

tag: alignedreads

tag: deduplicatedreads


title: B4_ROI_4_well_B10

description: Sample name: DSP-1004440003841-B-B10

tag: slide id


title: primary melanocyte CSD2

type: genomic

city: Rockville

first: Tongwu

state: MD

address: 9609 Medical Center Drive

department: Division of Cancer Epidemiology & Genetics

institute: National Cancer Institute

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridized to Illumina Infinium Human Methylation450 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: Cy3, Cy5

molecule: genomic DNA

source_name: Primary cultured melanocytes

label_protocol: Standard Illumina Protocol

extract_protocol: genomic DNA was extracted and purified from 106 samples using Gentra Puregene Cell Kit (158745, Qiagen)

tag: gender

tag: sample type

value: genomic

tag: cell type

value: melanocytes


title: 1019_T3

tag: Sex

value: Female

tag: treatment

value: T3 (after meditation)


title: primary melanocyte C34

value: Male


title: primary melanocyte C336


title: B4_ROI_5_well_B12

description: Sample name: DSP-1004440003841-B-B12

tag: roi number

value: Epidermis

tag: trimmedreads

tag: stitchedreads

tag: sequencingsaturation


title: HD2_No_Drug

description:
rawCounts.csv
normalizedCounts.csv

tag: drug

tag: donor


title: B4_ROI_3_well_B09

description: Sample name: DSP-1004440003841-B-B09

tag: tissue

tag: segment type

tag: disease state

tag: area

tag: roi x coordinate


title: primary melanocyte C91


title: 1019_T2

tag: age

value: Whole Blood


title: 1019_T4


title: THP1_IL4_PANOBINOSTAT_2

city: Charlestown

first: Alexander

middle: G

last: Marneros

state: MA

address: 13th Street

department: Department of Dermatology, Cutaneous Biology Research Center

institute: Massachusetts General Hospital, Harvard Medical School

data_processing:
We followed the nf-core/rnaseq workflow version 1.3 (https://github.com/nf-core/rnaseq) for all rna-seq data, with default parameters. The detail includes as following:
low-quality reads were eliminated using FastQC and trim_galory software, remaining only high quality reads.
The remaining clean reads were aligned against the iGenome Ensembl human referenece genome GRCh37 using by STAR. STAR is a read aligner designed for RNA sequencing.
Next, we generated counts relative to genes by featureCounts and StringTie with default parameters.
Genome_build: GRCh37
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample

growth_protocol: THP-1 cells were obtained from ATCC (ATCC Cat# TIB-202, RRID:CVCL_0006) and cultured in RPMI1640+10% FBS+1% Anti-Anti (Life technologies, 15240).

extract_protocol:
0.5X10^6 cells were harvested for mRNA using mRNeasy Mini Kit (Qiagen, No. 217004).
We used 0.4 μg total RNA for RNA-seq library preparation by TruSeq Ribo Profile Mammalian Kit (Illumina, RPHMR12126).

treatment_protocol: Primed THP-1 cells with PMA 50 nM were pre-treated with panobinostat (0.0034 μM, HDACs inhibitor) for one hour and then treated with either BSA (control), IL-4 (20 ng/ml, M2 polarization) or IFNγ (20 ng/ml) and LPS (10 ng/ml, M1 polarization) for 24 hours.

value: peripheral blood monocyte

tag: cell line


title: HD2_FTC

description:
rawCounts.csv
normalizedCounts.csv

value: FTC


title: 1019_T1

value: T1 (baseline)


title: primary melanocyte C87

tag: gender

tag: sample type


title: primary melanocyte C83

tag: cell type


title: THP1_IL4_PANOBINOSTAT_1


title: primary melanocyte C73


title: primary melanocyte CSD1


title: primary melanocyte C76


title: 1017_T4

tag: Sex

tag: treatment


title: THP1_IL4_DMSO_2


title: B4_ROI_1_well_B06

description: Sample name: DSP-1004440003841-B-B06

tag: slide id

tag: roi number

tag: roi y coordinate

tag: rawreads

tag: alignedreads

tag: deduplicatedreads

tag: trimmedreads


title: 1017_T3

tag: tissue


title: primary melanocyte C71


title: primary melanocyte C78


title: THP1_IL4_DMSO_1


title: primary melanocyte C80


title: 1017_T2

value: T2 (before meditation)


title: primary melanocyte C68


title: primary melanocyte C7


title: primary melanocyte C74


title: THP1_IFNyLPS_PANOBINOSTAT_2


title: primary melanocyte C8


title: primary melanocyte C77


title: A4_ROI_11_well_B04

description: Sample name: DSP-1004440003841-B-B04

value: skin

tag: segment type

value: Dermis

tag: disease state

tag: area

tag: stitchedreads

tag: sequencingsaturation


title: primary melanocyte C65

tag: gender

tag: sample type


title: B4_ROI_3_well_B08

description: Sample name: DSP-1004440003841-B-B08

value: SLE

tag: roi x coordinate


title: 1017_T1

tag: age

tag: Sex

tag: treatment


title: 1016_T4


title: THP1_IFNyLPS_PANOBINOSTAT_1

tag: cell type

tag: cell line


title: A4_ROI_10_well_B03

description: Sample name: DSP-1004440003841-B-B03

tag: slide id

tag: roi number

value: healthy

tag: roi y coordinate

tag: rawreads

tag: alignedreads


title: THP1_IFNyLPS_DMSO_2


title: 1016_T2

tag: tissue


title: A4_ROI_9_well_B02

description: Sample name: DSP-1004440003841-B-B02

tag: segment type

value: SMA+

tag: disease state

value: SCLE

tag: area

tag: deduplicatedreads

tag: trimmedreads


title: THP1_IFNyLPS_DMSO_1


title: A4_ROI_8_well_B01

description: Sample name: DSP-1004440003841-B-B01

tag: roi x coordinate

tag: stitchedreads

tag: sequencingsaturation


title: A4_ROI_7_well_A12

description: Sample name: DSP-1004440003841-B-A12


title: THP1_CTRL_PANOBINOSTAT_2


title: 1016_T3

tag: age

tag: Sex

tag: treatment


title: 1016_T1


title: primary melanocyte C72

tag: gender

tag: sample type

value: genomic

tag: cell type


title: B4_ROI_2_well_B07

description: Sample name: DSP-1004440003841-B-B07

tag: slide id

tag: roi number

tag: roi y coordinate

tag: rawreads


title: primary melanocyte C62

value: melanocytes


title: 1015_T4

value: T4 (three months after meditation)

tag: tissue


title: primary melanocyte C88


title: A4_ROI_7_well_A11

description: Sample name: DSP-1004440003841-B-A11

tag: segment type

tag: disease state

tag: area

tag: alignedreads


title: THP1_CTRL_DMSO_2

tag: cell line


title: THP1_CTRL_DMSO_1


title: A4_ROI_5_well_A09

description: Sample name: DSP-1004440003841-B-A09

tag: roi x coordinate

tag: deduplicatedreads

tag: trimmedreads

tag: stitchedreads

tag: sequencingsaturation


title: 1015_T3

tag: age

tag: Sex

tag: treatment

value: T3 (after meditation)


title: THP1_CTRL_PANOBINOSTAT_1

tag: cell type


title: 1015_T2

value: Male


title: A4_ROI_6_well_A10

description: Sample name: DSP-1004440003841-B-A10

tag: slide id

tag: roi number

value: Epidermis

tag: roi y coordinate


title: primary melanocyte C56

tag: gender

tag: sample type


title: A4_ROI_5_well_A08

description: Sample name: DSP-1004440003841-B-A08

tag: tissue

tag: segment type

tag: disease state

tag: area

tag: rawreads


title: primary melanocyte C55


title: primary melanocyte C64


title: BAGCE_Pioneiro

city: Juiz de Fora

first: Ana Luisa

middle: Sousa

last: Azevedo

state: Minas Gerais

address: Rua Eugenio do Nascimento, 610

country: Brazil

institute: Empresa Brasileira de Pesquisa Agropecuaria

data_processing:
The sequenced RNA quality control was evaluated using FastQC software v 0.11.8 (Babraham Bioinformatics, Babraham, England).
The sequenced reads were mapped to C. purpureus genome (Yan et al., 2021) through Spliced Transcripts Alignment to a Reference (STAR) software v. 2.5.2b (Dobin et al., 2012)
The BAM files were used to assemble the transcriptome in Stringtie v 2.0.4 software (Pertea et al., 2015).
The assembled transcriptome was used to a new reads mapping, using again STAR software v. 2.5.2b (Dobin et al., 2012).
Salmon v 0.7.2 software (Patro et al., 2017) was used to quantify the sequenced reads from transcriptome generated through Stringtie and mapping from second STAR analysis. The quantification files were used for differential expressed genes analysis.
Genome_build: GWHAORA00000000
Supplementary_files_format_and_content: tab-delimited text files include TPM values for each sample

organism: Cenchrus purpureus

source_name: Young stem

value: Young stem

value: High Lignin


title: 1015_T1

value: Whole Blood


title: 1014_T4

value: Female


title: BAGCE_98

value: Low Lignin


title: A4_ROI_4_well_A07

description: Sample name: DSP-1004440003841-B-A07

value: skin

tag: roi x coordinate

tag: alignedreads

tag: deduplicatedreads

tag: trimmedreads


title: A4_ROI_4_well_A06

description: Sample name: DSP-1004440003841-B-A06

tag: stitchedreads

tag: sequencingsaturation


title: 1014_T3

tag: age

tag: Sex

tag: treatment


title: BAGCE_82


title: A4_ROI_3_well_A05

description: Sample name: DSP-1004440003841-B-A05

tag: slide id

tag: roi number

tag: roi y coordinate


title: primary melanocyte C53

tag: gender

tag: sample type

tag: cell type


title: primary melanocyte C54


title: 1014_T2

value: T2 (before meditation)

tag: tissue


title: BAGCE_96


title: A4_ROI_2_well_A04

description: Sample name: DSP-1004440003841-B-A04

tag: segment type

tag: disease state

tag: area

tag: rawreads


title: 1014_T1

value: T1 (baseline)


title: BAGCE_32


title: BAGCE_10


title: BAGCE_7


title: A4_ROI_1_well_A03

description: Sample name: DSP-1004440003841-B-A03

tag: roi x coordinate

tag: alignedreads

tag: deduplicatedreads

tag: trimmedreads


title: primary melanocyte C6


title: A4_ROI_1_well_A02

description: Sample name: DSP-1004440003841-B-A02

tag: stitchedreads

tag: sequencingsaturation


title: BAGCE_5

tag: treatment


title: Full thickness skin - RDEB2 native skin

city: Minneapoilis

first: Julia

middle: Anne

last: Riedl

state: MN

address: 1600 Madison ST NE

department: Pediatrics

institute: University of Minnesota

data_processing:
CellRanger 2.1.0
The matrices underwent filtering, normalization, scaling, principal components analysis, and subsequent UMAP analysis using the Seurat 3.4.2 package and function SCTransform() in R software 3.6.0 (Butler et al., 2018, Hafemeister and Satija, 2019). SCTransform() function regresses out cells with high cell cycle and mitochondrial genes, normalizes data, finds variable features and scales data with final product being corrected read counts (log1p(counts)).
Number of PCs was chosen by running Jackstraw and Elbow plots and choosing PCs with p-values less than 1e-10. We used the first 20 primary components to construct the Shared Nearest Neighbor (SNN) graph for each sample. Resolution of 0.7 was chosen for all samples.
Genome_build: hg19
Supplementary_files_format_and_content: RDS files that were analyzed using Seurat package 3.4.2 on R version 3.6.0

source_name: Skin

extract_protocol:
Full-thickness 4-mm punch biopsies were obtained from RDEB patients or a healthy donor. Samples were kept on ice in DMEM with 1% gentamycin for no longer than one hour before their enzymatic and mechanical dissociation with the Whole Skin Dissociation kit for human material (Miltenyi Biotec, cat. no. 130-101-540) and the gentleMACS dissociator (Miltenyi Biotec), following the manufacturer’s instructions. Cell suspensions were then filtered through 70-μm cell strainers (Falcon). Full-thickness skin biopsies were incubated in enzyme mix for 8 hours, mechanically dissociated using Miltenyi gentleMACs and dead cells removed using Stem Cell Technologies EasySepTM Dead cell Removal (Annexin V) kit (catalog #17899) to remove dead cells and debris. Epidermal grafts were dissociated using Miltenyi Epidermal Dissociation Kit (#130-103-464), incubated in enzyme mix for one hour (due to decreased thickness of tissue) and then dead cells removed using Stem Cell Technologies kit as described above. Viability was between 30-60% for all samples. Samples were resuspended at 10,000 cells/mL in cold PB buffer (phosphate-buffered saline with 0.5% bovine serum albumin). Samples were kept on ice for immediate transport to the University of Minnesota Genome Core for library preparation.
Cells were subjected to 10X Genomics Chromium Single-Cell Platform manipulation (3’ library prep), followed by sequencing using Illumina NovaSeq 6000 system, and then results were run through Cell Ranger pipeline software for sequence alignment and basic filtering. Sequencing libraries were subsequently prepared following the Drop-seq methodology, using a Chromium Single Cell Controller and the v3 chemistry from 10X Genomics (cat. no. PN-1000075).

value: Recessive Dystrophic Epidermolysis Bullosa (RDEB)

tag: skin condition

value: native skin


title: 1013_T3

tag: age

tag: Sex


title: Full thickness skin - RDEB2 epidermal grafted site

value: epidermal grafted site


title: B4_ROI_1_well_B05

description: Sample name: DSP-1004440003841-B-B05

tag: slide id

tag: roi number

value: SLE

tag: roi y coordinate


title: primary melanocyte C43

tag: gender

tag: sample type

value: genomic

tag: cell type

value: melanocytes


title: 1013_T1

tag: tissue


title: spleen Treg_Day 4_Rep2

city: Shenyang

first: Hui

last: Feng

address: No.77 Puhe Road, Shenyang North New Area

country: China

institute: China Medical University

description:
micRNA expression in spleen Treg cells from BALB/c mice infected with P.y 17XL on day 4.
Mmu Treg_D4-2

hyb_protocol: 0.6 μg of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/μg cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 22.5μl containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers' instructions. On completion of the fragmentation reaction, 22.5μl of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Mice miRNA Release21.0（8*60K）for 20 hours at 55°C in a rotating Agilent hybridization oven. After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.400.            washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505C) using one color scan setting for 4x180k array slides (Scan Area 61x21.6 mm, Scan resolution 3um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 10.7.1.1 (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities as the raw data. Raw data were normalized in quantile algorithm with Genespring 13.0(Agilent). Probe that at least 1 out of 2 samples flagged as Detected were maintained (resulting in 278 data rows).

source_name: spleen Treg_Day 4

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.2 μg RNA using the One-Color Low RNA Input Linear Amplification PLUS kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA). Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: Spleen Treg cells were isolated by MACS sorting from P.y 17XL infected mice on day 4 after infection accroding to Treg_D4. Control Treg cells were from uninfected BALB/c mice accroding to Treg_D0.

extract_protocol: RNA was extracted by mirVanaTM RNA Isolation Kit (Applied Biosystem p/n AM1556 ) following the manufacturer's instructions.

treatment_protocol: BALB/c mice were infected with fresh 10^6 P.y 17XL-infected red blood cells.

tag: strain

value: BALB/c

value: female

tag: infected with

value: Plasmodium yoelii 17XL (P.y 17XL)

value: spleen

value: CD4+CD25+ Treg cells


title: 1013_T4

value: Male

value: T4 (three months after meditation)

value: Whole Blood


title: Full thickness skin - RDEB1 native skin

tag: disease state

value: skin


title: primary melanocyte C344


title: spleen Treg_Day 4_Rep1

description:
micRNA expression in spleen Treg cells from BALB/c mice infected with P.y 17XL on day 4.
Mmu Treg_D4-1


title: 1012_T4


title: primary melanocyte C38


title: Full thickness skin - RDEB1 epidermal grafted site


title: primary melanocyte C360


title: primary melanocyte C326


title: spleen Treg_Day 0_Rep2

description:
micRNA expression in spleen Treg cells from control mice
Mmu Treg_D0-2

source_name: spleen Treg_Day 0


title: primary melanocyte C363


title: 1012_T2

value: T2 (before meditation)


title: primary melanocyte C365


title: 1012_T3

value: T3 (after meditation)


title: Full thickness skin - RDEB1 nonwound

value: Recessive Dystrophic Epidermolysis Bullosa (RDEB)

value: nonwound


title: Full thickness skin - WT healthy donor

value: healthy

value: full thickness skin


title: Full thickness skin - RDEB1 wound

value: wound


title: 1011_T4


title: primary melanocyte C318

value: genomic

value: melanocytes


title: primary melanocyte C31


title: 1011_T3


title: Epidermal Graft - WT healthy donor

value: Epidermal Graft


title: 1012_T1

value: T1 (baseline)


title: N3 IP

city: Beijing

first: Zhuo

last: Liu

address: Yabao Road 2

institute: Capital Institute of Pediatrics

description: m6A methylated RNA expression of Wilms' tumor compared with Adjacent normal tissue

hyb_protocol: The cRNAs were combined together and hybridized onto Arraystar Mouse mRNA&lncRNA Epitranscriptomic Microarray (8x60K, Arraystar).

scan_protocol: After washing, slides were scanned with the Agilent Scanner G2505C.

data_processing: Agilent Feature Extraction software (version 11.0.1.1) was used to analyze acquired array images. Raw intensities of IP (immunoprecipitated, Cy5-labelled) and Sup (supernatant, Cy3-labelled) were normalized with average of log2-scaled Spike-in RNA intensities.

source_name: Adjacent normal tissue

label_protocol: Briefly, the total RNAs were immunoprecipitated with anti-N6-methyadenosine (m6A) antibody. The modified RNAs were eluted from the immunoprecipitated magnetic beads as the “IP”. The unmodified RNAs were recovered from the supernatant as “Sup”. The “IP” and “Sup” RNAs were labeled with Cy5 and Cy3 respectively as cRNAs in separate reactions using Arraystar Super RNA Labeling Kit.

extract_protocol: Total RNA extracted using Trizol following manufacturer's instructions

treatment_protocol: The tissue samples were immediately frozen in liquid nitrogen after tumor resection, and stored at −80°C until further analysis. All the patients did not receive chemotherapy before surgical resection.

value: 2 moths

tag: molecule type

value: MeRIP RNA


title: primary melanocyte C304

value: Male


title: 1011_T2


title: RSV+ZL0454-replicate 4

city: Middleton

first: Allan

last: Brasier

state: WI

address: 715 Highland

institute: university of Wissconsin

description: Wild type small airway epithelial cells

data_processing:
bar codes were removed by cutadapt
alignment and quantification were performed using Salmon
differential analysis was using DESeq2

source_name: hSAEC wild type

growth_protocol: hSAECs were grown in SAGM small airway epithelial cell growth medium (Lonza, cc-3118).

extract_protocol: Cells were harvested for RNA isolation using RNeasy kit with on-column DNase digestion (Qiagen). Synthesis of complementary DNAs (cDNAs) was done with First Strand cDNA Synthesis Kit (Thermo Scientific).

treatment_protocol: The human RSV Long strain was grown in Hep-2 cells and prepared by sucrose cushion .  Cells were infected with RSV at an MOI of 1 in the absence or presence of the BRD4 inhibitor, ZL0454

value: Wild type small airway epithelial cells

value: Infected 24 h + ZL0454


title: RSV+ZL0454-replicate 3

description: Wild type small airway epithelial cells


title: 1011_T1

value: Whole Blood


title: 1013_T2

value: T2 (before meditation)


title: primary melanocyte C290


title: RSV+ZL0454-replicate 2

description: Wild type small airway epithelial cells


title: N1 IP

value: 1 year and 5 months


title: RSV+ZL0454-replicate 1

description: Wild type small airway epithelial cells


title: spleen Treg_Day 0_Rep1

description:
micRNA expression in spleen Treg cells from control mice
Mmu Treg_D0-1

value: BALB/c

value: female

value: spleen

value: CD4+CD25+ Treg cells


title: primary melanocyte C291


title: T4 IP

source_name: Wilm' s tumor

value: Female

value: 5 moths


title: 1007_T2


title: 1007_T3

value: T3 (after meditation)


title: primary melanocyte C282

value: genomic

value: melanocytes


title: primary melanocyte C29


title: primary melanocyte C303


title: T3 IP

value: 2 moths


title: T2 IP

value: 11 moths

value: MeRIP RNA


title: T5 IP

value: Male

value: 1 year


title: 1007_T1

value: T1 (baseline)

value: Whole Blood


title: primary melanocyte C27


title: RSV-24 h-replicate 3

description: Wild type small airway epithelial cells

value: Wild type small airway epithelial cells

value: Infected 24 h


title: primary melanocyte C262


title: primary melanocyte C283


title: primary melanocyte C28


title: 1004_T2

value: T2 (before meditation)


title: T1 IP

value: 1 year and 5 months


title: RSV-24 h-replicate 2

description: Wild type small airway epithelial cells


title: primary melanocyte C355


title: 1004_T1


title: primary melanocyte C26


title: RSV-24 h-replicate 4

description: Wild type small airway epithelial cells


title: 0-replicate 4

description: Wild type small airway epithelial cells

value: uninfected (0h)


title: primary melanocyte C254


title: 1004_T3


title: N2 IP

value: Female


title: RSV-24 h-replicate 1

description: Wild type small airway epithelial cells


title: 1003_T4

value: T4 (three months after meditation)


title: primary melanocyte C252


title: N3 Sup

value: Supernatant RNA


title: N1 Sup


title: 0-replicate 3

description: Wild type small airway epithelial cells


title: 0-replicate 2

description: Wild type small airway epithelial cells


title: 1003_T2


title: primary melanocyte C250

value: genomic


title: primary melanocyte C251

value: melanocytes


title: N2 Sup


title: 0-replicate 1

description: Wild type small airway epithelial cells


title: 1003_T1


title: L_170_00: COVID19 patient 170 day 0

city: San Francisco

first: Zicheng

last: Hu

address: 490 Illinois Street

institute: University of California San Francisco

data_processing:
The transcript level count were quantified using Kallisto v0.46.1.
 Remove reads containing N > 10% (N represents the base cannot be determined).
Remove reads containing low quality (Qscore<= 5) base which is over 50% of the total base
Genome_build: GRCh38
Supplementary_files_format_and_content: Transcript count

source_name: Whole blood

extract_protocol:
First the samples were treated with Proteinase K, and then some extractions were performed using Quick-RNA MagBead Kit (R2132) on KingFisher.
Libraries were prepared using ZymoSeq RiboFree Total RNA Library Kit (R3000).

tag: subject

tag: time

value: day 0

tag: symptom severity

value: Moderate Symptomatic

tag: viral shedding

value: Whole blood


title: T5 Sup

value: Male

tag: age


title: 144 hr_Intracellular Dormant Mtb_Rep 2

city: Bangalore

first: Genotypic

last: technology

state: Karnataka

address: 259, Apoorva 4th cross,80 feet Road,RMV 2ND STAGE

country: India

institute: Genotypic Technology

description: Gene expression of Mtb extracted from THP-1 at 144 hr post-infection (dormant)

hyb_protocol: Labeled Cyanine 3-CTP cRNAs  were fragmented to an average size of approximately 50 to 100 nucleotides with fragmentation buffer at 60°C for 30 minutes and the reaction was stopped by adding 2X GE HI-RPM hybridization buffer (Agilent Technologies, In situ Hybridization kit, Part Number5190-0404).The samples were pipetted onto the gasket slide and hybridized onto array (AMADID 26323). The hybridization was carried out at 65°C for 16 hours.After hybridization, the slides were washed using Gene Expression Wash Buffer1 (Agilent Technologies, Part Number 5188-5325) at room temperature for 1 minute and Gene Expression Wash Buffer 2 (Agilent Technologies, Part Number 5188-5326) at 37 oC for 1 minute. The slides were then washed with Acetonitrile for 30 seconds.

scan_protocol: Agilent Scanner (Agilent Technologies, Part Number G2600D).

data_processing: Data extraction from Images was done using Feature Extraction software  and Normalization of the data was done using Limma package: Quantile Normalization

organism: Mycobacterium tuberculosis H37Rv

source_name: Intracellular Dormant Mtb (Vit C+INH), 144 hr, Replicate 2

label_protocol: The sample labeling was performed using Agilent Low Input Quick Amp  Labeling Kit, One Color (Agilent Technologies, Catalog  No: 5190-2331). 20ng of each samples were denatured along with WT primer with a T7 polymerase promoter (T7 polymerase is extremely promoter-specific. The WT primer mix provided in the kit contains a mixture of oligo dT and random nucleotide-based T7 promoter primers, thus enabling robust generation of cRNA from templates of both eukaryotic and prokaryotic origin.). The cDNA master mix was added to the denatured RNA sample and incubated at 40°C for 2 hours for double stranded cDNA synthesis.The cDNA synthesis reaction was stopped at 65°C for 15 min. Synthesized double stranded cDNA were used as template for cRNA generation. cRNA was generated by in vitro transcription and the dye Cy3 CTP incorporated during this step and incubated at 40°C for 2:30 hours. The Cyanine 3-CTP  labeled cRNA sample was purified using Qiagen RNeasy column (Qiagen, Cat No: 74106). The concentration of cRNA and dye incorporation were determined using Nanodrop-1000  and the specific activity was estimated.

growth_protocol: Mtb H37Rv culture was grown aerobically in Dubos medium supplemented with 0.5% BSA, 0.75% Glucose and 0.085% NaCl plus 0.1% Tween-80  (DTA medium) untill logarithmic phase (OD595 ~0.4-0.5). The culture was adjusted to 5x106/ml and frozen at -80°C. THP-1 cells that were cultured in RPMI media supplemented with 10% fetal bovine serum were infected with this frozen Mtb culture at MOI 10:1 (bacteria: THP-1).

extract_protocol: RNA was prepared using Qiagen RNeasy Micro Kit following the manufacturer's recommendations.

treatment_protocol: THP-1 cells were infected with Mtb H37Rv for 4 hours and then treated with 100 µM vitamin C. At 24 hours post-infection, the cells were treated with 4 µg/ ml isoniazid and incubation was continued for 96 and 144 hours post-infection. A parallel set of infected THP-1 cells served as untreated time-matched control.

tag: cell line for infection

value: PMA-differentiated THP-1

tag: bacteria

value: Intracellular Mtb (infected into PMA-differentiated THP-1 macrophages)


title: 1001_T4

tag: Sex

tag: treatment

value: Whole Blood


title: T4 Sup

tag: gender

value: 5 moths


title: primary melanocyte C245

tag: sample type


title: 1001_T3

value: T3 (after meditation)


title: L_012_05: COVID19 patient 012 day 5

value: day 5


title: 1003_T3


title: 144 hr_Intracellular Dormant Mtb_Rep 1

source_name: Intracellular Dormant Mtb (Vit C+INH), 144 hr, Replicate 1


title: T2 Sup

value: 11 moths


title: T3 Sup

value: 2 moths


title: 1001_T2

source_name: T2 (before meditation)_whole blood

value: T2 (before meditation)


title: T1 Sup

value: 1 year and 5 months


title: L_270_00: COVID19 patient 270 day 0

value: Female


title: L_127_05: COVID19 patient 127 day 5


title: 1001_T1

source_name: T1 (baseline)_whole blood

value: T1 (baseline)


title: 144 hr_Intracellular Control Mtb_Rep 1

description: Gene expression of Mtb extracted from THP-1 at 144 hr post-infection (control)

source_name: Intracellular Control Mtb, 144 hr, Replicate 1


title: L_228_00: COVID19 patient 228 day 0


title: 144 hr_Intracellular Control Mtb_Rep 2

source_name: Intracellular Control Mtb, 144 hr, Replicate 2


title: 96 hr_Intracellular Dormant Mtb_Rep 2

description: Gene expression of Mtb extracted from THP-1 at 96 hr post-infection (dormant)

source_name: Intracellular Dormant Mtb (Vit C+INH), 96 hr, Replicate 2


title: SGC7901 SNAI2 OE

city: Shiyan

first: Qin

last: Shanshan

address: Renmin Road 30, Maojian District

institute: Institute of Basic Medical Sciences, School of Basic Medical Sciences, Hubei University of Medicine

data_processing:
Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts. In this step, clean data (clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data. At the same time, Q20, Q30 and GC content the clean data were calculated. All the downstream analyses were based on the clean data with high quality.
Reads were mapped to human genome assembly GRCh38 (ftp://ftp.ensembl.org/pub/release-89/fasta/homo_sapiens/dna/Homo_sapiens.GRCh38.dna.toplevel.fa.gz) using HISAT2 with default parameters.
HTSeq v0.11.2 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene. GTF file:ftp://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_human/release_26/gencode.v26.annotation.gtf.gz.
Genome_build: GRCh38
Supplementary_files_format_and_content: tab-delimited text file include count and FPKM values for each Sample

source_name: gastric cancer cell

growth_protocol: The human gastric cancer cell line  SGC7901 were purchased from the Shanghai Cell Bank of Chinese Academy of Sciences (Shanghai, China). The SGC7901 cell line was cultured in DMEM medium containing 10% fetal bovine serum (FBS), 100 U/mL penicillin, 100 U/mL streptomycin and 0.03% glutamine at 37 oC in 5% CO2.

extract_protocol:
The established gastric cancer cell lines were grown in 6-well plates. After 48 hours, remove the medium and directly add 800μL Trizol into the 6-well plate to harvest samples. Total RNA was extracted using Trizol reagent (Invitrogen, USA) according to the manufacturer’s instructions. The RNA purity and concentration was checked using the NanoPhotometer spectrophotometer (IMPLEN, CA, USA).
A total amount of 1.5 µg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext Ultra RNA Library Prep Kit for Illumina (NEB, USA) following manufacturer's recommendations and index codes were added to attribute sequences to each sample.

treatment_protocol: The lentiviruses for overexpression of SNAI1 and SNAI2 in GC cell lines were purchased from GeneChem (Shanghai, China). Transfection was performed according to the manufacturer’s instructions.

tag: cell type

tag: transfection

value: Lentivirus-SNAI2 Overexpressing


title: L_303_00: COVID19 patient 303 day 0

value: day 0

value: Severe

tag: tissue


title: primary melanocyte C244

source_name: Primary cultured melanocytes

value: genomic

value: melanocytes


title: SGC7901 SNAI1 OE

value: Lentivirus-SNAI1 Overexpressing


title: primary melanocyte C25

value: Male


title: L_006_00: COVID19 patient 006 day 0

value: Whole blood


title: 96 hr_Intracellular Control Mtb_Rep 2

description: Gene expression of Mtb extracted from THP-1 at 96 hr post-infection (control)

source_name: Intracellular Control Mtb, 96 hr, Replicate 2

value: PMA-differentiated THP-1

value: Intracellular Mtb (infected into PMA-differentiated THP-1 macrophages)


title: SGC7901 NC

value: Lentivirus-Negative Control


title: L_327_00: COVID19 patient 327 day 0

value: Moderate Symptomatic


title: 96 hr_Intracellular Dormant Mtb_Rep 1

source_name: Intracellular Dormant Mtb (Vit C+INH), 96 hr, Replicate 1


title: SGC7901_ILF3_siRNA#2

growth_protocol: The human gastric cancer cell line SGC7901 was purchased from the Shanghai Cell Bank of Chinese Academy of Sciences (Shanghai, China). The gastric cancer cell line SGC7901 was cultured in DMEM medium containing 10% fetal bovine serum (FBS), 100 U/mL penicillin, 100 U/mL streptomycin and 0.03% glutamine at 37 oC in 5% CO2.

extract_protocol:
Gastric cancer cells were grown in 6-well plates and transfected with NC siRNAs and the ILF2/ILF3-targeted siRNAs. After 48 hours, remove the medium and directly add 800μL Trizol into the 6-well plate to harvest samples. Total RNA was extracted using Trizol reagent (Invitrogen, USA) according to the manufacturer’s instructions. The RNA purity and concentration was checked using the NanoPhotometer spectrophotometer (IMPLEN, CA, USA).
A total amount of 1.5 µg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext Ultra RNA Library Prep Kit for Illumina (NEB, USA) following manufacturer's recommendations and index codes were added to attribute sequences to each sample. MRNA was purified from total RNA using poly-T oligo-attached magnetic beads.

treatment_protocol: SGC7901 cells were seeded into 6-well plates and grown overnight. The next day, when the cell plating density reached 20%-30%, GC cells were transfected with NC siRNAs and the ILF2/ILF3-targeted siRNAs (final concentration, 50 nM) by Lipofectamine 2000 (Invitrogen) according to the manufacturer’s instructions. At 48 h post-transfection, cells were harvested for RNA sequencing.

value: ILF3 siRNA#2


title: 96 hr_Intracellular Control Mtb_Rep 1

source_name: Intracellular Control Mtb, 96 hr, Replicate 1


title: L_138_05: COVID19 patient 138 day 5

value: day 5


title: SGC7901_ILF3_siRNA#1

value: ILF3 siRNA#1


title: primary melanocyte C241


title: L_215_05: COVID19 patient 215 day 5


title: SGC7901_NC_2

value: negative control siRNA


title: 0 hr_Intracellular Mtb_Rep 1

description: Gene expression of Mtb extracted from THP-1 at 0 hr post-infection

source_name: Intracellular Mtb, 0hr, Replicate 1


title: primary melanocyte C240


title: SGC7901_ILF2_siRNA#2

value: ILF2 siRNA#2


title: 0 hr_Intracellular Mtb_Rep 2

source_name: Intracellular Mtb, 0hr, Replicate 2


title: L_267_00: COVID19 patient 267 day 0


title: L_215_00: COVID19 patient 215 day 0


title: SGC7901_ILF2_siRNA#1

value: ILF2 siRNA#1


title: primary melanocyte C24


title: L_200_05: COVID19 patient 200 day 5


title: primary melanocyte C234


title: OE18-1

city: Harbin

first: Jingli

last: Yang

address: Hexing Road 51

institute: Northeast Forestry University

description: drought for 2 weeks

data_processing:
In order to guarantee the data quality which was used to analysis, the useful Perl script was used to filter the original data (Raw Data)
The reference genomes and the annotation file were downloaded from  the Populus genome (version3.0,https://phytozome.jgi.doe.gov/pz/portal.html#!info?alias=Org_Ptrichocarpa ). Bowtie2 v2.2.3 was used for building the genome index, and Clean Data was then aligned to the reference genome using HISAT2 v2.1.0.
Genome_build: Populus trichocarpa v3.0 (https://phytozome.jgi.doe.gov/pz/portal.html#!info?alias=Org_Ptrichocarpa)
Supplementary_files_format_and_content: FPKM

organism: Populus ussuriensis

source_name: fully expanded leaf

growth_protocol: Seedling grown in greenhouse

extract_protocol:
Fully expanded leaces were harvested, flash frozen on dry ice, and RNA was isolated using CTAB method.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: 6-month old of  WT, OE14 and OE18 plants were grown in greenhouse under dewatered conditions (water withheld) for 1 week

value: leaf

tag: genotype

value: high level overexpression of LbDREB6


title: L_118_05: COVID19 patient 118 day 5

tag: disease state

value: Severe


title: OE18-3

description: drought for 2 weeks


title: primary melanocyte C239

value: genomic

value: melanocytes


title: OE14-3

description: drought for 2 weeks

value: moderate level overexpression of LbDREB6


title: PDC026 SSC

city: London

first: Combiz

last: Khozoie

address: 726 Sir Michael Uren Hub

department: Brain Sciences

country: United Kingdom

institute: Imperial College London

data_processing:
Illumina sequencing files were aligned to the genomic sequence (introns and exons) using GRCh38 (gencode v30) annotation in Cell Ranger v3.0.2
Genome_build: GRCh38_gencode_v30_pre_mRNA
Supplementary_files_format_and_content: Filtered Feature-Barcode Matrix Generated by Cell Ranger Version 3.0.2

molecule: nuclear RNA

source_name: post-mortem cortex

extract_protocol:
Nuclei were isolated from fresh frozen cortical grey matter from AD and control brains using a protocol based on Krishnaswami et al. (2016). Single-nuclei capture was performed using 10X Genomics Single Cell Gene Expression kit v3
10X Genomics Single Cell 3’ Gene Expression kit v3

treatment_protocol: Post-mortem delay < 24hr. Grey matter isolated (white matter removed).

value: post-mortem cortex

value: Non-disease control

tag: braak tangle stage

tag: brain region (somatosensory or entorhinal cortex)

value: SSC

value: female

tag: rin

tag: ptau immunostaining (%ptau positive cells)

tag: amyloid immunostaining (%area stained)


title: primary melanocyte C238

last: Zhang

value: Male


title: primary melanocyte C223


title: primary melanocyte C230


title: SGC7901_NC_1


title: L_199_00: COVID19 patient 199 day 0

source_name: Whole blood

tag: subject

tag: time

value: day 0

tag: age

tag: symptom severity

value: Moderate Symptomatic

tag: viral shedding

value: Whole blood


title: PDC026 EC

value: EC

tag: Sex


title: primary melanocyte C225

tag: gender

tag: sample type


title: L_206_00: COVID19 patient 206 day 0

value: Female


title: primary melanocyte C219

tag: cell type


title: OE14-2

description: drought for 2 weeks

tag: tissue


title: primary melanocyte C220


title: L_126_00: COVID19 patient 126 day 0


title: primary melanocyte C236


title: PDC016 EC


title: WT3

description: drought for 2 weeks

tag: genotype

value: wild type plant


title: L_164_00: COVID19 patient 164 day 0

tag: disease state


title: A319/11 SSC

tag: braak tangle stage

value: male


title: L_143_05: COVID19 patient 143 day 5

value: day 5


title: A277/12 EC

value: AD

tag: brain region (somatosensory or entorhinal cortex)


title: WT2

description: drought for 2 weeks

value: leaf


title: OE18-2

description: drought for 2 weeks

value: high level overexpression of LbDREB6


title: WT1

description: drought for 2 weeks


title: L_313_00: COVID19 patient 313 day 0

value: Asymptomatic


title: A277/12 SSC

value: post-mortem cortex

tag: rin


title: Young2_TetNeg_Lung_P1

city: Cambridge

first: Rebecca

middle: H

last: Herbst

address: 415 Main Street

department: Klarman Cell Observatory

institute: Broad Institute of MIT and Harvard

description:
Full-length RNAseq (SMART-Seq2) reads
processed data file: ss2_rna_data.mtx

data_processing:
10X - Sample demultiplexing, barcode processing, alignment, filtering, UMI counting, and csv files of TCR clonality were performed using the Cell Ranger analysis pipeline (v3.0.2)
Smart-Seq2 - BAM files were converted to de-multiplexed FASTQs using Illumina’s Bcl2Fastq software package v2.17.1.14.
Genome_build: mm10
Supplementary_files_format_and_content: Unique molecular identifiers (UMI) counts table (mtx file), with separate file for cell barcodes and genes. Exported for single-cell and single-nucleus RNA-seq data separatel.

source_name: lung resident T cells

growth_protocol: KP mice were infected with 25,000 titer/units of lentivirus expressing the LucOS construct (Dupage et al 2012).

extract_protocol:
10x: H-2Kb/SIINFEKL specific CD8+ T cells from KrasG12D+/-  Trp53-/- lung adenocarcinoma bearing lungs at different timepoints were sorted and loaded into the 10X Chromium Controller using the Chromium Single Cell 5' Library and Gel Bead Kit (10X Genomics)
Smart-Seq2: H-2Kb/SIINFEKL specific CD8+ T cells from KrasG12D+/-  Trp53-/- lung adenocarcinoma bearing lungs at different timepoints were sorted into 96-well plates with 5 µl lysis buffer comprised of Buffer TCL (Qiagen 1031576) plus 1% 2-mercaptoethanol (Sigma 63689). Following sorting, plates were spun down for one minute at 3,000 rpm and immediately frozen at −80°C.
10X: 10X Chromium Single Cell V(D)J kits (5' gene expression with paired T cell receptor sequencing, and for some samples Feature Barcode detection); Smart-Seq2: For preparation of single-cell libraries we thawed the cells and purified them with 2.2x RNAClean SPRI beads (Beckman Coulter Genomics) without final elution (Shalek et al., 2013). The RNA captured beads were air-dried and processed immediately for cDNA synthesis. We performed SMART-seq2 following the published protocol (Picelli et al., 2013).

treatment_protocol: Mice did not receive any treatments.

tag: strain

tag: mouse id

value: lung resident T cells

value: TetNeg


title: L_227_00: COVID19 patient 227 day 0

tag: subject


title: A319/11 EC

value: Non-disease control

tag: ptau immunostaining (%ptau positive cells)

tag: amyloid immunostaining (%area stained)


title: 6407_TetNeg_Lung_P1


title: L_315_05: COVID19 patient 315 day 5

tag: time

tag: age

tag: symptom severity


title: primary melanocyte C204

tag: gender

value: Male

value: genomic

value: melanocytes


title: A297/16 SSC

value: SSC

tag: Sex


title: primary melanocyte C200

tag: sample type

tag: cell type


title: 832_TetPos_Lung_P1

value: TetPos


title: primary melanocyte C218


title: A297/16 EC

tag: tissue

value: EC


title: primary melanocyte C206


title: primary melanocyte C22


title: primary melanocyte C20


title: PDC016 SSC

tag: disease state

value: female


title: L_108_05: COVID19 patient 108 day 5

value: Moderate Symptomatic

tag: viral shedding

value: Whole blood


title: A169/10 EC

value: AD

tag: braak tangle stage

tag: brain region (somatosensory or entorhinal cortex)


title: 6226_TetNeg_Lung_P1

tag: strain


title: primary melanocyte C205


title: 4351_TetPos_Lung_P1

tag: mouse id


title: primary melanocyte C202


title: A402/14 EC

value: male

tag: rin


title: L_218_05: COVID19 patient 218 day 5

tag: subject

value: day 5


title: L_124_00: COVID19 patient 124 day 0

value: day 0


title: 4351_TetNeg_Lung_P1


title: OE14-1

description: drought for 2 weeks

value: leaf

tag: genotype

value: moderate level overexpression of LbDREB6


title: A053/11 EC

value: post-mortem cortex

tag: ptau immunostaining (%ptau positive cells)

tag: amyloid immunostaining (%area stained)


title: primary melanocyte C21


title: L_135_00: COVID19 patient 135 day 0

tag: time

value: Female

tag: age

tag: symptom severity


title: L_205_05: COVID19 patient 205 day 5

tag: Sex

value: Male


title: 4267_TetPos_Lung_P1

tag: cell type

value: lung resident T cells


title: primary melanocyte C197

tag: gender

tag: sample type

value: genomic

value: melanocytes


title: 4227_TetPos_Lung_P1

value: TetPos


title: A169/10 SSC

tag: tissue

tag: disease state

value: SSC


title: A402/14 SSC

tag: braak tangle stage

tag: brain region (somatosensory or entorhinal cortex)


title: L_165_05: COVID19 patient 165 day 5

tag: viral shedding


title: A163/17 EC

value: EC

tag: rin


title: 4227_TetNeg_Lung_P1

tag: strain

tag: mouse id

value: TetNeg


title: primary melanocyte C198


title: L_337_05: COVID19 patient 337 day 5

tag: subject

value: Moderate Symptomatic

value: Whole blood


title: primary melanocyte C193


title: 3964_TetPos_Lung_P1


title: L_124_05: COVID19 patient 124 day 5


title: A096/14 EC

value: AD

value: male

tag: ptau immunostaining (%ptau positive cells)

tag: amyloid immunostaining (%area stained)


title: A163/17 SSC

tag: age


title: L_136_00: COVID19 patient 136 day 0

tag: time

value: day 0

tag: symptom severity


title: 3964_TetNeg_Lung_P1

tag: cell type


title: L_252_00: COVID19 patient 252 day 0

tag: Sex


title: 3889_TetPos_Lung_P3


title: A282/14 EC

value: female


title: primary melanocyte C191

tag: gender

tag: sample type


title: A096/14 SSC

tag: tissue

tag: disease state


title: 3889_TetPos_Lung_P1


title: A127/11 EC

value: Non-disease control

tag: braak tangle stage

tag: brain region (somatosensory or entorhinal cortex)


title: primary melanocyte C192


title: L_283_05: COVID19 patient 283 day 5

value: day 5

tag: viral shedding


title: primary melanocyte C194


title: 3889_TetNeg_Lung_P2

tag: strain


title: A282/14 SSC

value: post-mortem cortex

tag: rin


title: L_141_05: COVID19 patient 141 day 5

tag: subject

value: Male


title: primary melanocyte C179


title: A053/11 SSC

tag: ptau immunostaining (%ptau positive cells)


title: 3839_TetPos_Lung_P1

tag: mouse id

value: lung resident T cells


title: L_228_05: COVID19 patient 228 day 5

tag: age


title: A127/11 SSC

tag: amyloid immunostaining (%area stained)


title: 3889_TetNeg_Lung_P1


title: L_202_00: COVID19 patient 202 day 0

tag: time

value: Female

tag: symptom severity


title: primary melanocyte C185

value: genomic

tag: cell type

value: melanocytes


title: L_281_00: COVID19 patient 281 day 0

tag: Sex


title: L_243_05: COVID19 patient 243 day 5


title: primary melanocyte C178

tag: gender

tag: sample type


title: 3839_TetNeg_Lung_P1


title: primary melanocyte C173


title: 717T-ADRN_input

city: Amsterdam

first: Richard

last: Volckmann

state: Noord-Holland

address: van der Boechorststraat 6a

department: Laboratory of Experimental Oncology and Radiobiology

country: Netherlands

institute: msterdam UMC and University of Amsterdam

library_source: genomic

data_processing:
Peaks were called using the RSEG algorithm using the following arguments (rseg-diff -d k41.hg19.bed  -m 2 -v -i 20 -c human.hg19.size.bed -o )
Genome_build: hg19
Supplementary_files_format_and_content: bed files: rseg-diff ouput files.

source_name: Neuroblatoma TIC line

extract_protocol: Cultured cells were fixed with 1% formaldehyde. Nuclei were isolated and the DNA was sheared to 200 to 300 bp fragments. Histon-bound DNA was precipitated using antibodies H3K27Ac (#4729, Abcam) and H3K4me3 (#04-745, Millipore).  De-crosslinked DNA was purified using Qiagen PCR purification kit (Qiagen) and quantified with Quant-IT Picogreen (Invitrogen). The DNA was used to generate sequencing libraries according to the manufactures procedure (Life Technologies): The DNA was end-polished, dA-tailed and adaptors with barcodes were ligated. The fragments were amplified (8 cycles) and quantified with a Bioanalyzer (Agilent). The libraries were prepped with the 5500W Flowchip v2 kit  (Life Technologies) and sequenced on the SOLiD Wildfire (Illumina) resulting in 50 bp reads.

tag: growth medium

value: neural stem cell medium

tag: chip antibody


title: L_275_00: COVID19 patient 275 day 0

tag: disease state

tag: tissue


title: NBLW-ADRN_input

source_name: Neuroblatoma cell line


title: 3642_TetNeg_Lung_P1

tag: strain


title: L_253_00: COVID19 patient 253 day 0

tag: viral shedding


title: NBLW-ADRN_H3K27ac


title: NBLW-MES_input


title: primary melanocyte C168


title: primary melanocyte C195


title: 338_TetPos_Lung_P1

value: TetPos


title: primary melanocyte C174


title: primary melanocyte C17


title: 338_TetNeg_Lung_P1

value: TetNeg


title: 3889_TetPos_Lung_P2


title: primary melanocyte C171


title: primary melanocyte C165


title: 337_TetPos_Lung_P1


title: 717T-ADRN_H3K27ac


title: 336_TetPos_Lung_P1


title: L_264_00: COVID19 patient 264 day 0

tag: subject

value: Moderate Symptomatic


title: NBLW-MES_H3K27ac


title: L_339_00: COVID19 patient 339 day 0

value: Whole blood


title: primary melanocyte C167


title: 336_TetNeg_Lung_P1


title: L_282_05: COVID19 patient 282 day 5


title: RS-A

city: Versailles

first: HAKIM

last: MIREAU

address: Route de Saint-Cyr

country: France

institute: INRAE

description: Ribosome footprints

data_processing:
Library strategy: Ribo-Seq
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence. After cytosolic, plastid and mitochondrial rRNA removal, reads comprised between 26-32 nucleotides were selected for mapping to the rapeseed mitochondrial genome using Bowtie 2 with default parameters but allowing 1 missmatch.
Genome_build: Brassica napus mitochondrial DNA (GenBank: AP006444.1) to which we manually added the orf138 gene.
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

organism: Brassica napus

source_name: Flower buds

extract_protocol:
Mitoribosome footprints were prepared from rapeseed flower buds as previously described (Planchard et al, 2018). Ribosome footprints were depleted from ribosomal RNA with the Ribo-Zero Plant kit (Illumina) following manufacturer’s recommendations. Ribo-Seq libraries were prepared using the TruSeq Small RNA library preparation kit (Illumina). For RNA-Seq, total RNAs were extracted from 1/10th of the lysates used for Ribo-Seq analysis and treated with the Ribo-Zero rRNA Removal Kit (Illumina). One hundred ng of the rRNA-depleted RNAs were used for library construction using the NEXTflex Rapid Directional qRNA-Seq Kit (Bioo Scientific) according the manufacturer’s instructions.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Pactol

value: Flower buds

tag: phenotype

value: Restored


title: RS-B

description: Ribosome footprints


title: primary melanocyte C140


title: primary melanocyte C15


title: L_248_05: COVID19 patient 248 day 5


title: 2771_TetNeg_Lung_P1

tag: mouse id


title: primary melanocyte C166


title: CMS-B

description: Ribosome footprints

value: Male sterile


title: primary melanocyte C160


title: 2768_TetNeg_Lung_P1


title: L_279_00: COVID19 patient 279 day 0

value: day 0

tag: age


title: 1073_TetPos_Lung_P1


title: primary melanocyte C146


title: 1073_TetNeg_Lung_P1


title: L_196_00: COVID19 patient 196 day 0


title: 24h

city: Chicago

first: Dolly

last: Mehta

state: Illinois

address: 835 S Wolcott Ave E403

department: Department of Pharmacology and Regenerative Medicine

institute: University of Illinois at Chicago

data_processing:
Libraries prepared sequenced using 75bp SE High Seq to generate FASTq files.
Fastq files for each sample indexed and aligned to mouse reference genome mm10 using Kalisto algorithem
FastqFiles aligned to mouse refference genome annoted using Ensemble transcriptome database
Gene expression comparable between samples calculated using RPKM (reads per Kilobase of transcript per Million) mapped reads.
Differential gene expression between the samples and QC of samples by Principle component analysis on log scaled normalized expression done using DEseq2
Genome_build: mm10
Supplementary_files_format_and_content: Differential expression of genes in pairwise comparisons

source_name: Lung

extract_protocol:
At experimental timepoints, lungs were surgically removed, minced, and digested in a collogenase solution for 50min at 37 degrees, followed by mechanical separation by repeatedly passing tissue through a narrow gauge syringe. Single cell suspension was stained with florescently tagged antibodies for myeloid cell surface markers. Cells were isolated by FACS sorting: GFP+ cells were selected, followed by ly6g negative gating to exclude neutrophils, and CD64+ cells for mature macrophages. RNA from the sorted cells was collected in Trizol and isolated from cells via ethanol precipitation, then submitted for RNA sequencing.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Acute lung injury was induced in LysM-GFP mice through nebulization of a solution of LPS in saline (1mg/ml).

value: Macrophages

tag: background strain

value: 6-8 weeks

tag: time point


title: L_223_00: COVID19 patient 223 day 0

tag: time

value: Male

tag: symptom severity


title: Δrok rep2 - IPOD interphase

city: Ann Arbor

first: Lydia

last: Freddolino

state: MI

address: 1150 W. Medical Center Dr., MSRB 3 room 3315

department: Biological Chemistry

institute: University of Michigan

data_processing:
Adapter removal using the common Illumina Truseq adapter sequences with cutadapt 1.8.1
Read ends were trimmed using Trimmomatic 0.33 in paired end mode, with the trimming steps ‘TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:10’
Reads were aligned using bowtie2 version 2.1.0 with ‘very sensitive’ end-to-end presets, and dovetailed alignments allowed
Surviving DNA reads with proper paired-end alignments were quantified using an in-house pipeline in which each read contributes a total signal of weight 1, divided over the length of the read. Further processing is described in detail in the accompanying paper
RNA reads were subject to quantitation using kallisto v0.43 and differential expression calling using sleuth 0.30.0
Genome_build: E. coli U00096.3
Supplementary_files_format_and_content: For all summary/processed files, note that we provide one file per experimental condition, which represents a consolidation of all replicates for that condition, as described in the accompanying manuscript. Ipod_vs_inp.gr files – Raw IPOD occupancy traces prior to ChIP subtraction, given as a log_2 ratio of extracted to input. The .gr file extension refers to a simple graph type, where the first column indicates a genomic position and the second a corresponding signal chip_vs_inp.gr files – RNA polymerase occupancy given as a log_2 ratio of extracted to input V6rzlog10p.gr files – ChIP-subtracted IPODHR occupancy, z-scored and then used to calculate enrichment p values as described in the text. Tsv files – differential expression calling from sleuth

organism: Escherichia coli str. K-12 substr. MG1655

source_name: Culture lysate

extract_protocol:
DNA samples: Frozen cell pellets were resuspended in 1x IPOD lysis buffer (10 mM Tris HCl, pH 8.0; 50 mM NaCl) containing 1x protease inhibitors (Roche Complete Mini, EDTA free) and 52.5 kU/mL of ready-lyse (Epicentre); 600 uL per pellet (stationary phase cells were diluted 10x prior to lysis due to the much higher biomass of those pellets). We incubated the resuspended pellet for 15 minutes at 30 C, and then placed it on ice. We then sonicated the cells using a Branson digital sonicator at 25% power, using three 10 second bursts with 10 second pauses between bursts. The cells were maintained in a wet ice bath throughout sonication. We then performed a calibrated DNA digestion to sub-200 bp fragments, by adding to the sonicated lysates 60 ug RNase A (Thermo Fisher), 6 uL DNase I (Fisher product #89835), 5.4 uL 100 mM MnCl2, and 4.5 uL 100 mM CaCl2, and then incubating on ice. While the appropriate digestion time must be calibrated for each particular sample type and batch of DNase, 30 minutes of digestion proved appropriate for all samples here. Reactions were quenched after completion by the addition of 50 uL 500 mM EDTA (pH 8.0), typically yielding 50-200 bp fragments. Samples were clarified by centrifugation for 10 minutes at 16,9000xg at 4 C. After clarification, the lysate was mixed with 1 volume of 100 mM Tris base and 2 volumes of 25:24:1 phenol:chloroform:isoamyl alcohol, vortexed, and then incubated for 10 minutes at room temperature. After incubation, the sample was spun at 21,130xg for two minutes at room temperature, allowing formation of a white disc at the aqueous-organic interface enriched for protein-DNA complexes. The complete aqueous phases were removed and discarded, and the remaining disc washed again with 350 microliters TE (10 mM Tris, pH 8.0; 1 mM EDTA), 350 microliters 100 mM Tris base, and 700 microliters 24:1 chloroform:isoamyl alcohol. The resulting mixture was vortexed vigorously, and again centrifuged for 2 minutes at 21,130xg. All liquid was again removed, and the wash was repeated using 700 microliters TE and 700 microliters 24:1 chloroform:isoamyl alcohol. After vortexing, centrifugation, and removal of the final wash (exactly as above), any residual liquid was removed by wicking with a laboratory wipe (if any substantial pools of liquid were present). Finally, the interface was resuspended in 500 microliters of elution buffer (described above), vortexed vigorously, and reverse crosslinked overnight at 65 C. After allowing the samples to cool to room temperature, we then added 100ug of RNase A (Thermo-Fisher), incubated 2 hours at 37 C, then added 200ug of proteinase K (Fermentas) and incubated an additional 2 hours at 50 C. DNA was then recovered via standard phenol-chloroform extraction and ethanol precipitation, following protocols from (Ausubel, 1998). We used Glycoblue (Ambion) as a co-precipitant, NaCl as a precipitating salt (due to the presence of SDS in our solution), and washed with ice-cold 95% ethanol to avoid loss of low molecular weight DNA. RNA: RNA was harvested using Qiagen RNAProtect. RNA was isolated, and rRNA depletion was performed according to the Illumina Ribo-Zero rRNA Removal Kit for Bacteria.
DNA samples: NEB Nebnext Ultra 2 DNA kit, but with a spin column replacing the first bead cleanup (see the accompanying paper for details).

tag: genotype

value: {delta}rok

tag: media

value: Lysogeny broth (LB)

tag: time of harvest

value: logarithmic phase


title: 4h

tag: cell type


title: L_257_00: COVID19 patient 257 day 0

tag: Sex

value: Female


title: L_254_00: COVID19 patient 254 day 0

tag: disease state


title: Δrok rep1 - IPOD RNA-pol ChIP


title: 0h


title: 3642_TetPos_Lung_P1

value: lung resident T cells


title: primary melanocyte C16

city: Rockville

first: Tongwu

address: 9609 Medical Center Drive

institute: National Cancer Institute

data_processing: BeadStudio software v3.2

extract_protocol: genomic DNA was extracted and purified from 106 samples using Gentra Puregene Cell Kit (158745, Qiagen)

tag: gender

tag: sample type

value: genomic

value: melanocytes


title: genomic DNA from ASD patient (ID: 9476)

city: Sao Paulo

first: Ana

middle: Carolina

last: Tahira

state: São Paulo

address: Avenida Vital Brasil, 1500 prédio 55

department: Parasitologia

institute: Instituto Butantan

description: whole blood of ASD patients

hyb_protocol: DNA from whole blood samples were treated using the EZ DNA Methylation kit (Zymo Research, Irvine, California,USA). The bisulfite converted DNA was hybridized in the BeadChip Human Methylation 450 microarrays (Illumina Inc., San Diego, California, USA) following the manufacturer’s protocol

scan_protocol: Arrays were imaged using iScan SQ scanner using the GenomeStudio software (v.2011.1), with the methylation module v.1.9.0 IDAT files

data_processing: Bioconductor packages in R (minfi, ComBat and ChAMP)

label: Cy5 and Cy3

source_name: whole blood

extract_protocol: Automated DNA extraction from peripheral blood was performed using the Maxwell® 1 Instrument (which uses magnetic particles to capture, wash and purify the genomic DNA molecules), following the manufacturer's protocol (Promega Corporation, Madison , Wisconsin, USA). The quality of the extracted DNA was verified by spectrophotometry (NanoDrop® ND-1000, ThermoScientific, Waltham, Massachusetts, USA), in order to guarantee the use of samples with a purity ratio of at least 1.8. DNA quantification was performed using the Qubit® instrument with the dsDNA BR Assay kit (Life Technologies Corporation, Carlsbad, California, USA), according to the manufacturer's instructions.

value: male

tag: tissue

value: Autism Spectrum Disorder

tag: cars

tag: iq

tag: snap


title: Δrok rep2 - IPOD input

tag: strain


title: L_158_00: COVID19 patient 158 day 0

tag: subject

tag: age

value: Moderate Symptomatic

tag: viral shedding

value: Whole blood


title: Δrok rep1 - IPOD input


title: L_225_05: COVID19 patient 225 day 5

tag: time

value: day 5

tag: symptom severity


title: L_266_00: COVID19 patient 266 day 0


title: Trachea, ControlWls_tr2

city: Cincinnati

first: John

middle: M.

last: Snowball

address: 3333 Burnet Ave

department: Pulmonary Research

institute: Cincinnati Childrens Hospital

description: Processed data file: trachea_raw_counts.txt

data_processing:
FASTQ files were aligned using Bowtie2 to mouse reference genome mm10.
RNAseq Normalized gene expressions were generated using Cufflinks.
RNAseq Gene counts were obtained using Bioconductor’s GenomicAlignment.
DeSeq was used to analyze the RNAseq raw gene counts and calculate differentially expressed genes
Genome_build: mm10
Supplementary_files_format_and_content: text file of RNA raw counts

source_name: Wls flox/flox

extract_protocol:
RNA was isolated using trizol according to manufacturer’s instructions
Nextera XT DNA Sample Preparation kits (Illumina Technologies)
RNA sequencing was performed by Cincinnati Children’s Hospital Medical Center’s Gene Expression Core utilizing the Ovation RNA-Seq System v2 (NuGEN)

treatment_protocol: e13.5 traches were dissected out of control and Wls flox/flox, ShhCre+, mutant mice.

value: trachea


title: Trachea, ControlWls_tr


title: genomic DNA from ASD patient (ID: 9481)

description: whole blood of ASD patients


title: PY79 rep2 - IPOD RNA-pol ChIP

tag: genotype

value: wild type

tag: media


title: L_258_05: COVID19 patient 258 day 5


title: primary melanocyte C130

source_name: Primary cultured melanocytes

tag: cell type


title: primary melanocyte C12


title: L_112_00: COVID19 patient 112 day 0

value: day 0

tag: Sex


title: genomic DNA from ASD patient (ID: 9491)

description: whole blood of ASD patients

tag: disease state


title: genomic DNA from ASD patient (ID: 9486)

description: whole blood of ASD patients

tag: gender

value: female


title: L_258_00: COVID19 patient 258 day 0


title: CMS-A

description: Ribosome footprints

value: Pactol

value: Flower buds

tag: phenotype

value: Male sterile


title: primary melanocyte C10

value: Male

tag: sample type


title: L_165_00: COVID19 patient 165 day 0

value: Female

tag: tissue


title: PY79 rep2 - IPOD interphase

value: Lysogeny broth (LB)

tag: time of harvest

value: logarithmic phase


title: PY79 rep1 - IPOD interphase


title: Trachea, WlsShh_tr

source_name: Wls flox/flox, ShhCre+


title: genomic DNA from ASD patient (ID: 9478)

description: whole blood of ASD patients

tag: cars

tag: iq

tag: snap


title: genomic DNA from ASD patient (ID: 9473)

description: whole blood of ASD patients

tag: age


title: agc1-4 rep1

city: Taian

first: yuying

last: zhang

address: No. 61 Mou Zong Street

institute: Shandong Agricultural University

data_processing:
After total RNA was extracted, eukaryotic mRNA was enriched by Oligo(dT) beads, while prokaryotic mRNA was enriched by removing rRNA by Ribo-ZeroTM Magnetic Kit (Epicentre).
Then the enriched mRNA was fragmented into short fragments using fragmentation buffer and reverse transcripted into cDNA with random primers.
Second-strand cDNA were synthesized by DNA polymerase I, RNase H, dNTP and buffer. Then the cDNA fragments were purified with QiaQuick PCR extraction kit, end repaired, poly(A) added, and ligated to Illumina sequencing adapters.
The ligation products were size selected by agarose gel electrophoresis, PCR amplified, and sequenced using Illumina HiSeqTM 2500 by Gene Denovo Biotechnology Co. (Guangzhou, China).
Removing reads containing adapters;  removing reads containing more than 10% of unknown nucleotides (N); removing low quality reads containing more than 50% of low quality (Q-value≤20) bases.
Supplementary_files_format_and_content: tab-delimited text file includes FPKM values and counts for each Sample

organism: Arabidopsis thaliana

source_name: agc1-4, silique

extract_protocol:
The siliques were removed, flash frozen by Liquid Nitrogen, and RNA was harvested using Trizol reagent.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: silique

tag: developmental stage

value: 3 days after pollination (DAP)


title: L_320_00: COVID19 patient 320 day 0

tag: subject

tag: time

tag: viral shedding


title: agc1-4 rep2

tag: genotype


title: agc1-4 rep3


title: L_344_00: COVID19 patient 344 day 0

tag: symptom severity

value: Asymptomatic


title: genomic DNA from ASD patient (ID: 9448)

description: whole blood of ASD patients

value: male

value: Autism Spectrum Disorder


title: genomic DNA from ASD patient (ID: 9488)

description: whole blood of ASD patients

value: Whole blood


title: genomic DNA from ASD patient (ID: 9483)

description: whole blood of ASD patients


title: L_144_00: COVID19 patient 144 day 0

tag: Sex

value: Moderate Symptomatic


title: PY79 rep2 - IPOD input

tag: strain

value: wild type

tag: media


title: WT rep3

source_name: WT, silique

value: WT


title: primary melanocyte C134

tag: gender

value: genomic

tag: cell type

value: melanocytes


title: L_115_05: COVID19 patient 115 day 5

tag: disease state

value: day 5

tag: tissue


title: PY79 rep1 - IPOD input

tag: time of harvest


title: Δrok rep1 - IPOD interphase

value: {delta}rok


title: WT rep2


title: WT rep1


title: Genomic DNA control

city: New York

first: Jun

last: Li

state: NY

address: 1425 Madsion Ave, 14th Fl, RM 14-02

department: Department of Genetics and Genomic Sciences

institute: Icahn School of Medicine at Mount Sinai

data_processing:
The ChIP-seq data was first checked for quality using the various metrics generated by FastQC (v0.11.2). Raw sequencing reads were then aligned to the mouse mm10 genome using default settings of Bowtie (v2.2.0). Only uniquely-mapped reads were retained and duplicates were removed.
Peak-calling was performed using MACS (v2.1.1) with qvalue (minimum FDR) cutoff of 0.05.
Motif enrichment analysis was performed using the Homer package (v4.8.3). The peak annotation and gene ontology analysis was performed using the GREAT program and Panther classification system.
Genome_build: mm10

source_name: Kidney

extract_protocol:
The tissues were fixed with 1%FA in PBS for 60 min at RT. After washing, the tissues were homogenized to a fine powder using BeadBugTM high-energy benchtop homogenizer in the lysis buffer. Chromatin shearing was performed using the Covaris E220 focused-ultrasonicator system. After preclearing with Protein A beads, the chromatin was immunoprecipitated with antibodies. After IP, the beads were washed in sequential low salt buffer, high salt buffer, LiCl washing buffer and TE buffer.
The libraries were prepared using the ThruPlex DNA-seq Kit (Rubicon Genomics) and according to the manufacturer's instructions.


title: L_251_05: COVID19 patient 251 day 5


title: PY79 rep1 - IPOD RNA-pol ChIP


title: Kidney_IgG_control

tag: antibody

value: IgG


title: L_209_05: COVID19 patient 209 day 5

value: Male


title: E13.5_WT_Kidney_H3K27ac_ChIP-seq


title: L_316_00: COVID19 patient 316 day 0

value: day 0


title: L_016_00: COVID19 patient 016 day 0

value: Female


title: L_327_05: COVID19 patient 327 day 5


title: genomic DNA from ASD patient (ID: 9450)

description: whole blood of ASD patients

tag: cars

tag: iq

tag: snap


title: genomic DNA from ASD patient (ID: 9442)

description: whole blood of ASD patients

value: female

tag: age


title: L_311_00: COVID19 patient 311 day 0

tag: subject

tag: time

value: Severe


title: genomic DNA from ASD patient (ID: 9453)

description: whole blood of ASD patients


title: L_209_00: COVID19 patient 209 day 0

tag: viral shedding


title: E13.5_WT_Kidney_Six2_ChIP-seq replicate 1

tag: developmental stage


title: E13.5_WT_Kidney_Six2_ChIP-seq replicate 3


title: L_181_00: COVID19 patient 181 day 0

tag: Sex

tag: symptom severity


title: primary melanocyte C136

tag: sample type


title: L_140_00: COVID19 patient 140 day 0


title: primary melanocyte C104

tag: gender


title: E13.5_WT_Kidney_Brg1_ChIP-seq replicate 2

tag: strain


title: genomic DNA from ASD patient (ID: 9430)

description: whole blood of ASD patients

tag: disease state


title: E13.5_WT_Kidney_Brg1_ChIP-seq replicate 3


title: genomic DNA from ASD patient (ID: 9459)

description: whole blood of ASD patients

tag: tissue


title: L_251_00: COVID19 patient 251 day 0


title: L_243_00: COVID19 patient 243 day 0


title: E13.5_WT_Kidney_Brg1_ChIP-seq replicate 1


title: CKO6_male

city: Burlington

first: Alyssa

last: Richman

state: VT

address: 106 Carrigan Dr, Rowell Building Rm302

department: Department of Biomedical and Health Sciences

institute: University of Vermont

data_processing:
CellRanger version 5.0.1 was used to align reads to the mm10 genome.
Seurat version 3.1.5 was used for further analysis.
Cells were filtered based on gene number and mitochondrial reads.
WT and CKO  samples were integrated and RNA expression data was log normalized.
Clustering was performed using UMAP with 7 dimensions and a resolution of 0.5, and cluster markers/DEGs were identified using default settings of the FindMarkers command.
Genome_build: mm10
Supplementary_files_format_and_content: Filtered feature-barcode matrices contain UMI counts per barcode and gene ID as output of CellRanger Count.

molecule: polyA RNA

source_name: Microglia

extract_protocol:
10x Genomics single cell 3’ V3 system
RNA libraries were prepared following 10X 3' system manufacturer instuctions.

treatment_protocol: Male p38αCKOCx3cr1-ER and WT control littermates were treated with tamoxifen to induce Cre activity, followed by EAE induction at 4 weeks post tamoxifen treatment. On day 20 post-EAE induction, microglia were isolated from the brain and spinal cord using FACS based on CD11b+ CD45int/lo CX3CR1+ Ly6C- Ly6G- TCRb- CD19- staining.

tag: cell type

value: Microglia

tag: condition

value: Conditional Knock Out

tag: treatment

value: EAE induced with 2XMOG/CFA


title: CKO5_male


title: ΔstpaΔhns RDM logarithmic rep 3 - IPOD RNA-pol ChIP

tag: genotype

value: {delta}stpa{delta}hns

tag: media

value: M9 Rich Defined Media (RDM) + glucose

tag: time of harvest

value: logarithmic phase


title: genomic DNA from ASD patient (ID: 9432)

description: whole blood of ASD patients

value: male

tag: age

value: Whole blood

value: Autism Spectrum Disorder

tag: cars

tag: iq

tag: snap


title: L_270_05: COVID19 patient 270 day 5

extract_protocol:
First the samples were treated with Proteinase K, and then some extractions were performed using Quick-RNA MagBead Kit (R2132) on KingFisher.
Libraries were prepared using ZymoSeq RiboFree Total RNA Library Kit (R3000).

tag: subject

tag: time

value: day 5

tag: Sex

value: Moderate Symptomatic

tag: viral shedding


title: genomic DNA from ASD patient (ID: 9462)

description: whole blood of ASD patients

tag: gender


title: ΔstpaΔhns RDM logarithmic rep 4 - IPOD RNA-pol ChIP

tag: strain


title: ΔstpaΔhns RDM logarithmic rep 2 - IPOD RNA-pol ChIP


title: primary melanocyte C14

tag: sample type

value: genomic

value: melanocytes


title: ΔstpaΔhns RDM logarithmic rep 1 - IPOD RNA-pol ChIP


title: L_303_05: COVID19 patient 303 day 5

tag: disease state

value: Male

tag: symptom severity

tag: tissue


title: L_295_00: COVID19 patient 295 day 0

value: day 0


title: genomic DNA from ASD patient (ID: 9456)

description: whole blood of ASD patients


title: genomic DNA from ASD patient (ID: 9427)

description: whole blood of ASD patients


title: genomic DNA from ASD patient (ID: 9444)

description: whole blood of ASD patients

value: female


title: Δstpa RDM logarithmic rep 2 - IPOD RNA-pol ChIP

tag: genotype

value: {delta}stpa


title: genomic DNA from ASD patient (ID: 9437)

description: whole blood of ASD patients


title: genomic DNA from ASD patient (ID: 9415)

description: whole blood of ASD patients


title: CKO4_male

tag: cell type

value: Microglia

tag: condition

tag: treatment


title: genomic DNA from ASD patient (ID: 9391)

description: whole blood of ASD patients

tag: age

tag: cars


title: WT3_male

value: p38alphaf/f Cre-

value: Wildtype


title: L_268_05: COVID19 patient 268 day 5

value: Female


title: genomic DNA from ASD patient (ID: 9403)

description: whole blood of ASD patients

tag: iq

tag: snap


title: WT2_male

value: EAE induced with 2XMOG/CFA


title: L_202_05: COVID19 patient 202 day 5

tag: subject

tag: time


title: genomic DNA from ASD patient (ID: 9394)

description: whole blood of ASD patients


title: L_162_05: COVID19 patient 162 day 5

tag: Sex

tag: viral shedding


title: WT1_male

tag: strain


title: genomic DNA from ASD patient (ID: 9406)

description: whole blood of ASD patients

tag: gender


title: CKO_female_HTO

description: HTO for three KO replicates: K6, K7, K8

data_processing:
CellRanger version 5.0.1 was used for read alignment to mm10 and quantification of hashing barcodes. Supplementary files conatin comma-delimited file for hashtag oligo mapping.
Seurat version 3.1.5 was used to demux samples based on centered log ratio normalized hashing barcode counts and for further analysis.
RNA expression data was log normalized and  scaled.
Cells were filtered based off number of genes and percent mitochondrial reads per cell.
Clustering was performed using UMAP with 7 dimensions and a resolution of 0.5.
Cluster markers and DEGs were identified using default settings of the FindMarkers command
Genome_build: mm10
Supplementary_files_format_and_content: Filtered feature-barcode matrices contain UMI/antibody hashtag counts per barcode and gene ID as output of CellRanger Count for feature barcodes.

extract_protocol:
10x Genomics single cell 3’ V3 system
RNA and HTO libraries were prepared following 10X 3' system manufacturer instuctions and CITE-seq protocols (Stoeckius et al, 2017)

treatment_protocol: Female p38αCKOCx3cr1-ER and WT control littermates were treated with tamoxifen to induce Cre activity, followed by EAE induction at 4 weeks post tamoxifen treatment. On day 20 post-EAE induction, microglia were isolated from the brain and spinal cord using FACS based on CD11b+ CD45int/lo CX3CR1+ Ly6C- Ly6G- TCRb- CD19- staining. Cell hashing was used to mark biological samples using barcoded antibodies for CD45 (clone 30-F11), MHC class I (clone M1/42), and control Rat IgG2a following CITE-seq and TotalSeq-B protocols(Stoeckius et al, 2017).

value: Conditional Knock Out


title: L_140_05: COVID19 patient 140 day 5

data_processing:
The transcript level count were quantified using Kallisto v0.46.1.
 Remove reads containing N > 10% (N represents the base cannot be determined).
Remove reads containing low quality (Qscore<= 5) base which is over 50% of the total base
Genome_build: GRCh38
Supplementary_files_format_and_content: Transcript count

tag: disease state


title: Δstpa RDM logarithmic rep 1 - IPOD RNA-pol ChIP

tag: media

value: M9 Rich Defined Media (RDM) + glucose

tag: time of harvest

value: logarithmic phase


title: ihfA::Kan infB::Chlor RDM logarithmic rep 1 - IPOD RNA-pol ChIP

tag: genotype

value: ihfA::Kan infB::Chlor


title: E13.5_WT_Kidney_Six2_ChIP-seq replicate 2

tag: developmental stage

tag: antibody


title: genomic DNA from ASD patient (ID: 8984)

description: whole blood of ASD patients

value: male

tag: tissue

value: Whole blood

value: Autism Spectrum Disorder


title: CKO_female_GEX

description: GEX for three KO replicates: K6, K7, K8

tag: condition

tag: treatment


title: ΔhupA hupB::kan RDM logarithmic rep 2 - IPOD RNA-pol ChIP

value: {delta}hupA hupB::kan


title: genomic DNA from ASD patient (ID: 9383)

description: whole blood of ASD patients

tag: age

tag: cars

tag: iq


title: L_306_00: COVID19 patient 306 day 0

tag: subject

tag: time

value: Male

tag: symptom severity

value: Moderate Symptomatic


title: ΔhupA hupB::kan RDM logarithmic rep 1 - IPOD RNA-pol ChIP

tag: strain


title: genomic DNA from ASD patient (ID: 9409 or 9282)

description: whole blood of ASD patients

tag: gender

tag: snap


title: L_268_00: COVID19 patient 268 day 0

tag: disease state

value: day 0

tag: Sex

tag: viral shedding


title: Δhns RDM logarithmic rep 4- IPOD RNA-pol ChIP

tag: genotype

value: {delta}hns

tag: media

tag: time of harvest


title: L_138_00: COVID19 patient 138 day 0

tag: tissue


title: WT_female_GEX

description: GEX for three WT replicates: W3, W4, W5

value: Microglia

tag: condition

tag: treatment


title: WT_female_HTO

description: HTO for three WT replicates: W3, W4, W5

value: p38alphaf/f Cre-


title: L_183_05: COVID19 patient 183 day 5

value: day 5

tag: age


title: Δhns RDM logarithmic rep 2 - IPOD RNA-pol ChIP


title: KO3_Ovary_ZC257

city: Chapel Hill

first: Alain

last: Laederach

state: NC

institute: UNC-Chapel Hill

data_processing:
355,122,201 reads were sequenced using an Illumina HiSeq by Genewiz (https://www.genewiz.com/). On average, 50-60 million reads per sample (4 WT and 4 L2-cKO) were trimmed to remove possible adapter sequences and nucleotides with poor quality using Trimmomatic v.0.36. In all cases over 97.5% of the trimmed reads were mapped to the Mus musculus GRCm38 reference genome available on ENSEMBL using the STAR aligner v.2.5.2b (43). The STAR aligner is a splice aligner that detects splice junctions and incorporates them to help align the entire read sequences. Unique gene hit counts were calculated by using featureCounts from the Subread package v.1.5.2. Only unique reads that fell within exon regions were counted in a strand-specific manner since the library was strand specific.
After extraction of gene hit counts, the gene hit counts table was used for downstream differential expression analysis. Using DESeq2, a comparison of gene expression between the customer-defined groups of samples was performed (44). The Wald test was used to generate p-values and log2 fold changes. Genes with an adjusted p-value < 0.05 and absolute log2 fold change > 1 were called as differentially expressed genes for each comparison.
Genome_build: GRCm38
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: ovary

growth_protocol: Conditional Zfp36l2 knockout mice carrying the loxP sites flanking exon 2 of Zfp36l2 (Zfp36l2fl/+) were generated by Xenogen Biosciences (Cranbury, NJ) using standard embryonic stem (ES) cell targeting techniques. Mice carrying both Zfp36l2 alleles containing loxP sites were kindly obtained from Dr. Blackshear by MTA and are referred here as Zfp36l2fl/fl (23). B6.CTg(CMV-Cre)1Cgn/J (stock#006054) mice were purchased from Jackson Laboratory. Deletion of Zfp36l2 by conditional knockout was obtained by crossing the CMV-Cre transgenic females with the Zfp36l2 floxed males (Zfp36l2fl/fl) to generate Zfp36l2fl/-;CMV-Cre in the first generation (F1). When Zfp36l2fl/-;CMV-Cre (F1) females were mated with Zfp36l2fl/-;CMV-Cre (F1) males, animals of both sex carrying the recombined Zfp36l2 alleles were generated on the second generation (Zfp36l2-/-;CMV-Cre), these animals are referred here as L2-cKO. Animals carrying both WT copies of Zfp36l2, as well as the Tg.CMV-Cre, were used as WT littermate controls for experiments (Suppl. Fig. 6). Animals were housed in the Dental School vivarium of UNC’s School of Medicine, Chapel Hill. All experiments were in revised and approved by Institutional Animal Care and Use Committee (IACUC) from the University of North Carolina at Chapel Hill.  Mice were genotyped by polymerase chain reaction. For the Zfp36l2flox,+ or-  the following primers used:  F: 5' AGATACCAAACACTTAGGTCTCAGATGAG 3' R: 5' CGACCATTACAGGACCCAGAAA 3'. For the presence of the Tg.CMV-Cre, we used as primers: F: 5' TGGGCCAGCTAAACATGCTT 3' and R: 5' GGTGTTATAAGCAATCCCCAGA 3'.

extract_protocol:
Trizol Plus RNA extraction kit (Thermo Fisher)
NEBNext Ultra II library prep kit with polyA RNA selection

value: F


title: Δhns RDM logarithmic rep 3 - IPOD RNA-pol ChIP


title: L_301_05: COVID19 patient 301 day 5

city: San Francisco

first: Zicheng

last: Hu

institute: University of California San Francisco

value: Severe


title: KO2_Ovary_ZC205


title: Δhns RDM logarithmic rep 1 - IPOD RNA-pol ChIP


title: genomic DNA from ASD patient (ID: 9412)

description: whole blood of ASD patients

tag: cars

tag: iq


title: KO1_Ovary_ZC151


title: genomic DNA from ASD patient (ID: 9385)

description: whole blood of ASD patients


title: genomic DNA from ASD patient (ID: 9397)

description: whole blood of ASD patients


title: L_118_00: COVID19 patient 118 day 0

tag: subject

tag: time


title: L_279_05: COVID19 patient 279 day 5

tag: symptom severity


title: Δhfq RDM logarithmic rep 3 - IPOD RNA-pol ChIP

tag: strain

value: {delta}hfq


title: E13.5_Six2_mutant_ Kidney_Brg1_ChIP-seq

tag: developmental stage

tag: antibody


title: Δhfq RDM logarithmic rep 2 - IPOD RNA-pol ChIP

value: M9 Rich Defined Media (RDM) + glucose


title: L_001_00: COVID19 patient 001 day 0

tag: disease state

tag: Sex

value: Female

value: Asymptomatic


title: WT2_Ovary_ZC210

tag: genotype

value: WT

tag: gender


title: L_142_00: COVID19 patient 142 day 0

tag: viral shedding

value: Whole blood


title: WT1_Ovary_ZC150


title: Δfis RDM logarithmic rep 2 - IPOD RNA-pol ChIP

value: {delta}fis

tag: media

tag: time of harvest

value: logarithmic phase


title: WT3_Ovary_ZC256


title: L_173_05: COVID19 patient 173 day 5

tag: tissue


title: Δfis RDM logarithmic rep 1 - IPOD RNA-pol ChIP


title: L_267_05: COVID19 patient 267 day 5

value: Male

tag: age


title: L_319_00: COVID19 patient 319 day 0

value: Moderate Symptomatic


title: Δhfq RDM logarithmic rep 1 - IPOD RNA-pol ChIP