title: PVP-3

description: PVP: Mixed samples of seed embryo seedling roots, stems and leaves in medium supplemented with PVP

value: Roots, stems and leaves mixed

value: Tissue culture 30 days after rooting

value: PVP


title: Nasal, ARDS-032-ND3

status: Public on Dec 24 2021

type: SRA

city: Cincinnati

first: Brian

middle: Michael

last: Varisco

state: OH

address: 3333 Burnet Avenue, MLC 7006

department: Critical Care Medicine

country: USA

institute: Cincinnati Children's Hospital Medical Center

library_source: transcriptomic

data_processing:
Specimens were sequenced, demultiplexed and each  aligned and counted using STAR.
Illumina Novaseq 6000
STAR Alignment to GRCh38
DESeq2
ToppGene
Genome_build: GRCh38
Supplementary_files_format_and_content: fastq

molecule: total RNA

organism: Homo sapiens

source_name: Nasal

extract_protocol:
Specimens stored in RNAProtect. 1:100 beta-mercaptoethanol added during thawing, cells extracted and RNA collected using QIAShredder and RNEasy columns.
RNA barcoded and amplified using NEBNext Low-Input RNA Kit.

tag: group

value: PARDS

tag: subgroup

value: A

tag: time

value: study day 3


title: SLX_14251_i710_i517

city: Cambridge

first: Bernhard

last: Blob

address: 47 Bateman Street

country: United Kingdom

institute: Sainsbury Laboratory, Cambridge University

data_processing:
De-multiplexed fastq files were aligned using HISAT2
Picard SortSam was used to create .bam from .sam files, Picard Merge2 to merge .bam files where necessary
Cuffquant was used to create abundance files
Cuffnorm was used with all abundance files from all cells to get read counts.
Genome_build: TAIR10, Release 36
Supplementary_files_format_and_content: tab-delimited text file with read counts for each cells and gene

organism: Arabidopsis thaliana

source_name: phloem root meristem

growth_protocol: Arabidopsis seeds were surface sterilized in a bleach solution (5% sodium hypochlorite with 0.02% tween 20) for 5 minutes with gentle rotation. Seeds were then thoroughly washed at least 5 times with sterile distilled water and imbibed for 2 – 5 days at 4 °C in the dark. Seeds were germinated on 1/2 strength Murashige and Skoog (½ MS) agar medium which contains 1% sucrose and 0.8% difco agar. Seedlings and adult plants were grown under long-day condition – 16 hours light (188 μmol m−2 s−1) and 8 hours dark at 23 °C.

extract_protocol:
Arabidopsis root protoplasts were isolated according to the published protocol (Clark et al., 2018). In short, sterilized seeds were plated onto the nylon mesh (57-103, Nitex) placed on the top of MS agar media. Two rows of seeds comprising approximately 100-150 seeds per row were then grown vertically for 5 days in long-day growth condition. To isolate root protoplasts, ⅓ of the root was cut and chopped on the surface of the mesh and collected in buffer containing cell wall degrading enzymes - 1.5 g Cellulase (C1794, Sigma) and 0.1 g Pectolyase (P3026, Sigma) in 100 ml protoplasting solution. After 1 hour of incubation with occasional stirring, the protoplasts were spun down (200 rcf for 6 min) in 15 ml Falcon tube and after removal of supernatant, cells were resuspended in 700 ul protoplasting solution without enzymes. After filtering with 70 um and 40 um cell strainers sequentially, FACS was performed using 70 micron nozzle at 10 psi. Fluorescence positive cells were collected in a round-bottom polystylene tube that contains 150 - 200 ul RLT buffer with beta-mercaptoethanol (10 ul / 1 ml RLT buffer, RNeasy micro kit protocol, Qiagen). Cell sorting was performed for about 15 min and collected cells were immediately frozen on dry ice and kept in -80 °C for up to one week. For single cell transcriptomics, protoplasts were produced and isolated as described here, but sorted individually into 96-well plates.
Libraries were prepared using Illumina Nextera XT DNA preparation kit and either Nextera XT index kit – 96 indexes or Nextera XT index kit v2.

tag: reporter line

tag: possible cell type

value: PSE

tag: developmental stage

value: protoplast of 5 day old root meristems


title: Nasal, ARDS-032-ND1

value: study day 1


title: PVP-2

city: Hefei

first: manman

last: Wang

address: 103 Meishan Road

country: China

institute: Anhui University of Chinese Medicine

data_processing:
De novo transcriptome assemblies
Quantification for assembled transcripts
Functional annotation of transcripts
Sequence mapping and differential expression analysis
Supplementary_files_format_and_content: tab-delimited text files include raw counts values for each Sample…

organism: Paeonia suffruticosa

source_name: Roots, stems and leaves mixed

extract_protocol:
Total RNA was isolated using a TRIzol total RNA extractibn kit,which yielded > 2 μg of total RNA per sample. RNA quality was examined by 0.8% agarose gel electrophoresis and spectrophotometry.
The library was sequenced using the Illumina NovaSeq 6000 sequencing platform (Paired end150) to generate raw reads

tag: tissue

tag: age

tag: treatment


title: SLX_14251_i710_i508


title: Nasal, ARDS-031-ND7

value: C

value: study day 7


title: PVP-1


title: AC-3

description: Mixed sample of seed embryo seedling roots, stems and leaves in medium supplemented with AC

value: AC


title: Nasal, ARDS-031-ND3


title: SLX_14251_i710_i506


title: SLX_14251_i710_i505


title: Nasal, ARDS-030-ND7


title: SLX_14252_i704_i517


title: SLX_14251_i710_i504


title: Outer.Unloaded.IL1.5

city: Durham

first: Amy

last: McNulty

state: NC

address: 203 Research Dr

department: Orthopaedic Surgery

institute: Duke University

data_processing:
Basecalling by Illumina RTA2
RNA-seq data was processed using the TrimGalore toolkit which employs Cutadapt to trim low quality bases and Illumina sequencing adapters from the 3’ end of the reads. Only reads that were 20nt or longer after trimming were kept for further analysis
Reads were mapped to the Sscrofa11.1v91 version of the pig genome and transcriptome using the STAR RNA-seq alignment tool.  Reads were kept for subsequent analysis if they mapped to a single genomic location
Gene counts were compiled using the HTSeq tool
Normalization and differential expression analysis was performed using the DeSeq2 BioConductor packge in the R statistical programming language
Genome_build: Sscrofa11.1v91
Supplementary_files_format_and_content: Matrix tables with raw gene counts and DESeq2 normalized counts for every gene and every sample

organism: Sus scrofa

source_name: medial meniscus

growth_protocol: Cylindrical explants from the inner or outer regions of porcine medial menisci were obtained using a 5mm biopsy punch and trimmed to a uniform 2mm thickness retaining the femoral surface, using a custom cutting jig. Explants were washed for 1 hour in DMEM-HG with 10X antibiotic/antimycotic, then transferred to complete culture media with ascorbic acid overnight before initiation of treatment.

extract_protocol:
Explants were pulverized in TRIzol under liquid nitrogen using a freezer mill. RNA was extracted by TRIzol/chloroform separation according to the manufacturer’s protocol, then resuspended in lysis buffer and column purified according to the Norgen RNA extraction kit protocol (Catalog # 48300; Norgen Biotek Corp.)
KAPA Stranded mRNA-Seq Kit--KK8421

treatment_protocol: Fresh culture media with or without 0.1 ng/mL IL-1α was added and explants were subjected to 10% dynamic compression in a sine wave pattern at 1Hz, using a custom bioreactor for 4 hrs. Loading was repeated every 24 hrs for a total of three loading sessions. Immediately following the final loading session, explants were rinsed in phosphate buffered saline, flash frozen in liquid nitrogen, and stored at -80C until RNA extraction was performed.

tag: zone

value: Outer

tag: treatment (load)

value: Unloaded

tag: treatment (il-1)


title: cDNA_rtf2_rep3

city: Brighton

first: Alice

last: Budden

address: Science Park Road

department: GDSC

institute: University of Sussex

description: derived from mRNA

data_processing:
Library strategy: Nanopore Direct cDNA-Sequencing
pychopper is used for processing and filtering for full length reads
processed reads are mapped to the reference genome using minimap2
mapped reads are then processed by stringtie in long read mode to evaluate the transcripts and produce a GFF annotation file
standard parameters were used as set in the nanopore pipeline used to produce the results (https://github.com/nanoporetech/pipeline-nanopore-ref-isoforms)
Genome_build: Schizosaccharomyces pombe reference sequence (http://www.pombase.org/downloads/genome-datasets)
Supplementary_files_format_and_content: files ending in .coverage.csv contain read counts for each position along the genome
Supplementary_files_format_and_content: files ending in .tracking.csv contain all transcripts identified by stringtie with associated transcript type allocation and their respective expression levels in FPKM and TPM

organism: Schizosaccharomyces pombe

source_name: Schizosaccharomyces pombe

growth_protocol: Cells were grown to mid log phase in YE media at 30C

extract_protocol:
Total RNA isolated from whole cells were used to isolate mRNA using poly-dT beads
cDNA libraries were constructed using mRNA following the Nanopore Direct cDNA Sequencing Protocol

tag: strain number

tag: genotype

value: rtf2{delta}::NAT, ade6-704, leu1-32, ura4-d18


title: SLX_14251_i710_i503


title: Nasal, ARDS-030-ND3-1

value: B


title: SLX_14251_i710_i507


title: SLX_14252_i705_i503


title: Outer.Unloaded.IL1.1


title: Nasal, ARDS-030-ND14

value: study day 14


title: cDNA_rtf2_rep2

description: derived from mRNA


title: PBMCs, Mother of proband, 7011.03 (mRNA)

type: RNA

city: Denver

first: Hara

last: Levy

state: CO

address: 1400 Jackson Street

department: Pediatrics

institute: National Jewish Health

description:
Gene expression data from PBMCs
Sample name: 7011.03

hyb_protocol: The labeled samples were then hybridized onto two arrays: Human Clariom D array (ThermoFisher Scientific),  GeneChip miRNA 4.0 array (ThermoFisher Scientific) for 16hrs at 45C

scan_protocol: GeneChips were scanned using a 7G Affymetrix Genechip Scanner

data_processing: Profiling data was normalized in the robust multi-array average (RMA) procedure and then processed using Transcriptome Analysis Console (ThermoFisher Scientific, version 4)

label: Biotin

source_name: Mother of proband

label_protocol: Biotinylated cRNA was prepared according to the Affymetrix protocol from at least 300ng RNA

growth_protocol: THP-1 cells were maintained in RPMI 1640 medium supplemented with 10% FBS and 2 mmol/L L-glutamine. THP-1 monocytes were differentiated into macrophages by adding 200 nM PMA to the media for 48 hours.

extract_protocol: Total RNA was isolated using Trizol (Invitrogen) according to manufacturer's  protocol.

treatment_protocol: THP-1 monocytes and macrophages were co-cultured for 9 hours with plasma (without PMA) collected from the enrolled subjects and healthy controls

tag: disease state

value: no known disease

value: -/+ CFTR

tag: cell type

value: Peripheral Blood Mononuclear cells (PBMCs)


title: PBMCs, Mother of proband, 7010.03 (mRNA)

description:
Gene expression data from PBMCs
Sample name: 7010.03


title: AC-1

value: Roots, stems and leaves mixed

value: Tissue culture 30 days after rooting


title: Outer.Unloaded.IL1.2


title: SLX_14251_i710_i502


title: PBMCs, CF proband, 7018.01 (mRNA)

description:
Gene expression data from PBMCs
Sample name: 7018.01

source_name: CF proband

value: classical CF

value: -/- CFTR


title: PBMCs, CF proband, 7011.01 (mRNA)

description:
Gene expression data from PBMCs
Sample name: 7011.01


title: PBMCs, CF proband, 7010.01 (mRNA)

description:
Gene expression data from PBMCs
Sample name: 7010.01


title: Nasal, ARDS-031-ND1

value: PARDS


title: SLX_14252_i708_i503

value: PSE

value: protoplast of 5 day old root meristems


title: PBMCs, CF proband, 7003.01 (mRNA)

description:
Gene expression data from PBMCs
Sample name: 7003.01


title: PBMCs, Mother of proband, 7008.03 (mRNA)

description:
Gene expression data from PBMCs
Sample name: 7008.03


title: PBMCs, CF proband, 7008.01 (mRNA)

description:
Gene expression data from PBMCs
Sample name: 7008.01


title: Outer.Loaded.IL1.2

value: Loaded


title: cDNA_rtf2_rep1

description: derived from mRNA


title: Nasal, ARDS-029-ND7

value: C

value: study day 7


title: PBMCs, Mother of proband, 7003.03 (mRNA)

description:
Gene expression data from PBMCs
Sample name: 7003.03


title: SLX_14251_i709_i517


title: Outer.Loaded.IL1.4

value: Outer


title: cDNA_WT_rep3

description: derived from mRNA


title: Nasal, ARDS-030-ND1-3

value: study day 1


title: Outer.Loaded.IL1.5


title: SLX_14251_i709_i508


title: AC-2

value: AC


title: SLX_14251_i709_i507


title: Nasal, ARDS-029-ND14

value: study day 14


title: cDNA_WT_rep2

description: derived from mRNA


title: cDNA_WT_rep1

description: derived from mRNA


title: SLX_14251_i709_i506


title: Inner.Unloaded.IL1.3

value: Inner

value: Unloaded


title: Inner.Unloaded.IL1.4


title: SLX_14251_i709_i505


title: Nasal, ARDS-029-ND3

value: A

value: study day 3


title: Inner.Unloaded.IL1.2


title: SLX_14251_i709_i504


title: Nasal, ARDS-029-ND1

value: D


title: SLX_14251_i709_i503


title: DP18211

city: Houston

first: Cintia

middle: S.

last: de Paiva

state: TX

address: 6565 Fannin Street NC505G

department: Ophthalmology

institute: Baylor College of Medicine

hyb_protocol: One hundred nanograms of total RNA were hybridized with the NanoString Technologies nCounter Gene Expression GE- Mouse -Immunology v2 Panel Codeset containing 594 unique pairs of 35-50bp reporter probes and biotin-labeled capture probes, including internal reference controls. Overnight hybridization occurred for 20 hours at 65°C. Removal of excess probes with magnetic bead purification was performed on the nCounter Prep Station (software v4.0.11.2) on the High Sensitivity assay. Briefly, the probe-mRNA structure was affinity purified by its 3’ end to remove excess reporter probes, then by its 5’ end to remove excess capture probes. Once unbound probes were washed away, the tripartite structure was bound to the streptavidin-coated cartridge by the biotin capture probe, aligned by an electric current (negative to positive), and immobilized. Photobleaching and fluorophore degradation was prevented with the addition of SlowFade.

scan_protocol: The cartridge containing immobilized samples was transferred to the nCounter Digital Analyzer (software v3.0.1.4) and scanned at 555 field of view (FOV). An epi-fluorescent microscope and CCD camera identified sets of fluorescent spots, which were tabulated for data output. Quality control metrics were recorded using the nSolver Analysis Software v4.0.6.2.

data_processing: Data processing was analyzed with nCounter and ROSALIND software. Data in Matrix is after normalization by ROSALIND.

organism: Mus musculus

source_name: nodes and spleens

extract_protocol: RNA was extracted using the Qiagen mini plus columns according to the manufacturer's protocol. RNA quantity and quality was measured with NanoDrop and Bioanalyzer.

treatment_protocol: Aged C57BL/6 mice of different ages were naïve and pooled by age. Ocular draining lymph nodes and spleens were made into a single cell suspension and Tregs (CD4+CD25+GIRTR+) or non-Tregs (CD4+CD25negGITRneg) were sorted. After sorting, cells were pelleted, and RNA lysis buffer from the Qiagen mini plus was added. Samples were stored at -80C until ready to be extracted.

tag: strain

tag: Sex

value: female

tag: age/group

value: young non-Treg

tag: cells

value: sorted cells

tag: origin

value: nodes and spleens

value: non-Treg

tag: age (months)

tag: cell population


title: Inner.Loaded.IL1.5

value: Loaded


title: DP18210

tag: group


title: SLX_14251_i708_i517

tag: reporter line

tag: possible cell type

value: PSE

tag: developmental stage

value: protoplast of 5 day old root meristems


title: DP18208

value: aged Treg

value: Treg


title: Nasal, ARDS-028-ND3-2

value: PARDS

tag: subgroup

tag: time


title: Inner.Loaded.IL1.4

tag: zone

tag: treatment (load)

tag: treatment (il-1)


title: DP18209


title: SLX_14251_i709_i502


title: Nasal, ARDS-026-ND7

value: C

value: study day 7


title: DP18206


title: Nasal, ARDS-027-ND1

value: study day 1


title: SLX_14251_i708_i508


title: SLX_14251_i708_i507


title: DP18207


title: Nasal, ARDS-028-ND7

value: B


title: DP18205

value: young Treg


title: Outer.Unloaded.2

value: Outer

value: Unloaded


title: Nasal, ARDS-026-ND3

value: study day 3


title: Nasal, ARDS-026-ND1

value: A


title: Inner.Loaded.IL1.3

value: Inner


title: Outer.Unloaded.6


title: SLX_14251_i708_i506


title: Outer.Unloaded.3


title: Outer.Loaded.1


title: Nasal, ARDS-025-ND3


title: SLX_14251_i708_i504


title: Nasal, ARDS-025-ND1


title: Outer.Loaded.3


title: SLX_14251_i708_i503


title: Outer.Loaded.2


title: Nasal, ARDS-024-ND7


title: DP18204

value: female

value: sorted cells

value: nodes and spleens


title: DP18202

value: aged non-Treg

value: non-Treg


title: DP18201


title: Inner.Unloaded.3


title: SLX_14251_i708_i502

value: PSE

value: protoplast of 5 day old root meristems


title: Nasal, ARDS-024-ND3

value: PARDS


title: Inner.Unloaded.2


title: DP18200


title: DP20323_12


title: DP18203

value: Treg


title: Inner.Unloaded.5


title: SLX_14251_i707_i508


title: Inner.Loaded.4

value: Loaded


title: Nasal, ARDS-024-ND1

value: study day 1


title: SLX_14251_i708_i505


title: DP20323_11

value: aged Treg


title: DP20323_10


title: SLX_14251_i707_i507


title: Inner.Loaded.1


title: SLX_14251_i707_i506


title: Nasal, ARDS-023-ND3

value: Unk


title: SLX_14251_i711_i503


title: SLX_14251_i707_i505


title: SLX_14251_i707_i517


title: Nasal, ARDS-023-ND14

value: study day 14


title: Inner.Loaded.5


title: Nasal, ARDS-024-ND14


title: Nasal, ARDS-023-ND1


title: DP20323_09


title: DP20323_08


title: SLX_14251_i707_i503


title: Nasal, ARDS-022-ND7

value: study day 7


title: SLX_14251_i707_i504


title: Nasal, ARDS-022-ND3

value: C

value: study day 3


title: Nasal, ARDS-023-ND7


title: SLX_14251_i707_i502


title: SLX_14251_i706_i517


title: Nasal, ARDS-021-ND7


title: DP20323_06

value: female

value: young Treg


title: DP20323_04

value: young non-Treg

value: sorted cells

value: nodes and spleens


title: Nasal, ARDS-021-ND3


title: DP20323_03


title: SLX_14251_i706_i507

value: PSE


title: Nasal, ARDS-021-ND14


title: Nasal, ARDS-021-ND1


title: DP20323_02

value: non-Treg


title: DP20323_07


title: DP20323_01


title: SLX_14251_i706_i505

value: protoplast of 5 day old root meristems


title: DP20323_05

value: Treg


title: SLX_14251_i706_i504


title: SLX_14251_i706_i508


title: Nasal, ARDS-020-ND3-2

value: PARDS


title: SLX_14251_i706_i506


title: Nasal, ARDS-020-ND1

value: study day 1


title: C300: controls: TB patients who receive anti-TB chemo-treatment but didn't get ATLI

type: genomic

city: Shanghai

first: Cong

last: Huai

address: No.1954. Huashang Rd.

institute: Shanghai Jiaotong University

description:
controls: TB patients who receive anti-TB chemo-treatment but didn't get ATLI
C300

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

scan_protocol: Scanned on an Agilent G2505C scanner. Images were quantified using Agilent Feature Extraction Software (version 10.7.1.1).

data_processing: Agilent Genomic Workbench 7.0 was used for background subtraction and Batman algorithm

molecule: genomic DNA

source_name: MeDIP pulled DNA

label_protocol: 3.5 µg of DNA were sheared for this expriment. 4/5 of the samples were immunoprecipitaed by anti-5'mc antibody and labeled using Cy5 dUTP, the other 1/5 were labed using Cy3 dUTP. The whole lableling procedure used SureTag DNA Labeling Kit

extract_protocol: Genomic DNA from peripheral blood of the subjects were extracted using QIAamp DNA blood Kits following manufacturer's instructions

treatment_protocol: All subjects are TB patients under anti-TB chem therapy

tag: disease state

value: TB patient without ATLI

tag: tissue

value: peripheral blood

tag: gender

value: male

tag: age

source_name: total genomic DNA


title: SLX_14251_i706_i503


title: C272: controls: TB patients who receive anti-TB chemo-treatment but didn't get ATLI

description:
controls: TB patients who receive anti-TB chemo-treatment but didn't get ATLI
C272

tag: Sex


title: C297: controls: TB patients who receive anti-TB chemo-treatment but didn't get ATLI

description:
controls: TB patients who receive anti-TB chemo-treatment but didn't get ATLI
C297


title: SLX_14251_i706_i502


title: C260: controls: TB patients who receive anti-TB chemo-treatment but didn't get ATLI

description:
controls: TB patients who receive anti-TB chemo-treatment but didn't get ATLI
C260


title: C226: controls: TB patients who receive anti-TB chemo-treatment but didn't get ATLI

description:
controls: TB patients who receive anti-TB chemo-treatment but didn't get ATLI
C226


title: C273: controls: TB patients who receive anti-TB chemo-treatment but didn't get ATLI

description:
controls: TB patients who receive anti-TB chemo-treatment but didn't get ATLI
C273


title: Nasal, ARDS-019-ND1

value: A


title: C225: controls: TB patients who receive anti-TB chemo-treatment but didn't get ATLI

description:
controls: TB patients who receive anti-TB chemo-treatment but didn't get ATLI
C225


title: C224: controls: TB patients who receive anti-TB chemo-treatment but didn't get ATLI

description:
controls: TB patients who receive anti-TB chemo-treatment but didn't get ATLI
C224


title: Nasal, ARDS-018-ND7

value: study day 7


title: Nasal, ARDS-018-ND3

value: study day 3


title: SLX_14251_i705_i508


title: Nasal, ARDS-018-ND14

value: study day 14


title: SLX_14251_i705_i517


title: SLX_14251_i705_i507


title: Hip16_WT_t18_l5_n3

city: Paris

first: Pierre

last: Billuart

address: 102 rue de la santé

department: IPNP

country: France

institute: INSERM

description: gene expression in hippocmpus from ophn1 WT male at t18 replicate3

hyb_protocol: 600 ng of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes.  Cy3-labelled cRNA were hybridized to SurePrint G3 Mouse GE 8x60K  (Agilent)  for 17 hours at 65Â°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed according to the manufacturer's instructions.

scan_protocol: Slides were scanned immediately after washing on the Agilent  Microarray Scanner (G2505C) using one color scan setting for 8x60k array slides.

data_processing: The scanned images were analyzed with Feature Extraction Software (Agilent) using default parameters (protocol GE1_107 and Grid: 028005_D_F_20110406) to obtain background subtracted and spatially detrended Processed Signal intensities.

source_name: Hippocampus, WT16, 18 hours

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 100ng RNA using the One-Color Low RNA Input Quick Amp Labeling kit (Agilent) according to the manufacturer's instructions.  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

extract_protocol: Hippocampi samples were snap-frozen in liquid Azote. Total RNA was extracted using RNA-PLUS (MP biomedicals), treated with rDNase (Macherey-Nagel) and cleaned with RNA clean-up kit (Macherey-Nagel). RNA transcripts were quantified on a Nanodrop (Thermoscientific) and controlled by a bioanalyzer 2100 (Agilent).

value: Hippocampus

value: Adult

tag: collection time (hours)


title: Hip14_WT_t18_l3_n1

description: gene expression in hippocmpus from ophn1 WT male at t18 replicate1

source_name: Hippocampus, WT14, 18 hours


title: Nasal, ARDS-017-ND7

value: C


title: SLX_14251_i705_i506


title: SLX_14251_i705_i505


title: Nasal, ARDS-017-ND3-2

value: B


title: Hip15_WT_t18_l4_n2

description: gene expression in hippocmpus from ophn1 WT male at t18 replicate2

source_name: Hippocampus, WT15, 18 hours


title: Nasal, ARDS-028-ND14


title: Hip12_WT_t12_l5_n3

description: gene expression in hippocmpus from ophn1 WT male at t12 replicate2

source_name: Hippocampus, WT12, 12 hours


title: Nasal, ARDS-018-ND1


title: Nasal, ARDS-028-ND1


title: Nasal, ARDS-017-ND14


title: C222: controls: TB patients who receive anti-TB chemo-treatment but didn't get ATLI

description:
controls: TB patients who receive anti-TB chemo-treatment but didn't get ATLI
C222


title: SLX_14251_i705_i504

value: PSE


title: Hip10_WT_t12_l4_n2

description: gene expression in hippocmpus from ophn1 WT male at t12 replicate1

source_name: Hippocampus, WT10, 12 hours


title: C183: controls: TB patients who receive anti-TB chemo-treatment but didn't get ATLI

description:
controls: TB patients who receive anti-TB chemo-treatment but didn't get ATLI
C183

value: female


title: C184: controls: TB patients who receive anti-TB chemo-treatment but didn't get ATLI

description:
controls: TB patients who receive anti-TB chemo-treatment but didn't get ATLI
C184


title: C180: controls: TB patients who receive anti-TB chemo-treatment but didn't get ATLI

description:
controls: TB patients who receive anti-TB chemo-treatment but didn't get ATLI
C180


title: Hip7_WT_t6_l5_n3

description: gene expression in hippocmpus from ophn1 WT male at t6 replicate3

source_name: Hippocampus, WT7, 6 hours


title: C181: controls: TB patients who receive anti-TB chemo-treatment but didn't get ATLI

description:
controls: TB patients who receive anti-TB chemo-treatment but didn't get ATLI
C181


title: SLX_14251_i705_i503

value: protoplast of 5 day old root meristems


title: Nasal, ARDS-017-ND1


title: Nasal, ARDS-016-ND7


title: SLX_14251_i705_i502


title: Hip5_WT_t6_l3_n1

description: gene expression in hippocmpus from ophn1 WT male at t6 replicate1

source_name: Hippocampus, WT5, 6 hours


title: Hip1_WT_t0_l3_n1

description: gene expression in hippocmpus from ophn1 WTmale at t0 replicate1

source_name: Hippocampus, WT1, 0 hour


title: Nasal, ARDS-016-ND14

source_name: Nasal


title: C172: controls: TB patients who receive anti-TB chemo-treatment but didn't get ATLI

description:
controls: TB patients who receive anti-TB chemo-treatment but didn't get ATLI
C172


title: C174: controls: TB patients who receive anti-TB chemo-treatment but didn't get ATLI

description:
controls: TB patients who receive anti-TB chemo-treatment but didn't get ATLI
C174


title: Nasal, ARDS-016-ND3


title: SLX_14251_i704_i517

source_name: phloem root meristem


title: SLX_14251_i704_i508


title: SLX_14251_i704_i507


title: Nasal, ARDS-016-ND1


title: Nasal, ARDS-015-ND3


title: Hip6_WT_t6_l4_n2

description: gene expression in hippocmpus from ophn1 WT male at t6 replicate2

source_name: Hippocampus, WT6, 6 hours


title: C177: controls: TB patients who receive anti-TB chemo-treatment but didn't get ATLI

description:
controls: TB patients who receive anti-TB chemo-treatment but didn't get ATLI
C177


title: SLX_14251_i704_i505


title: Hip13_KO_t18_l3_n1

description: gene expression in hippocmpus from ophn1 KO male at t18 replicate1

source_name: Hippocampus, KO13, 18 hours


title: Nasal, ARDS-015-ND1


title: Hip2_WT_t0_l4_n2

description: gene expression in hippocmpus from ophn1 WT male at t0 replicate2

source_name: Hippocampus, WT2, 0 hour


title: Hip15_KO_t18_l5_n3

description: gene expression in hippocmpus from ophn1 KO male at t18 replicate3

source_name: Hippocampus, KO15, 18 hours


title: SLX_14251_i704_i506


title: Hip14_KO_t18_l4_n2

description: gene expression in hippocmpus from ophn1 KO male at t18 replicate2

source_name: Hippocampus, KO14, 18 hours


title: Hip11_KO_t12_l5_n3

description: gene expression in hippocmpus from ophn1 KO male at t12 replicate3

source_name: Hippocampus, KO11, 12 hours


title: C171: controls: TB patients who receive anti-TB chemo-treatment but didn't get ATLI

description:
controls: TB patients who receive anti-TB chemo-treatment but didn't get ATLI
C171

source_name: MeDIP pulled DNA

source_name: total genomic DNA


title: Nasal, ARDS-014-ND1


title: Hip6_KO_t6_l4_n2

description: gene expression in hippocmpus from ophn1 KO male at t6 replicate2

source_name: Hippocampus, KO6, 6 hours


title: C151: controls: TB patients who receive anti-TB chemo-treatment but didn't get ATLI

description:
controls: TB patients who receive anti-TB chemo-treatment but didn't get ATLI
C151


title: C197: controls: TB patients who receive anti-TB chemo-treatment but didn't get ATLI

description:
controls: TB patients who receive anti-TB chemo-treatment but didn't get ATLI
C197


title: C169: controls: TB patients who receive anti-TB chemo-treatment but didn't get ATLI

description:
controls: TB patients who receive anti-TB chemo-treatment but didn't get ATLI
C169


title: C134: controls: TB patients who receive anti-TB chemo-treatment but didn't get ATLI

description:
controls: TB patients who receive anti-TB chemo-treatment but didn't get ATLI
C134


title: Hip7_KO_t6_l5_n3

description: gene expression in hippocmpus from ophn1 KO male at t6 replicate3

source_name: Hippocampus, KO7, 6 hours


title: C146: controls: TB patients who receive anti-TB chemo-treatment but didn't get ATLI

description:
controls: TB patients who receive anti-TB chemo-treatment but didn't get ATLI
C146


title: C135: controls: TB patients who receive anti-TB chemo-treatment but didn't get ATLI

description:
controls: TB patients who receive anti-TB chemo-treatment but didn't get ATLI
C135


title: SLX_14251_i704_i503


title: Hip10_KO_t12_l4_n2

description: gene expression in hippocmpus from ophn1 KO male at t12 replicate2

source_name: Hippocampus, KO10, 12 hours


title: Hip9_KO_t12_l3_n1

description: gene expression in hippocmpus from ophn1 KO male at t12 replicate1

source_name: Hippocampus, KO9, 12 hours


title: SLX_14251_i703_i508


title: Nasal, ARDS-014-ND14


title: SLX_14251_i704_i502


title: SLX_14251_i704_i504


title: Nasal, ARDS-013-ND7


title: SLX_14251_i703_i517


title: Nasal, ARDS-013-ND3

value: D


title: SLX_14251_i703_i507


title: Nasal, ARDS-012-ND7

value: PARDS


title: C211: controls: TB patients who receive anti-TB chemo-treatment but didn't get ATLI

description:
controls: TB patients who receive anti-TB chemo-treatment but didn't get ATLI
C211


title: Hip5_KO_t6_l3_n1

description: gene expression in hippocmpus from ophn1 KO male at t6 replicate1

source_name: Hippocampus, KO5, 6 hours


title: Crispr_2

city: Baltimore

first: Guofeng

last: Xie

state: MD

address: 22 South Greene St

institute: University of Maryland Baltimore

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

source_name: HT29 cells

extract_protocol:
Illumina TruSeq RNA Sample Prep Kit was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: cell type

value: Human colon cancer cell lines

tag: genotype/varation

value: ZNF277 KO


title: Nasal, ARDS-012-ND3

tag: group


title: Crispr_1


title: Nasal, ARDS-012-ND1

value: study day 1


title: Nasal, ARDS-013-ND1


title: Crispr_3


title: C207: controls: TB patients who receive anti-TB chemo-treatment but didn't get ATLI

description:
controls: TB patients who receive anti-TB chemo-treatment but didn't get ATLI
C207

value: TB patient without ATLI

value: peripheral blood

value: male


title: Hip2_KO_t0_l4_n2

description: gene expression in hippocmpus from ophn1 KO male at t0 replicate2

source_name: Hippocampus, KO2, 0 hour


title: SLX_14251_i702_i517

tag: reporter line


title: Control_1

value: WT


title: Nasal, ARDS-011-ND14

source_name: Nasal

value: study day 14


title: Input1

city: Beijing

first: Chen

last: Dong

address: Haidian District

department: Institute for Immunology and School of Medicine

institute: Tsinghua University

library_source: genomic

data_processing:
Sequencing reads were mapped to the mouse genome mm10 by bowtie2
PCR duplicates were removed using picard MarkDuplicates
The uniquely mapped reads were used to call peak with MACS2 using a p value cutoff 1e-4
ChIPseeker was used for peak annotation
Genome_build: mm10
Supplementary_files_format_and_content: bigwig file

source_name: Tfh-like cell

growth_protocol: pRV-Zfp831-HA transfected CD4+ T cell were cultured under IL-6 plus anti-IL2/IL-4/IFN-γ/TGFβ

extract_protocol:
The ChIP assay was performed using Active Motif’s ChIP assay kit (53035) according to manufacturer’s instructions with slight modifications.
ChIP-seq DNA library was constructed for deep sequencing by BGI Genomics.

tag: transfection

value: Spleen+Lymph nodes

value: Tfh-like cell

value: 1 days in vitro

tag: chip antibody


title: C116: controls: TB patients who receive anti-TB chemo-treatment but didn't get ATLI

description:
controls: TB patients who receive anti-TB chemo-treatment but didn't get ATLI
C116


title: SLX_14251_i703_i506

source_name: phloem root meristem

tag: possible cell type

tag: developmental stage


title: Control_3


title: SLX_14251_i703_i505


title: C132: controls: TB patients who receive anti-TB chemo-treatment but didn't get ATLI

description:
controls: TB patients who receive anti-TB chemo-treatment but didn't get ATLI
C132


title: Hip3_KO_t0_l5_n3

description: gene expression in hippocmpus from ophn1 KO male at t0 replicate3

source_name: Hippocampus, KO3, 0 hour

value: Hippocampus

value: Adult


title: C114: controls: TB patients who receive anti-TB chemo-treatment but didn't get ATLI

description:
controls: TB patients who receive anti-TB chemo-treatment but didn't get ATLI
C114


title: C088: controls: TB patients who receive anti-TB chemo-treatment but didn't get ATLI

description:
controls: TB patients who receive anti-TB chemo-treatment but didn't get ATLI
C088


title: C068: controls: TB patients who receive anti-TB chemo-treatment but didn't get ATLI

description:
controls: TB patients who receive anti-TB chemo-treatment but didn't get ATLI
C068


title: C071: controls: TB patients who receive anti-TB chemo-treatment but didn't get ATLI

description:
controls: TB patients who receive anti-TB chemo-treatment but didn't get ATLI
C071

value: female


title: Hip1_KO_t0_l3_n1

description: gene expression in hippocmpus from ophn1 KO male at t0 replicate1

source_name: Hippocampus, KO1, 0 hour


title: C067: controls: TB patients who receive anti-TB chemo-treatment but didn't get ATLI

description:
controls: TB patients who receive anti-TB chemo-treatment but didn't get ATLI
C067


title: Nasal, ARDS-011-ND7

tag: subgroup

value: A

tag: time

value: study day 7


title: C069: controls: TB patients who receive anti-TB chemo-treatment but didn't get ATLI

description:
controls: TB patients who receive anti-TB chemo-treatment but didn't get ATLI
C069


title: Nasal, ARDS-010-ND7

value: PARDS

value: C


title: SLX_14251_i702_i506

value: PSE

value: protoplast of 5 day old root meristems


title: Control_2

value: Human colon cancer cell lines


title: Nasal, ARDS-011-ND3

value: B

value: study day 3


title: SLX_14251_i703_i502


title: Tw2

city: changchun

first: yingying

last: sun

state: jilin

address: 5268 Renmin Street

department: school of life science

institute: northeast normal university

description: CD11b+Gr1+ cells in peripheral blood of tumor bearing mice for 2 weeks

data_processing:
Library construction and sequencing on an Illumina HiSeq 2500 instrument
Bowtie2 v2.2.3 was used for building the genome index
Clean data was then aligned to the reference genome using HISAT2 v2.1.0
Gene expression levels were quantified using a software package called FPKM
DEGseq v1.18.0 was used for differential gene expression analysis between two samples with non biological replicates
Genome_build: Mus musculus. GRCm38. 89
Supplementary_files_format_and_content: tab-delimited excel files include FPKM values for each Sample ...

source_name: G-MDSC

growth_protocol: G-MDSC cells were freshly isolated from peripheral blood of mice at different stages of tumor bearing

extract_protocol:
The cellular RNA was extracted using Trizol reagent followed by a genomic DNA elimination step. RNA purity was checked using the kaiaoK5500® Spectrophotometer. RNA integrity and concentration was assessed using the RNA Nano 6000 Assay Kit of the Bioanalyzer 2100 system.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: G-MDSC were sorted by using the AutoMACS sorter (Miltenyi Biotech) with a myeloid- derived suppressor cell isolation kit according to the manufacturer’s instructions.

tag: strain

value: peripheral blood

value: CD11b+Gr1+ cells

value: tumor-bearing mice for 2 months


title: Nasal, ARDS-010-ND14

value: study day 14


title: SLX_14251_i702_i508


title: SLX_14251_i702_i503


title: SLX_14251_i702_i507


title: Nasal, ARDS-011-ND1

value: study day 1


title: Nasal, ARDS-009-ND7


title: SLX_14251_i702_i502


title: Ab1

value: Spleen+Lymph nodes

value: Tfh-like cell

value: 1 days in vitro

value: HA-Tag (C29F4) Rabbit mAb, CST, 3724


title: SLX_14251_i701_i507


title: N57_1

data_processing:
 Raw counts have been aligned and mapped according to a standardized Bowtie 2 suit using the TAIR10 genome.
Feature Counts was used to obtain read counts
Differential gene expression analysis was performed using edgeR
Shannon-entropy based selection of tissue specific genes as described by Zambelli et al., 2018, using published root map RNA-seq data of other tissue types (Li S et al., 2016)
Genome_build: TAIR10
Supplementary_files_format_and_content: Tables with read counts, tab delimited text files.

source_name: FACS-isolated protoplasts

extract_protocol:
Arabidopsis root protoplasts were isolated according to the published protocol (Clark et al., 2018). In short, sterilized seeds were plated onto the nylon mesh (57-103, Nitex) placed on the top of MS agar media. Two rows of seeds comprising approximately 100-150 seeds per row were then grown vertically for 5 days in long-day growth condition. To isolate root protoplasts, ⅓ of the root was cut and chopped on the surface of the mesh and collected in buffer containing cell wall degrading enzymes - 1.5 g Cellulase (C1794, Sigma) and 0.1 g Pectolyase (P3026, Sigma) in 100 ml protoplasting solution. After 1 hour of incubation with occasional stirring, the protoplasts were spun down (200 rcf for 6 min) in 15 ml Falcon tube and after removal of supernatant, cells were resuspended in 700 ul protoplasting solution without enzymes. After filtering with 70 um and 40 um cell strainers sequentially, FACS was performed using 70 micron nozzle at 10 psi. Fluorescence positive cells were collected in a round-bottom polystylene tube that contains 150 - 200 ul RLT buffer with beta-mercaptoethanol (10 ul / 1 ml RLT buffer, RNeasy micro kit protocol, Qiagen). Cell sorting was performed for about 15 min and collected cells were immediately frozen on dry ice and kept in -80 °C for up to one week.
Frozen cells were quickly thawed by adding the same volume of EtOH (150 - 200 µl), and RNA extraction was done using RNeasy Micro Kit (Qiagen) as previously described by Clark et al., 2018. RNA integrity was measured with Agilent HS RNA TapeStation system following the manufacturer’s instructions. Samples of RNA integrity value (RIN) 6.3 and above were taken to the following cDNA synthesis step. Clontech Smarter Ultra Low Input Library Kit V4 was used for cDNA synthesis and amplification (18 PCR cycles). Samples were then submitted to Novogene for library construction and RNA sequencing on an Illumina HiSeq SE50 run.  The precise name of the instrument used to produce the reads is not available, although it was a HiSeq series instrument.

value: 5day old seedlings

value: FACS-isolated protoplasts

tag: line

value: pNAC57::2GFP pCALS7::H2B-RFP


title: Nasal, ARDS-009-ND14

value: PARDS

value: C


title: Th3

description: CD11b+Gr1+ cells in peripheral blood of tumor bearing mice for 3 weeks

tag: tissue

tag: disease state

value: tumor-bearing mice for 3 months


title: C066: controls: TB patients who receive anti-TB chemo-treatment but didn't get ATLI

description:
controls: TB patients who receive anti-TB chemo-treatment but didn't get ATLI
C066

value: TB patient without ATLI

tag: gender

value: male

tag: age


title: C064: controls: TB patients who receive anti-TB chemo-treatment but didn't get ATLI

description:
controls: TB patients who receive anti-TB chemo-treatment but didn't get ATLI
C064

value: peripheral blood

value: female

tag: Sex


title: C055: controls: TB patients who receive anti-TB chemo-treatment but didn't get ATLI

description:
controls: TB patients who receive anti-TB chemo-treatment but didn't get ATLI
C055


title: C065: controls: TB patients who receive anti-TB chemo-treatment but didn't get ATLI

description:
controls: TB patients who receive anti-TB chemo-treatment but didn't get ATLI
C065


title: C053: controls: TB patients who receive anti-TB chemo-treatment but didn't get ATLI

description:
controls: TB patients who receive anti-TB chemo-treatment but didn't get ATLI
C053


title: SLX_14251_i701_i506

value: PSE

value: protoplast of 5 day old root meristems


title: Nasal, ARDS-009-ND1

value: A

value: study day 1


title: N73_4

value: pNAC73::H2B-YFP pS32::erRFP


title: SLX_14251_i701_i505


title: SLX_14251_i702_i504


title: Nasal, ARDS-010-ND3

value: study day 3


title: N1

description: CD11b+Gr1+ cells in peripheral blood of normal mice

tag: cell type

value: CD11b+Gr1+ cells

value: normal mice


title: N73_2

value: 5day old seedlings

value: FACS-isolated protoplasts


title: Nasal, ARDS-010-ND1

value: PARDS


title: N57_4

value: pNAC57::2GFP pCALS7::H2B-RFP


title: N73_1


title: SLX_14251_i701_i503


title: SLX_14251_i702_i505


title: N57_2


title: SLX_14251_i701_i508


title: Nasal, ARDS-009-ND3


title: Nasal, ARDS-008-ND1

value: B


title: C023: controls: TB patients who receive anti-TB chemo-treatment but didn't get ATLI

description:
controls: TB patients who receive anti-TB chemo-treatment but didn't get ATLI
C023

value: TB patient without ATLI


title: C049: controls: TB patients who receive anti-TB chemo-treatment but didn't get ATLI

description:
controls: TB patients who receive anti-TB chemo-treatment but didn't get ATLI
C049


title: C033: controls: TB patients who receive anti-TB chemo-treatment but didn't get ATLI

description:
controls: TB patients who receive anti-TB chemo-treatment but didn't get ATLI
C033

value: male


title: N73_3


title: Bronchial, ARDS-008-TD1

source_name: Bronchial


title: SLX_14251_i701_i504


title: P1D_5


title: C044: controls: TB patients who receive anti-TB chemo-treatment but didn't get ATLI

description:
controls: TB patients who receive anti-TB chemo-treatment but didn't get ATLI
C044

source_name: MeDIP pulled DNA

value: peripheral blood


title: Nasal, ARDS-007-ND14

value: study day 14


title: Nasal, ARDS-008-ND7

value: C

value: study day 7


title: C048: controls: TB patients who receive anti-TB chemo-treatment but didn't get ATLI

description:
controls: TB patients who receive anti-TB chemo-treatment but didn't get ATLI
C048

source_name: total genomic DNA


title: C006: controls: TB patients who receive anti-TB chemo-treatment but didn't get ATLI

description:
controls: TB patients who receive anti-TB chemo-treatment but didn't get ATLI
C006


title: Nasal, ARDS-008-ND3

value: A


title: C045: controls: TB patients who receive anti-TB chemo-treatment but didn't get ATLI

description:
controls: TB patients who receive anti-TB chemo-treatment but didn't get ATLI
C045


title: P1_2


title: SLX_14251_i701_i502

value: PSE

value: protoplast of 5 day old root meristems


title: Nasal, ARDS-007-ND7

value: D


title: P1D_3


title: SLX_12100_i712_i508


title: SLX_12100_i712_i507


title: P1_3


title: P1_1


title: C020: controls: TB patients who receive anti-TB chemo-treatment but didn't get ATLI

description:
controls: TB patients who receive anti-TB chemo-treatment but didn't get ATLI
C020

value: female


title: Nasal, ARDS-005-ND14

description: RNA-Only

molecule: polyA RNA


title: CALS7_4

value: pCASL7::H2B-YFP pS32::erRFP


title: Nasal, ARDS-004-ND1

description: RNA-Only

value: study day 1


title: CALS7_3

value: 5day old seedlings

value: FACS-isolated protoplasts


title: SLX_12100_i712_i504


title: SLX_12100_i712_i503


title: C032: controls: TB patients who receive anti-TB chemo-treatment but didn't get ATLI

description:
controls: TB patients who receive anti-TB chemo-treatment but didn't get ATLI
C032


title: Nasal, ARDS-003-ND7

value: PARDS


title: Bronchial, ARDS-002-TD1-NEB


title: C019: controls: TB patients who receive anti-TB chemo-treatment but didn't get ATLI

description:
controls: TB patients who receive anti-TB chemo-treatment but didn't get ATLI
C019


title: Nasal, ARDS-002-ND3

description: RNA-Only

value: study day 3


title: SLX_12100_i712_i505


title: C013: controls: TB patients who receive anti-TB chemo-treatment but didn't get ATLI

description:
controls: TB patients who receive anti-TB chemo-treatment but didn't get ATLI
C013

value: TB patient without ATLI


title: C001: controls: TB patients who receive anti-TB chemo-treatment but didn't get ATLI

description:
controls: TB patients who receive anti-TB chemo-treatment but didn't get ATLI
C001

value: male


title: SJTU_380: case: TB patient who suffers ATLI

description:
case: TB patient who suffers ATLI
SJTU_380

value: TB patient with Anti-tuberculosis Drug Induced Liver Injury

value: peripheral blood


title: C003: controls: TB patients who receive anti-TB chemo-treatment but didn't get ATLI

description:
controls: TB patients who receive anti-TB chemo-treatment but didn't get ATLI
C003


title: Nasal, ARDS-002-ND7

description: RNA-Only

value: C


title: CALS7_2


title: SLX_12100_i711_i517


title: SLX_12100_i712_i502


title: CALS7_1


title: SLX_12100_i711_i508


title: Nasal, ARDS-002-ND1

description: RNA-Only


title: CD_3


title: CD_4


title: SLX_12100_i711_i507


title: SLX_12100_i711_i506


title: Nasal, ARDS-001-ND7

description: RNA-Only

value: study day 7


title: Nasal, ARDS-001-ND3

description: RNA-Only


title: Nasal, ARDS-001-ND1

description: RNA-Only


title: CD_2


title: Bronchial, ARDS-001-TD7


title: CD_1


title: SLX_12100_i711_i504


title: SLX_12100_i711_i502


title: CAC_20

city: Nashville

first: Danielle

middle: L

last: Michell

state: TN

address: 2220 Pierece Ave

department: Department of Medicine

institute: Vanderbilt Univ. Medical Center

data_processing:
Pipeline: TIGER (https://www.ncbi.nlm.nih.gov/pubmed/30128086)
To assess raw data quality, FastQC was performed at the raw read level to check for base quality, total read counts, and adapter identification. Cutadapt was then used to trim 3’ adapters from processed reads (-a TGGAATTCTCGGGTGCCAAGG). Cutadapt was then used to remove the first and last 4 bases from the trimmed reads and all trimmed reads <16 nts in length were removed (-m 16 -u 4 -u -4). After trimming, read length distributions were plotted and FastQC was performed on trimmed reads to validate the efficiency of adapter trimming. To generate identical read files, trimmed reads in each sample were collapsed into non-redundant “identical” reads in FASTQ format and copy numbers were recorded for downstream analysis.
In the Host Genome & Database alignment module, bowtie (v1.1.2) was used to map reads to a costumed database with option (-a -m 100 --best - strata -v 1) which allows 1 mismatch (MM) and
Genome_build: human GRCh37

source_name: HDL

extract_protocol:
Total RNA were isolated from equivalent amounts of HDL total protein using the miRNeasy Mini Kit (Qiagen)
Libraries were prepared using the BioO Scientific NEXTflex Small RNA-Seq Kit v3


title: CAC_21


title: BxPC3 cells, Erastin+Vitamin C 3

city: Zhengjiang

first: Yawen

last: Liu

address: Xuefu Road 301

institute: Jiangsu University

data_processing:
Illumina Casava1.7 software used for basecalling.
DEGseq was used for differential gene expression analysis between two samples with non biological replicates.
Reads Count for each gene in each sample was counted by HTSeq v0.6.0, and FPKM (Fragments Per Kilobase Millon Mapped Reads) was then calculated to estimate the expression level of genes in each sample
Genome_build: hg19
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: Pancreatic cancer

growth_protocol: BxPC3 cells were cultured in RPMI-1640 medium supplemented with 10% fetal bovine serum, 100 units/ml penicillin, and 100 mg/ml streptomycin.

extract_protocol:
Cells were washed with cold PBS twice, and total RNA was isolated using RNAiso Plus (Takara) following the manufacturer's protocol. After verifying its concentration and integrity, the qualified RNA samples were subjected to PCR amplification to construct a cDNA library. The cluster generation and sequencing were performed on Novaseq 6000 S4 platform, using NovaSeq 6000 S4 Reagent kit V1.5.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: BxPC3 cells were treated with DMSO, Erastin or /and Vitamin C.

value: Pancreatic cancer

value: Pancereatic cancer cell

tag: cell line

tag: treatment

value: Erastin+Vitamin C


title: SLX_12100_i710_i517

tag: reporter line

value: PSE

value: protoplast of 5 day old root meristems


title: BxPC3 cells, Erastin+Vitamin C 2


title: SLX_12100_i711_i503


title: SJTU_272: case: TB patient who suffers ATLI

description:
case: TB patient who suffers ATLI
SJTU_272

value: female


title: SJTU_367: case: TB patient who suffers ATLI

description:
case: TB patient who suffers ATLI
SJTU_367


title: BxPC3 cells, Erastin+Vitamin C 1


title: SJTU_246: case: TB patient who suffers ATLI

description:
case: TB patient who suffers ATLI
SJTU_246


title: SLX_12100_i710_i508


title: SJTU_307: case: TB patient who suffers ATLI

description:
case: TB patient who suffers ATLI
SJTU_307


title: SJTU_122: case: TB patient who suffers ATLI

description:
case: TB patient who suffers ATLI
SJTU_122


title: SJTU_248: case: TB patient who suffers ATLI

description:
case: TB patient who suffers ATLI
SJTU_248


title: CAC_17


title: CAC_18


title: SLX_12100_i710_i507


title: SJTU_134: case: TB patient who suffers ATLI

description:
case: TB patient who suffers ATLI
SJTU_134


title: BxPC3 cells, Vitamin C 3

value: Vitamin C


title: CAC_19


title: SJTU_107: case: TB patient who suffers ATLI

description:
case: TB patient who suffers ATLI
SJTU_107


title: SLX_12100_i710_i506


title: SJTU_101: case: TB patient who suffers ATLI

description:
case: TB patient who suffers ATLI
SJTU_101


title: BxPC3 cells, Vitamin C 2


title: SJTU_104: case: TB patient who suffers ATLI

description:
case: TB patient who suffers ATLI
SJTU_104


title: CAC_15


title: SLX_12100_i710_i505


title: SLX_12100_i710_i504


title: SJTU_089: case: TB patient who suffers ATLI

description:
case: TB patient who suffers ATLI
SJTU_089


title: SJTU_121: case: TB patient who suffers ATLI

description:
case: TB patient who suffers ATLI
SJTU_121


title: CAC_14


title: BxPC3 cells, Erastin 4

value: Erastin


title: BxPC3 cells, Erastin 3


title: CAC_13


title: CAC_16


title: CAC_12


title: BxPC3 cells, Erastin 2


title: BxPC3 cells, DMSO 4

value: DMSO


title: CAC_11


title: BxPC3 cells, Vitamin C 1


title: SLX_12100_i710_i502


title: SLX_12100_i709_i517


title: BxPC3 cells, DMSO 3


title: CAC_10


title: SLX_12100_i709_i507


title: SLX_12100_i710_i503


title: CAC_09


title: BxPC3 cells, DMSO 2


title: SLX_12100_i709_i506


title: CAC_08


title: BxPC3 cells, DMSO 1


title: SJTU_086: case: TB patient who suffers ATLI

description:
case: TB patient who suffers ATLI
SJTU_086


title: SJTU_085: case: TB patient who suffers ATLI

description:
case: TB patient who suffers ATLI
SJTU_085


title: SJTU_087: case: TB patient who suffers ATLI

description:
case: TB patient who suffers ATLI
SJTU_087


title: SLX_12100_i709_i508


title: SLX_12100_i709_i505


title: SLX_12100_i709_i504


title: CAC_06


title: SJTU_083: case: TB patient who suffers ATLI

description:
case: TB patient who suffers ATLI
SJTU_083


title: CAC_07


title: SJTU_080: case: TB patient who suffers ATLI

description:
case: TB patient who suffers ATLI
SJTU_080


title: FL19_CD13low_P7

city: Lund

first: Gunilla

last: Westergren-Thorsson

address: Sölvegatan 19, BMC C12

country: Sweden

institute: Lund University

data_processing:
Demultiplexing using the bcl2fastq2 software with default settings
Raw Quality Control (QC) using FastQC
Read Mapping was performed using the STAR software, and the reference genome sequence was from the Ensemble database, the Human GRCh38 primary assemply, and the annotation (GTF) from gencode version 33. Data is sorted by genomic coordinate.
Assembly of the alignments into full transcripts and quantification of the expression levels of each gene and transcript. This task was performed using the featureCounts software v2.0.1.
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited text file including feature lengths and featurecounts for all samples

source_name: Lung mesenchymal cells

extract_protocol:
Total RNA was extracted according the instructions for cell pellets in the PicoPure™ RNA Isolation Kit (Thermo Fisher Scientific, KIT0204).
cDNA libraries were prepared using SMART-Seq v4 Ultra Low Input RNA Kit for Sequencing (Takara Bio) and Nextera XT DNA Library Preparation Kit (Illumina).

tag: cell population

value: CD105+CD90+CD13- mesenchymal cells

value: Distal lung parenchyma

tag: tissue donor


title: SLX_12100_i709_i503

tag: possible cell type


title: FL19_CD13high_P8

value: CD105+CD90+CD13+ mesenchymal cells


title: SJTU_079: case: TB patient who suffers ATLI

description:
case: TB patient who suffers ATLI
SJTU_079


title: SJTU_078: case: TB patient who suffers ATLI

description:
case: TB patient who suffers ATLI
SJTU_078


title: CAC_05


title: FL18_CD13low


title: SLX_12100_i709_i502

tag: developmental stage


title: FL18_CD13high


title: SJTU_074: case: TB patient who suffers ATLI

description:
case: TB patient who suffers ATLI
SJTU_074

value: male


title: CAC_04


title: SLX_12100_i708_i517


title: FL17_CD13low_P7


title: FL17_CD13high_P8


title: CAC_03


title: SLX_12100_i712_i506


title: P1_4

value: 5day old seedlings

value: FACS-isolated protoplasts


title: SJTU_069: case: TB patient who suffers ATLI

description:
case: TB patient who suffers ATLI
SJTU_069

value: TB patient with Anti-tuberculosis Drug Induced Liver Injury

value: peripheral blood


title: SJTU_056: case: TB patient who suffers ATLI

description:
case: TB patient who suffers ATLI
SJTU_056


title: CAC_02


title: SJTU_057: case: TB patient who suffers ATLI

description:
case: TB patient who suffers ATLI
SJTU_057


title: CAC_01


title: FL16_CD13low


title: SJTU_054: case: TB patient who suffers ATLI

description:
case: TB patient who suffers ATLI
SJTU_054


title: SLX_12100_i708_i507


title: SLX_12100_i708_i506


title: SJTU_053: case: TB patient who suffers ATLI

description:
case: TB patient who suffers ATLI
SJTU_053


title: SJTU_050: case: TB patient who suffers ATLI

description:
case: TB patient who suffers ATLI
SJTU_050


title: Control_46

value: Healthy


title: SLX_12100_i708_i505


title: SLX_12100_i708_i508


title: FL16_CD13high


title: EOC349_primary_Peritoneum

city: Helsinki

first: Kaiyang

last: Zhang

state: Finland

address: Biomedicum Helsinki 1, Haartmaninkatu 8

department: Faculty of Medicine

country: Finland

institute: University of Helsinki

data_processing:
de-multiplexing, alignment, barcode processing and unique molecular identifier (UM)I quantification were performed using the Cell Ranger Software Suite (Version 3.1.0)
cell quality control was performed using Seurat v3
Genome_build: GRCh38.d1.vd1
Supplementary_files_format_and_content: Matrix table with raw UMI counts

source_name: Treatment-naive tumor tissue sample from patient EOC349

growth_protocol: Cells were not cultured

extract_protocol:
Tumor samples were dissected and enzymatically digested in a mixture of collagenase and hyaluronidase to obtain single-cell suspensions. Resulting cell suspensions were used without any selection/enrichment to create single-cell RNA sequencing libraries.
Chromium Single Cell 3′ Reagent Kit v. 2.0 (10x Genomics)
single cell RNA-seq

treatment_protocol: The post-NACT samples were collected from patients after neoadjuvant chemotherapy.

value: high-grade serous ovarian cancer (HGSOC)

tag: individual

value: patient EOC349

tag: treatment phase

value: Treatment-naive

tag: anatomical location

value: Peritoneum


title: Control_45


title: SJTU_393: case: TB patient who suffers ATLI

description:
case: TB patient who suffers ATLI
SJTU_393


title: SLX_12100_i708_i504

value: PSE

value: protoplast of 5 day old root meristems


title: EOC227_interval_Omentum

source_name: Post-NACT tumor tissue sample from patient EOC227

value: patient EOC227

value: Post-NACT

value: Omentum


title: EOC349_interval_Omentum

source_name: post-NACT tumor tissue sample from patient EOC349


title: SLX_12100_i708_i502


title: Control_44


title: Control_42


title: EOC227_primary_Omentum

source_name: Treatment-naive tumor tissue sample from patient EOC227


title: 182455_100118_PBMC_scRNA-seq_2018_Fresh_2

first: Ira

middle: Daniel Klein

last: Fleming

state: MA

address: 400 Main St

institute: MIT

description: scRNA-seq data of PBMCs

data_processing:
Reads aligned and pre-processed according to the DropSeq Computational Protocol v2.0 (https://github.com/broadinstitute/Drop-seq)
Summary:
1. Read one contains a cell barcode (first 12bp), and a unique molecular identifier (UMI). Paired reads are categorized by cell and by UMI.
2. Reads with low-quality bases are discarded and reads are trimmed for 5' primer sequences and 3' poly-A tails.
3. Read two is aligned to the human genome hg19 using STAR v2.5.1a with default parameters
4. Aligned sequences are merged by cell barcode and UMI (barcodes with a hamming edit distance of one are also merged)
Genome_build: hg19
Supplementary_files_format_and_content: Tab delimited text file containing a digital gene expression matrix giving the counts of unique UMIs per gene per cell ( UMIs by row and cells by column)

source_name: PBMCs

extract_protocol:
Single-cell RNA capture, barcoding, and multiplexing according to the Seq-Well method (Gierahn et al., Nature Methods 2017). An updated protocol using "second-strand synthesis" was applied in this case (Hughes et al.,  BioRxiv 2019): https://www.biorxiv.org/content/10.1101/689273v1
Illumina Nextera XT DNA Library Prep was used as specified in the Seq-Well protocol (Gierahn et al., Nature Methods 2017 and Hughes et al., BioRxiv 2019)

treatment_protocol: PBMCs isolated from whole blood in BD CPT vacutainer tubes with sodium-citrate anticoagulant (Cat. 362761), shipped cross-country (~12hr) and frozen in FBS  + 10% DMSO then thawed at a later date or processed fresh with Seq-Well  S3 methodology (first undergoing treatment with eBioscience RBC-lysis buffer)

value: West Nile Fever

tag: study time collected (days)

value: PBMC


title: Control_41


title: SLX_12100_i707_i507

data_processing:
De-multiplexed fastq files were aligned using HISAT2
Picard SortSam was used to create .bam from .sam files, Picard Merge2 to merge .bam files where necessary
Cuffquant was used to create abundance files
Cuffnorm was used with all abundance files from all cells to get read counts.
Genome_build: TAIR10, Release 36
Supplementary_files_format_and_content: tab-delimited text file with read counts for each cells and gene

extract_protocol:
Arabidopsis root protoplasts were isolated according to the published protocol (Clark et al., 2018). In short, sterilized seeds were plated onto the nylon mesh (57-103, Nitex) placed on the top of MS agar media. Two rows of seeds comprising approximately 100-150 seeds per row were then grown vertically for 5 days in long-day growth condition. To isolate root protoplasts, ⅓ of the root was cut and chopped on the surface of the mesh and collected in buffer containing cell wall degrading enzymes - 1.5 g Cellulase (C1794, Sigma) and 0.1 g Pectolyase (P3026, Sigma) in 100 ml protoplasting solution. After 1 hour of incubation with occasional stirring, the protoplasts were spun down (200 rcf for 6 min) in 15 ml Falcon tube and after removal of supernatant, cells were resuspended in 700 ul protoplasting solution without enzymes. After filtering with 70 um and 40 um cell strainers sequentially, FACS was performed using 70 micron nozzle at 10 psi. Fluorescence positive cells were collected in a round-bottom polystylene tube that contains 150 - 200 ul RLT buffer with beta-mercaptoethanol (10 ul / 1 ml RLT buffer, RNeasy micro kit protocol, Qiagen). Cell sorting was performed for about 15 min and collected cells were immediately frozen on dry ice and kept in -80 °C for up to one week. For single cell transcriptomics, protoplasts were produced and isolated as described here, but sorted individually into 96-well plates.
Libraries were prepared using Illumina Nextera XT DNA preparation kit and either Nextera XT index kit – 96 indexes or Nextera XT index kit v2.


title: SLX_12100_i707_i517


title: 182455_100118_PBMC_scRNA-seq_2018_Fresh_1

description: scRNA-seq data of PBMCs


title: SJTU_047: case: TB patient who suffers ATLI

description:
case: TB patient who suffers ATLI
SJTU_047

tag: tissue

value: male


title: SJTU_048: case: TB patient who suffers ATLI

description:
case: TB patient who suffers ATLI
SJTU_048

tag: disease state


title: SLX_12100_i707_i508


title: SLX_12100_i707_i506


title: Control_40


title: 182455_010719_PBMC_scRNA-seq_2018_Thawed_2

description: scRNA-seq data of PBMCs


title: Control_39


title: SLX_12100_i707_i505


title: 182455_010719_PBMC_scRNA-seq_2018_Thawed_1

description: scRNA-seq data of PBMCs


title: 182454_112919_PBMC_scRNA-seq_2018_Thawed_2

description: scRNA-seq data of PBMCs


title: SJTU_045: case: TB patient who suffers ATLI

description:
case: TB patient who suffers ATLI
SJTU_045

tag: gender


title: Control_38


title: SLX_12100_i707_i504


title: SJTU_038: case: TB patient who suffers ATLI

description:
case: TB patient who suffers ATLI
SJTU_038

tag: age


title: SJTU_042: case: TB patient who suffers ATLI

description:
case: TB patient who suffers ATLI
SJTU_042

value: female

tag: Sex


title: SJTU_029: case: TB patient who suffers ATLI

description:
case: TB patient who suffers ATLI
SJTU_029


title: SJTU_032: case: TB patient who suffers ATLI

description:
case: TB patient who suffers ATLI
SJTU_032


title: SJTU_033: case: TB patient who suffers ATLI

description:
case: TB patient who suffers ATLI
SJTU_033


title: Control_37


title: SLX_12100_i707_i503


title: Control_36


title: 182454_112919_PBMC_scRNA-seq_2018_Thawed_1

description: scRNA-seq data of PBMCs

tag: cell type


title: Control_35


title: SLX_12100_i707_i502


title: Control_34


title: 182454_112919_PBMC_scRNA-seq_2018_Fresh_1

description: scRNA-seq data of PBMCs


title: 182452_111518_PBMC_scRNA-seq_2018_Thawed_2

description: scRNA-seq data of PBMCs

value: Asymptomatic


title: SLX_12100_i706_i508


title: SLX_12100_i706_i507


title: 182452_111518_PBMC_scRNA-seq_2018_Thawed_1

description: scRNA-seq data of PBMCs


title: 182454_112919_PBMC_scRNA-seq_2018_Fresh_2

description: scRNA-seq data of PBMCs


title: SLX_12100_i706_i506


title: Control_32


title: Control_30


title: 182452_111518_PBMC_scRNA-seq_2018_Fresh_1

description: scRNA-seq data of PBMCs


title: SLX_12100_i706_i503


title: 182452_111518_PBMC_scRNA-seq_2018_Fresh_2

description: scRNA-seq data of PBMCs


title: SJTU_023: case: TB patient who suffers ATLI

description:
case: TB patient who suffers ATLI
SJTU_023

value: TB patient with Anti-tuberculosis Drug Induced Liver Injury


title: SLX_12100_i706_i502


title: Control_33


title: SJTU_018: case: TB patient who suffers ATLI

description:
case: TB patient who suffers ATLI
SJTU_018

value: peripheral blood


title: 182452_082118_PBMC_scRNA-seq_2018_Thawed_1

description: scRNA-seq data of PBMCs


title: E_DYDD5

city: Guangzhou

first: shanshan

last: Zhuang

state: Guangdong

address: Guangzhou, Guangdong, 510225, China

department: College of Light Industry and Food

institute: Zhongkai College of Agriculture and Engineering

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

organism: Escherichia coli

growth_protocol: Escherichia coli was incubated in TSB at 37 C for 8 h. During the logarithmic phase, 200 μL of bacterial solution was added to 200 mL of liquid medium, 200 μL of sterile water (control group; P_CK), or 50 mg/mL of DDDY solution (treatment group; P_DDDY). The bacteria were then cultured on a shaking table at 150 R/min and 37 C for 24 h, centrifuged at 6000 R/min and 4 C for 10 min, washed with PBS three times, and then collected and stored at -80 C.

extract_protocol:
Cells were removed, flash frozen on dry ice, and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: The bacteria were then cultured on a shaking table at 150 R/min and 37 C for 24 h.

tag: strain

value: DYDD


title: Control_28

value: Healthy


title: SLX_12100_i706_i504

first: Bernhard

last: Blob

address: 47 Bateman Street

institute: Sainsbury Laboratory, Cambridge University


title: SJTU_022: case: TB patient who suffers ATLI

description:
case: TB patient who suffers ATLI
SJTU_022


title: Control_31


title: SLX_12100_i705_i517


title: 182452_082118_PBMC_scRNA-seq_2018_Fresh_2

description: scRNA-seq data of PBMCs


title: Control_27


title: Control_29


title: SJTU_015: case: TB patient who suffers ATLI

description:
case: TB patient who suffers ATLI
SJTU_015


title: 182452_082118_PBMC_scRNA-seq_2018_Thawed_2

description: scRNA-seq data of PBMCs


title: SJTU_016: case: TB patient who suffers ATLI

description:
case: TB patient who suffers ATLI
SJTU_016


title: SLX_12100_i705_i508


title: E_DYDD4

tag: treatment


title: 182452_082118_PBMC_scRNA-seq_2018_Fresh_1

description: scRNA-seq data of PBMCs


title: SJTU_014: case: TB patient who suffers ATLI

description:
case: TB patient who suffers ATLI
SJTU_014


title: SJTU_005: case: TB patient who suffers ATLI

description:
case: TB patient who suffers ATLI
SJTU_005


title: SJTU_006: case: TB patient who suffers ATLI

description:
case: TB patient who suffers ATLI
SJTU_006


title: SJTU_003: case: TB patient who suffers ATLI

description:
case: TB patient who suffers ATLI
SJTU_003


title: Control_26


title: SJTU_011: case: TB patient who suffers ATLI

description:
case: TB patient who suffers ATLI
SJTU_011


title: SJTU_002: case: TB patient who suffers ATLI

description:
case: TB patient who suffers ATLI
SJTU_002


title: E_DYDD3


title: SLX_12100_i705_i507

tag: reporter line


title: 182443_111518_PBMC_scRNA-seq_2018_Thawed_2

description: scRNA-seq data of PBMCs


title: 182443_111518_PBMC_scRNA-seq_2018_Thawed_1

description: scRNA-seq data of PBMCs


title: SLX_12100_i705_i506


title: E_DYDD2


title: E_DYDD1


title: SLX_12100_i705_i505


title: Control_24


title: 182443_111518_PBMC_scRNA-seq_2018_Fresh_2

description: scRNA-seq data of PBMCs


title: E_CK5

value: untreated


title: Control_22


title: SLX_12100_i705_i504


title: 182443_111518_PBMC_scRNA-seq_2018_Fresh_1

description: scRNA-seq data of PBMCs


title: SLX_12100_i705_i503


title: 182443_081618_PBMC_scRNA-seq_2018_Fresh_2

description: scRNA-seq data of PBMCs


title: Control_21


title: Control_25


title: Control_20


title: SLX_12100_i705_i502


title: 182443_081618_PBMC_scRNA-seq_2018_Fresh_1

description: scRNA-seq data of PBMCs


title: E_CK3


title: E_CK2


title: SLX_12100_i706_i517


title: 182442_111518_PBMC_scRNA-seq_2018_Thawed_3

description: scRNA-seq data of PBMCs

value: West Nile Encephalitis


title: SLX_12100_i704_i517


title: Control_19


title: E_CK1


title: Control_23


title: 182442_111518_PBMC_scRNA-seq_2018_Thawed_2

description: scRNA-seq data of PBMCs


title: SLX_12100_i704_i508


title: SLX_12100_i704_i507


title: Control_18


title: SJTU_027: case: TB patient who suffers ATLI

description:
case: TB patient who suffers ATLI
SJTU_027


title: Control_17


title: smallRNA_Untransformed_D7M_2

city: Winnipeg

first: Nick

last: Wytinck

state: MB

address: 50 Sifton Road

department: Department of Biological Sciences

country: Canada

institute: University of Manitoba

description: small RNA

data_processing:
FastQ files were trimmed using Trimmomatic 0.33
adapter sequences, initial 12 bases of raw reads, low quality reads with a quality score under 20 over a sliding window of 4 bases and reads with an average quality score under 30 removed during the trimming process
Genome_build: B. napus genome from: Song, J. M., Guan, Z., Hu, J., Guo, C., Yang, Z., Wang, S., … Guo, L. (2020). Eight high-quality genomes reveal pan-genome architecture and ecotype differentiation of Brassica napus. Nature Plants, 6(1), 34–45. S. sclerotiorum genome from: Derbyshire, M., Denton-Giles, M., Hegedus, D., Seifbarghi, S., Rollins, J., Kan, J. Van, … Oliver, R. (2017). The complete genome sequence of the phytopathogenic fungus Sclerotinia sclerotiorum reveals insights into the genome architecture of broad host range pathogens. Genome Biology and Evolution, 9(3), 593–618. https://doi.org/10.1093/gbe/evx030 https://doi.org/10.1038/s41477-019-0577-7
Supplementary_files_format_and_content: Excel file with count of reads aligning to transgene sequence.  Genome-wide counts of small RNAs was not performed for this study.

organism: Brassica napus

source_name: stem cross-section

growth_protocol: Seeds of B. napus cv. Untransformed and the resultant transgenic lines were germinated in germination pouches (Phyto AB Inc.,  San Jose, CA, USA) and transplanted at the cotyledon stage into Sunshine Mix No. 1 (SunGro Horticulture, Agawam, MA, USA) at 22 °C and 50–70% humidity within greenhouse conditions. The plants were grown until the 30% flowering stage for use in infection experiments.

extract_protocol:
RNA was extracted from infected and uninfected plant tissue. For infected stems, cross-section disks (10 mm wide) were taken from the site of infection. The tissue was ground in an RNase-free mortar and RNA extracted using the Qiagen RNeasy Plant Mini kit (Toronto, ON, Canada). RNA was treated with Qiagen RNAse free DNAse (Toronto, ON, Canada), then cDNA synthesized using Quantabio qScript cDNA (Beverly, MA, USA). Quantity and purity were assessed spectrophotometrically and the quality of RNA samples verified using electropherogram profiles and RNA Integrity Numbers (RIN) (All samples had a RIN greater than 8.5) with an Agilent 2100 Bioanalyzer and RNA Pico Chips (Agilent, Santa Clara, CA, USA).
cDNA libraries were constructed by Genome Québec according to their mRNA stranded library protocol. The Illumina HISeq4000 was used to generate 100 bp PE reads.

treatment_protocol: A 3 x 3 mm cube of actively growing S. sclerotiorum from the leading edge of hyphae on a potato dextrose agar plate was collected using a syringe tip and placed onto the stem of a mature B. napus plant 30-50 mm above the soil. The fungus was sealed to the stem using a 30 x 20 mm strip of parafilm and lesion length was measured seven days post inoculation.

value: mature:30% flowering

value: stem, 30 mm above soil

value: control

tag: time


title: E_CK4


title: SLX_12100_i704_i506

city: Cambridge

source_name: phloem root meristem

value: PSE

value: protoplast of 5 day old root meristems


title: Control_16


title: 182442_111518_PBMC_scRNA-seq_2018_Fresh_2

description: scRNA-seq data of PBMCs


title: smallRNA_Untransformed_D7M_1

description: small RNA


title: smallRNA_Untransformed_D7M_3

description: small RNA


title: 182442_111518_PBMC_scRNA-seq_2018_Thawed_1

description: scRNA-seq data of PBMCs


title: Control_15


title: Control_14


title: 182442_081518_PBMC_scRNA-seq_2018_Thawed_2

description: scRNA-seq data of PBMCs


title: smallRNA_Untransformed_D1_2

description: small RNA


title: SLX_12100_i704_i503


title: 182442_081518_PBMC_scRNA-seq_2018_Thawed_1

description: scRNA-seq data of PBMCs


title: smallRNA_Untransformed_D1_1

description: small RNA


title: SLX_12100_i704_i502


title: Control_12


title: smallRNA_Untransformed_D0_3

description: small RNA


title: 182441_111818_PBMC_scRNA-seq_2018_Fresh_2

description: scRNA-seq data of PBMCs


title: 182441_111818_PBMC_scRNA-seq_2018_Fresh_1

description: scRNA-seq data of PBMCs


title: smallRNA_Untransformed_D0_2

description: small RNA


title: 182441_081018_PBMC_scRNA-seq_2018_Thawed_2

description: scRNA-seq data of PBMCs


title: Control_11


title: SLX_12100_i703_i508


title: SLX_12100_i704_i505


title: SLX_12100_i703_i507


title: 182441_081018_PBMC_scRNA-seq_2018_Thawed_1

description: scRNA-seq data of PBMCs


title: Control_10


title: smallRNA_Untransformed_D0_1

description: small RNA


title: smallRNA_1703_D7M_3

description: small RNA

value: treatment


title: Control_09


title: 182442_111518_PBMC_scRNA-seq_2018_Fresh_1

description: scRNA-seq data of PBMCs


title: SLX_12100_i704_i504


title: smallRNA_Untransformed_D1_3

description: small RNA


title: Control_13


title: Control_08


title: SLX_12100_i703_i506


title: 182440_102918_PBMC_scRNA-seq_2018_Fresh_2

description: scRNA-seq data of PBMCs

value: West Nile Fever


title: smallRNA_1703_D7M_2

description: small RNA


title: SLX_12100_i703_i517


title: SLX_12100_i703_i505


title: SLX_12100_i703_i504


title: 182440_073018_PBMC_scRNA-seq_2018_Thawed_2

description: scRNA-seq data of PBMCs

value: PBMC


title: smallRNA_1703_D7M_1

description: small RNA


title: smallRNA_1703_D1_3

description: small RNA


title: Control_06


title: Control_07


title: SLX_12100_i703_i502


title: SLX_12100_i703_i503


title: 182440_073018_PBMC_scRNA-seq_2018_Thawed_1

description: scRNA-seq data of PBMCs


title: Control_05


title: Control_04


title: smallRNA_1703_D1_1

description: small RNA


title: smallRNA_1703_D1_2

description: small RNA


title: 182439_102218_PBMC_scRNA-seq_2018_Fresh_2

description: scRNA-seq data of PBMCs


title: 182439_102218_PBMC_scRNA-seq_2018_Fresh_1

description: scRNA-seq data of PBMCs


title: smallRNA_1703_D0_3

description: small RNA


title: SLX_12100_i702_i508


title: Control_03


title: SLX_12100_i702_i517


title: 182439_072418_PBMC_scRNA-seq_2018_Fresh_2

description: scRNA-seq data of PBMCs


title: Control_43


title: Control_02


title: smallRNA_1703_D0_2

description: small RNA


title: 182440_102918_PBMC_scRNA-seq_2018_Fresh_1

description: scRNA-seq data of PBMCs


title: Control_01


title: SLX_12100_i702_i507


title: 182439_072418_PBMC_scRNA-seq_2018_Fresh_1

description: scRNA-seq data of PBMCs


title: SLX_12100_i702_i506


title: smallRNA_1703_D0_1

description: small RNA


title: 182438_102218_PBMC_scRNA-seq_2018_Fresh_2

description: scRNA-seq data of PBMCs


title: Down Syndrome - Epcam+ (rep. 3)

city: Milan

first: Stefano

last: Beretta

address: Via Olgettina, 60

country: Italy

institute: San Raffaele Telethon Institute for Gene Therapy

data_processing:
Basecalling using blc2fastq and trimming using cutadapt
Alignment using HISAT2 and gene abundance estimation using featurecounts
Differential gene expression computed using edgeR
Genome_build: GRCh38
Supplementary_files_format_and_content: Tab-separated count file

source_name: Human thymic epithelial cell

extract_protocol:
RNA was extracted from Epcam-enriched hTEC subsets by using ReliaPrepTM RNA MiniPrep System (Promega) according to manufacturer’s recommendations
Full-length RNA-seq libraries were prepared using the SMART-Seq2 protocol

value: Human thymic epithelial cell

tag: condition

value: Down Syndrome

tag: sorting

value: Epcam-positive


title: SJTU_044: case: TB patient who suffers ATLI

description:
case: TB patient who suffers ATLI
SJTU_044

value: TB patient with Anti-tuberculosis Drug Induced Liver Injury

value: male


title: 182438_102218_PBMC_scRNA-seq_2018_Fresh_1

description: scRNA-seq data of PBMCs

value: Asymptomatic


title: SLX_12100_i702_i505

tag: possible cell type

tag: developmental stage


title: Down Syndrome - Epcam- (rep. 3)

value: Epcam-negative


title: THP-1 macrophage incubated with CF Proband's Mother Plasma, 5059.03 (miRNA)

description:
miRNA profiling data from THP-1 macrophage incubated with CF Proband's Mother Serum
Sample name: 5059.03

data_processing: Profiling data was normalized in the robust multi-array average (RMA) procedure and then processed using Transcriptome Analysis Console (ThermoFisher Scientific, version 4)

extract_protocol: Total RNA was isolated using Trizol (Invitrogen) according to manufacturer's  protocol.

value: no known disease

value: THP-1 macrophage


title: SLX_12100_i702_i504


title: 182438_072318_PBMC_scRNA-seq_2018_Thawed_2

description: scRNA-seq data of PBMCs


title: SLX_12100_i702_i503


title: Down Syndrome - Epcam- (rep. 2)


title: 182438_072318_PBMC_scRNA-seq_2018_Thawed_1

description: scRNA-seq data of PBMCs


title: THP-1 macrophage incubated with CF Proband's Mother Plasma, 5064.03 (miRNA)

description:
miRNA profiling data from THP-1 macrophage incubated with CF Proband's Mother Serum
Sample name: 5064.03


title: 182438_072318_PBMC_scRNA-seq_2018_Fresh_1

description: scRNA-seq data of PBMCs


title: Down Syndrome - Epcam+ (rep. 1)


title: 182437_101518_PBMC_scRNA-seq_2018_Fresh_2

description: scRNA-seq data of PBMCs


title: Down Syndrome - Epcam- (rep. 1)


title: THP-1 macrophage incubated with CF Proband's Father Plasma, 5064.02 (miRNA)

description:
miRNA profiling data from THP-1 macrophage incubated with CF Proband's Father Serum
Sample name: 5064.02


title: SLX_12100_i701_i508


title: SLX_12100_i702_i502


title: 182437_101518_PBMC_scRNA-seq_2018_Fresh_1

description: scRNA-seq data of PBMCs


title: Healthy Donor - Epcam+ (rep. 3)

value: Healthy Donor


title: SLX_12100_i701_i507


title: 182437_071918_PBMC_scRNA-seq_2018_Fresh_2

description: scRNA-seq data of PBMCs


title: SLX_12100_i701_i517


title: 182437_071918_PBMC_scRNA-seq_2018_Fresh_1

description: scRNA-seq data of PBMCs


title: Down Syndrome - Epcam+ (rep. 2)


title: Healthy Donor - Epcam+ (rep. 2)


title: THP-1 macrophage incubated with CF Proband's Father Plasma, 6090.02 (miRNA)

description:
miRNA profiling data from THP-1 macrophage incubated with CF Proband's Father Serum
Sample name: 6090.02


title: Healthy Donor - Epcam- (rep. 2)


title: THP-1 macrophage incubated with CF Proband Plasma, 5064.01 (miRNA)

description:
miRNA profiling data from THP-1 macrophage incubated with CF Proband Serum
Sample name: 5064.01

value: classical CF

value: incubated with CF Proband Serum


title: Healthy Donor - Epcam+ (rep. 1)


title: THP-1 macrophage incubated with CF Proband Plasma, 5059.01 (miRNA)

description:
miRNA profiling data from THP-1 macrophage incubated with CF Proband Serum
Sample name: 5059.01


title: THP-1 macrophage incubated with CF Proband's Mother Plasma, 6090.03 (miRNA)

description:
miRNA profiling data from THP-1 macrophage incubated with CF Proband's Mother Serum
Sample name: 6090.03


title: 172169_111617_PBMC_scRNA-seq_2017_Thawed_1

description: scRNA-seq data of PBMCs

value: West Nile Encephalitis


title: SLX_12100_i701_i506

value: PSE

value: protoplast of 5 day old root meristems


title: SLX_12100_i701_i504


title: THP-1 macrophage incubated with CF Proband's Father Plasma, 5059.02 (miRNA)

description:
miRNA profiling data from THP-1 macrophage incubated with CF Proband's Father Serum
Sample name: 5059.02


title: THP-1 macrophage incubated with CF Proband Plasma, 6090.01 (miRNA)

description:
miRNA profiling data from THP-1 macrophage incubated with CF Proband Serum
Sample name: 6090.01


title: Healthy Donor - Epcam- (rep. 1)


title: THP-1 macrophage incubated with Healthy Control Plasma, HC1 (miRNA)

description:
miRNA profiling data from THP-1 macrophage incubated with healthy control serum
Sample name: HC1

value: healthy

value: incubated with healthy control serum


title: 172169_071717_PBMC_scRNA-seq_2017_Thawed_2

description: scRNA-seq data of PBMCs

value: PBMC


title: Healthy Donor - Epcam- (rep. 3)

value: Human thymic epithelial cell


title: SLX_12100_i701_i503


title: SLX_12100_i701_i502


title: 172169_071717_PBMC_scRNA-seq_2017_Thawed_1

description: scRNA-seq data of PBMCs


title: THP-1 macrophage incubated with Healthy Control Plasma, HC3 (miRNA)

description:
miRNA profiling data from THP-1 macrophage incubated with healthy control serum
Sample name: HC3


title: 172169_111617_PBMC_scRNA-seq_2017_Thawed_2

description: scRNA-seq data of PBMCs


title: SLX_12100_i701_i505


title: THP-1 macrophage incubated with Healthy Control Plasma, HC2 (miRNA)

description:
miRNA profiling data from THP-1 macrophage incubated with healthy control serum
Sample name: HC2


title: PBRM1KD_siHIF1_1

status: Public on Dec 23 2021

city: Chapel Hill

first: William

last: Kim

address: 450 West Dr

department: Lineberger Comprehensive Cancer Center

institute: UNC Chapel Hill

data_processing:
75b paired-end reads were sequenced on a NextSeq 500 Desktop Sequencer using a high output flow cell kit (Illumina), yielding an average of over 28M reads per sample.
QC-passed reads were aligned to theHERV reference genome using STAR
Transcript abundance estimates for each sample were performed using SALMON
Raw SALMON read counts for all RNAseq samples were normalized by total reads
Supplementary_files_format_and_content: Tab-delimited text files include Normalized count values for each sample
Genome_build: hg19

organism:
Homo sapiens
Human endogenous retroviruses

extract_protocol:
RNA was extracted with Qiagen RNeasy Plus Mini kit
Libraries were prepared using TruSeq Stranded mRNA Sample Prep Kit (Illumina)

tag: cell line


title: PBRM1KD_siHIF2_2


title: siHIF2_2


title: PBRM1KD_1


title: PBRM1KD_siHIF1_2


title: PBRM1KD_2


title: PBRM1KD_siHIF2_1


title: siHIF2_1


title: siHIF1_2


title: WT_2

value: shNS


title: siHIF1_1


title: WT_1


title: dUTP strand-specific RNA-seq log-phase cells of Schizosaccharomyces octosporus grown in BMW

first: Carl

middle: G

last: de Boer

address: 415 Main St

institute: The Broad Institute

data_processing:
For each of the 11 Ascomycota yeast species described above, the reads were merged and assembled using Trinity (Grabherr et al., 2011) (version ‘trinityrnaseq_r2012-05-18’) and mapped onto the assemblies to the respective genomes using GMAP (Wu and Watanabe, 2005). The Jaccard coefficient was used to join adjacent assemblies given enough connecting reads (a Jaccard cutoff of 0.35, the default in Trinity was used). Finally, upon mapping all of the reads to all of the merged assemblies, the Jaccard coefficient was used to clip assemblies which did not have enough support over a certain region. For each of the species, the reads were mapped to the genome sequence (Wapinski et al., 2007) using BLAT (Kent, 2002).
The RPKM used in the analysis described below were calculated for each transcript using RSEM (Li and Dewey, 2011), and only reads mapping to the sense mRNA strand were considered. Orthology between genes in different species was used as determined previously (Wapinski et al., 2007).
Genome_build: Various (from Wapinski et al, 2007, Nature)
Supplementary_files_format_and_content: tab delimited text containing all RPKM values for genes with S. cerevisiae orthologs

organism: Schizosaccharomyces octosporus

source_name: log-phase cells

growth_protocol: We conducted RNA-seq on the following 11 Ascomycota yeast species: Candida albicans, Candida glabrata, Kluyveromyces lactis, Kluyveromyces waltii, Saccharomyces bayanus, Naumovozyma castellii, Saccharomyces cerevisiae, Schizosaccharomyces japonicus, Schizosaccharomyces octosporus, Schizosaccharomyces pombe, Yarrowia lipolytica. Each of the 11 species was grown in BMW medium, chosen to minimize cross-species growth differences, as previously described (Thompson et al., 2013). N. castellii was grown at 25℃ while the rest of the species were grown at 30℃.

extract_protocol:
RNeasy Midi or Mini Kits (Qiagen, Valencia, CA) were used to isolate total RNA from log-phase cells by mechanical lysis using the manufacturer instructions as previously described (Thompson et al., 2013).
dUTP strand-specific RNA-seq libraries were constructed as previously described (Yassour et al., 2010) with the following modifications. (1) The polyA+-selected RNA was fragmented in a 40 µl reaction containing 1x Fragmentation Buffer (Affymetrix) by heating at 80℃ for 4 minutes followed by cleanup via ethanol precipitation for all libraries (except Y. lipolytica, S. pombe, S. japonicus, and S. octosporus; for these species, the conditions described previously were used (Yassour et al., 2010)), followed by cleanup via 1.8x RNAClean XP beads (Beckman Coulter Genomics). (2) For C. glabrata, K. lactis, S. bayanus, S. pombe, S. japonicus, and S. octosporus libraries, the adapter ligation was performed overnight at 16℃. For the rest, this was done at 16 degrees for 2 hours as described previously (Yassour et al., 2010). (3) Normalization was carried out based on the cDNA input and pooling of selected Illumina barcoded-adaptor-ligated cDNA products followed by gel size selection occurred as follows: range of 275 to 575 bp for pooled C. albicans, K. polysporus, K. waltii, and N. castellii libraries, and 375 to 575 bp for C. glabrata, K. lactis, and S. bayanus libraries. For the other libraries, no pooling was performed before gel size-selection – range of 310 to 510 bp for Y. lipolytica and 350 to 550 bp for S. pombe, S. japonicus, and S. octosporus. (4) The final PCR product was purified by 1.8x AMPure XP beads (Beckman Coulter Genomics) followed by a second gel size-selection for the range of 300 to 575 bp for C. albicans, K. polysporus, K. waltii, and S. castellii libraries, but no gel size-selection was performed for the other libraries. The pooled final library was sequenced on one to four lanes of HiSeq2000 (Illumina) with 68 base (Y. lipolytica had 76 base) paired-end reads and 8 base index reads.

tag: media

value: BMW

tag: growth temperature (celcius)

tag: growth phase

value: log phase


title: control virgin females treated with βAla repeat3

city: Dallas

first: James

middle: J.

last: Collins

address: 5323 Harry Hines Blvd.

department: Pharmacology

institute: UT Southwestern

data_processing:
Illumina Casava1.9 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to the Schistosoma mansoni genome (v7) using STAR.
Pairwise comparisons of differential gene expression were performed with DESeq2.
Genome_build: Schistosoma mansoni v7
Supplementary_files_format_and_content: .csv file containing analysis of data of reads per gene and data generated from one-to-one comparison of three replicates of each group within the same treatment by the Wald test in DESeq2

organism: Schistosoma mansoni

source_name: single sex adult female parasites

growth_protocol: Virgin females were cultured in ABC169 media with fresh media change every two days in 6-well plates. A 40 µm cell strainer was placed in each well with equal amount of virgin males co-culturing but separated from the females. Each treatment per experiment  contained two wells of 20 virgin females + 20 virgin males (so in total 40 females + 40 males as one bio-repeat)

extract_protocol:
All parasites were  flash frozen in liquid N2 and stored in 150 µL Trziol at -80℃ until all three biological replicates were collected for the sequencing. Total RNA was extracted and purified using a Zymo Direct-zol RNA miniprep kit before Illumina sequencing.
RNA libraries were prepared for sequencing using Illumina Truseq stranded mRNA library preparation kit.

treatment_protocol: 5 µM BATT or βAla was supplemented in the culture media with every media change. The culture lasted for 8 days.

value: NMRI (Puerto Rico)

tag: tissue

value: whole worm extract

value: 6 weeks intra-mammalian


title: control, (HeLa), rep1

city: Gainesville

first: Eric

middle: T

last: Wang

state: FL

address: 2033 Mowry Road

department: Molecular Genetics and Microbiology

institute: University of Florida

data_processing:
pseudoalignment (transcript level), kallisto 0.43.0
Genome_build: hg19
Supplementary_files_format_and_content: tab-separated values, TPM estimates from kallisto 0.43.0 for each sample

source_name: HeLa

growth_protocol: HeLa cells were maintained in 10% FBS growth medium (Dulbecco’s modified eagle medium (DMEM) + 10% fetal bovine serum (FBS) + 1% penicillin/streptomycin) in a humidity-controlled 5% CO2 incubator at 37°C.

extract_protocol:
RNA was extracted with 300 uL TRIzol and purified using the Direct-zol RNA Miniprep Kit.
Ribosomal RNA was depleted from 300 ng total RNA using the NEBNext rRNA Depletion Kit (NEB, #E6310L), and libraries were generated for next-generation sequencing using the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina (NEB, #E7760L) according to the manufacturer protocol. Libraries were multiplexed with Illumina i5 and i7 barcoding primers, pooled at 4 nM, and sequenced in a 2x76 bp paired-end format on an Illumina NextSeq 500. >14 million paired end reads were sequenced per library and recorded in FASTQ format.

treatment_protocol: Cells were passaged to 12-well tissue culture plates at a density of 1.5×10^5 cells/well (3.9×10^4 cells/cm2) and transfected with 500 ng plasmid DNA using 2 uL of TransIT-X2 transfection reagent (Mirus Bio, #MIR6005) and 100 uL Opti-MEM I reduced serum medium (ThermoFisher Scientific, #31985088) according to the manufacturer’s protocol. Cells were incubated with transfection reagent for 20 hr, after which the culture medium was aspirated and replaced with 10% FBS growth medium. Cells were then incubated for an additional 48 hr for 3-day experiments, followed by RNA isolation for further analysis.

value: HeLa

tag: approach

tag: target seq

tag: rep


title: control, (HeLa), rep3


title: vrigin females treated with 5 µM BATT repeat2

tag: age


title: vrigin females treated with 5 µM BATT repeat1

tag: strain


title: control, (HeLa), rep4


title: vrigin females treated with 5 µM BATT repeat3


title: control virgin females treated with βAla repeat1


title: control virgin females treated with βAla repeat2


title: Non-targeting, shRNA, rep2

value: shRNA

value: NT


title: Non-targeting, shRNA, rep3


title: Non-targeting, shRNA, rep1


title: CUG1, shRNA, rep3

value: CUGn


title: CUG1, shRNA, rep2


title: CUG1, shRNA, rep1


title: dCas9, -gRNA, rep2


title: dCas9, -gRNA, rep1


title: dCas9, -gRNA, rep3


title: dCas9, +CAG0, gRNA, rep3


title: Cas13d, -gRNA, rep3


title: Cas13d, -gRNA, rep2


title: Cas13d, +CUG1, gRNA, rep3


title: dCas9, +CAG0, gRNA, rep1


title: Cas13d, -gRNA, rep1


title: dCas9, +CAG0, gRNA, rep2


title: Cas13d, +CUG1, gRNA, rep2


title: SH-SY5Y SNCA-AS sample 4

first: Letizia

last: Messa

address: Piazza Leonardo Da Vinci 32

department: Electronics, Informatics and Bioengineering

institute: Politecnico di Milano

data_processing:
FastQ files were generated via llumina bcl2fastq2 Version 2.17.1.14
Gene and transcript intensities were computed using STAR/RSEM software using GRCh38 (Gencode release 27) as a reference, using the “-strandness forward” option. Differential expression analysis for mRNA and lncRNA was performed using R package DESeq2
Genome_build: HG19

source_name: Neuroblastoma cell line (SH-SY5Y)

growth_protocol: The human neuroblastoma cell line SH-SY5Y (ATCC) was grown in DMEM supplemented with 15% fetal bovine serum, 1% L-Glutammine and 1% penicillin/streptomycin, at 37 °C in a 5% CO2 atmosphere.

extract_protocol:
Samples were homogenized and total RNA was isolated by Trizol® reagent (Life Science Technologies, Italy) following the manufacturer’s specifications. RNAs were quantified using a Nanodrop ND-100 Spectrophotometer (Nanodrop Technologies, Wilmington, USA) and a 2100 Bioanalyzer (Agilent RNA 6000 Nano Kit, Waldbronn, Germany); RNAs with a 260:280 ratio of ≥1.5 and an RNA integrity number of ≥8 were subjected to deep sequencing.
SENSE Total RNA-Seq Library Prep Kit (Lexogen) using 500 ng total RNA and sequenced by Illumina NextSeq 550 sequencer.

treatment_protocol: Cells were transfected with a pCMV6-AC-GFP construct.

tag: cell type

value: Neuroblastoma

tag: treatment

value: Overexpression of SNCA-AS


title: control, (HeLa), rep2


title: SH-SY5Y SNCA-AS sample 3


title: SH-SY5Y SNCA-AS sample 2


title: SH-SY5Y SNCA sample 2

value: Overexpression of SNCA


title: SH-SY5Y SNCA sample 4


title: SH-SY5Y SNCA sample 1


title: SH-SY5Y SNCA sample 3


title: 1

city: changsha

first: Zhaoyu

last: Yang

address: 87 of xiangya road

institute: xiangya hospital

description: tiRNA and tRF

data_processing:
Illumina NextSeq 500 raw sequencing read data that passed the Illumina chastity filter were used for the following analysis. Sequencing quality was examined by FastQC software.
After that, the sequencing reads were 5’, 3’-adaptor trimmed, filtered for more than 15 nt by Cutadapt software, and for exactly aligned to mature-tRNA and pre-tRNA sequences from GtRNAdb (http://gtrnadb.ucsc.edu/) using NovoAlign software (v2.07.11).
The tsRNA expression levels were measured and normalized as tag counts per million of total aligned tRNA reads (TPM). For each tRNA sequence-based profile, the number of tRNA sequence reads could be used to estimate expression level of each tsRNA.
Genome_build: Human NCBI genome build 36 (NCBI36)
Supplementary_files_format_and_content: Sample_All_Comparisons_of_Expresseds_tDR.xlsx: Excel file includes tag count and TPM values for each Sample.
Supplementary_files_format_and_content: *_human_novoalign_alignment_tRNA_raw.txt

source_name: myocardial papilla

extract_protocol:
Total RNAs were extracted according to the manufacturer’s instruction (Qiagen, USA). The purity and concentration of total RNA samples were determined with NanoDrop ND-1000. Then we did the following treatments to remove some RNA modifications which might interfere with small RNA-sequencing library construction: 3’-aminoacyl (charged) deacylation to 3’-OH (hydroxyl group) for 3’ adaptor ligation, 3’-cP (2’,3’-cyclic phosphate) removal to 3’-OH for 3’ adaptor ligation, 5’-OH phosphorylation to 5’-P for 5’-adaptor ligation, N1-methyladenosine and N3-methylcytidine demethylation for efficient reverse transcription. All procedures were performed using rtStar tRF&tiRNA Pretreatment Kit (Arraystar) protocols.
Total RNA samples were sequentially ligated to 3’ and 5’ small RNA adapters using NEBNext Multiplex Small RNA Library Prep Set for Illumina (New England Biolabs, USA). cDNA was then synthesized and amplified using Illumina’s proprietary reverse transcription primers and amplification primers. Subsequently, 135-170 bp PCR amplified fragments (corresponding to 15-50 nt small RNA size range) were extracted and purified from the PAGE gel. The completed libraries were quantified by Agilent 2100 Bioanalyzer. Libraries were mixed in equal amounts according to the quantification results and used for sequencing on the instrument. And then, the DNA fragments in well-mixed libraries were denatured to generate single-stranded DNA molecules and loaded onto the reagent cartridge. Finally, the sequencing run was performed on Illumina NextSeq 500 system using NextSeq 500/550 V2 kit (Illumina) according to the manufacturer’s instructions. Sequencing was carried out by running 50 cycles.

value: myocardial papilla

tag: diagnosis

value: RHD without AF


title: SH-SY5Y SNCA-AS sample 1


title: 5

description: tiRNA and tRF

value: RHD with AF


title: 6

description: tiRNA and tRF


title: 3

description: tiRNA and tRF


title: 4

description: tiRNA and tRF