title: HC-075

city: Vancouver

first: Robert

middle: E. W.

last: Hancock

state: British Columbia

address: 2259 - Lower Mall Research Station

department: Department of Microbiology & Immunology

institute: University of British Columbia

data_processing:
BBDuk (version 38.26) was used to trim adapter sequences and polyA tails (trimpolya=10)
STAR (version 2.6.1b) was used to align trimmed reads to the indexed human genome.
SAMtools (version 1.9) was used to merge alignments or samples sequenced across multiple lanes of the flowcell.
HTSeq-count (version 0.9.1) was used to generate raw count data from alignments using the "union" mode and "reverse" stranded options.
Genome_build: GRCh38/hg38 (version 94) from Ensembl
Supplementary_files_format_and_content: Tab-delimited count matrix of raw counts for all samples from HTSeq-count

source_name: blood

extract_protocol:
2.5ml of whole blood was collected from each participant into PAXgene Blood RNA tubes (PreAnalytiX GmbH, Switzerland). RNA was isolated from each samples using the RiboPure RNA purification kit (Ambion ThermoFisher; Waltham, MA, USA) following the manufacturer’s protocol. Quantification and quality assessment of total RNA was performed using an Agilent 2100 Bioanalyzer (Santa Clara, CA, USA). Poly-adenylated RNA was captured using the NEBNext Poly(A) mRNA Magnetic Isolation Module (catalogue no.: E7409L, NEB; Ipswich, MA, USA).
Strand-specific cDNA libraries were generated from poly-adenylated RNA using the KAPA Stranded RNA-Seq Library Preparation Kit (cat. no.: 07277253001, Roche; Basel, Switzerland).

value: whole blood

tag: pathology

value: Healthy control


title: HC-078

status: Public on Mar 01 2022

type: SRA

country: Canada

library_source: transcriptomic

molecule: total RNA

organism: Homo sapiens

tag: tissue


title: HC-077


title: NT12571_1

city: Cambridge

first: Pedro

last: Beltrao

address: Wellcome Genome Campus

country: United Kingdom

institute: EMBL-EBI

description: batch: Galardini_HC3HYBGX9

data_processing:
Raw single-ended Illumina reads were trimmed to remove the TruSeq3 adaptors using trimmomatic v0.36.
Trimmed reads were pseudo-aligned to the NC_000913.3 E. coli K-12 genome’s transcripts using kallisto v0.44.0 with the sequence based bias correction and using an average fragment length of 130bp (70bp standard deviation).
Genome_build: NC_000913.3
Supplementary_files_format_and_content: Files starting with the “kallisto_” prefix contain the transcripts counts

organism: Escherichia coli

source_name: E. coli strain culture

growth_protocol: Samples were grown in LB media until an O.D. concentration of about 0.2

extract_protocol:
Total RNA was extracted using the RNeasy kit (QIAGEN) followed by Dnaze treatment
Samples were subject ro rRNA depletion prior to library preparation

tag: strain

value: NILS 38

tag: growth condition

value: LB media


title: BCM2

city: Birmingham

first: Kai-Michael

last: Toellner

state: West Midlands

address: 4th Floor IBR, Wolfson Drive

department: Institute of Immunology and Immunotherapy

institute: University of Birmingham

data_processing:
Reads were aligned against the GCRm38 genome assembly with Ensembl release 86 transcript annotations and expected gene-level counts were calculated using either STAR v2.7.3a or Partek Flow.
Count data were rounded to integers and normalized for differences in sample library size using the standard median ratio method in DESeq2 (Anders and Huber, 2010).
Genome_build: GRCm38
Supplementary_files_format_and_content: Normalized log2 counts in tab-delimited text format.  Gene ids are represented by Ensembl v86 identifiers.

organism: Mus musculus

source_name: IgG1+ Bmem

extract_protocol:
Single cell suspensions from lymph nodes were depleted of erythrocytes by ACK lysis buffer and stained with live/dead marker and respective antibodies in FACS buffer (1x PBS with EDTA and FCS). Cells were directly sorted into 500ul of Trizol. The total RNA was purified using the RNeasy Plus Micro kit (QIAGEN) according to the manufacturer’s instructions.
Un-stranded, non-rRNA, non-polyA+ selected libraries were prepared using the SMARTer Ultra Low Input RNA kit for Sequencing v3 (Clontech Laboratories).
The libraries were sequenced on the Illumina HiSeq 2000 platform (Illumina, Crick advanced sequencing) as 75 bp paired-end runs.

treatment_protocol: Mice received adoptive cell transfers of 1x10^5 NP+B220+ splenocytes from IgHNP QM k-/- Cg1cre mTmG splenocytes, 24 hours later were immunised with 20µg/µl NP-CGG in alum precipitate with heat-inactivated bordetella pertussis adjuvant on the plantar surface of hind feet. At day 8 post-immunisation GC and emigrating memory B cells were isolated from popliteal (draining) lymph nodes and naive B cells and circulating memory B cells were isolated from distal (pooled axillary and brachial) lymph nodes were collected. All mice were aged 8-12 weeks.

tag: Sex

value: male

tag: organ

value: distLN


title: HC-076


title: NAIVE3

source_name: naïve from host


title: NT12567_1

description: batch: Galardini_HC3HYBGX9

value: NILS 34


title: DB_HB013H_1_2_redo

city: San Francisco

first: Hanbing

last: Song

state: CA

address: 513 Parnassus Ave, HSE

department: Department of Medicine

country: USA

institute: UCSF

data_processing:
Demultiplexed pair-end FASTQ files were aligned to mm8 whole genome using dropseq_workflow pipeline on Terra
Genome_build: hg19
Supplementary_files_format_and_content: txt format matrix table with raw gene counts for every gene and every cell barcode

source_name: Hepatoblastoma Patient Paired Normal Tissue Sample

extract_protocol:
Tumor and adjacent normal liver tissues were dissociated by mincing tissue in 1-2mm squares, followed by incubation in Liver Perfusion Medium (ThermoFisher Scientific) for 15 min at 37°C in a rotating oven. After being washed in PBS (ThermoFisher Scientific), tissues were incubated with Liver Digest Medium (ThermoFisher Scientific) supplemented with HEPES and collagenase type IV (Worthington Biochemical, Lakewood, NJ) (600 to 800 U/ml) for 30 min at 37°C with rotation. Further dissociation was achieved by pipetting 10 times through a 25 mL serological pipette. Single cells were then separated from clumps using a 70 µm strainer (Fisher Scientific, Hampton, NH). After lysis of red blood cells with ACK RBC Lysis Buffer (Fisher Scientific), single cells were counted using a LUNA™ Automated Cell Counter (Logos biosystems, South Korea) and processed for scRNA-seq analysis. Patient derived spheroids embedded in Matrigel were washed with PBS, then digested in TrypLE 1X (ThermoFisher Scientific) for 30 to 45 min at 37°C with rotation to obtain a single cell suspension. Cells were washed, then, filtered through a 70-µm strainer, counted using a LUNA™ Automated Cell Counter, and processed for scRNA-seq analysis.
Libraries were prepared for each pool, using 800-1000 pg of DNA and the Nextera XT DNA Library Preparation Kit. They were dual-indexed with N700 and N500 oligonucleotides. Library products were purified using SPRI beads, first at 0.6x and then at a 1x volumetric ratio. Libraries were then run on an HSD1000 tape (Agilent, Cat: 50675584) to determine the concentration between 100-1000 bp. For each library, 3 nM dilutions were prepared. These dilutions were pooled for sequencing on a NovaSeq S4 flow cell.

tag: sample type

value: Paired Normal

value: liver

tag: patient


title: NT12564_1

description: batch: Galardini_HC3HYBGX9

value: NILS 31


title: DB_HB015H_2


title: Ngn3 Weak posi

type: RNA

city: Tokyo

first: Ami

last: Watanabe

address: 1-1-1 yayoi, Bunkyo-ku

department: Institute of Molecular and Cellular Biosciences

country: Japan

institute: University of Tokyo

hyb_protocol: 0.6 ug of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes following the manufacturer’s instructions (Gene Expression Hybridization Kit <5188-5242>). On completion of the fragmentation reaction, hybridization buffer was added to the fragmentation mixture and hybridized to Agilent SurePrint G3 Human Gene Expression 8x60K v3 Microarray <G4851C> for 17 hours at 65 ℃ in a rotating Agilent hybridization oven <G2545Ａ，Ｇ2530-60029>. After hybridization, microarrays were washed 1 minute at room temperature with Gene Expression Wash Buffer Kit <5188-5327> Wash Buffer 1 (Agilent) and 1 minute with 37℃ Wash buffer 2, then dried immediately.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505C) using one color scan setting for 8x60k array slides (Scan Area 61x21.6 mm, Scan resolution 3um, Dye channel is set to Green is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction <version 10.10.1.1> (Agilent) using default parameters (protocol GE１_1010_Sep10 and Grid template: 072363_D_F_20150612) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

source_name: Ngn3 Low expression cells

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 1 ug RNA using the One-Color Low Input Quick Amp Labering kit, one-color <5190-2305> and Agilent RNA Spike-In kit (Agilent) according to the manufacturer's instructions, followed by RNeasy mini kit <74106> (Qiagen).  Dye incorporation and RNA yield were checked with the Nanodrop ND1000 <version 3.5.2> (Thermo Fisher Scientific).

extract_protocol: Total RNA was isolated from NGN3 posi, NGN3 weak posi, and Ngn3 mature cells using Qiashredder and RNeasy Mini Kit (Qiagen).

tag: cell type

value: iPS cells

tag: genotype

value: Ngn3 weak expression

tag: time

value: differentiation day 22

tag: cell line


title: NT12552_1

description: batch: Galardini_HC3HYBGX9

value: NILS 19


title: BCM1


title: HC-074


title: HC-073


title: BCM4


title: Ngn3 posi

source_name: Ngn3 high expression cells

value: Ngn3 high expression


title: NT12551_1

description: batch: Galardini_HC3HYBGX9

value: NILS 18


title: DB_HB012T_2_S18_L001

source_name: Hepatoblastoma Patient Paired Tumor Tissue Sample

value: Paired Tumor


title: NAIVE2


title: NAIVE1


title: DB_HB012T_1_S34_L002


title: HC-072

value: whole blood


title: HC-067

value: Healthy control


title: NT12393_1

description: batch: Galardini_HC3HYBGX9


title: DSP-1010992704701-G-G11

city: Seattle

first: Stephanie

last: Zimmerman

state: WA

address: 530 Fairview Ave N

institute: NanoString Technologies

data_processing:
Library strategy: GeoMx Seq
GeoMx NGS Pipeline v2.3.3.10 with the following parameters: quality-trim-score = 20, 2color-trimming = True, adapter1 = AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC, adapter2 = AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT, adapter-trim-match-length = 10, adapter-trim-max-mismatch = 3, barcode-max-mismatch = 1, stitching-max-mismatch = 2
Genome_build: NA
Supplementary_files_format_and_content: Digital Count Conversion (DCC) files: format outputted from GeoMx NGS Pipeline, contains software versions, scan attributes, GeoMx NGS pipeline parameters and output metrics, Q30 scores, and list of deduplicated counts per RTS_ID (probe barcode)
Supplementary_files_format_and_content: mouse_organs_RawCounts: xlsx file outputted from the GeoMx DSPDA analysis software containing sample annotations, probe information, and raw probe count matrix for each probe and sample
Supplementary_files_format_and_content: mouse_organs_CollapsedTargetCounts: xlsx file outputted from the GeoMx DSPDA analysis software containing sample annotations, processing information, and target-level count matrix for each gene target and sample
Supplementary_files_format_and_content: mouse_organs_NormalizedCounts: xlsx file outputted from the GeoMx DSPDA analysis software containing sample annotations, processing information, and Q3 normalized count matrix for each gene target and sample, filtered for genes expressed above background

molecule: other

source_name: adult mouse FFPE tissue

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

tag: panel

value: (v1.0) 06 E2E Set 1 WTA, (v1.0) 07 E2E Set 2 WTA, (v4.0) Mouse Whole Transcriptome Dev

tag: roilabel

tag: area

value: Colon


title: NT12442_1

description: batch: Galardini_HC3HYBGX9

value: LB media


title: HC-066


title: HC-063


title: NT12285_1

description: batch: Galardini_HC3HYBGX9


title: NT12292_1

description: batch: Galardini_HC3HYBGX9


title: DB_HB009H_Pool_C


title: HC-061


title: HC-064


title: DB_HB009H_Pool_B


title: DSP-1010992704701-G-H01


title: DSP-1010992704701-G-G12


title: NT12286_1

description: batch: Galardini_HC3HYBGX9


title: NT12223_1

description: batch: Galardini_HC3HYBGX9


title: DSP-1010992704701-G-G08

value: Intenstine


title: HC-062


title: HC-060


title: DSP-1010992704701-G-G09


title: NT12194_3

description: batch: Galardini_HC3HYBGX9


title: DB_HB008T_Pool_B


title: DB_HB010T_Pool_C


title: HC-059


title: DB_HB011H_1_S33_L002


title: NT12332_3

description: batch: Galardini_HC3HYBGX9


title: NT12192_2

description: batch: Galardini_HC3HYBGX9


title: DB_HB008T_Pool_A


title: DB_HB011H_2_S17_L001


title: DSP-1010992704701-G-G06


title: DB_HB009H_Pool_A


title: DSP-1010992704701-G-G10


title: DSP-1010992704701-G-G05

value: Spleen


title: NT12177_1

description: batch: Galardini_HC3HYBGX9


title: DSP-1010992704701-G-G03


title: DB_HB007N_Pool_B

value: Paired Normal


title: DSP-1010992704701-G-G07


title: NT12169_3

description: batch: Galardini_HC3HYBGX9


title: DB_HB007N_Pool_C

value: liver


title: HC-056


title: NT12167_1

description: batch: Galardini_HC3HYBGX9


title: DB_HB007H_Pool_C


title: HC-055


title: DSP-1010992704701-G-G02


title: DSP-1010992704701-G-G04


title: HC-054


title: DSP-1010992704701-G-G01

value: Kidney


title: HC-053


title: DSP-1010992704701-G-F12


title: DB_HB006T_Pool_C


title: HC-057


title: NT12153_1

description: batch: Galardini_HC3HYBGX9


title: NT12148_1

description: batch: Galardini_HC3HYBGX9


title: DB_HB007H_Pool_A_B


title: HC-058


title: HC-051


title: NT12165_1

description: batch: Galardini_HC3HYBGX9


title: DB_HB007N_Pool_A


title: DSP-1010992704701-G-F09

value: Lung


title: HC-040


title: DSP-1010992704701-G-F11


title: NT12140_1

description: batch: Galardini_HC3HYBGX9


title: NT12136_1

description: batch: Galardini_HC3HYBGX9


title: HC-052


title: HC-050


title: HC-038


title: NT12160_1

description: batch: Galardini_HC3HYBGX9


title: DB_HB004T_Pool_B


title: DB_HB004T_Pool_A_C


title: HC-039


title: NT12119_1

description: batch: Galardini_HC3HYBGX9


title: DB_HB005H_Pool_C


title: DB_HB005H_Pool_B


title: DSP-1010992704701-G-F07


title: HC-037


title: DSP-1010992704701-G-F06


title: NT12113_1

description: batch: Galardini_HC3HYBGX9


title: DB_HB006T_Pool_A


title: NT12110_1

description: batch: Galardini_HC3HYBGX9


title: HC-036


title: DB_HB005H_Pool_A


title: DSP-1010992704701-G-F05

value: Brain


title: DB_HB003H_Pool_C


title: DSP-1010992704701-G-F08


title: DB_HB003N_Pool_A_B_C


title: NT12118_1

description: batch: Galardini_HC3HYBGX9


title: DSP-1010992704701-G-F04


title: NT12105_1

description: batch: Galardini_HC3HYBGX9


title: DSP-1010992704701-G-F03


title: HC-027


title: DB_HB003H_Pool_A


title: DSP-1010992704701-G-F02


title: NT12098_3

description: batch: Galardini_HC3HYBGX9


title: HC-028


title: HC-025


title: DB_HB002T_Pool_A_C


title: DB_HB002T_Pool_B


title: NT12096_3

description: batch: Galardini_HC3HYBGX9


title: PANWES006

value: Mild AP


title: DSP-1010992704701-G-F01

value: Liver


title: NT12089_3

description: batch: Galardini_HC3HYBGX9


title: NT12095_3

description: batch: Galardini_HC3HYBGX9


title: DB_HB001N_Pool_C


title: DSP-1010992704701-G-E12


title: PANWES004

value: Severe AP


title: PANWES003


title: DB_HB001H_Pool_C


title: DB_HB001N_Pool_A


title: NT12084_1

description: batch: Galardini_HC3HYBGX9


title: DSP-1010992704701-G-E10


title: DSP-1010992704701-G-E09

value: NOD

value: (v4.0) Mouse Whole Transcriptome Dev, (v1.0) 06 E2E Set 1 WTA, (v1.0) 07 E2E Set 2 WTA


title: PANWES002

value: whole blood


title: DB_HB001H_Pool_A_B


title: DSP-1010992704701-G-E08


title: PANWES005


title: PANSEP008


title: NT12082_1

description: batch: Galardini_HC3HYBGX9


title: NT12068_1

description: batch: Galardini_HC3HYBGX9


title: PANSEP007

value: Moderately-severe AP


title: DSP-1010992704701-G-E11

value: (v1.0) 06 E2E Set 1 WTA, (v1.0) 07 E2E Set 2 WTA, (v4.0) Mouse Whole Transcriptome Dev


title: DB_HB001N_Pool_B


title: NT12027_1

description: batch: Galardini_HC3HYBGX9


title: NT12044_1

description: batch: Galardini_HC3HYBGX9


title: DSP-1010992704701-G-E06

value: Colon


title: MDA-MB-231_MEL-18 T334A_rep2

city: Seoul

first: Gu

last: Kong

address: 17 Haengdang-dong, Seongdong-gu

department: Department of Pathology

country: South Korea

institute: College of Medicine, Hanyang University

data_processing:
Illumina Casava 1.8 software used for basecalling
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to hg19 whole genome using STAR v2.5.3a
Raw counts were calculated using featureCounts from Subread package v1.5.3
Genome_build: hg19
Supplementary_files_format_and_content: Tab-delimited text files include raw counts for each sample

source_name: breast cancer cell line

growth_protocol: Cells were cultured in DMEM supplemented with 10% FBS at 37°C in a humidified 5% CO2 incubator.

extract_protocol:
Total RNA was extracted using TRIzol reagents. RNA integrity was confirmed by a bioanalyzer using an Agilent RNA 6000 Pico Kit (Agilent, Santa Clara, CA). The isolated total RNA was processed for preparing mRNA sequencing library using TruSeq stranded mRNA sample preparation kit (illumina, San Diego, CA) according to manufacturer’s instruction. Simply, mRNAs were isolated from 400 ng total RNA by RNA purification bead using polyA capture, and followed by enzyme shearing.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: MDA-MB-231 cells were infected with lentiviruses encoding either control (pLVX vectror), MEL-18 wild type (pLVX-MEL-18 WT) or MEL-18 T334A (pLVX-MEL-18 T334A)

value: mammary gland/breast

value: epithelial

tag: lentivirus

value: pLVX-MEL-18 T334A

tag: disease

value: adenocarcinoma


title: MDA-MB-231_MEL-18 T334A_rep3


title: DSP-1010992704701-G-E05

value: Intenstine


title: PANSEP005

tag: pathology


title: NT12055_1

description: batch: Galardini_HC3HYBGX9

value: LB media


title: DSP-1010992704701-G-E07

tag: tissue


title: PANSEP006


title: MDA-MB-231_MEL-18 T334A_rep1


title: DSP-1010992704701-G-E03

tag: strain


title: MDA-MB-231_MEL-18 WT_rep2

value: pLVX-MEL-18 WT


title: PANSEP003


title: DSP-1010992704701-G-E04


title: PANSEP004


title: DSP-1010992704701-G-E02


title: NT12020_3

description: batch: Galardini_HC3HYBGX9

tag: growth condition


title: DSP-1010992704701-G-E01

value: Spleen


title: MDA-MB-231_CON_rep3

value: pLVX vectror


title: MDA-MB-231_MEL-18 WT_rep3


title: MDA-MB-231_MEL-18 WT_rep1


title: NT12015_3

description: batch: Galardini_HC3HYBGX9


title: NT12004_3

description: batch: Galardini_HC3HYBGX9


title: DSP-1010992704701-G-D12


title: NT12002_3

description: batch: Galardini_HC3HYBGX9


title: PANSEP001


title: DSP-1010992704701-G-F10

value: Kidney


title: NT12023_3

description: batch: Galardini_HC3HYBGX9


title: PANNE085


title: MDA-MB-231_CON_rep1


title: NT12704_2

description: batch: 2017-05-30-HTYY2BGX2


title: NT12001_3

description: batch: Galardini_HC3HYBGX9


title: PANNE082


title: PANNE081

value: Mild AP


title: DSP-1010992704701-G-D10

value: NOD


title: DSP-1010992704701-G-D11

value: (v4.0) Mouse Whole Transcriptome Dev, (v1.0) 06 E2E Set 1 WTA, (v1.0) 07 E2E Set 2 WTA


title: NT12616_2

description: batch: 2017-05-30-HTYY2BGX2


title: NT12616_1

description: batch: 2017-05-30-HTYY2BGX2


title: PANNE080

value: whole blood


title: PANNE079


title: DSP-1010992704701-G-D09


title: PANSEP002

value: Moderately-severe AP


title: DSP-1010992704701-G-D08


title: NT12525_2

description: batch: 2017-05-30-HTYY2BGX2

value: metR-E


title: PANNE078


title: MDA-MB-231_CON_rep2


title: PANNE077


title: DSP-1010992704701-G-D05

value: Lung


title: DSP-1010992704701-G-D07


title: DSP-1010992704701-G-D06


title: PANNE075

value: Severe AP


title: NT12525_1

description: batch: 2017-05-30-HTYY2BGX2


title: DSP-1010992704701-G-D03


title: NT12514_2

description: batch: 2017-05-30-HTYY2BGX2

value: ptsI-D


title: NT12514_1

description: batch: 2017-05-30-HTYY2BGX2


title: DSP-1010992704701-G-D04


title: NT12521_1

description: batch: 2017-05-30-HTYY2BGX2

value: hisH-E


title: PANNE076


title: NT12506_2

description: batch: 2017-05-30-HTYY2BGX2

value: tyrA-D


title: FGF2 Organoid scRNA Sequencing

city: Albany

first: Nicholas

last: Moskwa

state: New York

address: 1400 Washington Avenue

institute: University at Albany

data_processing:
Clean reads were analyzed with mouse reference genome using the Cell Ranger v4.0
Genome_build: mm10-2020-A
Supplementary_files_format_and_content: tsv and mtx files containing cell barcodes and gene count matrix

extract_protocol:
Capture 5023 cells for control and 10107 cells for FGF2 organoids using the 10x Chromium System
Libraries were prepared according to 10x Genomics Chrmoium Next GEM Single Cell 3' GEM Kit instructions (Cat# 1000130). Briefly, single cells were emulsified in 10X Chromium system and each cell's RNA was barcoded. cDNA was amplified, fragmented and indexed primers 10-13 cycles and library fragments of ~400 bp. The cDNA was flowed onto a Illumina flow cell for cluster generation. Libraries were sequenced on 4 lanes of a Illumina NextSeq500 for high output PE75 v2.5 following the manufacturer's protocols.
scRNA-Seq / Drop-Seq

value: Salivary Gland

tag: age


title: PANNE073


title: Control Organoid scRNA Sequencing


title: DSP-1010992704701-G-D01

value: Brain


title: NT12506_1

description: batch: 2017-05-30-HTYY2BGX2

value: LB media


title: PANNE072


title: DSP-1010992704701-G-C12


title: NT12521_2

description: batch: 2017-05-30-HTYY2BGX2


title: Mouse inducible PDAC cells-Off Dox-4 days, pool2-AK-B6

city: Buffalo

first: Prasenjit

last: Dey

state: NY

address: Elm & Carlton Sts. CGP/BLSC-L5 307

department: Immunology

institute: Roswell Park Comprehensive Cancer Center

description: Dey-14wtRNA-pool2-AK-B6-Off-4d_190520-NB500999-0276-AHGMLMBGXB-1-GTGAAA

data_processing:
STAR 2.7 MAPPING
HTSEQ and RPKM for gene expression normalization
Genome_build: mm10
Supplementary_files_format_and_content: exp_14_sample_htseq_count.txt

source_name: Mouse PDAC tumor

growth_protocol: PDAC cancer cells are routinely cultured in RPMI+10% FBS and 1 ug/ml doxycycline (Dox). Dox Off cells are cultured in media without Dox for the time point described.

extract_protocol:
RNA was extracted using standard Qiagen kit using their protocol
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: 1 ug/ml doxycycline (Dox)-On Dox

value: pancreatic cancer cell

tag: treatment

value: Untreated, 4 days


title: NT12489_1

description: batch: 2017-05-30-HTYY2BGX2

value: proB-C


title: PANNE071

value: Mild AP


title: PANNE070


title: NT12489_2

description: batch: 2017-05-30-HTYY2BGX2


title: DSP-1010992704701-G-C11

value: NOD


title: PANNE074


title: DSP-1010992704701-G-C10

value: (v4.0) Mouse Whole Transcriptome Dev, (v1.0) 06 E2E Set 1 WTA, (v1.0) 07 E2E Set 2 WTA


title: Mouse inducible PDAC cells-On Dox, pool2-AK-B6

description: Dey-14wtRNA-pool2-AK-B6-On-Day_190520-NB500999-0276-AHGMLMBGXB-1-CCGTCC

value: Dox


title: Mouse inducible PDAC cells-Off Dox-2 days, pool2-AK-B6

description: Dey-14wtRNA-pool2-AK-B6-Off-2d_190520-NB500999-0276-AHGMLMBGXB-1-GTCCGC

value: Untreated, 2 days


title: Mouse inducible PDAC cells-Off Dox-2 days, pool2-14838

description: Dey-14wtRNA-pool2-14838-Off-2d_190520-NB500999-0276-AHGMLMBGXB-1-AGTTCC


title: Mouse inducible PDAC cells-Off Dox-4 days, pool2-14838

description: Dey-14wtRNA-pool2-14838-Off-4d_190520-NB500999-0276-AHGMLMBGXB-1-ATGTCA


title: PANNE069

value: whole blood


title: DSP-1010992704701-G-D02

value: Lung


title: PANNE066

value: Severe AP


title: NT12485_1

description: batch: 2017-05-30-HTYY2BGX2

value: thrA-B


title: PANNE065


title: PANNE068


title: DSP-1010992704701-G-C06

value: Liver


title: NT12460_2

description: batch: 2017-05-30-HTYY2BGX2


title: PANNE064


title: Mouse inducible PDAC cells-Off Dox-4 days, pool1-4298

description: Dey-14wtRNA-pool1-4298-Off-4d_190521-NB501070-0146-AHGMLKBGXB-1-CTTGTA


title: NT12190_2

description: batch: 2017-05-30-HTYY2BGX2


title: Mouse inducible PDAC cells-On Dox, pool1-14838

description: Dey-14wtRNA-pool1-14838-On-Day_190521-NB501070-0146-AHGMLKBGXB-1-AGTCAA


title: DSP-1010992704701-G-C08


title: DSP-1010992704701-G-C07


title: NT12460_1

description: batch: 2017-05-30-HTYY2BGX2


title: Mouse inducible PDAC cells-On Dox, pool1-4298

description: Dey-14wtRNA-pool1-4298-On-Day_190521-NB501070-0146-AHGMLKBGXB-1-GCCAAT


title: Mouse inducible PDAC cells-Off Dox-2 days, pool1-4298

description: Dey-14wtRNA-pool1-4298-Off-2d_190521-NB501070-0146-AHGMLKBGXB-1-CAGATC


title: NT12485_2

description: batch: 2017-05-30-HTYY2BGX2


title: DSP-1010992704701-G-C04

value: BALBC

value: Colon


title: PANNE063


title: NT12183_1

description: batch: 2017-05-30-HTYY2BGX2


title: NT12183_2

description: batch: 2017-05-30-HTYY2BGX2


title: DSP-1010992704701-G-C05


title: DSP-1010992704701-G-C02


title: PANNE060


title: DSP-1010992704701-G-C01

value: Intenstine


title: NT12178_2

description: batch: 2017-05-30-HTYY2BGX2

value: LB media


title: NT12190_1

description: batch: 2017-05-30-HTYY2BGX2


title: Mouse inducible PDAC cells-On Dox, pool1-4217

description: Dey-14wtRNA-pool1-4217-On-Day_190521-NB501070-0146-AHGMLKBGXB-1-CGATGT

value: pancreatic cancer cell


title: NT12178_1

description: batch: 2017-05-30-HTYY2BGX2


title: DSP-1010992704701-G-C03


title: PANNE058


title: DSP-1010992704701-G-C09


title: DSP-1010992704701-G-B11


title: DSP-1010992704701-G-B12


title: Mouse inducible PDAC cells-Off Dox-2 days, pool1-4217

description: Dey-14wtRNA-pool1-4217-Off-2d_190521-NB501070-0146-AHGMLKBGXB-1-TGACCA


title: PANNE059

value: Moderately-severe AP


title: PANNE062


title: Replicate 3 mPGES-1 KO

city: Frankfurt

first: Andreas

last: Weigert

address: Theodor-Sern-Kai 7

department: Medicine

country: Germany

institute: Goethe-University

data_processing:
Read sequence quality was monitored with FastQC ( v 0.11.5) and PicardTools CollectRnaSeqMAtrics (v 2.17.2)
Adapter sequences were removed from 3'ends with Felxbar (v 3.0.3) using parameters -q WIN -qt 20 -qw 5
Reads were mapped to mm10 with STAR using GENCODE gene annotation m16 with parameters --outFilterMismatchNmax 5 --outFilterMultimapNmax 1
Read overlaps with annotated exons were counted using GenomicAlignments (v 1.18.) mode "union"
Genome_build: mm10
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: PyMT mammary tumor

extract_protocol:
mRNA-isolation and cDNA transcription were performed immediately after fibroblast sorting from tumors using SMART-Seq v4 Ultra Low Input RNA Kit for Sequencing (Takara) according to the manufacturer’s instructions. cDNA was amplified by 16 PCR cycles and samples were purified after cDNA synthesis with AMPure XP beads for PCR Purification (Beckman Coulter). For the determination of cDNA content, a Qubit® 3.0 Fluorometer in combination with Qubit™ 1x dsDNA HS Assay Kit (both Thermo Fisher Scientific) were used. Fragment sizes were determined using High Sensitivity DNA Kit with 2100 Bioanalyzer (both Agilent). The Covaris M220 system was used for controlled cDNA shearing (2 min at 20°C, Peak Power 75W, 20% Duty Factor, Burst Cycle set at 200).
Library preparation was performed with SMARTer ThruPLEX DNA-Seq Kit (Takara). Samples were purified after library synthesis with AMPure XP beads for PCR Purification (Beckman Coulter). Six samples were subjected to an indexed single-read sequencing run with 1 x 75 cycles on an Illumina NextSeq™ 500 system.

treatment_protocol: PyMT mice were divided into two groups according to genotype (WT, samples 1-3; mPGES-1 KO, samples 4-6). Tumors were harvested after 16-20 weeks. Afterwards, cancer-associated fibroblasts were isolated by FACS-sorting.

value: Cancer-associated fibroblasts

value: mPGES-1 KO


title: PANNE057

value: Mild AP


title: Replicate 2 mPGES-1 KO


title: PANNE056


title: NT12171_2

description: batch: 2017-05-30-HTYY2BGX2


title: NT12171_1

description: batch: 2017-05-30-HTYY2BGX2


title: Mouse inducible PDAC cells-Off Dox-4 days, pool1-4217

description: Dey-14wtRNA-pool1-4217-Off-4d_190521-NB501070-0146-AHGMLKBGXB-1-ACAGTG

value: Untreated, 4 days


title: NT12163_2

description: batch: 2017-05-30-HTYY2BGX2


title: DSP-1010992704701-G-B09

value: (v4.0) Mouse Whole Transcriptome Dev, (v1.0) 06 E2E Set 1 WTA, (v1.0) 07 E2E Set 2 WTA

value: Spleen


title: PANNE054

value: whole blood


title: DSP-1010992704701-G-B08


title: Replicate 1 mPGES-1 KO


title: NT12162_2

description: batch: 2017-05-30-HTYY2BGX2


title: Replicate 3 WT

value: WT


title: NT12163_1

description: batch: 2017-05-30-HTYY2BGX2


title: DSP-1010992704701-G-B07


title: Replicate 1 WT


title: PANNE052


title: Replicate 2 WT


title: PANNE055


title: PANNE053


title: NT12162_1

description: batch: 2017-05-30-HTYY2BGX2


title: PANNE051


title: DSP-1010992704701-G-B05

value: Kidney


title: X17: Ptdss1 knockdown tumor cell in WT mice

data_processing:
Sequencing data were analyzed using SeqBox software (Beccuti et al., 2018).
Adapter trimming with done with skewer (Jiang et al., 2014)
STAR (Dobin & Gingeras, 2015) was used to map the reads to the mouse reference genome (mm10)
RSEM (Li & Dewey, 2011) was used for gene and isoform-level quantification
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include log2normalized_counts values for each sample

source_name: PyMT cell mammary tumor

extract_protocol:
mRNA-isolation and cDNA transcription were performed immediately after tumor-associated macrophage sorting using SMART-Seq v4 Ultra Low Input RNA Kit for Sequencing (Takara) according to the manufacturer’s instructions. cDNA was amplified by 16 PCR cycles and samples were purified after cDNA synthesis with AMPure XP beads for PCR Purification (Beckman Coulter). For the determination of cDNA content, a Qubit® 3.0 Fluorometer in combination with Qubit™ 1x dsDNA HS Assay Kit (both Thermo Fisher Scientific) were used. Fragment sizes were determined using High Sensitivity DNA Kit with 2100 Bioanalyzer (both Agilent). The Covaris M220 system was used for controlled cDNA shearing (2 min at 20°C, Peak Power 75W, 20% Duty Factor, Burst Cycle set at 200).
Library preparation was performed with SMARTer ThruPLEX DNA-Seq Kit (Takara). Samples were purified after library synthesis with AMPure XP beads for PCR Purification (Beckman Coulter). Ten samples were subjected to an indexed single-read sequencing run with 1 x 75 cycles on an Illumina NextSeq™ 500 system.

treatment_protocol: Mice were divided into three groups according to genotype and injected tumor cell genotype (WT tumor cells in WT mice (samples X5, X9, X10); WT tumor cells in macrophage-specific MerTK KO mice (samples X2, X6, X7, X8); Ptdss1 knockdown tumor cell in WT mice (samples X13, X14, X17)). All mice received injection of tumor cells into two mammary glands and and tumors were monitored for five weeks. Afterwards,  tumor-associated macrophages wereisolated by FACS-sorting.

value: macrophage

tag: treatment duration

value: tumor growth for 5 weeks


title: DSP-1010992704701-G-B06

value: BALBC


title: PANNE050


title: NT12151_1

description: batch: 2017-05-30-HTYY2BGX2


title: DSP-1010992704701-G-B04


title: NT12150_1

description: batch: 2017-05-30-HTYY2BGX2


title: DSP-1010992704701-G-B10


title: DSP-1010992704701-G-B03


title: X10: WT tumor cells in WT mice


title: DSP-1010992704701-G-B02


title: X9: WT tumor cells in WT mice


title: PANNE045


title: NT12150_2

description: batch: 2017-05-30-HTYY2BGX2


title: PANNE047


title: PANNE048


title: PANNE044


title: X5: WT tumor cells in WT mice


title: DSP-1010992704701-G-A11

value: Lung


title: DSP-1010992704701-G-A12


title: X14: Ptdss1 knockdown tumor cell in WT mice


title: X13: Ptdss1 knockdown tumor cell in WT mice


title: DSP-1010992704701-G-B01


title: NT12151_2

description: batch: 2017-05-30-HTYY2BGX2


title: DSP-1010992704701-G-A10


title: NT12143_2

description: batch: 2017-05-30-HTYY2BGX2


title: NT12144_1

description: batch: 2017-05-30-HTYY2BGX2


title: X7: WT tumor cells in macrophage-specific MerTK KO mice


title: NT12144_2

description: batch: 2017-05-30-HTYY2BGX2


title: NT12143_1

description: batch: 2017-05-30-HTYY2BGX2


title: PANNE049


title: PANNE043


title: DSP-1010992704701-G-A09

value: Brain


title: X6: WT tumor cells in macrophage-specific MerTK KO mice


title: X2: WT tumor cells in macrophage-specific MerTK KO mice


title: NT12111_2

description: batch: 2017-05-30-HTYY2BGX2

value: LB media


title: NT12111_1

description: batch: 2017-05-30-HTYY2BGX2


title: X8: WT tumor cells in macrophage-specific MerTK KO mice


title: PANNE041


title: DSP-1010992704701-G-A08


title: NT12106_2

description: batch: 2017-05-30-HTYY2BGX2


title: PANNE042


title: PANNE040


title: CBA_26M_SV_C_L004

city: Omaha

first: David

middle: ZZ

last: He

state: Nebraska

address: 2500 California Plaza

department: Biomedical Sciences

institute: Creighton University

data_processing:
All data processing was performed using the CLC Genomics Workbench (version 20.0.2) including trimming of reads, alignment, read counts, and normalization using the default paramaters.
Genome_build: mm10, build name GRCm38
Supplementary_files_format_and_content: Normalized RPKM values and relevant statistics were exported to Excel.

source_name: Stria vascularis

extract_protocol:
Cells were separately suspended in RNALater (~100 µL in total volume) and total RNA, including small RNAs (> ~18 nucleotides), were extracted and purified using the Qiagen RNeasy mini plus Kit (Qiagen, Germantown, MD). On-column DNase digestion was performed to eliminate DNA contamination in the collected RNA.
Libraries were prepared using the SMARTer Low Input RNA kit (Clontech Laboratories, Mountain View, CA) to generate cDNA in combination with the Nextera Library preparation kit (Illumina, San Diego, CA). Library size and concentration were assessed using an Agilent 2100 Bioanalyzer and a Quibit fluorometer (Invitrogen, Thermo Fisher Scientific) to ensure the inserts were the appropriate size and determine concentration prior to sequencing. Transcriptome libraries were sequenced using the HiSeq 2500 Sequencing System (Illumina).

value: CBA

value: 26 months

value: Stria vascularis


title: CBA_26M_SV_C_L003


title: PANNE039


title: NT12106_1

description: batch: 2017-05-30-HTYY2BGX2


title: DSP-1010992704701-G-A06


title: NT12020_1

description: batch: 2017-05-30-HTYY2BGX2


title: DSP-1010992704701-G-A07


title: CBA_26M_SV_C_L002


title: NT12021_2

description: batch: 2017-05-30-HTYY2BGX2


title: DSP-1010992704701-G-A04

value: Liver


title: NT12012_2

description: batch: 2017-05-30-HTYY2BGX2

value: HS


title: DSP-1010992704701-G-A05


title: CBA_26M_SV_B_L004


title: CBA_26M_SV_C_L001


title: DSP-1010992704701-G-A03


title: NT12007_2

description: batch: 2017-05-30-HTYY2BGX2


title: DSP-1010992704701-G-A02


title: CBA_26M_SV_B_L002


title: CBA_26M_SV_B_L003


title: NT12705_2

description: batch: 2017-05-26-HTKNLBGX2


title: CBA_26M_SV_B_L001


title: DSP-1010992704701-G-A01

value: No Template Control


title: NT12705_1

description: batch: 2017-05-26-HTKNLBGX2


title: CBA_26M_SV_A_L004


title: DAS_2

city: Houston

first: sangbae

last: Kim

address: 1 baylor plaza

institute: Baylor College of Medicine

data_processing:
Illumina Casava software used for basecalling.
FASTQ sequences were mapped to human genome hg19 (GRCh37) downloaded from UCSC genome browser website and aligned using TopHat2
Transcript structure and abundance were estimated using HTseq and Cufflelink
Read count profile were analyzed for the differential expression analysis using DESeq2 (version 1.10.1)
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include read count values for each Sample.

source_name: SOX7 (-/-)_null Tube 2 June 14

extract_protocol:
RNA was harvested using Trizol reagent from retinal organoids/cultures at the time points.
RNA libraries were prepared from ∼500 ng total RNA with the TruSeq Stranded Total RNA Library Prep Kit according to the manufacturer’s directions (Illumina).

value: Heart Tube

tag: culture time

tag: genotype/variation


title: NT12704_1

description: batch: 2017-05-26-HTKNLBGX2


title: CBA_26M_SV_A_L003


title: CBA_26M_SV_A_L002


title: NT12619_2

description: batch: 2017-05-26-HTKNLBGX2


title: NT12619_1

description: batch: 2017-05-26-HTKNLBGX2


title: UPN119 cells, patient PRO028 post VSL3 supplements plasma

city: Milwaukee

first: Martin

last: Hessner

state: WI

address: 8701 Watertown Plank Road

department: Pediatrics

institute: Medical College of Wisconsin

description: Gene expression data from UPN119 cells stimulated with post VSL3 supplements plasma

hyb_protocol: The Affymetrix GeneChip Human Genome U133 plus 2.0 array was selected for these studies for its overall comprehensive coverage.

scan_protocol: Affymetrix

data_processing: Image data were normalized and analyzed Partek Genomic Suite (Partek GS) to determine signal log intensity/ratios.  The statistical significance of differential gene expression and false discovery rates (FDR) were derived through ANOVA function in Partek GS.

label: biotin

source_name: UPN119 cells stimulated with PRO028POST plasma

label_protocol: cRNA was synthesized, labeled, fragmented, and hybridized to an array in accordance to the Affymetrix GeneChip expression analysis technical manual.

growth_protocol: Commercial cryopreserved PBMCs of healthy Caucasian male donor UPN119 were thawed and washed per the manufacturer’s protocol (Cellular Technology Ltd., Shaker Heights, OH).

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions.

treatment_protocol: Gene expression was accomplished by culturing PBMCs at 37°C in 5% CO2 with 40% of unaffected siblings of diabetes patients' pre/post VSL3 probiotic supplements plasma.  Cultures were prepared in a Costar 24-well plate (Corning) using 500,000 cells/well and in RPMI 1640 medium supplemented with 100U/ml penicillin and 100ug/ml streptomycin in a total of 500 µl.  After culture (9 hours optimal for cryopreserved PBMCs) total RNA was extracted using TRIzol reagent (Invitrogen Life Technologies).

value: UPN119 cells


title: NT12527_2

description: batch: 2017-05-26-HTKNLBGX2

value: ptsI-E


title: UPN119 cells, patient PRO027 post VSL3 supplements plasma

source_name: UPN119 cells stimulated with PRO027POST plasma


title: UPN119 cells, patient PRO030 pre VSL3 supplements plasma

description: Gene expression data from UPN119 cells stimulated with pre VSL3 supplements plasma

source_name: UPN119 cells stimulated with PRO030PRE plasma


title: UPN119 cells, patient PRO030 post VSL3 supplements plasma

source_name: UPN119 cells stimulated with PRO030POST plasma


title: UPN119 cells, patient PRO028 pre VSL3 supplements plasma

source_name: UPN119 cells stimulated with PRO028PRE plasma


title: UPN119 cells, patient PRO027 pre VSL3 supplements plasma

source_name: UPN119 cells stimulated with PRO027PRE plasma


title: CBA_9M_SV_C_L004

value: 9 months


title: NT12527_1

description: batch: 2017-05-26-HTKNLBGX2

source_name: E. coli strain culture


title: OT1cells_2hr_Rep2_FP

city: Zurich

first: Gunnar

last: Rätsch

state: -None-

address: Universitatstrasse 6

department: Institute for Machine Learning

country: Switzerland

institute: ETH Zürich

data_processing:
XPRESSPipe was used for alignment, processing an abundance estimation: https://doi.org/10.1371/journal.pcbi.1007625
In brief: RNA-seq and ribosomal foot printing reads were aligned using STAR v2.5. using the Ensembl mouse genome reference, mm10 (GRCm38.Ensembl78). RNA-seq and ribosomal profiling reads were aligned using a singularity instance of XPRESSpipe, with the following parameters: 3′ adapter sequence: CTGTAGGCAC, minimum read length of 17, splice junction overhang (sjdbOverhang) of 49, removal of duplicates, removal of rRNA aligning sequences, and two-pass STAR alignment.
Genome_build: mm10
Supplementary_files_format_and_content: Tab-delimited text files with raw counts across CDS

source_name: Primed OT1 cells

extract_protocol: See Ignolia et al., Nature Protocols 2012 PMID: 22836135

treatment_protocol: Primed OT1 cells were either activated with CD3/CD28 beads or left in resting state for 2 hours, followed with cycloheximide treatment for 10 minutes

value: Stimulated

tag: rna type

value: Ribosome protected RNA


title: DAS_3

source_name: SOX7 WT_ Tube 3 June 14

value: wild type


title: NT12524_2

description: batch: 2017-05-26-HTKNLBGX2

value: serB-E


title: CBA_9M_SV_C_L003


title: OT1cells_T0_Rep3_FP

value: Unstimulated

tag: time


title: OT1cells_T0_Rep2_FP

tag: cell line


title: UPN119 cells, patient PRO026 pre VSL3 supplements plasma

source_name: UPN119 cells stimulated with PRO026PRE plasma


title: CBA_9M_SV_C_L002


title: UPN119 cells, patient PRO026 post VSL3 supplements plasma

source_name: UPN119 cells stimulated with PRO026POST plasma


title: UPN119 cells, patient PRO024 pre VSL3 supplements plasma

source_name: UPN119 cells stimulated with PRO024PRE plasma


title: OT1cells_2hr_Rep3_FP


title: DAS_1

source_name: SOX7 (-/-)_null Tube 1 June 14


title: NT12524_1

description: batch: 2017-05-26-HTKNLBGX2


title: CBA_9M_SV_C_L001


title: CBA_26M_SV_A_L001


title: OT1cells_T0_Rep1_FP


title: OT1cells_2hr_Rep3_RNA

value: total RNA


title: CBA_9M_SV_B_L004


title: NT12517_1

description: batch: 2017-05-26-HTKNLBGX2

value: carA-D

value: LB media


title: OT1cells_2hr_Rep2_RNA


title: NT12507_2

description: batch: 2017-05-26-HTKNLBGX2

value: ilvE-D


title: CBA_9M_SV_B_L002

value: CBA

value: Stria vascularis


title: OT1cells_2hr_Rep1_RNA


title: NT12507_1

description: batch: 2017-05-26-HTKNLBGX2


title: UPN119 cells, patient PRO022 pre VSL3 supplements plasma

source_name: UPN119 cells stimulated with PRO022PRE plasma


title: UPN119 cells, patient PRO023 post VSL3 supplements plasma

source_name: UPN119 cells stimulated with PRO023POST plasma


title: NT12505_2

description: batch: 2017-05-26-HTKNLBGX2

value: hisH-D


title: CBA_9M_SV_A_L004

source_name: Stria vascularis


title: NT12505_1

description: batch: 2017-05-26-HTKNLBGX2


title: UPN119 cells, patient PRO021 post VSL3 supplements plasma

source_name: UPN119 cells stimulated with PRO021POST plasma


title: UPN119 cells, patient PRO022 post VSL3 supplements plasma

source_name: UPN119 cells stimulated with PRO022POST plasma


title: OT1cells_T0_Rep2_RNA


title: OT1cells_T0_Rep1_RNA


title: NT12517_2

description: batch: 2017-05-26-HTKNLBGX2


title: NT12498_2

description: batch: 2017-05-26-HTKNLBGX2

value: argB-C


title: CBA_9M_SV_B_L003


title: UPN119 cells, patient PRO020 post VSL3 supplements plasma

source_name: UPN119 cells stimulated with PRO020POST plasma


title: CBA_9M_SV_A_L002


title: CBA_9M_SV_A_L003


title: NT12498_1

description: batch: 2017-05-26-HTKNLBGX2


title: UPN119 cells, patient PRO023 pre VSL3 supplements plasma

source_name: UPN119 cells stimulated with PRO023PRE plasma


title: UPN119 cells, patient PRO020 pre VSL3 supplements plasma

source_name: UPN119 cells stimulated with PRO020PRE plasma


title: FL5.12_mycER_OHT_IACS_2

city: Milan

first: Marco

last: Filipuzzi

address: Via Giuseppe Ripamonti, 435

country: Italy

institute: IEO

data_processing:
Read filtering with fastx toolkit 0.0.13.2: fastq_masker -Q33 -q 20 -r N -v -i
alignment with tophat version 2.0.8: tophat -r 170 -p 8 --no-novel-juncs --no-novel-indels --library-type fr-unstranded --transcriptome-index transcriptome_index reffile fastq_file_R1 fastq_file_R2
Removing duplicate reads: samtools rmdup -sS bamfile
Quantifying read counts over features with featureCounts v. 1.4.5-p1: featureCounts -T 2 -p -P -a gtffile
Idendifying Differentially Expressed Genes (DEG) using DESeq2 R Bioconductor package
Genome_build: mm9
Supplementary_files_format_and_content: txt file reporting the RPKM, log2FC and padj from DESEq2 output

source_name: cells grown in vitro

extract_protocol:
Cells were collected and washed in PBS, then lysed in RNA lysis buffer (Zymo, #R1054). Total RNA was purified from these lysates onto Quick-RNA Miniprep columns (Zymo, #R1054) and treated on-column with DNaseI. After RNA quality was checked with the Agilent 2100 Bioanalyser (Agilent Technologies),  0.5-1 µg RNA for each sample were used to prepare RNA-seq libraries using the TruSeq stranded total RNA Sample Prep Kit (Illumina, #20020596) following manufacturer's instructions. RNA-seq libraries were then run on an Agilent 2100 Bioanalyser (Agilent Technologies) for quantification and quality control, then sequenced on an Illumina instrument.
Libraries were prepared for Illumina sequencing using the Stranded Total RNA Sample Preparation Protocol, consisting in Ribo-zero depletion and RNA fragmentation, First Strand cDNA Synthesis, Second Strand cDNA synthesis, addition of dA overhangs, ligation of Illumina adapters, selection with AMPure beads and PCR with index primers.
Strand Specific RNA-Seq

treatment_protocol: FL5.12 MycER-expressing cells, either primed or not for 48 hour with 100 nM 4-hyrdroxytamoxifen (OHT), were seeded at a concentration of 120^3 cells/mL in normal growth medium (supplemented with 100 nM OHT where required), or in medium containing 135 nM IACS-010759. After 24 hours cells were harvested for RNA extraction.

value: BALB/c

value: prolymphocytic cell line FL5.12

tag: genotype

value: expressing MycER

tag: treatment protocol


title: CBA_9M_SV_A_L001

value: 9 months


title: FL5.12_mycER_OHT_IACS_3


title: NT12467_2

description: batch: 2017-05-26-HTKNLBGX2

value: metR-A


title: CBA_9M_SV_B_L001


title: OT1cells_T0_Rep3_RNA


title: UPN119 cells, patient PRO019 post VSL3 supplements plasma

source_name: UPN119 cells stimulated with PRO019POST plasma

value: UPN119 cells


title: UPN119 cells, patient PRO021 pre VSL3 supplements plasma

source_name: UPN119 cells stimulated with PRO021PRE plasma


title: UPN119 cells, patient PRO019 pre VSL3 supplements plasma

source_name: UPN119 cells stimulated with PRO019PRE plasma


title: CBA_P30_SV_C_L004

value: P30_1 month


title: NT12467_1

description: batch: 2017-05-26-HTKNLBGX2

source_name: E. coli strain culture


title: FL5.12_mycER_IACS_3

value: IACS


title: CBA_P30_SV_C_L003


title: CBA_P30_SV_C_L002


title: NT12457_1

description: batch: 2017-05-26-HTKNLBGX2


title: FL5.12_mycER_IACS_2


title: FL5.12_mycER_IACS_1


title: CBA_P30_SV_C_L001


title: FL5.12_mycER_OHT_3

value: OHT


title: CBA_P30_SV_B_L004


title: FL5.12_mycER_OHT_2


title: FL5.12_mycER_OHT_IACS_1


title: UPN119 cells, patient PRO018 pre VSL3 supplements plasma

source_name: UPN119 cells stimulated with PRO018PRE plasma


title: NT12197_1

description: batch: 2017-05-26-HTKNLBGX2


title: CBA_P30_SV_B_L002


title: FL5.12_mycER_OHT_1


title: UPN119 cells, patient PRO018 post VSL3 supplements plasma

source_name: UPN119 cells stimulated with PRO018POST plasma


title: NT12179_1

description: batch: 2017-05-26-HTKNLBGX2


title: UPN119 cells, patient PRO017 pre VSL3 supplements plasma

source_name: UPN119 cells stimulated with PRO017PRE plasma


title: NT12179_2

description: batch: 2017-05-26-HTKNLBGX2


title: FL5.12_mycER_untreated_3

value: untreated


title: CBA_P30_SV_B_L001


title: NT12176_2

description: batch: 2017-05-26-HTKNLBGX2


title: UPN119 cells, patient PRO016 post VSL3 supplements plasma

source_name: UPN119 cells stimulated with PRO016POST plasma


title: NT12457_2

description: batch: 2017-05-26-HTKNLBGX2


title: FL5.12_mycER_untreated_2


title: UPN119 cells, patient PRO017 post VSL3 supplements plasma

source_name: UPN119 cells stimulated with PRO017POST plasma


title: CBA_P30_SV_A_L004


title: UPN119 cells, patient PRO015 post VSL3 supplements plasma

source_name: UPN119 cells stimulated with PRO015POST plasma


title: NT12197_2

description: batch: 2017-05-26-HTKNLBGX2


title: UPN119 cells, patient PRO016 pre VSL3 supplements plasma

source_name: UPN119 cells stimulated with PRO016PRE plasma


title: NT12176_1

description: batch: 2017-05-26-HTKNLBGX2


title: UPN119 cells, patient PRO014 pre VSL3 supplements plasma

source_name: UPN119 cells stimulated with PRO014PRE plasma


title: UPN119 cells, patient PRO015 pre VSL3 supplements plasma

source_name: UPN119 cells stimulated with PRO015PRE plasma


title: UPN119 cells, patient PRO014 post VSL3 supplements plasma

source_name: UPN119 cells stimulated with PRO014POST plasma


title: FL5.12_mycER_untreated_1


title: NT12164_2

description: batch: 2017-05-26-HTKNLBGX2


title: CBA_P30_SV_A_L003

source_name: Stria vascularis


title: CBA_P30_SV_A_L002


title: CBA_P30_SV_A_L001


title: NT12158_2

description: batch: 2017-05-26-HTKNLBGX2


title: NT12164_1

description: batch: 2017-05-26-HTKNLBGX2


title: UPN119 cells, patient PRO013 pre VSL3 supplements plasma

source_name: UPN119 cells stimulated with PRO013PRE plasma


title: NT12158_1

description: batch: 2017-05-26-HTKNLBGX2


title: Veh_p103_rep4_reused

city: Taipei

first: Chia-Lang

last: Hsu

address: No. 7, Zhongshan S. Rd.

department: Department of Medical Research

country: Taiwan

institute: National Taiwan University Hospital

description:
BNL-MEA tumor-bearing Balb/c mice treated with vehicle (p103)
GSM4486535

data_processing:
Trimming adaptor sequences and removing reads of low quality were performed by cutadapt (v2.4).
Quantified reads were aligned to the mouse genome (GRCm38) by STAR (v2.7.2a) and then gene-level read counts were generated based on the annotations of Gencode (vM19).
Genome_build: GRCm38
Supplementary_files_format_and_content: Tab-delimited text file includes gene-level read counts.

source_name: BNL-MEA tumor-bearing Balb/c mice treated with anti-PD1 (p103)

extract_protocol:
Total RNA was extracted from frozen snaps using an AllPrep DNA/RNA mini kit (Qiagen,  Hilden, Germany).
Libraries were constructed using Illumina TruSeq Stranded mRNA kit according to the manufacturers

value: vehicle

tag: mouse strain

value: BNL-MEA tumor-bearing Balb/c mice

tag: cell type

value: hepatocellular carcinoma

tag: batch


title: NT12152_2

description: batch: 2017-05-26-HTKNLBGX2

value: LB media


title: Veh_p103_rep3_reused

description:
BNL-MEA tumor-bearing Balb/c mice treated with vehicle (p103)
GSM4486534


title: Veh_p103_rep2_reused

description:
BNL-MEA tumor-bearing Balb/c mice treated with vehicle (p103)
GSM4486533


title: NT12146_2

description: batch: 2017-05-26-HTKNLBGX2


title: NT12152_1

description: batch: 2017-05-26-HTKNLBGX2


title: Veh_p103_rep1_reused

description:
BNL-MEA tumor-bearing Balb/c mice treated with vehicle (p103)
GSM4486532


title: PD1_p103_rep3

description: BNL-MEA tumor-bearing Balb/c mice treated with anti-PD1 (p103)


title: UPN119 cells, patient PRO012 post VSL3 supplements plasma

source_name: UPN119 cells stimulated with PRO012POST plasma


title: KRIB-H8B

first: Richard

middle: Eric

last: Davis

state: TX

address: 7455 Fannin Street

institute: MD Anderson Cancer Center

description: replicate 2

hyb_protocol: Amplified cRNA was hybridized to Illumina human HT12v4.0 whole-transcriptome arrays.

scan_protocol: As per Illumina instructions, with detection by Streptavidin-Cy3 conjugate.

data_processing: The non-normalized data were generated by GenomeStudio with background correction. The normalized data were generated by starting from the non-normalized data, then modified by methods previously described (PMID: 20805315). In brief, probe-level values were quantile-normalized and adjusted by a model-based background correction method (PMID: 18450815). After this, the only probe results that are kept for the normalized matrix are those for reliable probes (PMID: 19923232) in which the detection p value is <0.05, in at least 25% of the samples.

source_name: KRIB cells, IL11RA shRNA H8

label_protocol: 100 nanograms of total RNA was amplified and biotin-labeled through a two-round Eberwine procedure using MessageAmp II and Illumina TotalPrep RNA amplification kits (Ambion).

growth_protocol: KRIB cells were  maintained at 37 °C in 5% CO2 in DMEM with 10% FBS and 10 mg/mL penicillin-streptomycin.

extract_protocol: Total RNA of harvested cells was extracted using a mirVana miRNA Isolation Kit (Invitrogen). RNA integrity was determined using the 2100 Bioanalyzer and RNA 6000 Nano Kit (Agilent Technologies).

treatment_protocol: KRIB cells were transduced with GIPZ lentivirus for shRNA expression and isolated by sorting for GFP expression, as previously described (PMID: 28698375).

value: KRIB


title: UPN119 cells, patient PRO012 pre VSL3 supplements plasma

source_name: UPN119 cells stimulated with PRO012PRE plasma


title: KRIB-H8C

description: replicate 3


title: NT12146_1

description: batch: 2017-05-26-HTKNLBGX2

data_processing:
Raw single-ended Illumina reads were trimmed to remove the TruSeq3 adaptors using trimmomatic v0.36.
Trimmed reads were pseudo-aligned to the NC_000913.3 E. coli K-12 genome’s transcripts using kallisto v0.44.0 with the sequence based bias correction and using an average fragment length of 130bp (70bp standard deviation).
Genome_build: NC_000913.3
Supplementary_files_format_and_content: Files starting with the “kallisto_” prefix contain the transcripts counts

source_name: E. coli strain culture

extract_protocol:
Total RNA was extracted using the RNeasy kit (QIAGEN) followed by Dnaze treatment
Samples were subject ro rRNA depletion prior to library preparation


title: KRIB-H2B

description: replicate 2

source_name: KRIB cells, IL11RA shRNA H2


title: PD1_p103_rep2


title: UPN119 cells, patient PRO011 post VSL3 supplements plasma

source_name: UPN119 cells stimulated with PRO011POST plasma


title: KRIB-H2A

description: replicate 1


title: UPN119 cells, patient PRO024 post VSL3 supplements plasma

source_name: UPN119 cells stimulated with PRO024POST plasma


title: UPN119 cells, patient PRO010 pre VSL3 supplements plasma

source_name: UPN119 cells stimulated with PRO010PRE plasma


title: UPN119 cells, patient PRO010 post VSL3 supplements plasma

source_name: UPN119 cells stimulated with PRO010POST plasma


title: NT12141_2

description: batch: 2017-05-26-HTKNLBGX2


title: PD1_p103_rep1


title: NT12141_1

description: batch: 2017-05-26-HTKNLBGX2


title: KRIB-G2C

description: replicate 3

source_name: KRIB cells, IL11RA shRNA G2


title: UPN119 cells, patient PRO008 post VSL3 supplements plasma

source_name: UPN119 cells stimulated with PRO008POST plasma


title: KRIB-H8A

description: replicate 1


title: iron_PD1_p106_rep3

description: BNL-MEA tumor-bearing Balb/c mice treated with ironized anti-PD1 (p106)

value: ironized anti-PD1


title: KRIB-G2B

description: replicate 2


title: NT12077_2

description: batch: 2017-05-26-HTKNLBGX2


title: UPN119 cells, patient PRO011 pre VSL3 supplements plasma

source_name: UPN119 cells stimulated with PRO011PRE plasma


title: KRIB-H2C

description: replicate 3


title: iron_PD1_p106_rep2

source_name: BNL-MEA tumor-bearing Balb/c mice treated with ironized anti-PD1 (p106)


title: UPN119 cells, patient PRO008 pre VSL3 supplements plasma

source_name: UPN119 cells stimulated with PRO008PRE plasma


title: KRIB-G2A

description: replicate 1


title: NT12077_1

description: batch: 2017-05-26-HTKNLBGX2


title: iron_PD1_p106_rep1


title: UPN119 cells, patient PRO013 post VSL3 supplements plasma

source_name: UPN119 cells stimulated with PRO013POST plasma


title: NT12028_2

description: batch: 2017-05-26-HTKNLBGX2


title: NT12028_1

description: batch: 2017-05-26-HTKNLBGX2


title: KRIB-C1B

description: replicate 2

source_name: KRIB cells, IL11RA shRNA C1


title: NT12021_1

description: batch: 2017-05-26-HTKNLBGX2


title: Veh_p106_rep2

description: BNL-MEA tumor-bearing Balb/c mice treated with vehicle (p106)


title: UPN119 cells, patient PRO005 post VSL3 supplements plasma

source_name: UPN119 cells stimulated with PRO005POST plasma


title: CBA_P30_SV_B_L003

source_name: Stria vascularis

value: CBA

value: Stria vascularis


title: UPN119 cells, patient PRO005 pre VSL3 supplements plasma

source_name: UPN119 cells stimulated with PRO005PRE plasma


title: KRIB-C1A

description: replicate 1


title: UPN119 cells, patient PRO006 post VSL3 supplements plasma

source_name: UPN119 cells stimulated with PRO006POST plasma


title: Veh_p106_rep1

source_name: BNL-MEA tumor-bearing Balb/c mice treated with vehicle (p106)


title: NT12012_1

description: batch: 2017-05-26-HTKNLBGX2

source_name: E. coli strain culture

value: HS


title: KRIB-WC

description: replicate 3

source_name: KRIB cells, control


title: KRIB-WB

description: replicate 2


title: KRIB-C1C

description: replicate 3


title: F308_d245_PI_Spleen

city: New Haven

first: Hanah

last: Georges

state: Connecticut

address: 333 Cedar St

institute: Yale University

library_source: genomic

data_processing:
reads were trimmed using fastp then mapped to the bostau9 genome using bismark
bam files were input into R, analyzed using the methylKit R package
Genome_build: bosTau9
Supplementary_files_format_and_content: differentially methylated regions analyzed by methylkit R package
Tandem mass spectra were extracted, charge state deconvoluted and deisotoped by ProteoWizard MsConvert version 3.0
spectra were searched using Mascot against reverse concatenated Uniprot_Bovine_rev_102819 and cRAP_rev_100518 databases
Search results imported and combined using Scaffold software.
Supplementary_files_format_and_content: Relative quantitation by spectral counting, students T test with BH correction

molecule: genomic DNA

organism: Bos taurus

source_name: Fetal Spleen Tissue (1ug)

growth_protocol: BVDV naïve heifers were bred by AI then fetuses were collected on day 245 of gestation

extract_protocol:
DNA from frozen splenic tissue was homogenized then extracted with the Qiagen Dneasy kit
Libraries were prepared by Zymo Research

treatment_protocol: On day 75 of gestation, 3 heifers were inoculated with BVDV and 4 were inoculated with sham media

value: Spleen

tag: gestational day

value: PI


title: F307_d245_PI_Spleen

tag: tissue


title: NT12189_2

first: Pedro

last: Beltrao

address: Wellcome Genome Campus

institute: EMBL-EBI

description: batch: 2016-12-22-HGHNHBBXX

tag: strain


title: NT12193_2

description: batch: 2016-12-22-HGHNHBBXX

tag: growth condition


title: F250_d245_Control_Spleen

value: Control


title: F278_d245_Control_Spleen


title: KRIB-WA

description: replicate 1


title: NT12510_2

description: batch: 2016-12-22-HGHNHBBXX

value: serB-D


title: NT12447_2

description: batch: 2016-12-22-HGHNHBBXX


title: NT12007_1

description: batch: 2017-05-26-HTKNLBGX2


title: UPN119 cells, patient PRO006 pre VSL3 supplements plasma

source_name: UPN119 cells stimulated with PRO006PRE plasma

value: UPN119 cells


title: UPN119 cells, patient PRO002 pre VSL3 supplements plasma

source_name: UPN119 cells stimulated with PRO002PRE plasma


title: LN4-Veh

description: replicate 4

hyb_protocol: Amplified cRNA was hybridized to Illumina mouse WG-6 version 2.0 mouse whole-genome arrays.

data_processing:
The non-normalized data were generated by GenomeStudio with background correction. The normalized data were generated from bead-level data by methods previously described (PMID: 20805315). In brief, bead-level values were quantile-normalized, adjusted by a model-based background correction method (PMID: 18450815), trimmed by the 3-MAD method employed by Illumina, and then averaged to give a single probe-level value. After this, the only probe results that are kept for the normalized matrix are those in which the detection p value is <0.05, in at least 25% of the samples.
Cy3 fluorescence intensity

source_name: Control lymph node

growth_protocol: B16 tumors were established by subcutaneous inoculation, and allowed to grow until 30-40 mm2 in size

extract_protocol: Total RNA of dissected tumors was extracted using the RNAqueous kit (Ambion). The RNA quality was checked by using a Bioanalyzer 2100 instrument (Agilent).

treatment_protocol: Tumors were injected intratumorally once with 3M-052 or vehicle control, then 4 days later draining lymph nodes were excised.

value: lymph node


title: UPN119 cells, patient PRO004 pre VSL3 supplements plasma

source_name: UPN119 cells stimulated with PRO004PRE plasma


title: UPN119 cells, patient PRO002 post VSL3 supplements plasma

source_name: UPN119 cells stimulated with PRO002POST plasma


title: F842_d245_PI_Spleen


title: F268_d245_Control_Spleen


title: F272_d245_Control_Spleen


title: UPN119 cells, patient PRO001 post VSL3 supplements plasma

source_name: UPN119 cells stimulated with PRO001POST plasma


title: UPN119 cells, patient PRO004 post VSL3 supplements plasma

source_name: UPN119 cells stimulated with PRO004POST plasma


title: LN3-Veh

description: replicate 3


title: NT12145_2

description: batch: 2016-12-22-HGHNHBBXX


title: LN2-Veh

description: replicate 2


title: UPN119 cells, patient PRO001 pre VSL3 supplements plasma

source_name: UPN119 cells stimulated with PRO001PRE plasma


title: FRC CD49a+ cells from Healthy donor's tonsil, biological rep 5

city: Rennes

first: Delphine

last: Rossille

address: 2 avenue du Pr. Léon Bernard

country: France

institute: INSERM U1236-MOBIDIC

hyb_protocol: Hybridization was processed onto Affymetrix GeneChip™ Genome U133 Plus 2.0 oligonucleotide arrays according to the manufacturer's instructions.

scan_protocol: Probe arrays were scanned using the Affymetrix software to obtain .CEL files.

data_processing: Raw data were RMA-normalized with adjustment for GC content. Data were processed with Partek® Genomics Suite (version 6.5, Partek Inc., St Louis, MO, USA).   The data were pre-filtered by excluding probesets with linear scale expression less than 20 for each of the 10 samples.

source_name: Healthy donor 6, tonsil, FRC CD49a+ cells, at T0

label_protocol: RNA was amplified and converted into cDNA by a linear amplification method with the Ovation PicoSL WTA System V2 (NuGEN) then cDNA was labeled with the Encore Biotin Module.

extract_protocol: Tonsil tissues from 6 healthy donors were collected and enzymatically dissociated. After depletion of hematopoietic cells (Dynal, Dynabeads CD45) three stromal cell subsets (FRC, FDC, DN) where sorted by FACS based on their phenotype. RNA extraction (QIAGEN, RNeasy Micro Kit) was performed on 10 000 cells. Quality control was performed using the Agilent RNA 6000 Pico Kit.

tag: subject

value: tonsil

tag: phenotype

value: stroma cells

tag: cell subtype

value: Fibroblastic reticular cells CD49a+


title: NT12515_2

city: Cambridge

description: batch: 2016-12-22-HGHNHBBXX

value: metL-D


title: LN1-Veh

description: replicate 1


title: LN4-3M

description: replicate 4

source_name: Treated lymph node


title: NT12169_2

description: batch: 2016-12-22-HGHNHBBXX


title: NT12487_2

description: batch: 2016-12-22-HGHNHBBXX

value: gltA-C


title: NT12172_2

description: batch: 2016-12-22-HGHNHBBXX

value: LB media


title: NT12533_2

description: batch: 2016-12-22-HGHNHBBXX


title: LN2-3M

description: replicate 2


title: NT12079_2

description: batch: 2016-12-22-HGHNHBBXX


title: FRC CD49a+ cells from Healthy donor's tonsil, biological rep 1

source_name: Healthy donor 1, tonsil, FRC CD49a+ cells, at T0


title: LN3-3M

description: replicate 3


title: FRC CD49a+ cells from Healthy donor's tonsil, biological rep 3

source_name: Healthy donor 3, tonsil, FRC CD49a+ cells, at T0


title: NT12189_1

description: batch: 2016-12-22-HGHNHBBXX


title: MTZ+ Rapamycin 4dpi rep3

city: Pittsburgh

first: Jeffrey

last: Gross

state: PA

department: Ophthalmology

institute: University of Pittsburgh School Of Medicine

data_processing:
All processing of raw data was performed using the CLC Genomics Workbench (v20) Toolbox
Reads were trimmed using quality trim limit = 0.05, ambiguous trim = 2, and automatic read-through adapter trimming enabled (Trim Reads tool v2.4)
Reads were mapped to the zebrafish reference genome, GRCz11, and TPM expression values were caluclated using the RNA-seq Analysis tool (v2.2) in CLC Genomics Workbench
Genome_build: GRCz11

molecule: polyA RNA

organism: Danio rerio

source_name: retinal pigment epithelium

growth_protocol: Zebrafish were maintained at 28.5°C under a 14-hour light/10-hour dark cycle. Embryos and larvae used for subsequent experiments were kept in an incubator at 28.5°C in the dark until being euthanized

extract_protocol:
1000 GFP-positive cells from each sample were FACS-sorted directly into buffer from the SMART-Seq HT Ultra Low Input RNA Kit from Takara Bio, Inc. cDNA synthesis, amplification, and purification was performed using the SMART-Seq HT Ultra Low Input RNA Kit.
Libraries were prepared using the Nextera XT DNA Library Preparation Kit from Illumina, following manufacterer's instructions

treatment_protocol: A subset of larvae derived form rpe65:nfsb-eGFP X AB crosses went through MTZ mediated RPE ablation and drug treatment. Samples were collected at 2 and 4 days post abaltion.

value: retinal pigment epithelium

tag: treatment

value: MTZ+ Rapamycin

tag: time point

tag: replicate


title: MTZ+ Rapamycin 4dpi rep2


title: FDC cells from Healthy donor's tonsil, biological rep 4

source_name: Healthy donor 4, tonsil, FDC cells, at T0

value: FDC

value: Follicular dendritic cells


title: NT12447_1

description: batch: 2016-12-22-HGHNHBBXX

source_name: E. coli strain culture


title: FDC cells from Healthy donor's tonsil, biological rep 3

source_name: Healthy donor 3, tonsil, FDC cells, at T0


title: MTZ+ Rapamycin 4dpi rep1


title: LN1-3M

description: replicate 1


title: ARCS17

first: Alison

middle: J.

last: Kriegel

address: 8701 Watertown Plank Rd.

department: Physiology

description:
ARCS17
KriegelARCS17_CGATGT

data_processing:
Adapter sequences were removed from the output RNA-Seq sequence reads using cutadapt (http://code.google.com/p/cutadapt/)
Reads with low base quality (<13) were further trimmed and, if less than 25 base pairs, removed by FastQC (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/).
The trimmed sequence reads were then aligned to the rat reference genome and gene annotation database (rn5) using TopHat2 (v2.1.1) with mammalian default parameters (PMID:23618408)
Transcripts in all of the sequencing libraries were assembled by Stringtie (PMID:25690850)
Transcripts present in less that 50% of samples (expression of zero) in each group were removed.
Differential expression analysis was performed by using Cufflinks (v2.2.1) (PMID: 20436464 )
The Benjamini-Hochberg procedure was used for controlling false discovery rates in multiple comparisons
Supplementary_files_format_and_content: Group log2 fold-change, p-value and q-value are represented for each transcript and isoform in the group comparison processed data files.

organism: Rattus norvegicus

source_name: Sham control group

growth_protocol: Rats were purchased from Envigo Laboratories at 9 weeks of age and placed on 0.4% Dyets chow upon delivery.  Food and water were provided ad libitum.  Surgery was performed at 10 weeks of age.  Rats were phenotyped before tissue collection 6 weeks later. Kidney tissues were flash frozen in liquid nitrogen for RNA extraction.

extract_protocol:
Total RNA was extracted using a Trizol-based method and quantified by Nanodrop. Small RNA deep sequencing and analysis was performed as previously described by the Human Molecular Genetic Center at the Medical College of Wisconsin (Kriegel et al, Physiol Genomics, 2013; PMID 24085797).
Small RNA libraries were constructed from each sample using the Illumina TruSeq Stranded Total RNA.
Samples were multiplexed on a 400 GB flow cell and pair-end sequenced using an Illumina HiSeq 2500.

treatment_protocol: No experimental treatment was provided.

value: Sprague Dawley

tag: surgical model

value: Sham-operated control

value: Kidney

tag: Sex

value: male


title: MTZ+ DMSO 4dpi rep3

value: MTZ+ DMSO


title: DN cells from Healthy donor's tonsil, biological rep 3

source_name: Healthy donor 3, tonsil, DN cells, at T0

value: DN

value: Double negative cells


title: NT12533_1

description: batch: 2016-12-22-HGHNHBBXX


title: ACKR4 neg cells mouse 5

city: Hannover

first: Berislav

last: Bosnjak

address: Carl-Neuberg Straße 1

department: Institute of Immunology

institute: Hannover Medical School

description: Gene expression in spleen endothelial cells, Ackr4-

hyb_protocol: cRNA fragmentation, hybridization and washing steps were carried-out as recommended in the ‘One-Color Microarray-Based Gene Expression Analysis Protocol V5.7’, except that 150 ng of each fluorescently labeled cRNA population were used for hybridization.

scan_protocol: Slides were scanned on the Agilent Micro Array Scanner G2565CA (pixel resolution 3 µm, bit depth 20).

data_processing: Data extraction was performed with the ‘Feature Extraction Software V10.7.3.1’ using the extraction protocol file ‘GE1_107_Sep09.xml’. Measurements of on-chip replicates (quadruplicates) were averaged using the geometric mean of processed intensity values of the green channel, ‘gProcessedSignal’ (gPS) to retrieve one resulting value per unique non-control probe. Single Features were excluded from averaging, if they i) were manually flagged, ii) were identified as Outliers by the Feature Extraction Software, iii) lay outside the interval of ‘1.42 x interquartile range‘ regarding the normalized gPS distribution of the respective on-chip replicate population, or, iv) showed a coefficient of variation of pixel intensities per Feature that exceeded 0.5.   Averaged gPS values were normalized by global linear scaling: All gPS values of one sample were multiplied by an array-specific scaling factor. This factor was calculated by dividing a ‘reference 75th Percentile value’ (set as 1500 for the whole series) by the 75th Percentile value of the particular Microarray to be normalized (‘Array i’ in the formula shown below). Accordingly, normalized gPS values for all samples (microarray data sets) were calculated by the following formula:   normalized gPSArray i = gPSArray i x (1500 / 75th PercentileArray i)  Finally, a lower intensity threshold (surrogate value) was defined based on intensity distribution of negative control features. This value was fixed at 15 normalized gPS units. All of those measurements that fell below this intensity cutoff were substituted by the respective surrogate value of 15.  Differentially expressed genes were identified using the filtering option in the Excel-based analysis software RCUTAS (Research Core Unit Transcriptomics Analysis System). Gene sets were clustered with the gene set enrichment tool Enrichr (Chen et al., 2013; Kuleshov et al., 2016) and heat maps were generated using Heatmapper (Babicki et al., 2016) with the normalized gPS values for selected genes.

label: Alexa Fluor 555 Reactive Dye

source_name: DAPI-CD45-CD31+ACKR4- spleen cells from Ackr4GFP/wt mouse, replicate 2

label_protocol: 6-20 ng of total RNA were used to prepare aminoallyl-UTP-modified (aaUTP) cRNA (Amino Allyl MessageAmp™ II Kit, life technologies) applying one-round of amplification as suggested by the company, with the exception that a twofold downscaling of all reaction volumes was used. aaUTP-cRNA was labeled with Alexa Fluor 555 Reactive Dye (Thermo Fisher Scientific) according to the manufacturer’s guidelines except a twofold downscaling of reaction volumes.

extract_protocol: Total RNA was extracted using an RNeasy Plus Micro kit (QUIAGEN) according to the manufacturer’s protocol.

treatment_protocol: 1-2 ml of a digestion cocktail containing 0.2 mg/ml Dispase Grade I, 0.2 mg/ml Collagenase D, and 0.025 mg/ml DNase I (all from Roche) in RPMI-1640 (Gibco) were injected into spleens of Ackr4GFP/wt mice (Heinzel et al., 2007, Proc Natl Acad Sci U S A 104, 8421) at multiple sites using a 27 G needle. After 45 min incubation at 37°C, spleens were cut into small pieces and transferred into another 2 ml of the same digestion cocktail. During the following 20 min incubation at 37°C, the suspension was mixed thoroughly every 7 to 10 min. Subsequently, digestion was quenched by addition of 25 ml FACS buffer (3 % FCS and 4 mM EDTA in PBS) and suspension was filtered through a 100 µm cell strainer (BD Biosciences). Cells were washed with FACS buffer and red blood cells were lysed. For enrichment of endothelial cells, CD45+ cells were depleted by 30 min incubation with anti-CD45 mAb (clone 30-F11, BioLegend) followed by 30 min incubation with 1.2 x 108 sheep anti-rat Dynabeads (Invitrogen) at 4°C with gentle tilting and collection of the supernatant in a DynaMag 15 (Invitrogen). Afterwards, cell suspesnion was counterstained with Anti-CD45 mAb (clone 30-F11, PE, Biolegend), anti-CD31 mAb (clone 390, Alexa Fluor 647, Biolegend),  and DAPI. The following fluorescent-activated cell sorting was performed at the Core Facility Cell Sorting at Hannover Medical School using a FACSAria Fusion (BD Biosciences). Cell fractions were pre-gated on CD45- DAPI- single cells and sorted as CD31+ ACKR4-GFP+ or CD31+ ACKR4 GFP-, respectively. Cells were pooled from two to three mice per experiment to reach sufficient cell numbers of both populations.

value: spleen endothelial cells, Ackr4-


title: FDC cells from Healthy donor's tonsil, biological rep 1

source_name: Healthy donor 1, tonsil, FDC cells, at T0

value: tonsil

value: stroma cells


title: ACKR4 pos cells mouse 4

description: Gene expression in spleen endothelial cells, Ackr4+

source_name: DAPI-CD45-CD31+ACKR4+ spleen cells from Ackr4GFP/wt mouse, replicate 1

value: spleen endothelial cells, Ackr4+


title: DN cells from Healthy donor's tonsil, biological rep 5

source_name: Healthy donor 5, tonsil, DN cells, at T0


title: ACKR4 pos cells mouse 5

source_name: DAPI-CD45-CD31+ACKR4+ spleen cells from Ackr4GFP/wt mouse, replicate 2


title: ARCS16

description:
ARCS16
KriegelARCS16_GAGTGG


title: MTZ+ DMSO 4dpi rep2


title: NT12510_1

description: batch: 2016-12-22-HGHNHBBXX

value: serB-D


title: ARCS15

description:
ARCS15
KriegelARCS15_GTCCGC


title: DN cells from Healthy donor's tonsil, biological rep 2

source_name: Healthy donor 2, tonsil, DN cells, at T0


title: ARCS14

description:
ARCS14
KriegelARCS14_GGCTAC


title: ACKR4 neg cells mouse 4

source_name: DAPI-CD45-CD31+ACKR4- spleen cells from Ackr4GFP/wt mouse, replicate 1


title: MTZ+ DMSO 4dpi rep1


title: DN cells from Healthy donor's tonsil, biological rep 6

source_name: Healthy donor 6, tonsil, DN cells, at T0


title: NT12145_1

description: batch: 2016-12-22-HGHNHBBXX

value: LB media


title: vero_168h_ctrl_zn018

city: Santa Cruz

first: Jeremy

last: Sanford

address: 1156 High St

department: Molecular, Cell and Developmental Biology

institute: UC Santa Cruz

description: mRNA (100bp)

data_processing:
Reads were mapped against human/African Green Monkey repeat elements in their respective genomes for initial repeat-filtering using Bowtie 2
Repeat-filtered reads were then mapped against their respective STAR indexes (joint hg38-wuhCor1 or chlSab2-wuhCor1) using STAR v2.5.3a "--alignEndsType EndToEnd" option
Gene-level quantification and comparisons using DESeq2
Called peaks in sRNA-seq data mapped to wuhCor1 using Piranha v1.2.1
Quantified unique wuhCor1-mapped sRNA-seq coordinates using in-house python script
Predicted duplexes between host (human or African Green Monkey) transcripts and SARS-CoV-2 sRNAs using RNAhybrid v2.1.2
Genome_build: UCSC (hg18, chlSab2 and wuhCor1)
Supplementary_files_format_and_content: Gene-level counts [mRNA mapping to host quantified with DESeq2 (.csv), sRNA mapping to host quantified with DESeq2 (.csv), sRNA mapping to SARS-CoV-2 quantified with in-house script (.csv)], SARS-CoV-2 sRNA peaks [called with Piranha (.bed)], sRNA Interactions [predicted with RNAhybrid (.csv)]

organism: Chlorocebus aethiops

source_name: kidney cells – Vero-E6

growth_protocol: DMEM + 1% heat inactivated FBS, 100U/mL penicillin, 100 μg/mL streptomycin in 5% CO2 at 37°C

extract_protocol:
Trypsin-EDTA 0.25% (ThermoFIsher Scientific), then 250 μl Trizol
NEXTFLEX Poly(A) Beads Kit 2.0, then NEXTFLEX Rapid Directional RNA-Seq Kit 2.0 (Perkin Elmer Applied Genomics)

tag: cell line

value: kidney cells

value: control (uninfected)

tag: hours post-treatment

tag: moi


title: vero_216h_ctrl_zn021

description: mRNA (100bp)

tag: cell type


title: MTZ- Rapamycin 4dpi rep3

value: retinal pigment epithelium

value: MTZ- Rapamycin


title: vero_216h_cov2_zn019

description: mRNA (100bp)

value: Infected – SARS-CoV-2


title: NT12096_2

description: batch: 2016-12-22-HGHNHBBXX


title: ARCS13

description:
ARCS13
KriegelARCS13_ACTGAT

value: Sprague Dawley

value: Sham-operated control


title: MTZ- Rapamycin 4dpi rep2


title: NT12487_1

description: batch: 2016-12-22-HGHNHBBXX

value: gltA-C


title: ARCS12

description:
ARCS12
KriegelARCS12_ACTTGA

source_name: 1/3 nephrectomy group

value: 1/3 nephrectomy

value: Kidney

value: male


title: ARCS11

description:
ARCS11
KriegelARCS11_GTGGCC


title: vero_120h_ctrl_zn015

description: mRNA (100bp)


title: NT12518_2

description: batch: 2016-12-22-HGHNHBBXX

value: gltA-E


title: vero_120h_cov2_zn013

description: mRNA (100bp)


title: vero_168h_cov2_zn016

description: mRNA (100bp)


title: ARCS10

description:
ARCS10
KriegelARCS10_TAGCTT


title: NT12193_1

description: batch: 2016-12-22-HGHNHBBXX


title: ARCS9

description:
ARCS9
KriegelARCS9_ATCACG


title: NT12147_2

description: batch: 2016-12-22-HGHNHBBXX


title: vero_120h_cov2_zn014

description: mRNA (100bp)


title: NT12194_2

description: batch: 2016-12-22-HGHNHBBXX


title: MTZ- DMSO 4dpi rep1

value: MTZ- DMSO


title: MTZ- DMSO 4dpi rep3


title: MTZ- Rapamycin 4dpi rep1


title: ARCS8

description:
ARCS8
KriegelARCS8_GTTTCG


title: vero_072h_cov2_zn011

description: mRNA (100bp)


title: Veh_p106_rep3

source_name: BNL-MEA tumor-bearing Balb/c mice treated with vehicle (p106)

value: vehicle

tag: mouse strain

value: BNL-MEA tumor-bearing Balb/c mice

value: hepatocellular carcinoma

tag: batch


title: NT12518_1

description: batch: 2016-12-22-HGHNHBBXX

value: LB media


title: ARCS7

description:
ARCS7
KriegelARCS7_GTGAAA

tag: tissue


title: ARCS6

description:
ARCS6
KriegelARCS6_ATGTCA

source_name: 5/6 nephrectomy group

tag: strain

value: 5/6 nephrectomy


title: vero_048h_ctrl_zn009

description: mRNA (100bp)

value: kidney cells

value: control (uninfected)


title: ARCS5

description:
ARCS5
KriegelARCS5_ACAGTG


title: MTZ+ Rapamycin 2dpi rep1

source_name: retinal pigment epithelium

value: retinal pigment epithelium

value: MTZ+ Rapamycin


title: vero_048h_cov2_zn008

description: mRNA (100bp)

value: Infected – SARS-CoV-2


title: NT12172_1

description: batch: 2016-12-22-HGHNHBBXX

source_name: E. coli strain culture

tag: growth condition


title: MTZ+ Rapamycin 2dpi rep3


title: MTZ+ DMSO 2dpi rep3

value: MTZ+ DMSO


title: vero_072h_ctrl_zn012

description: mRNA (100bp)


title: NT12515_1

description: batch: 2016-12-22-HGHNHBBXX

value: metL-D


title: NT12332_2

description: batch: 2016-12-22-HGHNHBBXX


title: vero_072h_cov2_zn010

description: mRNA (100bp)


title: vero_048h_cov2_zn007

description: mRNA (100bp)


title: ARCS3

description:
ARCS3
KriegelARCS3_CTTGTA

value: Sprague Dawley


title: NT12098_2

description: batch: 2016-12-22-HGHNHBBXX


title: MTZ+ DMSO 2dpi rep2


title: MTZ+ Rapamycin 2dpi rep2


title: MTZ+ DMSO 2dpi rep1


title: ARCS4

description:
ARCS4
KriegelARCS4_AGTTCC

value: Kidney


title: NT12079_1

description: batch: 2016-12-22-HGHNHBBXX


title: ARCS2

description:
ARCS2
KriegelARCS2_AGTCAA

value: male


title: vero_024h_cov2_zn005

description: mRNA (100bp)


title: NT12147_1

description: batch: 2016-12-22-HGHNHBBXX


title: ARCS1

description:
ARCS1
KriegelARCS1_GCCAAT


title: vero_024h_cov2_zn004

description: mRNA (100bp)


title: NT12192_1

description: batch: 2016-12-22-HGHNHBBXX


title: vero_024h_ctrl_zn006

description: mRNA (100bp)


title: MTZ- Rapamycin 2dpi rep2

value: MTZ- Rapamycin


title: PANNE038

city: Vancouver

first: Robert

last: Hancock

address: 2259 - Lower Mall Research Station

institute: University of British Columbia

data_processing:
BBDuk (version 38.26) was used to trim adapter sequences and polyA tails (trimpolya=10)
STAR (version 2.6.1b) was used to align trimmed reads to the indexed human genome.
SAMtools (version 1.9) was used to merge alignments or samples sequenced across multiple lanes of the flowcell.
HTSeq-count (version 0.9.1) was used to generate raw count data from alignments using the "union" mode and "reverse" stranded options.
Genome_build: GRCh38/hg38 (version 94) from Ensembl
Supplementary_files_format_and_content: Tab-delimited count matrix of raw counts for all samples from HTSeq-count

source_name: blood

extract_protocol:
2.5ml of whole blood was collected from each participant into PAXgene Blood RNA tubes (PreAnalytiX GmbH, Switzerland). RNA was isolated from each samples using the RiboPure RNA purification kit (Ambion ThermoFisher; Waltham, MA, USA) following the manufacturer’s protocol. Quantification and quality assessment of total RNA was performed using an Agilent 2100 Bioanalyzer (Santa Clara, CA, USA). Poly-adenylated RNA was captured using the NEBNext Poly(A) mRNA Magnetic Isolation Module (catalogue no.: E7409L, NEB; Ipswich, MA, USA).
Strand-specific cDNA libraries were generated from poly-adenylated RNA using the KAPA Stranded RNA-Seq Library Preparation Kit (cat. no.: 07277253001, Roche; Basel, Switzerland).

value: whole blood

tag: pathology

value: Mild AP


title: MTZ- Rapamycin 2dpi rep3


title: MTZ- Rapamycin 2dpi rep1


title: MTZ- DMSO 2dpi rep3

value: MTZ- DMSO


title: PANNE036


title: NT12194_1

description: batch: 150306_C5HH0ACXX


title: vero_004h_cov2_zn001

description: mRNA (100bp)


title: NT12098_1

description: batch: 150306_C5HH0ACXX


title: PANNE035

value: Moderately-severe AP


title: MTZ- DMSO 2dpi rep2


title: vero_216h_ctrl_zn051

description: small RNA (100bp)

extract_protocol:
Trypsin-EDTA 0.25% (ThermoFIsher Scientific), then 250 μl Trizol
NEXTFLEX small RNA-Seq Kit v3 (Perkin Elmer Applied Genomics)


title: vero_004h_ctrl_zn003

description: mRNA (100bp)


title: M-19-23

type: genomic

city: Manchester

first: Caroline

last: Dive

address: Cancer Research UK Manchester Institute, The University of Manchester, Wilmslow Road

institute: Cancer Research UK Manchester Institute

description: Whole blood genomic DNA  of healthy control subject ()

hyb_protocol: Bisulphite converted DNA was amplified, fragmented and hybridized to the Illumina Infinium EPIC Beadchip using standard Illumina protocol

scan_protocol: Illumina HiScan

data_processing: Raw Illumina Infinium EPIC Beadchip array (i.e., the ‘850K array’) data was extracted using GenomeStudio. Methylation data preprocessing was performed using the minfi R package. CpGs were discarded from analysis that had single nucleotide polymorphisms within either the interrogated CpG or at the single nucleotide extension, that represented cross-reactive probes that are listed within the maxprobes R package, or that had detection p-values of greater than 0.01 in more than ten percent of samples. CpGs within sex chromosomes were excluded in order to exclude biases associated with analysis of sex chromosome DNAm in samples of mixed sexes.

label: Cy5 and Cy3

source_name: Whole blood

label_protocol: Standard Illumina Protocol

extract_protocol: DNA and RNA were extracted simultaneously from 1ml fresh whole blood, using the AllPrep DNA/RNA Mini kit (Qiagen). DNA was bisulfite converted using the EZ DNAm kit (Zymo Research).  DNA and RNA were extracted simultaneously from 1ml fresh whole blood, using the AllPrep DNA/RNA Mini kit (Qiagen). DNA was bisulfite converted using the EZ DNAm kit (Zymo Research).

tag: case control status

value: Control

tag: participant type

value: Age and sex matched donor

tag: age (years)

value: M

tag: self-declared ancestry

value: Unknown (Anonymous blood donor)


title: M-24-28


title: MTZ- DMSO 2dpi rep1

value: retinal pigment epithelium

tag: treatment

tag: time point

tag: replicate


title: PANNE033


title: 3425-P

description: Whole blood genomic DNA of individual with Sotos syndrome

value: Case

value: Proband

tag: Sex

value: Asian


title: PANNE034


title: Huh7_siDHX37_rep2

city: Shanghai

first: Xianghuo

address: No 270, Dong An Road

country: China

institute: Fudan University

data_processing:
Sequenced reads were trimmed for adaptor sequence and low-quality bases, then mapped to hg38 whole genome using Bowtie with standard alignment parameters.
PCR duplicates were marked with the Picard “Mark Duplicates” utility and removed from further analysis.
Bam files were converted to BigWig files using deepTools.
Peaks were identified using the MACS2 peak caller with the following parameters: –f BAMPE –keep-dup all –g hs –q 0.01
Genome_build: hg38
Supplementary_files_format_and_content: wig files were generated using deepTools.

source_name: Huh 7

growth_protocol: Huh 7 was cultured in Dulbecco’s modified Eagle’s medium (DMEM) (Invitrogen, Carlsbad, CA, USA) containing 10% fetal bovine serum (FBS) (HyClone, Logan, UT, USA) and antibiotics (penicillin and streptomycin, Invitrogen) at 37 °C in 5% CO2.

extract_protocol:
ChIP-seq was performed as described previously (Schmidt D, Wilson MD, Spyrou C, Brown GD, Hadfield J, Odom DT. ChIP-seq: using high-throughput sequencing to discover protein-DNA interactions. Methods.2009;48:240-8).
For the ChIPseq, input amounts of DNA was converted into high quality libraries for next-generation sequencing on the Illumina platform using the NEBNext Ultra II DNA Library Prep Kit. Bead based size selection was performed for final library size selection to obtain ChIP-seq libraries containing fragments of 250 bp to 500 bp.   For the RNA-seq, the sequencing library was prepared using an Illumina mRNA-seq sample preparation kit and was then subjected to paired-end sequencing on the Illumina HiSeq platform.   CUT&Tag was performed according to the manufacturer's protocol (Novoprotein, Shanghai, China). The DNA was mixed with a universal i5 and a uniquely barcoded i7 primer. The sample was placed in a Thermocycler for PCR, and post-PCR clean-up was performed by bead based size selection and cleanup.

treatment_protocol: Before siRNA transfection, around 0.4 million Huh 7 cells  were seeded in to 6 well plate per well. Next day, cells in each well were transfected with 5μl of siRNA or NC (5μM) using Lipofectamine RNAiMAX. To set up DHX37-overexpression stable cell lines, Huh 7 cells were transfected with Flag-DHX37 lentivirus, renew the medium after 8 hours later, for another 24 hours, sorting the positive cells with puromycin.

value: HCC

tag: chip antibody

tag: cell line

value: transfected with siDHX37 using Lipofectamine RNAiMAX.


title: vero_216h_cov2_zn049

description: small RNA (100bp)

tag: cell type

value: kidney cells

value: Infected – SARS-CoV-2

tag: hours post-treatment

tag: moi


title: NT12096_1

description: batch: 150306_C5HH0ACXX

value: LB media


title: vero_216h_cov2_zn050

description: small RNA (100bp)


title: vero_168h_ctrl_zn048

description: small RNA (100bp)

value: control (uninfected)


title: NT12089_2

description: batch: 150306_C5HH0ACXX


title: NT12095_2

description: batch: 150306_C5HH0ACXX


title: NT12004_2

description: batch: 150306_C5HH0ACXX


title: F-16-20

value: F


title: Huh7_siDHX37_rep1


title: NT12015_2

description: batch: 150306_C5HH0ACXX


title: vero_168h_cov2_zn047

description: small RNA (100bp)


title: pooled_PC

description: Pooled whole blood genomic DNA of unaffected parents of individuals with Sotos syndrome including father and mother of 3425-P, father and mother of 8658-P, and father of 5767-P (N=5 parents total).

value: Pooled controls

value: Pooled parent controls


title: PANNE030

tag: tissue

value: whole blood

value: Moderately-severe AP


title: Huh7_siNC_rep2

value: transfected with siNC using Lipofectamine RNAiMAX.


title: 8658-P

value: M

value: White


title: vero_168h_cov2_zn046

description: small RNA (100bp)


title: 5767-P

value: Case


title: NT12002_2

description: batch: 150306_C5HH0ACXX

tag: strain


title: PANNE032

value: Mild AP


title: Huh7_siNC_rep1


title: PANNE029


title: vero_120h_ctrl_zn045

description: small RNA (100bp)


title: NT12001_2

description: batch: 150306_C5HH0ACXX

tag: growth condition


title: PANNE028

tag: pathology


title: PANNE031


title: vero_120h_cov2_zn044

description: small RNA (100bp)


title: Huh7_siDHX37_Input

value: transfected with siDHX37 using Lipofectamine RNAiMAX, renew the medium after 8 hours later, for another 24 hours.


title: vero_120h_cov2_zn043

description: small RNA (100bp)


title: Huh7_DHX37

data_processing:
Library strategy: Cut & Tag
Sequenced reads were trimmed for adaptor sequence and low-quality bases, then mapped to hg38 whole genome using Bowtie with standard alignment parameters.
PCR duplicates were marked with the Picard “Mark Duplicates” utility and removed from further analysis.
Bam files were converted to BigWig files using deepTools.
Peaks were identified using the MACS2 peak caller with the following parameters: –f BAMPE –keep-dup all –g hs –q 0.01
Genome_build: hg38
Supplementary_files_format_and_content: wig files were generated using deepTools.

value: HCC

value: Flag, sigma,F1804

value: transfected with Flag-DHX37 lentivirus, renew the medium after 8 hours later, for another 24 hours,sorting the positive cells with puromycin.


title: PANNE026


title: PANNE025


title: vero_072h_ctrl_zn042

description: small RNA (100bp)

value: kidney cells


title: MTZ- DMSO 4dpi rep2

value: retinal pigment epithelium

value: MTZ- DMSO


title: Huh7_siDHX37_H3K27ac

value: H3K27ac, Active motif, 39133


title: PR0126_13_b

city: Gunma

first: Hiroki

last: Tanemura

address: 2716-1 Kurakake, Akaiwa, Chiyoda-machi, Ohra-gun

institute: Daiichi sankyo co., LTD.

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to chinese hamster whole genome (NW_003613580:NW_003722730) using bowtie v1.0.0 with parameters -v3 -all -m 30 --best --strata
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Mortazavi et al., Nature Methods, 2008. 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: Matrix table with calculated RPKM value, raw gene counts for every gene and every sample

organism: Cricetulus griseus

source_name: Chinese hamster ovary cells

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

value: CHO-K1 (CCL-61; ATCC)

value: ovary cells


title: PANNE024

value: whole blood

value: Severe AP


title: vero_072h_cov2_zn041

description: small RNA (100bp)

value: Infected – SARS-CoV-2


title: Huh7_siNC_Input

last: He

value: transfected with siNC using Lipofectamine RNAiMAX, renew the medium after 8 hours later, for another 24 hours.


title: PR0126_14_b


title: PANNE023


title: PR0126_12_b


title: vero_072h_cov2_zn040

description: small RNA (100bp)


title: vero_048h_ctrl_zn039

description: small RNA (100bp)

value: control (uninfected)


title: PR0126_10_b


title: Huh7_PLRG1

value: PLRG1, proteintech,11914-1-AP

value: untreated


title: PANNE020

value: Mild AP


title: Huh7_ATAC

extract_protocol:
ChIP-seq and ATAC were performed as described previously (Buenrostro JD, Giresi PG, Zaba LC, Chang HY, Greenleaf WJ. Transposition of native chromatin for fast and sensitive epigenomic profiling of open chromatin, DNA-binding proteins and nucleosome position. Nat Methods.2013;10:1213-8, and Schmidt D, Wilson MD, Spyrou C, Brown GD, Hadfield J, Odom DT. ChIP-seq: using high-throughput sequencing to discover protein-DNA interactions. Methods.2009;48:240-8).
DNA-seq and ATAC-seq library preparation

treatment_protocol: untreated

value: HCC


title: PR0126_15_b


title: vero_048h_cov2_zn038

description: small RNA (100bp)


title: PR0126_09_b


title: PANNE019


title: Huh7_Input_DNA


title: vero_048h_cov2_zn037

description: small RNA (100bp)


title: Huh7_H3K4me3

value: H3K4me3, Active motif, 39016


title: PR0126_08_b


title: PANNE018


title: Huh7_H3K4me1

value: H3K4me1, Active motif, 39297


title: vero_024h_cov2_zn035

description: small RNA (100bp)

value: kidney cells


title: PR0126_07_b


title: PR0126_06_b


title: Huh7_H3K27ac


title: PANNE016


title: PANNE017


title: vero_024h_cov2_zn034

description: small RNA (100bp)


title: PANNE021


title: PANNE015


title: PR0126_11_b


title: PR0126_05_b


title: vero_004h_ctrl_zn033

description: small RNA (100bp)


title: HepG2_Input_DNA

growth_protocol: HepG2 was cultured in Dulbecco’s modified Eagle’s medium (DMEM) (Invitrogen, Carlsbad, CA, USA) containing 10% fetal bovine serum (FBS) (HyClone, Logan, UT, USA) and antibiotics (penicillin and streptomycin, Invitrogen) at 37 °C in 5% CO2.


title: PR0126_04_b


title: Huh7_siNC_H3K27ac


title: HepG2_H3K4me1


title: vero_004h_cov2_zn032

description: small RNA (100bp)


title: vero_004h_cov2_zn031

description: small RNA (100bp)


title: PANNE013


title: HepG2_H3K27ac


title: PANNE014


title: PR0126_01_b


title: vero_024h_ctrl_zn036

description: small RNA (100bp)


title: PR0126_03_b


title: HepG2_H3K4me3


title: PR0126_02_b


title: 4A rep3

city: Washington DC

first: huadong

last: Pei

state: District of Columbia

address: 800 22ND ST NW

institute: BioChemistry and Molecular Medicine

data_processing:
Illumina 1.9 solfware was used for base-calling
STAR 2.7.0 with reference genome(GRCh38) and annotation file (GRCh38.95) were used for sequence alignment.
If the quality of alignment file meets standard QC, HT-Seq 0.11.2 was used to count the gene expression
Differential expression analysis is done using DE-Seq 1.22.2.
Genome_build: GRCh38
Supplementary_files_format_and_content: Text files of gene expression normalized counts for samples were generated.

source_name: MCF7 (ATCC® HTB-22)

extract_protocol:
MCF7 were harvsted , flash frozen on dry ice, mRNA were extracted mannually . NEBNext Ultra RNA library 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: shRNA

value: stably expressing shRNA targeting SRPK2 (PLKO.1-puro-shSRPK2-7）

tag: genotype/variation

value: stably overexpressing SRPK2 4A


title: PANNE010

value: Moderately-severe AP


title: PANNE009


title: 4A rep1


title: HepG2_ATAC


title: Control_1

city: NANJING

first: yue

last: yang

address: 639 LONGMIAN AVENUE

institute: china pharmaceutical university

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to hg38 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: hg18
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample …

source_name: breast cancer cells

growth_protocol: Cells were cultured in DMEM medium (Gibco, Grand Island, NY, USA) at 37 °C under a humidified atmosphere with 5% CO2, and supplemented with 10% FBS (Gibco), 80 U/ml penicillin, and 0.08 mg/ml streptomycin.

extract_protocol:
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: MDA-MB-231 cells were treated with CPUL119(4.5 μM), CPUL129(1.8 μM), CPUL149(0.9 μM) for 48 h, and subjected to  deep sequencing, in triplicate, using Illumina GAIIx.

value: Breast cancer cell line


title: Control_2


title: CPUL149_1