title: H17.7350589.scRNA-seq

value: 6 somite stage


title: 198CS23

status: Public on Feb 11 2021

type: SRA

city: Cambridge

first: Philip

last: Wigge

address: 47 Bateman street

department: Sainsbury Laboratory

country: United Kingdom

institute: Cambridge University

library_source: genomic

data_processing:
Genome_build: TAIR10
Adapters were trimmed off from raw reads with Trimmomatic with argument "ILLUMINACLIP:$FA_ADAPTER:6:30:10 LEADING:3 TRAILING:3 MINLEN:36 SLIDINGWINDOW:4:15". Raw reads were mapped to the genome "TAIR10" with Bowtie2 under argument:"--no-mixed --no-discordant --no-unal -k2". Any read that mapped to more than one genomic location was discarded. PCR duplicate reads were removed with Picard using default setting.
Genomic binding profile was quantified in RPKM (Reads Per Kilobase per Million mapped reads) using a bin-size of 10bp. "deeptools.bamCoverage" is used.
For each treated ChIP-Seq library, peaks were called against a chipseq input sample 195CS13 using MACS2 with argument "--keep-dup 1 -p 0.1".
Supplementary_files_format_and_content:  *.narrowPeak: containing MACS2-called peaks. as described
Supplementary_files_format_and_content:  *_RPKM.bw: RPKM-normalised bigwig track at 10bp resolution

molecule: genomic DNA

organism: Arabidopsis thaliana

source_name: seedling

growth_protocol:
Seeds were surface-sterilised using ethanol or vapour-phase sterilisation (Clough & Bent, 1998) and stratified in respective growth media in the dark at 4˚C for 72 hours. Growth cabinets were maintained at 65% relative humidity and 170 µmol/m2/s light, unless specified otherwise, and as specified per experiment seedlings were grown at 20˚C with a 12-hour photoperiod or at 22˚C with either continuous light, a 16-hour long-day photoperiod or an 8-hour short-day photoperiod.
For ChIP-seq, A. thaliana seedlings were grown for 8 days on 1-mm-pore nylon mesh rafts placed on half-strength MS medium (pH 5.7) with 0.8% w/v agar (P1001, Duchefa) (‘MS agar’ hereafter) (22˚C long days).

extract_protocol:
The seedling were grown for 10 days and treated as indicated. 3 g plant material for each treatment was fixed under vacuum for 20min in 1xPBS (10 mM PO43−, 137 mM NaCl, and 2.7 mM KCl) containing 1% Formaldehyde (F8775 SIGMA). The reaction was quenched by adding glycine to a final concentration of 62mM. Chromatin immunoprecipitation (ChIP) was performed as described (Jaeger et al), with the exception that 100μl of ANTI-FLAG® M2 Affinity Gel (A2220 Sigma) were used for immunoprecipitation.
Sequencing libraries were prepared using TruSeq ChIP Sample Preparation Kit (Illumina, IP-202-1024) and prepared according to manufacturer instructions. DNA libraries were quantified using a Qubit fluorometer, and liibrary profiles were analysed using a TapeStation 2200 with High Sensitivity D1000 ScreenTapes (5067-5584, Agilent). Libraries were sequenced on a NextSeq-500 (Illumina; single end, 75bp reads) according to Illumina guidelines.

tag: cultivar

tag: genotype

value: CAMTA3-FLAG in camta123

tag: tissue

value: seedling

tag: photoperiod

value: long days (16L/8D)

tag: temperature

tag: replicate

value: single

tag: fragmentation method

value: sonication

tag: chip antibody

value: FLAG M2 agarose affinity gel antibody SIGMA A2235

tag: age

value: 8 days

tag: objective time


title: I02.7350589.scRNA-seq

city: Palo Alto

first: Antoine

last: Zalc

address: 265 Campus Drive

country: USA

institute: Stanford University

library_source: transcriptomic

data_processing:
bcl2fastq2 2.18 (Illumina) was used to generate fastq files
Reads within fastq files were trimmed for base call quality (PHRED score > = 21) and for adaptor sequences at 3’ end using Skewer
Trimmed reads were then aligned to mouse genome version mm10 using STAR 2.6
Raw read counts were generated by STAR
Genome_build: mm10
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

molecule: total RNA

organism: Mus musculus

source_name: Cranial neural crest cells

extract_protocol:
Single cell were sorted directly into lysis buffer by flow cytometry from Wnt1::Cre; Rosa26TdTomato embryos dissected at indicated developmental stage
RNA libraries were prepared for sequencing using standard Illumina protocols Nextera XT DNA Library Prep kit
single cell RNA-Seq (Smart-Seq2)

tag: developmental stage

tag: strain

tag: cell type

value: Cranial neural crest cells


title: H14.7350589.scRNA-seq


title: 198CS21

value: CAMTA2-FLAG in camta123

value: FLAG M2 agarose affinity gel antibody SIGMA A2233


title: H13.7350589.scRNA-seq


title: H12.7350589.scRNA-seq


title: 198CS20

value: FLAG M2 agarose affinity gel antibody SIGMA A2232


title: 198CS2

value: FLAG M2 agarose affinity gel antibody SIGMA A2231


title: H11.7350589.scRNA-seq


title: 198CS19

value: CAMTA1-FLAG in camta123

value: FLAG M2 agarose affinity gel antibody SIGMA A2230


title: H10.7350589.scRNA-seq


title: H09.7350589.scRNA-seq


title: 198CS17

value: FLAG M2 agarose affinity gel antibody SIGMA A2228


title: 198CS18

value: FLAG M2 agarose affinity gel antibody SIGMA A2229


title: H08.7350589.scRNA-seq

value: 6 somite stage


title: 198CS16

value: FLAG M2 agarose affinity gel antibody SIGMA A2227


title: H07.7350589.scRNA-seq


title: 198CS13

value: seedling

value: FLAG M2 agarose affinity gel antibody SIGMA A2224


title: 198CS14

value: long days (16L/8D)

value: single

value: FLAG M2 agarose affinity gel antibody SIGMA A2225


title: H01.7350589.scRNA-seq


title: 198CS11

value: CAMTA3-FLAG in camta123

value: sonication

value: FLAG M2 agarose affinity gel antibody SIGMA A2222

value: 8 days


title: 198CS15

value: FLAG M2 agarose affinity gel antibody SIGMA A2226


title: G23.7350589.scRNA-seq

value: Cranial neural crest cells


title: 198CS1

value: FLAG M2 agarose affinity gel antibody SIGMA A2220


title: obese+NAM4

city: Graz

first: Andreas

last: Prokesch

state: Styria

address: Harrachgasse 21/7

department: Institute of Cell Biology, Histology, and Embryology

country: Austria

institute: Medical University Graz

data_processing:
FastQ sequencing files were processed and analyzed with the web tool RaNA-seq (Pietro et al., Bioinformatics, 2020)
Differentially expressed genes between groups were determined using moderated t-test with Limma and adjusted by Benjamini-Hochberg (P<0.1)
TPM values were generated using RaNA-seq (Pietro et al., Bioinformatics, 2020)
Genome_build: Rnor_6.0
Supplementary_files_format_and_content: TPM_lean_obese_obese+NAM.txt (TPM counts)

organism: Rattus norvegicus

source_name: ZSF1 rats - obese + NAM

growth_protocol: Rats were housed under conventional conditions in a 12-h light and 12-h dark cycle with ad libitum access to water and food.

extract_protocol:
RNA was isolated using TRIzol® Reagent and RNeasy mini kits (QIAGEN)
NEBNext® Ultra™ II Directional RNA Library Prep Kit (New England Biolabs, Massachusetts, USA)

treatment_protocol: 24 mM NAM in the drinking water from 8 till 20 weeks of age

value: cardiac muscle

tag: treatment

value: died-induced obese treated with NAM


title: 198CS12

value: FLAG M2 agarose affinity gel antibody SIGMA A2223


title: H03.7350589.scRNA-seq

value: 6 somite stage


title: H02.7350589.scRNA-seq


title: H04.7350589.scRNA-seq


title: G24.7350589.scRNA-seq


title: G22.7350589.scRNA-seq


title: obese+NAM3


title: 198CS10

value: FLAG M2 agarose affinity gel antibody SIGMA A2221


title: obese+NAM2


title: G21.7350589.scRNA-seq


title: obese+NAM1


title: G20.7350589.scRNA-seq


title: obese4

source_name: ZSF1 rats - obese

value: diet-indcued obese


title: G18.7350589.scRNA-seq


title: obese2


title: obese3


title: H06.7350589.scRNA-seq


title: H05.7350589.scRNA-seq


title: obese1


title: G16.7350589.scRNA-seq


title: lean4

source_name: ZSF1 rats - lean

value: lean control


title: G15.7350589.scRNA-seq


title: lean3


title: lean2


title: lean1


title: G12.7350589.scRNA-seq


title: G10.7350589.scRNA-seq


title: G13.7350589.scRNA-seq


title: G09.7350589.scRNA-seq


title: G06.7350589.scRNA-seq


title: G17.7350589.scRNA-seq


title: G19.7350589.scRNA-seq


title: G08.7350589.scRNA-seq


title: G05.7350589.scRNA-seq


title: G03.7350589.scRNA-seq


title: G04.7350589.scRNA-seq


title: G14.7350589.scRNA-seq


title: G02.7350589.scRNA-seq


title: G07.7350589.scRNA-seq


title: G11.7350589.scRNA-seq


title: G01.7350589.scRNA-seq


title: F23.7350589.scRNA-seq


title: F22.7350589.scRNA-seq


title: F24.7350589.scRNA-seq


title: Uninfected vs. Infected MDBK cells after 24 hours of incubation with BVDV-1b field strain - rep3

type: RNA

city: Puławy

first: Paweł

last: Mirosław

address: 57, Partyzantow Avenue

department: Department of Virology

country: Poland

institute: NATIONAL VETERINARY RESEARCH INSTITUTE

description: Infected cell line (BVDV-1b) compared to uninfected cell line after 24h of incubation. Biological replication 2. Sample 1.

hyb_protocol: Following fragmentation, 100 µl of solution with fragmented cRNA were applied to microarrays enclosed in Agilent SureHyb-enabled hybridization chambers and hybridized for 17 h at 65C. After hybridization, slides were washed sequential.

scan_protocol: Scanned on an Agilent SureScan Dx Microarray Scanner. Images were quantified using Agilent Feature Extraction Software (version 12.0.3.1).

data_processing: Agilent Feature Extraction Software (version 12.0.3.1) was used for background subtraction and Linear Lowess normalization.

organism: Bos taurus

source_name: bovine kidney cell line

label_protocol: The synthesis of labeled cRNA was carried out using the Low Input Quick Amp Labeling Kit (Agilent Technologies). The reaction mixture contained 0.75 µL of nuclease-free water, 3.2 µL of 5x reaction buffer, 0.6 µL of 0.1 M DTT, 1 µL of NTP mix, 0.21 µL of T7 RNA polymerase, 0.24 µL of Cyanine 3 or Cyanine 5, and 10 µL of cDNA.

growth_protocol: Madin-darby bovine kidney cells (MDBK, ATCC) were cultured in Minimum Essential Medium Eagle (MEM-E, Sigma) containing 10 % foetal calf serum (Gibco) and 1% of antibiotics (Sigma).

extract_protocol: Total RNA was extracted using a Qiagen RNeasy Mini kit following the supplied protocol. The Low Input Quick Amp Labeling Kit (Agilent Technologies) was used for cDNA synthesis at 40°C for 2h.

treatment_protocol: MDBK cells were infected with BVDV strain 59-GB/11 (BVDV-1f) or 60-GB/11 (BVDV-1b). RNA were isolated at 24 or 72 hours post-infection. At the same time, RNA was isolated from uninfected cells.

tag: cell line

value: MDBK

tag: virus strain infection

value: Uninfected

tag: incubation time


title: Uninfected vs. Infected MDBK cells after 72 hours of incubation with BVDV-1b field strain - rep1

description: Infected cell line (BVDV-1b) compared to uninfected cell line after 72h of incubation. Biological replication 1. Sample 1.


title: Uninfected vs. Infected MDBK cells after 72 hours of incubation with BVDV-1b field strain - rep4

description: Infected cell line (BVDV-1b) compared to uninfected cell line after 72h of incubation. Biological replication 2. Sample 2.


title: Uninfected vs. Infected MDBK cells after 24 hours of incubation with BVDV-1b field strain - rep4

description: Infected cell line (BVDV-1b) compared to uninfected cell line after 24h of incubation. Biological replication 2. Sample 2.


title: Uninfected vs. Infected MDBK cells after 24 hours of incubation with BVDV-1b field strain - rep1

description: Infected cell line (BVDV-1b) compared to uninfected cell line after 24h of incubation. Biological replication 1. Sample 1


title: F20.7350589.scRNA-seq


title: F21.7350589.scRNA-seq


title: F19.7350589.scRNA-seq


title: Pdpk1 KO Treg, rep_2 [Hemizygous]

city: Jersey City

first: Thomas

middle: S

last: Postler

state: New Jersey

address: 95 Greene Street 5-018

department: Discovery Science

institute: International AIDS Vaccine Initiative

data_processing:
Read alignment with STAR
Remove batch effect with ComBat function of sva package v3.18.0
Analysis with DESeq2
Genome_build: mm10
Supplementary_files_format_and_content: xlsx file with log2-transformed DESeq2-normalized gene counts

molecule: polyA RNA

source_name: CD4+ YFP+ Treg from spleen and peripheral lymph nodes

growth_protocol: Treg cells were purified by FACS immediately after isolation of spleen and peripheral lymph nodes.

extract_protocol:
RNA was extracted by RNeasy Mini Kit (Qiagen) according to protocol.
poly-A pull-down, Illumina TruSeq RNA prep kit.

treatment_protocol: No treatment.

tag: mouse strain

value: Foxp3 YFP-Cre/0 Pdpk1 FL/FL


title: Uninfected vs. Infected MDBK cells after 72 hours of incubation with BVDV-1b field strain - rep2

description: Infected cell line (BVDV-1b) compared to uninfected cell line after 72h of incubation. Biological replication 1. Sample 2.


title: Uninfected vs. Infected MDBK cells after 72 hours of incubation with BVDV-1b field strain - rep3

description: Infected cell line (BVDV-1b) compared to uninfected cell line after 72h of incubation. Biological replication 2. Sample 1.


title: Pdpk1 KO Treg, rep_1 [Hemizygous]

tag: genotype


title: Uninfected vs. Infected MDBK cells after 24 hours of incubation with BVDV-1b field strain - rep2

description: Infected cell line (BVDV-1b) compared to uninfected cell line after 24h of incubation. Biological replication 1. Sample 2


title: Uninfected vs. Infected MDBK cells after 72 hours of incubation with BVDV-1f field strain - rep4

description: Infected cell line (BVDV-1f) compared to uninfected cell line after 72h of incubation. Biological replication 2. Sample 2.


title: F18.7350589.scRNA-seq


title: WT Treg, rep_2 [Hemizygous]

value: Foxp3 YFP-Cre/0 Pdpk1 +/+


title: WT Treg, rep_1 [Hemizygous]


title: F17.7350589.scRNA-seq


title: Uninfected vs. Infected MDBK cells after 72 hours of incubation with BVDV-1f field strain - rep2

description: Infected cell line (BVDV-1f) compared to uninfected cell line after 72h of incubation. Biological replication 1. Sample 2.


title: Uninfected vs. Infected MDBK cells after 24 hours of incubation with BVDV-1f field strain - rep4

description: Infected cell line (BVDV-1f) compared to uninfected cell line after 24h of incubation. Biological replication 2. Sample 2.


title: Uninfected vs. Infected MDBK cells after 24 hours of incubation with BVDV-1f field strain - rep3

description: Infected cell line (BVDV-1f) compared to uninfected cell line after 24h of incubation. Biological replication 2. Sample 1.


title: Uninfected vs. Infected MDBK cells after 72 hours of incubation with BVDV-1f field strain - rep1

description: Infected cell line (BVDV-1f) compared to uninfected cell line after 72h of incubation. Biological replication 1. Sample 1.


title: Uninfected vs. Infected MDBK cells after 72 hours of incubation with BVDV-1f field strain - rep3

description: Infected cell line (BVDV-1f) compared to uninfected cell line after 72h of incubation. Biological replication 2. Sample 1.


title: Uninfected vs. Infected MDBK cells after 24 hours of incubation with BVDV-1f field strain - rep2

description: Infected cell line (BVDV-1f) compared to uninfected cell line after 24h of incubation. Biological replication 1. Sample 2


title: Uninfected vs. Infected MDBK cells after 24 hours of incubation with BVDV-1f field strain - rep1

description: Infected cell line (BVDV-1f) compared to uninfected cell line after 24h of incubation. Biological replication 1. Sample 1


title: F16.7350589.scRNA-seq


title: F11.7350589.scRNA-seq


title: F13.7350589.scRNA-seq


title: F15.7350589.scRNA-seq


title: F12.7350589.scRNA-seq


title: F09.7350589.scRNA-seq


title: F08.7350589.scRNA-seq


title: F05.7350589.scRNA-seq


title: F07.7350589.scRNA-seq


title: F06.7350589.scRNA-seq


title: F03.7350589.scRNA-seq


title: Blood_Day7_200400360011_D

city: Memphis

first: Zhaohui

last: Xu

state: TN

address: 262 Danny Thomas Place

department: Infectious Diseases

institute: St. Jude Children's Research Hospital

hyb_protocol: Amplified labeled RNA were hybridized overnight to Illumina HumanHT-12 v4 Beadchips (Illumina).

scan_protocol: Data was scanned on Illumina Beadstation 500

data_processing: Illumina GenomeStudio software was used for background subtraction and to scale average signal intensities

label: biotin

organism: Homo sapiens

source_name: Whole blood

label_protocol: Following RNA extraction and quality control analysis, Globin mRNA was depleted from a portion of each total RNA sample using the GLOBINclear 96-well format kit (Ambion). Globin reduced RNA from all samples passing quality control were then amplified and labeled using the Illumina TotalPrep-96 RNA Amplification Kit (Ambion).

extract_protocol: Blood was collected in Tempus tubes (Applied Biosystems, Foster City, CA), immediately placed on ice and stored within 2-4 hours at -20°C until further analyses in batches. RNA was extracted, amplified, quantified and globin reduced according to manufacturer's instructions.

tag: subject

tag: time

value: day 7 (post-vaccination)

tag: tissue

value: Whole blood


title: Blood_Day7_200400360009_B


title: Blood_Day7_200400360014_H


title: Blood_Day7_200400360002_L


title: Blood_Day7_200400360020_L


title: Blood_Day7_200400360007_G


title: Blood_Day7_200400360021_A


title: Blood_Day7_200400360011_A


title: Blood_Day7_200400360005_H


title: Blood_Day7_200400360020_B


title: F01.7350589.scRNA-seq


title: Blood_Day7_200400360014_I


title: F14.7350589.scRNA-seq


title: Blood_Day7_200400360011_I


title: F04.7350589.scRNA-seq


title: F10.7350589.scRNA-seq


title: E24.7350589.scRNA-seq


title: E23.7350589.scRNA-seq


title: E22.7350589.scRNA-seq


title: E20.7350589.scRNA-seq


title: F02.7350589.scRNA-seq


title: Blood_Day7_200400360007_L


title: E18.7350589.scRNA-seq


title: Blood_Day7_200400360004_H


title: E19.7350589.scRNA-seq


title: Blood_Day7_200400360005_J


title: E21.7350589.scRNA-seq


title: Blood_Day7_200400360024_H


title: Blood_Day7_200400360021_B


title: Blood_Day7_200400360005_G


title: Blood_Day7_200400360022_B


title: Blood_Day7_200400360020_E


title: Blood_Day7_200400360024_C


title: E16.7350589.scRNA-seq


title: E13.7350589.scRNA-seq


title: E12.7350589.scRNA-seq


title: E14.7350589.scRNA-seq


title: Blood_Day7_200400360021_C


title: E11.7350589.scRNA-seq


title: E10.7350589.scRNA-seq


title: E17.7350589.scRNA-seq


title: Blood_Day7_200400360015_D


title: E09.7350589.scRNA-seq


title: E08.7350589.scRNA-seq


title: E15.7350589.scRNA-seq


title: E07.7350589.scRNA-seq


title: Blood_Day7_200400360005_I


title: Blood_Day7_200400360014_D


title: Blood_Day7_200400360002_H


title: Blood_Day7_200400360003_B


title: Blood_Day7_200400360020_F


title: Blood_Day7_200400360015_L


title: E02.7350589.scRNA-seq


title: E06.7350589.scRNA-seq


title: E01.7350589.scRNA-seq


title: Blood_Day7_200400360022_D


title: Blood_Day7_200400360022_E


title: Blood_Day7_200400360024_F


title: Blood_Day7_200400360009_C


title: D24.7350589.scRNA-seq


title: E05.7350589.scRNA-seq


title: E04.7350589.scRNA-seq


title: Blood_Day7_200400280054_K


title: Blood_Day7_200400360015_I


title: D20.7350589.scRNA-seq


title: E03.7350589.scRNA-seq


title: Blood_Day7_200400360018_A


title: D23.7350589.scRNA-seq


title: D22.7350589.scRNA-seq


title: Blood_Day7_200400360021_D


title: D17.7350589.scRNA-seq


title: Blood_Day7_200400360020_A


title: D18.7350589.scRNA-seq


title: Blood_Day7_200400280054_C


title: Blood_Day7_200400360011_C


title: D21.7350589.scRNA-seq


title: D14.7350589.scRNA-seq


title: D16.7350589.scRNA-seq


title: Blood_Day7_200400360022_H


title: D19.7350589.scRNA-seq


title: D15.7350589.scRNA-seq


title: Blood_Day7_200400360018_J


title: D12.7350589.scRNA-seq


title: D13.7350589.scRNA-seq


title: Blood_Day7_200400360020_C


title: Blood_Day1_200400360015_G

value: day 1 (post-vaccination)


title: Blood_Day1_200400360008_D


title: Blood_Day7_200400360021_K


title: D11.7350589.scRNA-seq


title: Blood_Day1_200400360002_A


title: Blood_Day1_200400360022_G


title: Blood_Day1_200400360011_K


title: Blood_Day1_200400360022_K


title: D10.7350589.scRNA-seq


title: D09.7350589.scRNA-seq


title: Blood_Day1_200400360004_F


title: D08.7350589.scRNA-seq


title: D07.7350589.scRNA-seq


title: D06.7350589.scRNA-seq


title: D05.7350589.scRNA-seq


title: D04.7350589.scRNA-seq


title: D03.7350589.scRNA-seq


title: D01.7350589.scRNA-seq


title: C22.7350589.scRNA-seq


title: D02.7350589.scRNA-seq


title: C21.7350589.scRNA-seq


title: C24.7350589.scRNA-seq


title: C23.7350589.scRNA-seq


title: Blood_Day1_200400360015_C


title: Blood_Day1_200400360005_F


title: C20.7350589.scRNA-seq


title: C18.7350589.scRNA-seq


title: C19.7350589.scRNA-seq


title: Blood_Day1_200400360005_K


title: C17.7350589.scRNA-seq


title: Blood_Day1_200400360009_A


title: Blood_Day1_200400360021_J


title: Blood_Day1_200400360022_J


title: Blood_Day1_200400280054_E


title: C16.7350589.scRNA-seq


title: Blood_Day1_200400280054_J


title: Blood_Day1_200400360015_E


title: Blood_Day1_200400360004_A


title: Blood_Day1_200400360009_G


title: Blood_Day1_200400360021_G


title: Blood_Day1_200400360003_K


title: Blood_Day1_200400360011_F


title: Blood_Day1_200400360003_H


title: Blood_Day1_200400360018_E


title: Blood_Day1_200400360007_I


title: C14.7350589.scRNA-seq


title: C13.7350589.scRNA-seq


title: Blood_Day1_200400360009_I


title: C12.7350589.scRNA-seq


title: C15.7350589.scRNA-seq


title: C11.7350589.scRNA-seq


title: C07.7350589.scRNA-seq


title: C10.7350589.scRNA-seq


title: C09.7350589.scRNA-seq


title: Blood_Day1_200400360014_C


title: C05.7350589.scRNA-seq


title: C08.7350589.scRNA-seq


title: Blood_Day1_200400360004_I


title: C06.7350589.scRNA-seq


title: C04.7350589.scRNA-seq


title: C03.7350589.scRNA-seq


title: Blood_Day1_200400360009_D


title: C02.7350589.scRNA-seq


title: Blood_Day1_200400360009_E


title: C01.7350589.scRNA-seq


title: Blood_Day1_200400360020_H


title: Blood_Day1_200400360007_B


title: Blood_Day1_200400360007_F


title: Blood_Day1_200400280054_D


title: Blood_Day1_200400360009_F


title: Blood_Day1_200400360004_K


title: Igf1r_Mutant3

city: Cincinnati

first: John

middle: M.

last: Snowball

state: OH

address: 3333 Burnet Ave

department: Pulmonary Research

institute: Cincinnati Childrens Hospital

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

source_name: Rosa-EGFP, Igf1r Flox/Flox, Gli1creER+ Lung Cells

extract_protocol:
Cell sorting was performed on MoFlo XDP ccell sorter.  RNA was isolated using Rneasy Mini plus kit.
NEDNext Ultra RNA Library Prep Kit
Sequencing was conducted on Illumina HiSeq 4000 to generate 150-bp pair-end reads.

treatment_protocol: Mutant and Control mice were given (Tamoxifen 100 ug/pup) at Day P0 and P1 before haverst and GFP Facs sorting at P6.

value: lung

value: Fibroblast Cells


title: Blood_Day1_200400360024_J


title: Blood_Day1_200400360020_K


title: Blood_Day1_200400360003_D


title: Blood_Day1_200400360002_F


title: Blood_Day1_200400360010_E


title: Blood_Day1_200400360015_H


title: Blood_Day1_200400360011_G


title: Blood_Day1_200400360005_A


title: B24.7350589.scRNA-seq

value: Cranial neural crest cells


title: Igf1r_Mutant2


title: B22.7350589.scRNA-seq


title: Igf1r_Mutant1


title: Blood_Day1_200400360014_F


title: B21.7350589.scRNA-seq


title: B20.7350589.scRNA-seq


title: Igf1r_Control1

source_name: Rosa-EGFP, Igf1r Flox/Wildtype, Gli1creER+ Lung Cells


title: B19.7350589.scRNA-seq


title: B18.7350589.scRNA-seq


title: B23.7350589.scRNA-seq


title: Igf1r_Control2


title: Blood_Day0_200400360010_J

value: day 0 (pre-vaccination)


title: frozen skin cells

city: Lincoln

first: Chi

last: Zhang

state: NE

address: 1901 Vine Street

institute: University of Nebraska - Lincoln

data_processing:
Cell Ranger pipeline version 4.0.0.
The single-cell RNA-seq reads were mapped using STAR aligner (v. 2.5.1b) against the reference transcriptome
Genome_build: Sscrofa11.1

organism: Sus scrofa

source_name: pig skin

extract_protocol:
fresh skin tissues were dissociated into single cells using the Miltenyi Biotec Whole Skin Dissociation kit and Gentle MACS Dissociator28. Single cells were frozen in 90% FBS+10% DMSO, stored in liquid nitrogen34,38. Cells were thawed, and dead cells were removed via FACS right before preparing libraries using the 10x Genomics Chromium technology. Alternatively, dead cells could be removed via MACS using the Miltenyi Dead Cell Remove Kit
Cells were suspended in DMEM-10% FBS. The density and viability of the cells were estimated using Countess II FL Automated Cell Counter (ThermoFisher) upon staining with trypan blue 0.2%.   For each replicate, about 8,000 cells were used as an input to generate RNA-seq libraries following the 10X Genomics Chromium Next GEM Single Cell 3′ kit V3 protocol without modification. Libraries were sequenced using Illumina technology

value: frozen

value: skin


title: Blood_Day0_200400360002_B


title: fresh skin cells


title: Blood_Day0_200400360015_J


title: Blood_Day0_200400360014_B


title: B17.7350589.scRNA-seq

value: 6 somite stage


title: B16.7350589.scRNA-seq


title: Blood_Day0_200400360008_E


title: B15.7350589.scRNA-seq


title: Blood_Day0_200400360005_B


title: Blood_Day0_200400360003_C


title: 12G

city: chapel hill

first: Seth

last: Weir

address: 115 mason farm rd

institute: UNC Chapel Hill

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on Genechip Mouse Gene 2.1 ST arrays. Arrays were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip Scanner 3000 7G.

data_processing: The data were analyzed with partek Genomics Suite version using RMA normalization method.

source_name: G-Smo medulloblastoma

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: pups raised frm birth to P15 then tumors harvested

extract_protocol: total RNA extracted using Qiagen kit (QIAGEN, cat#74104) according to the manufacturers protocol.

treatment_protocol: Mice were decapitated under anesthesia and medullblastomas were rapidly dissected free and snap frozen in a dry ice-ethanol bath. Frozen tisue was homogenized while frozen and processed for RNAextraction. Samples 1-12 no treatment, samples 13-24 10gy x-ray radiation 2 hr prior to harvesting tumors

value: freshly harvested tumor

value: G-Smo

tag: developmental status

value: 10gy x-ray radiation 2hr prior to harvesting tumor


title: Blood_Day0_200400360003_L


title: Blood_Day0_200400360010_C


title: Blood_Day0_200400360003_A


title: Blood_Day0_200400360024_E


title: Blood_Day0_200400360018_G


title: Blood_Day0_200400360021_E


title: Blood_Day0_200400360008_J


title: Blood_Day0_200400360008_C


title: Blood_Day0_200400360007_D


title: B14.7350589.scRNA-seq


title: B13.7350589.scRNA-seq


title: B11.7350589.scRNA-seq


title: B12.7350589.scRNA-seq


title: B10.7350589.scRNA-seq


title: SAS_rep3

city: Changsha

first: Nian

last: Liu

state: Hunan

address: Xiangya road 87#

department: Department of Dermatology

country: China

institute: Xiangya Hospital, Central South University

data_processing:
The raw data was checked by FastQC v
Clean reads were aligned to the Mus musculus genome using HISAT
The expression of the transcript was calculated by FPKM using  Bowtie2
Differentially expression transcripts were determined using DEGseq
Function and signaling pathway enrichment analysis using GO and KEGG database
Genome_build: RN6
Supplementary_files_format_and_content: Differential gene excel

source_name: B16F10 melanoma cells

extract_protocol:
B16F10 melanoma cells were incubated with various concentrations of SAS  or a vehicle control (DMSO<0.1%) for 24 hours, and total RNA was harvested using Tripure reagent
RNA libraries were prepared for sequencing using standard BGISEQ-500 protocols

value: B16F10 melanoma cells

value: Treated with 500μm SAS for 24 hours


title: SAS_rep2


title: SAS_rep1


title: B09.7350589.scRNA-seq


title: B08.7350589.scRNA-seq


title: Vehicle_rep3

value: Treated with 0.05% DMSO


title: B06.7350589.scRNA-seq


title: B07.7350589.scRNA-seq


title: Vehicle_rep2


title: Vehicle_rep1


title: 12M

source_name: M-Smo medulloblastoma

value: M-Smo


title: B05.7350589.scRNA-seq


title: 9G


title: WHK_CON2

city: Tianjin

first: Liu

last: Zhiqiang

address: 22 Qxiangtai Rd

institute: Tianjin Medical University

data_processing:
Basecalls performed using BGISEQ-500
SOAPnuke was used to get the "clean reads".
Mapping clean reads to hg19 whole genome using BWA.
Bowtie2 was used to get the mapping ratio.
Fragments Per Kilobase Million (FPKM) was calculated based on the RSEM.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include fpkm values for each Sample ...

growth_protocol: LP-1 cell was cultured in 1640 medium with 10% FBS.

extract_protocol:
RNA was harvested using Trizol reagent.
RNA libraries were prepared for sequencing using BGI protocols

treatment_protocol: Non-target control and knockdown HRP2 LP-1 cells by letivirus sgRNA

value: B lymphoblast

tag: tumor type

value: multiple myeloma

value: HRP2 knockdown


title: 8G


title: 11G


title: Blood_Day0_200400360010_K

value: Whole blood


title: 7G


title: 7M


title: Blood_Day0_200400360004_L


title: WHK_CON1


title: 10M


title: Blood_Day0_200400360003_E


title: Blood_Day0_200400360024_I


title: Blood_Day0_200400360005_E


title: Blood_Day0_200400360020_I


title: Blood_Day0_200400360005_L


title: Blood_Day0_200400360008_L


title: 8M


title: Blood_Day0_200400360014_A


title: 10G


title: 11M


title: Blood_Day0_200400360018_D


title: Patient_Two_E

city: Dunedin

first: Amber

last: Helliwell

address: 710 Cumberland Road

department: Biochemistry Department

country: New Zealand

institute: University of Otago

data_processing:
reads were adaptor trimmed using bismark that used a file of adaptor sequences and trimmed three bases back from any detected adaptor to delete the C invorporated and rejecting any reads that were trimmed to less than 10bp
reads were aligned to the hg19 genome using bismark with the following specifications: a tolerance for one non-bisulfite mismatch per read, the default minimum alignment score (L,O, -02), and with ignore - quals in order to calculate the mismatch penalty by considering the quality value at the mismatched position to be the highest possible
bam files generated by Bismark alignment were then processed using DMAP to compare control vs. patients with  the following specifications: Chi squared test on fragments 40-220bp in length, with the fragment requireing at lest 2 CpGs  to have 10 or more sequence reads. The differential methylation file was then annotated with protein coding gene information using the DMAP command identgeneloc. DMAPmatrix.csv file contains this data.
Genome_build: hg19
Supplementary_files_format_and_content: Individual .txt files for each sample containing C and T frequency per base and coverage. C012_Full, ME007_Full and ME016_Full are excel files that contain, for the control, patient one, and patient two respectively, information about the per fragment methylation data including, genomic location, gene feature information, CpG relative location and fragment size.

source_name: Peripheral Blood Mononuclear Cells

extract_protocol:
DNA was extracted from 200ul of PBMCs
MSPI digestion (purify), end repair (purify), A-tialing and adaptor ligation (purify), PCR amplification (purify), Gel size selection and gel extraction (purify)

tag: disease state

value: myalgic encephalomyelitis/chronic fatigue syndrome

tag: individual

tag: time point

value: E

value: Peripheral Blood Mononuclear Cells


title: 9M


title: Blood_Day0_200400360002_E

value: day 0 (pre-vaccination)


title: Blood_Day0_200400360007_J


title: Patient_Two_D

value: D


title: WV2_CON2

value: Non-target control


title: B04.7350589.scRNA-seq

tag: developmental stage

value: 6 somite stage

value: Cranial neural crest cells


title: Blood_Day0_200400360010_F


title: Blood_Day0_200400360004_B


title: Blood_Day0_200400360021_H


title: WV2_CON1


title: B03.7350589.scRNA-seq

tag: strain


title: B01.7350589.scRNA-seq

tag: cell type


title: Blood_Day0_200400360008_A


title: Blood_Day0_200400360002_I


title: Patient-derived organoid NCO 2

city: Berlin

first: Nils

last: Blüthgen

address: Chariteplatz 1

department: Institute of Pathology

country: Germany

institute: Charite Universitätsmedizin Berlin

description: single-cell RNA SLAM sequencing

data_processing:
raw reads were assigned and count matrices produced by cellranger, version 3.0.2, reference GRCh38
different samples were demultiplexed by SNP using cellsnp-lite --version and vireo 0.3.2, and additionally different conditions were demultiplexed using HTO tags in Seurat, using HTODemultiplex
new and old counts were called using a custom script that marks UMIs/transcripts as new whenever there is at least one T->C conversion that is not a common SNP
Genome_build: GRCh38
Supplementary_files_format_and_content: meta data: Meta data of the cells, one row per cell, contains information about cell type clusters, and signature scores. Comma separated values
Supplementary_files_format_and_content: total counts: total gene expression couts per cell
Supplementary_files_format_and_content: old counts: unlabeled (old) gene expression couts per cell
Supplementary_files_format_and_content: new counts: labeled (new) gene expression couts per cell

source_name: Colon

growth_protocol: organoids were grown in matrigel using defined medium

extract_protocol:
drop seq
10x genomics 3' v2
scRNA-seq, scSLAMSeq

treatment_protocol: organoids were treated with inhibitors or different media for 2 days, and labeled with 4SU 2h before harvesting

tag: tumor/normal

value: normal

tag: growth medium

value: EGF+WNT

tag: mutations in braf/kras

tag: perturbations


title: A24.7350589.scRNA-seq


title: Patient_Two_A

value: A


title: B02.7350589.scRNA-seq


title: A23.7350589.scRNA-seq


title: Patient_One_D


title: Patient_One_E


title: Patient-derived organoid P009T 3

description: single-cell RNA SLAM sequencing

value: tumor


title: Patient_Two_B

value: B


title: Blood_Day0_200400360003_F


title: Patient_One_C

value: C


title: A21.7350589.scRNA-seq


title: Patient-derived organoid P013T 2

description: single-cell RNA SLAM sequencing

value: EGF


title: Blood_Day0_200400360014_J


title: Patient_One_B


title: A20.7350589.scRNA-seq


title: Patient-derived organoid P013T 3

description: single-cell RNA SLAM sequencing


title: A22.7350589.scRNA-seq


title: A19.7350589.scRNA-seq


title: C012E

value: Control


title: Blood_Day0_200400360018_C

value: Whole blood


title: A18.7350589.scRNA-seq


title: Patient-derived organoid NCO 1

description: single-cell RNA SLAM sequencing


title: Patient-derived organoid (inhibitors) P009T 1

description: single-cell RNA SLAM sequencing

value: DMSO, BRAF,  EGFR, EGFR + BRAF, EGFR + MEK, MEK


title: C012D


title: Blood_Day0_200400360007_E


title: Blood_Day0_200400360021_F


title: A17.7350589.scRNA-seq


title: Patient-derived organoid (inhibitors) OT302

description: single-cell RNA SLAM sequencing


title: Blood_Day0_200400360018_L


title: Blood_Day0_200400360009_L


title: Patient-derived organoid (inhibitors) P013T 1

description: single-cell RNA SLAM sequencing


title: C012C


title: A16.7350589.scRNA-seq


title: Blood_Day0_200400360011_B


title: Patient-derived organoid (inhibitors) OT227

description: single-cell RNA SLAM sequencing


title: WT_p18_STAT5_rep2

city: Bethesda

first: Hye Kyung

last: Lee

state: MD

address: 8 CENTER DR RM 107

department: National Institute of Diabetes and Digestive and Kidney (NIDDK)

institute: National Institutes of Health (NIH)

description: STAT5A (Santa Cruz Biotechnology, sc-271542)

data_processing:
The fastq files were subjected to QC analyses using the FastQC tool (version 0.11.9) (https://www.bioinformatics.babraham.ac.uk/projects/fastqc/). Quality filtering and alignment of the raw reads was done using Trimmomatic27 (version 0.36) and Bowtie28 (version 1.2.2) and Samtools29 (version 1.8), with the parameter ‘-m 1’ to keep only uniquely mapped reads, using the reference genome mm10. Homer30 (version 4.8.2) software was applied to generate bedGraph files, seperately. Integrative Genomics Viewer31 (version 2.5.3) was used for visualization.  (Langmead et al., Nature methods, 2012)  with the parameter of -m 1 to retrieve only uniquely mapped reads, and Picard Tools (Broad Institute. Picard, http://broadinstitute.github.io/picard/.) to remove duplicates. Homer software (Heinz et al., Mol. Cell, 2010) was applied  for the generation of bedGraph files.
Genome_build: mm10
Supplementary_files_format_and_content: bedgraph of ChIP-seq

source_name: Mammary gland

growth_protocol: Mouse mammary gland tissues were harvested at day one and ten of lactation (L1 and L10).

extract_protocol:
Chromatin was fixed with formaldehyde (1% final concentration) for 15 min at room temperature, and then quenched with glycine (0.125 M final concentration). Samples were processed as previously described. The following antibodies were used for ChIP-seq: H3K27ac (Abcam, ab4729), RNA polymerase II (Abcam, ab5408), H3K4me1 (Active Motif, 39297) and H3K4me3 (Millipore, 07-473). Libraries for next-generation sequencing were prepared and sequenced with a HiSeq 3000 instrument (Illumina). Libraries for sequencing were prepared using standard Illumina protocols.
Libraries for sequencing were prepared using standard Illumina protocols.

value: Pregnancy day 18

value: wild-type


title: Patient-derived organoid P009T 2

description: single-cell RNA SLAM sequencing


title: A15.7350589.scRNA-seq


title: C012B

value: Peripheral Blood Mononuclear Cells


title: WT_p18_STAT5_rep1


title: WT_p18_PolII_rep1

description: RNA polymerase II (Abcam, ab5408)


title: Patient-derived organoid (inhibitors) C2-019

description: single-cell RNA SLAM sequencing


title: A14.7350589.scRNA-seq


title: C012A


title: Patient-derived organoid (inhibitors) B2-040

description: single-cell RNA SLAM sequencing


title: Blood_Day0_200400360024_A

value: day 0 (pre-vaccination)


title: WT_p18_H3K27ac_rep2

description: H3K27ac (Abcam, ab4729)


title: Patient026 tumor

description: single-cell RNA sequencing

data_processing:
raw reads were assigned and count matrices produced by cellranger, version 3.0.2, reference GRCh38
raw data was loaded, merged and filtered in R using Seurat 2
Genome_build: GRCh38
Supplementary_files_format_and_content: meta data (meta_data.tsv.gz): Meta data of the cells, one row per cell, contains information about cell type clusters, and signature scores. Tab delimited files
Supplementary_files_format_and_content: other files (p0XXt/n.tsv.gz): contain the raw expression counts for all cells of a sample. Each row is a gene, each column is a cell. Cell ids correspond to the cell ids in the meta data table.

source_name: C18.9 (Colon)

extract_protocol:
drop seq
10x genomics 3' v2

treatment_protocol: surgical resection

tag: morphology (icdo3)

value: M8140/3 (Adenokarzinom o.n.A.)

tag: Stage

value: pT1 pN0 G2

tag: immunohistology

value: MSI

tag: grade


title: Blood_Day0_200400360011_J

tag: subject

tag: time

tag: tissue


title: A13.7350589.scRNA-seq

source_name: Cranial neural crest cells

value: 6 somite stage

value: Cranial neural crest cells


title: Blood_Day0_200400360009_J


title: WT_p18_H3K27ac_rep1

description: H3K27ac (Abcam, ab4729)

tag: genotype


title: A12.7350589.scRNA-seq


title: Patient025 tumor

description: single-cell RNA sequencing

value: pT3 pN0 G2

value: MSS


title: WT_p18_GR_rep2

description: GR (Thermo Fisher Scientific, PA1-511A)


title: A10.7350589.scRNA-seq


title: Patient025 normal

description: single-cell RNA sequencing


title: A11.7350589.scRNA-seq


title: CM-9

city: McAllen

first: Satish

last: Kumar

state: Texas

address: 5300 North L Street (MBMRF-2.219)

department: Division of Human Genetics & South Texas Diabetes and Obesity Institute, UTRGV School of Medicine

institute: University of Texas Rio Grande Valley

description: iPSCs & iPSC-CMs_mRNA_Data.txt

data_processing:
Raw fastq sequence files were generated and demultiplexed using Illumina bcl2fastq software (Illumina, Inc., San Diego, CA, USA).
After pre-alignment QCs, sequences were aligned to human genome assembly GRCh38 (hg38) and mapped to RefSeq transcripts using StrandNGS software v3.4 (Strand Life Sciences Pvt. Ltd., Bangalore, India).
The aligned reads were filtered based on read quality metrics and only high-quality aligned sequencing reads were retained and quantified using NGS software v3.4 (Strand Life Sciences Pvt. Ltd., Bangalore, India).
The gene expression values as raw counts of sequencing reads were obtained and log2 transformation and ‘DESeq’ normalization was applied.
Genome_build: hg38
Supplementary_files_format_and_content: Tab-delimited text file of raw sequencing read counts and log2 transformed and DESeq normalized values formatted as genes-vs-samples matrix table .

source_name: Cardiomyocytes (CMs)

growth_protocol: iPSCs cultured in feeder-free conditions until 70% to 80% confluent were harvested using Gibco StemPro Accutase and then seeded on GeltrexTM (both from Thermo Fisher Scientific, Waltham, MA, USA) coated tissue culture plates at a density of ~4 x 104 cells/cm2 in mTeSR-1 medium (Stem Cell Technologies Inc., Cambridge, MA, USA) supplemented with 10 µM ROCK inhibitor Y27632 (ATCC, Manassas, VA, USA). The mTeSR-1 medium was changed daily for the following two days or until the culture reached 50% to 70% confluency. On day 4, when iPSC cultures were 50% to 70% confluent, medium was switched to Gibco Cardiomyocytes Differentiation Medium A. On day 6, the medium was replaced with Gibco Cardiomyocytes Differentiation Medium B and from day 8 onwards, the differentiating cells were maintained in Gibco Cardiomyocyte Maintenance Medium until day 14, medium was changed every other day (the Gibco Cardiomyocytes Differentiation -Medium A, -Medium B and the Gibco Cardiomyocyte Maintenance Medium were all part of the Gibco PSC Cardiomyocyte Differentiation Kit). On day 14, the twelve-iPSC differentiated spontaneously contracting CM lines were harvested for characterization and total RNA extraction.

extract_protocol:
Total RNA was extracted from snap frozen cell pellets (~3-5 x 106 cells) of twelve well characterized, validated iPSC lines and their differentiated CM lines using commercially available RNeasy Mini Kit (Qiagen, Germantown, MD, USA) and the manufacturer protocol. RNA quality and quantity were assessed using a NanoDrop 2000 Spectrophotometer (Thermo Fisher Scientific,Waltham, MA, USA) and an Agilent 2200 TapeStation system (Agilent, Santa Clara, CA, USA).
1µg of total RNA per sample was used to prepare mRNA sequencing libraries. The sequencing libraries were prepared using Illumina TruSeq RNA sample preparation kit v2 and following manufacturer protocol.

tag: sample type

value: CMs differentiated from validated iPSCs


title: Patient021 tumor

description: single-cell RNA sequencing

source_name: C18.6 - Colon descendens


title: CM-11

description: iPSCs & iPSC-CMs_mRNA_Data.txt


title: A09.7350589.scRNA-seq


title: WT_L10_NFIB_rep2

description: NFIB (Sigma-Aldrich, HPA003956)

value: Lactation day 10


title: WT_p18_GR_rep1

description: GR (Thermo Fisher Scientific, PA1-511A)


title: A08.7350589.scRNA-seq


title: Patient021 normal

description: single-cell RNA sequencing


title: CM-8

description: iPSCs & iPSC-CMs_mRNA_Data.txt


title: CM-12

description: iPSCs & iPSC-CMs_mRNA_Data.txt


title: CM-7

description: iPSCs & iPSC-CMs_mRNA_Data.txt


title: WT_L10_NFIB_rep1

description: NFIB (Sigma-Aldrich, HPA003956)


title: Patient020 tumor

description: single-cell RNA sequencing


title: A07.7350589.scRNA-seq


title: CM-6

description: iPSCs & iPSC-CMs_mRNA_Data.txt


title: CM-5

description: iPSCs & iPSC-CMs_mRNA_Data.txt


title: A06.7350589.scRNA-seq


title: Patient017 tumor

description: single-cell RNA sequencing

source_name: C18.2 (Colon ascendens)


title: CM-4

description: iPSCs & iPSC-CMs_mRNA_Data.txt


title: WT_L10_H3K4me1_rep3

description: H3K4me1 (Active Motif, 39297)


title: A05.7350589.scRNA-seq


title: Patient017 normal

description: single-cell RNA sequencing


title: A04.7350589.scRNA-seq


title: WT_L10_H3K4me1_rep2

description: H3K4me1 (Active Motif, 39297)


title: WT_L10_H3K4me3_rep2

description: H3K4me3 (Millipore, 07-473)


title: Patient016 tumor

description: single-cell RNA sequencing

source_name: C20.9 (Rektum o.n.A.)


title: WT_L10_H3K4me3_rep1

description: H3K4me3 (Millipore, 07-473)


title: CM-2

description: iPSCs & iPSC-CMs_mRNA_Data.txt


title: A03.7350589.scRNA-seq


title: Patient016 normal

description: single-cell RNA sequencing


title: CM-10

description: iPSCs & iPSC-CMs_mRNA_Data.txt


title: A02.7350589.scRNA-seq


title: CM-1

description: iPSCs & iPSC-CMs_mRNA_Data.txt


title: Patient020 normal

description: single-cell RNA sequencing


title: A01.7350589.scRNA-seq


title: WT_L1_PolII_rep2

description: RNA polymerase II (Abcam, ab5408)

value: Lactation day 1


title: iPSC-12

description: iPSCs & iPSC-CMs_mRNA_Data.txt

source_name: induced pluripotent stem cells (iPSCs)

value: validated iPSCs reprogrammed from cryopreserved lymphoblastoid cell line


title: Patient014 tumor

description: single-cell RNA sequencing


title: WT_L10_H3K4me1_rep1

description: H3K4me1 (Active Motif, 39297)


title: iPSC-11

description: iPSCs & iPSC-CMs_mRNA_Data.txt


title: WT_L1_PolII_rep1

description: RNA polymerase II (Abcam, ab5408)


title: Patient014 normal

description: single-cell RNA sequencing


title: EV3

city: Groningen

first: Leonid

last: Bystrykh

state: Groningen

address: A. Deusinglaan 1

department: European Research Institute for the Biology of Ageing - ERIBA

country: Netherlands

institute: University Medical Center Groningen

description: Sample name: 5

data_processing:
After demultiplexing, run quality was evaluated using FastQC 0.11.8
FASTQ files were merged for each sample
FASTQ files were aligned to the reference genome using STAR aligner 020201 with standard arguments
In order to determine the strandness of the reads, piccard CollectRnaSeqMetrics 2.18.0 was used
Differently expressed analysis was done using edgeR 3.24.3
Genome_build: mm10 M21
Supplementary_files_format_and_content: Normalized read counts with differential expression and gene name annotation

source_name: Hematopoietic Stem Cells

extract_protocol:
2000 cells were directly sorted into NEBNext cell lysis buffer supplemented with RNAse inhibitor and snap frozen.
Library prep was performed with NEBNext single cell/low input RNA library prep kit for Illumina according to manufacturer's protocol.

value: miR-125a expression, endogenous

value: 12weeks after TX

value: bone marrow cells (lineage-Sca+)


title: CM-3

description: iPSCs & iPSC-CMs_mRNA_Data.txt


title: Patient013 normal

description: single-cell RNA sequencing

value: pT4a pN1b (3/18) pM1a G2 R0 L1 V1 Pn0


title: Patient013 tumor

description: single-cell RNA sequencing


title: iPSC-9

description: iPSCs & iPSC-CMs_mRNA_Data.txt


title: iPSC-10

description: iPSCs & iPSC-CMs_mRNA_Data.txt


title: delCsn1s2b-P_L10_STAT5_rep1


title: delS1-4_L1_NFIB_rep1

description: NFIB (Sigma-Aldrich, HPA003956)


title: Patient012 tumor

description: single-cell RNA sequencing

source_name: C18.4 (Colon transversum)

value: pTis pN0(0/26) G2 L0 V0 Pn0 R0


title: 125a2

description: Sample name: 4

value: miR-125a expression, overexpression


title: Patient012 normal

description: single-cell RNA sequencing

value: M8140/3 (Adenokarzinom o.n.A.)


title: 125a1

description: Sample name: 3


title: delCsn1s2b-P_L10_PolII_rep1

description: RNA polymerase II (Abcam, ab5408)


title: delS1-4_L1_NFIB_rep2

description: NFIB (Sigma-Aldrich, HPA003956)


title: delCsn1s2b-P_L10_NFIB_rep1

description: NFIB (Sigma-Aldrich, HPA003956)


title: EV2

description: Sample name: 2


title: iPSC-8

description: iPSCs & iPSC-CMs_mRNA_Data.txt


title: Patient009 tumor 1

description: single-cell RNA sequencing

source_name: C18.7 (Colon sigmoideum)


title: delCsn1s2b-P_L10_H3K27ac_rep1

description: H3K27ac (Abcam, ab4729)


title: EV1

description: Sample name: 1


title: Patient009 normal 2

description: single-cell RNA sequencing


title: Patient009 tumor 2

description: single-cell RNA sequencing


title: 125a3

description: Sample name: 6


title: delCsn1s2b-P_L10_H3K4me3_rep1

description: H3K4me3 (Millipore, 07-473)


title: iPSC-6

description: iPSCs & iPSC-CMs_mRNA_Data.txt


title: delCsn1s2b-P_L10_H3K4me1_rep1

description: H3K4me1 (Active Motif, 39297)


title: iPSC-4

description: iPSCs & iPSC-CMs_mRNA_Data.txt


title: Patient009 normal 1

description: single-cell RNA sequencing


title: Immunotherapy_nonResponder15

city: Gang-nam gu

first: Sehoon

state: Seoun

address: Ilwon

department: Division of Hematology-Oncology, Department of Medicine

country: South Korea

institute: SAMSUNG MEDICAL CENTER

data_processing:
STAR version 2.4.0
RSEM version 1.2.18
Genome_build: hg19
Supplementary_files_format_and_content: expression txt file

source_name: Lung cancer

extract_protocol:
The library was prepared following the manufacturer’s instructions using the TruSeq RNA Access Library Prep Kit (Illumina, USA).
RNA libraries were prepared for sequencing using standard Illumina protocols

value: lung

tag: treatment

value: pre-treatment

tag: disease state

value: advanced stage


title: Patient008 tumor

description: single-cell RNA sequencing

source_name: C18.0 (Coecum)


title: Immunotherapy_nonResponder14


title: iPSC-3

description: iPSCs & iPSC-CMs_mRNA_Data.txt


title: Immunotherapy_nonResponder13


title: delCsn1s2b-P_L10_GR_rep1

description: GR (Thermo Fisher Scientific, PA1-511A)

tag: strain


title: iPSC-7

description: iPSCs & iPSC-CMs_mRNA_Data.txt


title: iPSC-2

description: iPSCs & iPSC-CMs_mRNA_Data.txt


title: Patient008 normal

description: single-cell RNA sequencing


title: delCsn1s2b-IE_L10_STAT5_rep2


title: delCsn1s2b-IE_L10_STAT5_rep1


title: Immunotherapy_nonResponder12


title: Immunotherapy_nonResponder11


title: iPSC-1

description: iPSCs & iPSC-CMs_mRNA_Data.txt


title: iPSC-5

description: iPSCs & iPSC-CMs_mRNA_Data.txt


title: Patient007 tumor

description: single-cell RNA sequencing


title: delCsn1s2b-IE_L10_PolII_rep1

description: RNA polymerase II (Abcam, ab5408)


title: Patient007 normal

description: single-cell RNA sequencing


title: delCsn1s2b-IE_L10_PolII_rep2

description: RNA polymerase II (Abcam, ab5408)


title: Immunotherapy_nonResponder9


title: Immunotherapy_nonResponder10


title: Immunotherapy_nonResponder8


title: delCsn1s2b-IE_L10_NFIB_rep1

description: NFIB (Sigma-Aldrich, HPA003956)


title: Immunotherapy_nonResponder6


title: Immunotherapy_nonResponder7


title: Ctrl_LHC-17_IGF0005582

city: London

first: Marina

last: Botto

address: Du Cane Road

institute: Imperial College London

data_processing:
RawData production and quality check: Illumina bcl2fastq software used for basecalling and using FastQC (v.0.11.2)
Clean read :Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence using trimmomatic(v.0.36)
Alignment tools and ref genome and annotation using tophat2(v.2.1.0: -b2-sensitive,--library-type fr-firststrand )
Genome_build: GRCh38.primary_assembly.genome.fa
Genome_build: gencode.v25.annotation.gtf
Quality check after alignment using four tools:using FastQC (v.0.11.2),samtools(v.1.2),picard(v.2.6.0) and rseqc(2.6.4)  for mapping quality or rate, duplicates metric,read distribution, gene body coverage and GC content and rRNA contamination
Tools and parameter for get raw counting of genes usings HT-Seq-count (Anders et al. 201, v 0.6.1 ) with strict "-m intersection-strict” mode
Tools and parameter for diff exp and platform,using DESeq2 (Love et al. 2014,v. 1.14.1)
Threshold selection for significant gene exp lists,using fold change at 1.5 times and below 1 % FDR level
Supplementary_files_format_and_content: text file of count.table of each sample

source_name: Ctrl_Peripheral blood

extract_protocol:
Total RNA was extracted using RNeasy Plus Mini kits (Qiagen)  based on the manufacturer’s instruction. Total RNA quality and concentration was analysed using a NanoDrop 1000 spectrophotometer (ThermoFisher Scientific) and verified using Qubit meter (Invitrogen). All total RNA samples were subjected to level of degradation measurement using Agilent 2100 Bioanalyzer (Agilent Tech Inc.) and RIN values for all samples were ≥ 9.0.
RNA libraries were prepared for sequencing using standard Illumina protocols: TruSeq Stranded mRNA HT kits (Catlogue No:RS-122-2103)

tag: disease status

value: Ctrl

value: Blood

tag: cell type

value: CD 8 T cell


title: Ctrl_LHC-15_IGF0005580


title: Ctrl_LHC-16_IGF0005581


title: WT2_scRNAseq

city: Chicago

first: Raghavendra

middle: G

last: Mirmira

state: IL

address: 900 E. 57th Street

department: Medicine

institute: University of Chicago

data_processing:
CellRanger 3.0.2 was utilized to process the raw sequence data generated. The filtered gene-cell barcode matrices generated by CellRanger were used for further analysis.
Seurat 3.1.0 was used for data normalization, data scaling, graph-based clustering, cluster marker genes idenfification, and integrative analysis of multiple samples.
muscat was used for differential gene expression analysis between conditions within a cell cluster of the intergrative analysis
Genome_build: mm10
Supplementary_files_format_and_content: HDF5 file of filtered gene-barcode matrices

source_name: Cells from pancreatic islets

extract_protocol:
Single cell 3’ RNA-seq experiment was conducted using the Chromium single cell system (10x Genomics, Inc). Appropriate number of cells were loaded on a multiple-channel micro-fluidics chip of the Chromium Single Cell Instrument (10x Genomics). Single cell gel beads in emulsion containing barcoded oligonucleotides and reverse transcriptase reagents were generated with the v3 single cell reagent kit (10X Genomics). Following cell capture and cell lysis, cDNA was synthesized and amplified. Illumina sequencing library was then prepared with the amplified cDNA.
10X genomics 3' RNA-seq V3 single cell reagent kit

tag: age

value: 8 weeks old


title: WT1_scRNAseq


title: Ctrl_LHC-13_IGF0005577


title: Immunotherapy_nonResponder5


title: delCsn1s2b-IE_L10_H3K27ac_rep1

description: H3K27ac (Abcam, ab4729)

value: Lactation day 10


title: Ctrl_LHC-12_IGF0005576


title: delCsn1s2b-IE_L10_GR_rep2

description: GR (Thermo Fisher Scientific, PA1-511A)


title: delCsn1s2b-IE_L10_NFIB_rep2

description: NFIB (Sigma-Aldrich, HPA003956)


title: delCsn1s2b-IE_L10_GR_rep1

description: GR (Thermo Fisher Scientific, PA1-511A)


title: KO-DTX.3

city: St. Louis

first: Katherine

middle: N.

last: Weilbaecher

state: MO

address: 660 S. Euclid Ave., Box 8069

institute: Washington University School of Medicine

description: Integrin β3 kockout 4T1 cells treated with 10nM docetaxel, rep 3

data_processing:
Basecalls and demultiplexing were performed with Illumina’s bcl2fastq software and a custom python demultiplexing program with a maximum of one mismatch in the indexing read
RNA-Seq reads were then aligned to the Ensembl release 76 primary assembly with STAR version 2.5.1a
Gene counts were derived from the number of uniquely aligned unambiguous reads by Subread:featureCount version 1.4.6-p5
Genome_build: Ensembl 76 (Mus musculus)
Supplementary_files_format_and_content: 4T1_gene_counts.txt

source_name: 4T1 murine breast cancer cells

growth_protocol: 4T1 β3WT and β3KO cells were cultured in biological triplicate on poly-L-lysine-coated 6-well petri dishes in DMEM (10% FBS, 1% pen-strep)

extract_protocol:
Cells were lysed and RNA extracted using the Rneasy Plus Mini Kit according to manufacturer's directions.
Library preparation was performed with 1ug of total RNA. Ribosomal RNA was removed by an RNase-H method using RiboErase kits (Kapa Biosystems). mRNA was then fragmented in reverse transcriptase buffer and heated to 94 degrees for 8 minutes. mRNA was reverse transcribed to yield cDNA using SuperScript III RT enzyme (Life Technologies, per manufacturer’s instructions) and random hexamers. A second strand reaction was performed to yield ds-cDNA. cDNA was blunt ended, had an A base added to the 3’ ends, and then had Illumina sequencing adapters ligated to the ends. Ligated fragments were then amplified for 12 cycles using primers incorporating unique dual index tags. Fragments were sequenced on an Illumina NovaSeq 6000 using paired end reads extending 150 bases.

treatment_protocol: Cells were cultured for 24hr in the presence of either DMSO or 10nM docetaxel, then given a 48hr drug-free recovery period in fresh media prior to harvest.

value: BALB/c

value: 4T1 murine breast cancer (triple-negative)

value: integrin beta 3 knockout

value: 10nM docetaxel 24hr


title: KO5_scRNAseq

value: NOD.Alox15fl/fl Pdx1PB-CreERTM or deltaislets


title: KO-DTX.2

description: Integrin β3 kockout 4T1 cells treated with 10nM docetaxel, rep 2


title: Immunotherapy_nonResponder3


title: Ctrl_LHC-9_IGF0005575


title: KO4_scRNAseq


title: KO-DTX.1

description: Integrin β3 kockout 4T1 cells treated with 10nM docetaxel, rep 1


title: KO-DMSO.3

description: Integrin β3 kockout 4T1 cells treated with DMSO, rep 3

value: DMSO 24hr


title: delCsn1s2b-IE_L1_STAT5_rep2

value: Lactation day 1


title: Immunotherapy_nonResponder1


title: Ctrl_LHC-8_IGF0005574


title: Ctrl_LHC-14_IGF0005579


title: Ctrl_LHC-6_IGF0005572


title: delCsn1s2b-IE_L1_STAT5_rep1


title: Immunotherapy_Responder6


title: Immunotherapy_nonResponder4


title: Ctrl_LHC-18_IGF0005583


title: delCsn1s2b-IE_L1_PolII_rep1

description: RNA polymerase II (Abcam, ab5408)


title: Ctrl_LHC-7_IGF0005573


title: KO-DMSO.2

description: Integrin β3 kockout 4T1 cells treated with DMSO, rep 2


title: Ctrl_LHC-5_IGF0005571


title: WT-DTX.3

description: Integrin β3 wild-type 4T1 cells treated with 10nM docetaxel, rep 3

value: integrin beta 3 wild-type


title: Immunotherapy_Responder7


title: delCsn1s2b-IE_L10_H3K27ac_rep2

description: H3K27ac (Abcam, ab4729)


title: delCsn1s2b-IE_L1_NFIB_rep1

description: NFIB (Sigma-Aldrich, HPA003956)


title: delCsn1s2b-DE-S2-S3_L10_STAT5_rep2


title: WT-DTX.1

description: Integrin β3 wild-type 4T1 cells treated with 10nM docetaxel, rep 1


title: Ctrl_LHC-1_IGF0005569


title: Ctrl_LHC-4_IGF0005570


title: delCsn1s2b-IE_L1_H3K27ac_rep1

description: H3K27ac (Abcam, ab4729)


title: SLE less active_CDR-64_IGF0005568

source_name: SLE less active_Peripheral blood

value: SLE Less Active


title: Immunotherapy_nonResponder2

value: lung


title: Immunotherapy_Responder4

value: pre-treatment


title: delCsn1s2b-DE-S2-S3_L10_STAT5_rep1

source_name: Mammary gland


title: Immunotherapy_Responder3

value: advanced stage


title: Immunotherapy_Responder5


title: Immunotherapy_Responder2


title: SLE less active_CDR-61_IGF0005567


title: KO-DMSO.1

description: Integrin β3 kockout 4T1 cells treated with DMSO, rep 1


title: WT-DMSO.1


title: delCsn1s2b-DE-S2-S3_L10_PolII_rep1

description: RNA polymerase II (Abcam, ab5408)


title: WT-DMSO.2

description: Integrin β3 wild-type 4T1 cells treated with DMSO, rep 2


title: SLE less active_CDR-57_IGF0005565


title: Immunotherapy_Responder1


title: SLE less active_CDR-59_IGF0005566


title: WT 4VChP from E18.5 - Input

city: Shanghai

first: Feizhen

last: Wu

state: Shanghai

address: Zhangheng Road 825, Pudong

department: Intelligent Medicine Institute

institute: Fudan Univ, Shanghai, China

data_processing:
Raw reads were aligned to mm9 genome using bowtie(v1.2.3), producing bam file to save mapped reads. The mm9 genome was obtained from UCSC.
The bam file was converted into BED file;
remove PCR-duplicated reads;
the mapped reads were extended 300bp from 5' to 3'-end;
Genome_build: mm9
Supplementary_files_format_and_content: BED format

source_name: 4th ventricle choroid plexus

extract_protocol:
Tissue lysates were cross-linked, sonicated and isolated with antibody.
Libraries were prepared according to Illumina's instructions accompanying the NEBNext DNA library preparation reagents (E6000).

tag: chip antibody

value: none (input)

value: wild type

value: 4th ventricle choroid plexus


title: delCsn1s2b-DE-S2-S3_L10_NFIB_rep2

description: NFIB (Sigma-Aldrich, HPA003956)


title: WT-DTX.2

description: Integrin β3 wild-type 4T1 cells treated with 10nM docetaxel, rep 2


title: WT 4VChP from E18.5 - Meis1 ChIP

value: Meis1 (abcam 19867)


title: IAOM3_14D

city: Guangzhou

first: Yihuang

last: Lin

state: Guangdong

address: No.1838 North of Guangzhou Avenue

department: Orthopaedics

institute: Nanfang Hospital, Southern Medical University

data_processing:
Raw data  of fastq format were firstly processed through in-house perl scripts. In this step, clean data (clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data. At the same time, Q20, Q30 and GC content the clean data were calculated. All the downstream analyses were based on the clean data with high quality.
Index of the reference genome was built using Hisat2 v2.0.5 and paired-end clean reads were aligned to the reference genome using Hisat2 v2.0.5.
The featureCounts v1.5.0-p3 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene.
Genome_build: mm10
Supplementary_files_format_and_content: Excel files include read counts and FPKM values for each gene and sample

source_name: Bone tissue

extract_protocol:
The right femur was collected and pulverized in liquid nitrogen and total RNA was extracted by TRIzol. A total amount of 1 µg RNA per sample was used as input material for the RNA sample preparations.
Sequencing libraries were generated using NEBNext Ultra RNA Library Prep Kit for Illumina (NEB, USA) following manufacturer’s protocols and index codes were added to attribute sequences for each sample. PCR products were purified using AMPure XP system (Beckman Coulter, USA) and library quality was assessed on the Agilent Bioanalyzer 2100 system. The clustering of the index-coded samples was performed on a cBot Cluster Generation System using TruSeq PE Cluster Kit v3-cBot-HS (Illumia) according to the manufacturer’s instructions. After cluster generation, the library preparations were sequenced on an Illumina sequencing platform and 150 bp paired-end reads were generated.

treatment_protocol: Prior to surgery, mice were anesthetized by intraperitoneal injection of tribromoethanol (125 mg/kg). After the right hind femur was shaved followed by disinfection with iodine, a 5 mm incision was made on the dorsal side of the femur. After the femoral mid-shaft was exposed by blunt separation of the muscles, a canal was drilled by a 27-gauge syringe needle with care not to penetrate the contralateral cortex of the femur. Next, a 2 mm sterile stainless pin (0.3 mm in diameter) was inserted into the bone marrow cavity through the canal. Finally, 2 μl S. aureus solution at 1 × 10e6 CFU/ml was slowly injected into the bone marrow cavity using a micro-syringe for IAOM mice while an equal volume of sterile PBS for the controls. The hole was then sealed with bone wax and the incision was closed with a 5-0 suture. Right femurs were collected on days 3 and 14  for RNA-seq.

value: IAOM

value: Femur

value: S. aureus

tag: days

value: 14 days post-operation


title: SLE less active_CDR-56_IGF0005564

value: Blood

value: CD 8 T cell


title: delCsn1s2b-DE-S2-S3_L10_NFIB_rep1

description: NFIB (Sigma-Aldrich, HPA003956)

value: Lactation day 10


title: WT-DMSO.3

description: Integrin β3 wild-type 4T1 cells treated with DMSO, rep 3

value: BALB/c

value: 4T1 murine breast cancer (triple-negative)

value: DMSO 24hr


title: IAOM1_14D


title: delCsn1s2b-DE-S2-S3_L10_PolII_rep2

description: RNA polymerase II (Abcam, ab5408)


title: SLE less active_CDR-55_IGF0005563

value: SLE Less Active


title: delCsn1s2b-DE-S2-S3_L10_H3K27ac_rep2

description: H3K27ac (Abcam, ab4729)


title: SLE less active_CDR-54_IGF0005562


title: SLE less active_CDR-53_IGF0005561


title: LTS group

city: Wuhan

last: Feng

state: Hubei

address: 13 Hangkong Road, Hankou

department: School of Basic Medicine

institute: Huazhong University of Science and Technology

data_processing:
Cell Ranger, the official analysis software of 10X, was used for cell typing and differential analysis, and then functional enrichment of these differential genes was performed to identify the functional characteristics of the subpopulations.
Genome_build: mm10
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: Brain orthotropic G422-glioma

extract_protocol:
Brains were harvested at day 7 and  homogenized using enzymatic (1.5 mg/mL collagenase IV,  200 U/mL DNase I, HBSS with calcium and magnesium) and  mechanical tissue disaggregation.The solution was filtered twice over a 40 μm nylon filter and centrifuged. The cells were resuspended in 5 ml 70% standard isotonic percoll (SIP, GE Healthcare)  diluted in 1× Hanks’ buffered salt solution and gently overlaid with 5 ml of 37%  SIP, followed by a 5 ml layer of 30% SIP, forming a three-layered density gradient  (centrifuged at 800g, 4 °C, 30 min without acceleration/braking). The 70/37%  interphase containing immune cells was collected.
RNA libraries were prepared with chromium single cell 3' Reagent v3 Kits according to the manufacturer's protocol.

value: orthotropic G422-glioma tissue cells

value: Kunming

tag: group

value: LTS

value: treatment

tag: cell line


title: delCsn1s2b-DE-S2-S3_L10_H3K27ac_rep1

description: H3K27ac (Abcam, ab4729)


title: delCsn1s2b-DE-S2-S3_L10_GR_rep1

description: GR (Thermo Fisher Scientific, PA1-511A)


title: Control group

value: control

value: untreated


title: Ctrl2_14D

value: PBS


title: SLE less active_CDR-52_IGF0005560


title: delCsn1s2b-DE-S2-S3_L10_GR_rep2

description: GR (Thermo Fisher Scientific, PA1-511A)


title: Pdpk1 KO Treg, rep_4

city: Jersey City

first: Thomas

last: Postler

address: 95 Greene Street 5-018

institute: International AIDS Vaccine Initiative

data_processing:
Clipping and trimming with Trimmomatic v0.39
Read alignment with STAR v2.7.6a
Convert SAM files to coordinate-sorted BAM files with SAMtools v1.11
Count aligned reads with featureCounts in Subread v2.0.1
Analysis with DESeq2 v1.21
Genome_build: GRCm38.102
Supplementary_files_format_and_content: tab-separated-value text file with DESeq2-normalized gene counts

source_name: CD4+ YFP+ Treg from spleen and peripheral lymph nodes

extract_protocol:
RNA was extracted by RNeasy Plus Micro Kit(Qiagen) according to protocol.
Library construction was done using NEBNext Ultra™ II RNA Library Prep Kit for Illumina according to the protocol

tag: mouse strain

tag: mouse genotype

value: Foxp3 YFP-Cre/+ Pdpk1 FL/FL


title: Pdpk1 KO Treg, rep_2


title: delCsn1s2b-DE-S2_L10_STAT5_rep2


title: Ctrl1_14D

value: Femur


title: IAOM3_3D

value: IAOM

value: S. aureus

value: 3 days post-operation


title: Pdpk1 KO Treg, rep_3


title: SLE less active_CDR-51_IGF0005559

value: Blood

value: CD 8 T cell


title: delCsn1s2b-DE-S2_L10_STAT5_rep1

value: Lactation day 10


title: SLE less active_CDR-50_IGF0005558


title: IAOM2_14D

value: 14 days post-operation


title: Ctrl3_14D


title: Pdpk1 KO Treg, rep_1


title: IAOM2_3D


title: delCsn1s2b-DE-S2_L10_PolII_rep2

description: RNA polymerase II (Abcam, ab5408)


title: WT Treg, rep_4

value: Foxp3 YFP-Cre/+ Pdpk1 +/+


title: WT Treg, rep_2


title: WT Treg, rep_1


title: Ctrl3_3D


title: Ctrl2_3D


title: Ctrl1_3D


title: IAOM1_3D


title: WT Treg, rep_3


title: delCsn1s2b-DE-S2_L10_PolII_rep1

description: RNA polymerase II (Abcam, ab5408)


title: delCsn1s2b-DE-S2_L10_NFIB_rep2

description: NFIB (Sigma-Aldrich, HPA003956)


title: SLE less active_CDR-45_IGF0005555

value: SLE Less Active


title: SLE less active_CDR-48_IGF0005557


title: SLE less active_CDR-37_IGF0005553


title: SLE less active_CDR-23_IGF0005551


title: SLE active_CDR-65_IGF0005548

source_name: SLE active_Peripheral blood

value: SLE Active


title: SLE active_CDR-67_IGF0005550


title: SLE less active_CDR-29_IGF0005552


title: SLE less active_CDR-46_IGF0005556


title: SLE less active_CDR-41_IGF0005554


title: SLE active_CDR-63_IGF0005547


title: delCsn1s2b-DE-S2_L10_GR_rep2

description: GR (Thermo Fisher Scientific, PA1-511A)


title: delCsn1s2b-DE-N-S3_L10_STAT5_rep1


title: delCsn1s2b-DE-S2_L10_H3K27ac_rep2

description: H3K27ac (Abcam, ab4729)


title: delCsn1s2b-DE-S2_L10_GR_rep1

description: GR (Thermo Fisher Scientific, PA1-511A)


title: delCsn1s2b-DE-S2_L10_NFIB_rep1

description: NFIB (Sigma-Aldrich, HPA003956)


title: delCsn1s2b-DE-S2_L10_H3K27ac_rep1

description: H3K27ac (Abcam, ab4729)


title: SLE active_CDR-60_IGF0005546


title: delCsn1s2b-DE-N-S3_L10_STAT5_rep2


title: SLE active_CDR-36_IGF0005545


title: delCsn1s2b-DE-N-S3_L10_PolII_rep1

description: RNA polymerase II (Abcam, ab5408)


title: delCsn1s2b-DE-N-S3_L10_PolII_rep2

description: RNA polymerase II (Abcam, ab5408)


title: delCsn1s2b-DE-N-S3_L10_NFIB_rep2

description: NFIB (Sigma-Aldrich, HPA003956)


title: shA_3

city: Sapporo

first: Keisuke

last: Aoshima

state: Hokkaido

address: Kita 18 Nishi 9

department: Faculty of Veterinary Medicine

country: Japan

institute: Hokkaido University

data_processing:
Raw data was trimmed by AnnoRoad
Sequencing reads were mapped to the canine reference genome CanFam3.1 using STAR and aligned using RSEM (Dobin et al., 2013; Li and Dewey, 2011).
Genome_build: CanFam3.1
Supplementary_files_format_and_content: An excel file include TPM values for each Sample.

organism: Canis lupus familiaris

extract_protocol:
RNA was extracted with Nucleospin® RNA isolation kit (Macherey-Nagel GmbH & Co.) following the manufacturer’s instructions.
RNA-seq libraries were constructed using NEBNext® Ultra RNA Library Prep Kit for llumina® (New England Biolabs, MA, USA)

value: KDM2B knockdown by shRNA

value: hemangiosarcoma cell line


title: CD8 T Cell Eomes- Rep 1

city: Portland

first: Dana

middle: Alexander

last: Emerson

state: OR

address: 3181 SW Sam Jackson Park Road L220

department: Molecular Microbiology & Immunology

institute: OHSU

description: Gene expression data from tumor infiltrating lymphocytes (CD8 T cells), day 19 post tumor implant

hyb_protocol: Biotin labeled cRNA samples were fragmented and then hybridized to the Affymetrix GeneChip Mouse Genome Array

scan_protocol: Affymetrix GeneChip Scanner 3000 with GCOS software according to manufactuer's protocol

data_processing: Gene Chips were analyzed with the Transcriptome Analysis Console software and normalized using the MAS5 algorithm.

label_protocol: Biotin

growth_protocol: MCA-205 tumors were implanted into C57BL/6 Eomes-GFP mice

extract_protocol: RNA was extracted using Trizol reagent (Invitrogen) according to the manufacturer’s instructions

treatment_protocol: Mice were treated with 250ug aOX40 on days 12 and 16, and with 200ug aCTLA-4 on days 12, 14, and 16. Tumors were harvested for sort into trizol on day 19

value: Tumor infiltrating lymphocytes (CD8 T cells), day 19 post tumor implant


title: CD8 T Cell Eomes+ Rep 2

source_name: Tumor infiltrating lymphocytes (CD8 T cells)


title: CD8 T Cell Eomes- Rep 2


title: shA_2


title: CD8 T Cell Eomes+ Rep 1


title: CD8 T Cell Eomes- Rep 3


title: CD8 T Cell Eomes+ Rep 3


title: scr1_3

value: scramble shRNA expression


title: delCsn1s2b-DE-N-S3_L10_NFIB_rep1

description: NFIB (Sigma-Aldrich, HPA003956)


title: SLE active_CDR-34_IGF0005543


title: delCsn1s2b-DE-N-S3_L10_H3K27ac_rep2

description: H3K27ac (Abcam, ab4729)


title: SLE active_CDR-27_IGF0005542


title: scr1_2


title: shA_1


title: SLE active_CDR-35_IGF0005544


title: SLE active_CDR-25_IGF0005541


title: delCsn1s2b-DE-N-S3_L10_H3K27ac_rep1

description: H3K27ac (Abcam, ab4729)


title: JuB2

value: non-treated


title: delCsn1s2b-DE-N-S3_L10_GR_rep2

description: GR (Thermo Fisher Scientific, PA1-511A)


title: EC

source_name: CnAOEC

value: normal endothelial cell


title: delCsn1s2b-DE-N-S3_L10_GR_rep1

description: GR (Thermo Fisher Scientific, PA1-511A)


title: SLE active_CDR-21_IGF0005539


title: SLE active_CDR-24_IGF0005540


title: delCsn1s2b-DE-N-S2_L10_STAT5_rep2


title: Mixture_C4_72_R

city: Koblenz

first: Andreas

last: Schüttler

address: Am Mainzer Tor 1

department: Department Biochemistry and Ecotoxicology

institute: German Federal Institute of Hydrology

description: whole zebrafish embryo, exposed to Mixture, 102.93 micromol per liter, 24hpf-72hpf, subsequently transferred into clean water till 96hpf

hyb_protocol: Agilent Gene Expression Hybridisation Kit, according to manufacturer's protocol (Agilent Technologies, Waldbronn, Germany)

scan_protocol: Agilent DNA Microarray Scanner and Agilent Feature Extraction Software V11.5.1.1, according to manufacturer's protocol.

data_processing: Cyclic loess normalization between all arrays. Software for data normalization: R v3.3.1.

organism: Danio rerio

source_name: whole embryo, exposed to Mixture, 24hpf-96hpf, 102.93 micromol per liter

label_protocol: One-Color Quick Amp Labeling Kit, according to manufacturer's protocol (Agilent Technologies, Waldbronn, Germany)

extract_protocol: Trizol followed by RNeasy MiniKit cleanup (Qiagen) using the manufacturers’ protocols

tag: substance

value: Mixture


title: SLE active_CDR-13_IGF0005537


title: SLE active_CDR-20_IGF0005538


title: Mixture_Control_72_C.1

description: whole zebrafish embryo, exposed to Mixture, 24hpf-96hpf, 0 micromol per liter

source_name: whole embryo, exposed to Mixture, 24hpf-96hpf, 0 micromol per liter


title: Mixture_C5_72_R.1

description: whole zebrafish embryo, exposed to Mixture, 122.51 micromol per liter, 24hpf-72hpf, subsequently transferred into clean water till 96hpf

source_name: whole embryo, exposed to Mixture, 24hpf-96hpf, 122.51 micromol per liter


title: Mixture_Control_72_C


title: Mixture_C5_72_T.1

description: whole zebrafish embryo, exposed to Mixture, 24hpf-96hpf, 122.51 micromol per liter


title: delCsn1s2b-DE-N-S2_L10_STAT5_rep1

description: STAT5A (Santa Cruz Biotechnology, sc-271542)

tag: time


title: Mixture_C1_72_T

description: whole zebrafish embryo, exposed to Mixture, 24hpf-96hpf, 43.1 micromol per liter

source_name: whole embryo, exposed to Mixture, 24hpf-96hpf, 43.1 micromol per liter


title: Mixture_C1_72_T.1


title: Mixture_C2_72_T.1

description: whole zebrafish embryo, exposed to Mixture, 24hpf-96hpf, 61.06 micromol per liter

source_name: whole embryo, exposed to Mixture, 24hpf-96hpf, 61.06 micromol per liter


title: Mixture_C5_72_R


title: Mixture_C2_72_T


title: Mixture_C5_72_T


title: HT-29_Oxy_miRNA_rep2

city: Moscow

first: Stepan

last: Nersisyan

address: Vavilova str 7

department: Faculty of Biology and Biotechnology

country: Russia

institute: HSE University

description:
miRNA_counts.tsv
miRNA_CPM.tsv

data_processing:
Quality of FASTQ files were assessed with FastQC v0.11.9, three miRNA-seq replicates (Caco-2_Control_miRNA_rep3, HT-29_CoCl2_miRNA_rep1 and HT-29_Oxy_miRNA_rep3) had not passed the quality control
Adapters were trimmed with cutadapt v2.10
Trimmed mRNA-seq reads were mapped on the reference human genome (GENCODE GRCh38.p13) with STAR v2.7.5b, GENCODE genome annotation (release 34) was used to generate the count matrix.
MiRNA count matrix was generated by miRDeep2 v2.0.1.2 with the use of bowtie v1.1.1 and miRBase v22.1
Sequencing library sizes were normalized with the Trimmed Mean of M-values (TMM) algorithm available in edgeR v3.30.3 package. The same package was used to generate TMM-normalized Reads Per Kilobase of transcript per Million mapped reads (RPKM) and Counts Per Million mapped reads (CPM) matrices for mRNA-seq and miRNA-seq data, respectively.
Genome_build: GRCh38.p13
Supplementary_files_format_and_content: Tab-separated matrices containing raw read counts and TMM-normalized (edgeR) RPKM and RPM values

source_name: HT-29 cells

growth_protocol: HT-29 cells  (ATCC, Manassas, VA, USA) were grown in McCoy's 5A medium, supplemented with 10% fetal bovine serum, 2 mM glutamine, 1% non-essential amino acids, penicillin (100 U/mL) and streptomycin (100 mg/mL).  Caco-2 cells were obtained from the Russian Vertebrate Cell Culture Collection (Institute of Cytology, Russian Academy of Sciences, Russia). The cells were incubated under conditions for differentiation for 21 days in Eagle’s MEM with 20% FBS, 2 mM glutamine, 0.1 mM non-essential amino acids, 0.1% penicillin-streptomycin.  All cell culture reagents were obtained from Gibco, Waltham, MA, USA. Both cell lines were maintained in a humidified atmosphere at 37ºC and 5% CO2, changing medium every 3 days.

extract_protocol:
Cells were lysed with the Qiazol Lysis Reagent (Qiagen, Hilden, Germany) for subsequent extraction of RNA using the Qiagen miRNeasy Mini Kit (Qiagen, Hilden, Germany). Nanodrop (Thermo Fisher Scientific, Waltham, MA, USA) was used to assess quality (260/280) and quantity. Total RNA samples were also QC checked using the Agilent High Sensitivity DNA Kit (Agilent Technologies, Santa Clara, CA, USA).
Libraries for mRNA sequencing were prepared from total RNA samples using Illumina Stranded mRNA Library Prep Kit (Illumina, San Diego, CA, USA). Each sample was sequenced on the Illumina NextSeq 550 to generate single-end 75 nucleotide reads. Libraries for miRNA sequencing were prepared from total RNA samples using NEBNext Multiplex Small RNA Library Prep Kit for Illumina. Each sample was sequenced on the Illumina NextSeq 550 to generate single-end 50 nucleotide reads.

treatment_protocol: A fresh stock solution 0.3 M cobalt chloride (CoCl2) was prepared in water and added to the medium to obtain desired final concentration 300 µM for 24 hours. The second treatment included a fresh portion containing oxyquinoline derivative 4896-3212 (ChemDiv Research Institute, Khimki, Russia) in DMSO (10 mM). The final concentration of oxyquinoline in the medium was 5 μM (0.5 μl of the solution in DMSO per 1 ml medium). In the control, the cells were incubated in a medium with 0.5 μl DMSO per 1 ml medium (without CoCl2 or oxyquinoline).

value: Oxyquinoline for 24 hours


title: HT-29_Oxy_miRNA_rep3

description:
miRNA_counts.tsv
miRNA_CPM.tsv


title: Mixture_C3_72_R

description: whole zebrafish embryo, exposed to Mixture, 86.49 micromol per liter, 24hpf-72hpf, subsequently transferred into clean water till 96hpf

source_name: whole embryo, exposed to Mixture, 24hpf-96hpf, 86.49 micromol per liter


title: HT-29_Oxy_miRNA_rep1

description:
miRNA_counts.tsv
miRNA_CPM.tsv


title: SLE active_CDR-10_IGF0005536

tag: tissue


title: SLE active_CDR-6_IGF0005535


title: scr1_1


title: HT-29_CoCl2_miRNA_rep3

description:
miRNA_counts.tsv
miRNA_CPM.tsv

value: CoCl2 for 24 hours


title: delCsn1s2b-DE-N-S2_L10_PolII_rep1

description: RNA polymerase II (Abcam, ab5408)

tag: genotype


title: delCsn1s2b-DE-N-S2_L10_NFIB_rep2

description: NFIB (Sigma-Aldrich, HPA003956)


title: Mixture_C4_72_T.1

description: whole zebrafish embryo, exposed to Mixture, 24hpf-96hpf, 102.93 micromol per liter


title: HT-29_CoCl2_miRNA_rep2

description:
miRNA_counts.tsv
miRNA_CPM.tsv


title: HT-29_CoCl2_miRNA_rep1

description:
miRNA_counts.tsv
miRNA_CPM.tsv


title: delCsn1s2b-DE-N-S2_L10_NFIB_rep1

description: NFIB (Sigma-Aldrich, HPA003956)


title: Ctrl_LHC-19_IGF0006255

source_name: Ctrl_Peripheral blood

value: Ctrl

value: Peripheral blood

tag: cell

value: T cell


title: delCsn1s2b-DE-N-S2_L10_PolII_rep2

description: RNA polymerase II (Abcam, ab5408)

value: Lactation day 10


title: Mixture_C3_72_T.1

description: whole zebrafish embryo, exposed to Mixture, 24hpf-96hpf, 86.49 micromol per liter


title: HT-29_Control_miRNA_rep3

description:
miRNA_counts.tsv
miRNA_CPM.tsv

tag: treatment

value: No treatment


title: delCsn1s2b-DE-N-S2_L10_H3K27ac_rep2

description: H3K27ac (Abcam, ab4729)


title: Ctrl_LHC-17_IGF0005629


title: Ctrl_LHC-16_IGF0005628


title: Ctrl_LHC-15_IGF0005627


title: delCsn1s2b-DE-N-S2_L10_H3K27ac_rep1

description: H3K27ac (Abcam, ab4729)


title: delCsn1s2b-DE-N-S2_L10_GR_rep2

description: GR (Thermo Fisher Scientific, PA1-511A)


title: Mixture_Control_12_C.1

description: whole zebrafish embryo, exposed to Mixture, 24hpf-36hpf, 0 micromol per liter

source_name: whole embryo, exposed to Mixture, 24hpf-36hpf, 0 micromol per liter


title: HT-29_Control_miRNA_rep2

description:
miRNA_counts.tsv
miRNA_CPM.tsv


title: HT-29_Control_miRNA_rep1

description:
miRNA_counts.tsv
miRNA_CPM.tsv


title: Mixture_Control_12_C


title: Mixture_C4_72_T


title: HT-29_Oxy_mRNA_rep3

description:
mRNA_counts.tsv
mRNA_RPKM.tsv


title: SLE active_CDR-2_IGF0005534

value: Blood

value: CD 8 T cell


title: Mixture_C3_72_T


title: Mixture_C5_12_T.1

description: whole zebrafish embryo, exposed to Mixture, 24hpf-36hpf, 122.51 micromol per liter

source_name: whole embryo, exposed to Mixture, 24hpf-36hpf, 122.51 micromol per liter


title: Ctrl_LHC-14_IGF0005626


title: delCsn1s2b-DE-N-S2_L10_GR_rep1

description: GR (Thermo Fisher Scientific, PA1-511A)

source_name: Mammary gland


title: Ctrl_LHC-13_IGF0005624


title: HT-29_Oxy_mRNA_rep2

description:
mRNA_counts.tsv
mRNA_RPKM.tsv


title: Ctrl_LHC-12_IGF0005623


title: delCsn1s2b-DE-N-S1-S3_L10_STAT5_rep2


title: HT-29_Oxy_mRNA_rep1

description:
mRNA_counts.tsv
mRNA_RPKM.tsv


title: delCsn1s2b-DE-N-S1-S3_L10_STAT5_rep1


title: Mixture_C2_12_T

description: whole zebrafish embryo, exposed to Mixture, 24hpf-36hpf, 61.06 micromol per liter

source_name: whole embryo, exposed to Mixture, 24hpf-36hpf, 61.06 micromol per liter


title: delCsn1s2b-DE-N-S1-S3_L10_PolII_rep2

description: RNA polymerase II (Abcam, ab5408)


title: Mixture_C4_12_T

description: whole zebrafish embryo, exposed to Mixture, 24hpf-36hpf, 102.93 micromol per liter

source_name: whole embryo, exposed to Mixture, 24hpf-36hpf, 102.93 micromol per liter


title: HT-29_CoCl2_mRNA_rep3

description:
mRNA_counts.tsv
mRNA_RPKM.tsv


title: Ctrl_LHC-9_IGF0005622


title: delCsn1s2b-DE-N-S1-S3_L10_PolII_rep1

description: RNA polymerase II (Abcam, ab5408)


title: Mixture_C5_12_T


title: HT-29_CoCl2_mRNA_rep2

description:
mRNA_counts.tsv
mRNA_RPKM.tsv


title: Mixture_Control_6_C.1

description: whole zebrafish embryo, exposed to Mixture, 24hpf-30hpf, 0 micromol per liter

source_name: whole embryo, exposed to Mixture, 24hpf-30hpf, 0 micromol per liter


title: HT-29_CoCl2_mRNA_rep1

description:
mRNA_counts.tsv
mRNA_RPKM.tsv


title: delCsn1s2b-DE-N-S1-S3_L10_NFIB_rep1

description: NFIB (Sigma-Aldrich, HPA003956)


title: Ctrl_LHC-6_IGF0005619


title: HT-29_Control_mRNA_rep3

description:
mRNA_counts.tsv
mRNA_RPKM.tsv


title: Ctrl_LHC-5_IGF0005618


title: delCsn1s2b-DE-N-S1-S3_L10_NFIB_rep2

description: NFIB (Sigma-Aldrich, HPA003956)


title: delCsn1s2b-DE-N-S1-S3_L10_H3K27ac_rep2

description: H3K27ac (Abcam, ab4729)


title: Ctrl_LHC-4_IGF0005617


title: delCsn1s2b-DE-N-S1-S3_L10_H3K27ac_rep1

description: H3K27ac (Abcam, ab4729)


title: delCsn1s2b-DE-N-S1-S3_L10_GR_rep2

description: GR (Thermo Fisher Scientific, PA1-511A)


title: HT-29_Control_mRNA_rep1

description:
mRNA_counts.tsv
mRNA_RPKM.tsv


title: Caco-2_Oxy_miRNA_rep3

description:
miRNA_counts.tsv
miRNA_CPM.tsv

source_name: Caco-2 cells


title: Mixture_Control_6_C


title: Mixture_C1_12_T

description: whole zebrafish embryo, exposed to Mixture, 24hpf-36hpf, 43.1 micromol per liter

source_name: whole embryo, exposed to Mixture, 24hpf-36hpf, 43.1 micromol per liter


title: Mixture_C3_12_T

description: whole zebrafish embryo, exposed to Mixture, 24hpf-36hpf, 86.49 micromol per liter

source_name: whole embryo, exposed to Mixture, 24hpf-36hpf, 86.49 micromol per liter


title: Mixture_C5_6_T

description: whole zebrafish embryo, exposed to Mixture, 24hpf-30hpf, 122.51 micromol per liter

source_name: whole embryo, exposed to Mixture, 24hpf-30hpf, 122.51 micromol per liter


title: delCsn1s2b-DE-N-S1-S3_L10_GR_rep1

description: GR (Thermo Fisher Scientific, PA1-511A)


title: Caco-2_Oxy_miRNA_rep2

description:
miRNA_counts.tsv
miRNA_CPM.tsv


title: Mixture_C5_6_T.1


title: Mixture_C3_6_T

description: whole zebrafish embryo, exposed to Mixture, 24hpf-30hpf, 86.49 micromol per liter

source_name: whole embryo, exposed to Mixture, 24hpf-30hpf, 86.49 micromol per liter


title: SLE less active_CDR-64_IGF0005615

source_name: SLE Less Active_Peripheral blood

value: SLE Less Active


title: Mixture_C4_6_T

description: whole zebrafish embryo, exposed to Mixture, 24hpf-30hpf, 102.93 micromol per liter

source_name: whole embryo, exposed to Mixture, 24hpf-30hpf, 102.93 micromol per liter


title: SLE less active_CDR-61_IGF0005614


title: HT-29_Control_mRNA_rep2

description:
mRNA_counts.tsv
mRNA_RPKM.tsv


title: delCsn1s2b-DE-N_L10_STAT5_rep2


title: Caco-2_Oxy_miRNA_rep1

description:
miRNA_counts.tsv
miRNA_CPM.tsv


title: Caco-2_CoCl2_miRNA_rep3

description:
miRNA_counts.tsv
miRNA_CPM.tsv


title: delCsn1s2b-DE-N_L10_STAT5_rep1


title: SLE less active_CDR-59_IGF0005613


title: Ctrl_LHC-1_IGF0005616


title: Mixture_C2_6_T

description: whole zebrafish embryo, exposed to Mixture, 24hpf-30hpf, 61.06 micromol per liter

source_name: whole embryo, exposed to Mixture, 24hpf-30hpf, 61.06 micromol per liter


title: delCsn1s2b-DE-N_L10_PolII_rep2

description: RNA polymerase II (Abcam, ab5408)


title: Mixture_Control_3_C.1

description: whole zebrafish embryo, exposed to Mixture, 24hpf-27hpf, 0 micromol per liter

source_name: whole embryo, exposed to Mixture, 24hpf-27hpf, 0 micromol per liter


title: SLE less active_CDR-57_IGF0005612


title: Caco-2_CoCl2_miRNA_rep2

description:
miRNA_counts.tsv
miRNA_CPM.tsv


title: delCsn1s2b-DE-N_L10_PolII_rep1

description: RNA polymerase II (Abcam, ab5408)


title: Mixture_Control_3_C


title: Caco-2_CoCl2_miRNA_rep1

description:
miRNA_counts.tsv
miRNA_CPM.tsv


title: Mixture_C1_6_T

description: whole zebrafish embryo, exposed to Mixture, 24hpf-30hpf, 43.1 micromol per liter

source_name: whole embryo, exposed to Mixture, 24hpf-30hpf, 43.1 micromol per liter


title: delCsn1s2b-DE-N_L10_NFIB_rep2

description: NFIB (Sigma-Aldrich, HPA003956)


title: SLE less active_CDR-56_IGF0005611


title: Mixture_C5_3_T.1

description: whole zebrafish embryo, exposed to Mixture, 24hpf-27hpf, 122.51 micromol per liter

source_name: whole embryo, exposed to Mixture, 24hpf-27hpf, 122.51 micromol per liter


title: Caco-2_Control_miRNA_rep3

description:
miRNA_counts.tsv
miRNA_CPM.tsv


title: SLE less active_CDR-54_IGF0005609


title: delCsn1s2b-DE-N_L10_NFIB_rep1

description: NFIB (Sigma-Aldrich, HPA003956)


title: SLE less active_CDR-55_IGF0005610


title: Caco-2_Control_miRNA_rep1

description:
miRNA_counts.tsv
miRNA_CPM.tsv


title: Caco-2_Control_miRNA_rep2

description:
miRNA_counts.tsv
miRNA_CPM.tsv


title: SLE less active_CDR-52_IGF0005607


title: delCsn1s2b-DE-N_L10_H3K27ac_rep2

description: H3K27ac (Abcam, ab4729)


title: SLE less active_CDR-53_IGF0005608


title: Caco-2_Oxy_mRNA_rep3

description:
mRNA_counts.tsv
mRNA_RPKM.tsv


title: Mixture_C5_3_T


title: SLE less active_CDR-51_IGF0005606


title: delCsn1s2b-DE-N_L10_GR_rep2

description: GR (Thermo Fisher Scientific, PA1-511A)


title: Caco-2_Oxy_mRNA_rep2

description:
mRNA_counts.tsv
mRNA_RPKM.tsv


title: delCsn1s2b-DE-N_L10_H3K27ac_rep1

description: H3K27ac (Abcam, ab4729)


title: Mixture_C3_3_T

description: whole zebrafish embryo, exposed to Mixture, 24hpf-27hpf, 86.49 micromol per liter

source_name: whole embryo, exposed to Mixture, 24hpf-27hpf, 86.49 micromol per liter


title: Mixture_C4_3_T

description: whole zebrafish embryo, exposed to Mixture, 24hpf-27hpf, 102.93 micromol per liter

source_name: whole embryo, exposed to Mixture, 24hpf-27hpf, 102.93 micromol per liter


title: Mixture_C2_3_T

description: whole zebrafish embryo, exposed to Mixture, 24hpf-27hpf, 61.06 micromol per liter

source_name: whole embryo, exposed to Mixture, 24hpf-27hpf, 61.06 micromol per liter


title: Mixture_C1_3_T

description: whole zebrafish embryo, exposed to Mixture, 24hpf-27hpf, 43.1 micromol per liter

source_name: whole embryo, exposed to Mixture, 24hpf-27hpf, 43.1 micromol per liter


title: Mixture_Control_24_C.1

description: whole zebrafish embryo, exposed to Mixture, 24hpf-48hpf, 0 micromol per liter

source_name: whole embryo, exposed to Mixture, 24hpf-48hpf, 0 micromol per liter


title: Mixture_C5_24_T.1

description: whole zebrafish embryo, exposed to Mixture, 24hpf-48hpf, 122.51 micromol per liter

source_name: whole embryo, exposed to Mixture, 24hpf-48hpf, 122.51 micromol per liter


title: Caco-2_CoCl2_mRNA_rep3

description:
mRNA_counts.tsv
mRNA_RPKM.tsv

source_name: Caco-2 cells


title: SLE less active_CDR-50_IGF0005605


title: Caco-2_Oxy_mRNA_rep1

description:
mRNA_counts.tsv
mRNA_RPKM.tsv


title: delCsn1s2b-DE-N_L10_GR_rep1

description: GR (Thermo Fisher Scientific, PA1-511A)

source_name: Mammary gland


title: Caco-2_CoCl2_mRNA_rep2

description:
mRNA_counts.tsv
mRNA_RPKM.tsv


title: SLE less active_CDR-46_IGF0005604


title: SLE less active_CDR-41_IGF0005602


title: Caco-2_Control_mRNA_rep3

description:
mRNA_counts.tsv
mRNA_RPKM.tsv


title: human induced pluripotent stem cell-derived Muller Glial cells_2

city: Paris

first: Xavier

last: Guillonneau

address: 17 rue Moreau

department: Institut de la vision

country: France

institute: INSERM

data_processing:
Raw reads were filtered with Trimmomatic to obatin Pass-filtered reads
Pass-filtered reads were mapped using HiSAT2 and aligned to human reference genome GRCh38.95
The count table of the gene features was obtained using HTSeq
Normalization and differential expression analysis values were computed with DESeq2
TPM were determined using Libinorm using htseq mode
Genome_build: GRCh38.95
Supplementary_files_format_and_content: The MGCs_raw_counts.tsv file contains, raw counts and  RPKM, TPM for the processed 6 samples. Data are in a tab-separated format
Supplementary_files_format_and_content: The  hiMGC_vs_pMGC_DE_&_TPM_FC.tsv contains fold change values with pavalues <0.05 generated by Desq2. Data are in a tab-separated format

source_name: Muller Glial cell

growth_protocol: pMGCs and hiMGCs were plated at 50 000 cell/cm² in T-25 cm² flask previously coated with Geltrex matrix (ThermoFischer Scientific) and incubated at 37°C in a standard 5% CO2 / 95% air incubator. Medium was changed every 2-3 days until cell processing

extract_protocol:
Total RNA were extracted from  hiMGCs and pMGCsusing the Nucleospin RNA II kit (Macherey-Nagel) according to the manufacturer’s protocol, RNA quality and quantity were evaluated using BioAnalyzer 2100 (Agilent Technologies,) with the RNA 6000 Nano Kit (Agilent Technologies)
RNA sequencing libraries were constructed from 1 μg of total RNA using a modified TruSeq RNA Sample preparation kit protocol

value: human induced pluripotent stem cell-derived cells


title: SLE less active_CDR-37_IGF0005601


title: SLE less active_CDR-29_IGF0005600


title: human induced pluripotent stem cell-derived Muller Glial cells_3


city: New York

first: Joseph

middle: C

last: Devlin

state: NY

address: 430 East 29th Street

department: Microbiology

institute: New York University Langone Health

data_processing:
The Cellranger software suite version 3.0.1 (https://support.10xgenomics.com/single-cell-gene- expression/software/pipelines/latest/what-is-cell-ranger) from 10X was used to demultiplex cellular barcodes, align reads to the human genome (GRCh38 ensemble, http://useast.ensembl.org/Homo_sapiens/Info/Index) and perform UMI counting
Hashtag Oligos were quantified by kallisto kb-count version 0.24.4
From filtered counts Seurat1 version 3.1.3 was used to process the single cell data including HTO demultipleximg with HTODemux, normalization, dimension reduction, UMAP representation
Genome_build: GRCh38
Supplementary_files_format_and_content: SingleCellCounts.mtx.gz is a gzipped tab delimited count table where cells are columns and genes are rows. SingleCellBarcodes.tsv.gz contains the cell barcodes. SingleCellGenes.tsv.gz contains the gene names. SingleCellMetadata.txt.gz contains the metadata for clustering and HTO demultiplexing.
Supplementary_files_format_and_content: seurat_obj.rds is an R summaraized experiment object with clustering, dimension reduction and cellular metadata.
Supplementary_files_format_and_content: HTO-ref.csv is the hashtag reference barcode for demultiplexing

growth_protocol: Basal-like human airway progenitor cells (Bci-NS1.1) were obtained from Dr. Ronald G. Crystal and were used for cytotoxicity assays and for the generation of polarized human airway epithelial cultures (HAEC). They were maintained in BEGM Medium (Lonza, cat no. CC-3171 and CC-4175), while Pneumacult Ex Plus medium (StemCell, cat no. 05040) was used to culture Bci-NS1.1 cells for the generation of human airway epithelial cultures. To generate HAEC, Bci-NS1.1 were plated (7.5 E + 04 cells/well) on rat-tail collagen type 1-coated permeable transwell membrane supports (6.5 mm; Corning, cat no. 3470), and immersed apically and basolaterally in Pneumacult Ex Plus medium (StemCell, cat no. 05040). Upon reaching confluency, medium was removed from the apical side (“airlift”), and medium in the basolateral chamber was changed to Pneumacult ALI maintenance medium (StemCell, cat no. 05001). Medium in the basolateral chamber was exchanged with fresh Pneumacult ALI maintenance medium every 2-3 days for 12-15 days to form differentiated, polarized cultures that resemble in vivo pseudostratified mucociliary epithelium. Cultures were used within 4-6 weeks of differentiation.

extract_protocol:
6-week-old human airway cultures were used for the single-cell RNA-seq analysis.  The apical surface was washed once to remove mucus by adding 100 µL of PBS and incubating for 30 min at 37°C. Cells were dissociated by cutting out the transwell membrane and incubating it in 700 µL TrpLE 10x (Thermo Fisher cat no.  A1217701) for 30 min rocking at 37°C. To increase dissociation cells were pipetted through wide-bore tips every 10 min during the incubation time. When cells were visually dissociated 700µl of ALI maintenance medium supplemented with 0.1% Pluronic (Thermo Fisher cat. No. 24040032) was added and cells were carefully pipetted again using wide-bore tips. The cell suspension was centrifuged through a 10 µM filter at 300 x g for 5 min to break up any remaining cell clumps. The cell pellet was washed once with 200 µL ALI maintenance medium supplemented with 0.1% Pluronic before cell number and viability was assed using the Countess II (Thermo Fisher) to calculate cell numbers used in the following steps for single-cell RNA-seq analysis.
Single cell transcriptome profiling of dissociated organoids was carried out using the Chromium Next GEM Single Cell 5’ Library & Gel Bead Kit and Chromium controller (10X genomics). To enable multiplexing and doublet detection, cells were stained with barcoded antibodies described previously (Mimitou et al., 2019). Briefly, approximately 200,000 cells per sample were resuspended in staining buffer (PBS, 2% BSA, 0.01% Tween) and incubated for 10 minutes with Fc block (TruStain FcX, Biolegend; FcR blocking reagent, Miltenyi). Cells were then incubated with barcoded hashing antibodies for 30 min at 4 °C. After staining, cells were washed 3 times in staining buffer. After the final wash, cells were resuspended in PBS + 0.04% BSA, filtered, and counted. Cells were pooled and loaded onto the Chromium chips. For each lane, we pooled 5 samples, ~10,000 cells per sample (we might also want to just include a table that shows how the samples were pooled, how many cells we were targeting, etc).
The single-cell capturing, barcoding, and cDNA library preparation were performed using the Chromium Next GEM Single Cell 5’ Library & Gel Bead Kit by following the protocols recommended by the manufacturer. HTO additive oligonucleotide was spiked into the cDNA amplification PCR and the HTO library was prepared as described previously.   The Cellranger software suite (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger) from 10X was used to demultiplex cellular barcodes, align reads to the human genome (GRCh38 ensemble, http://useast.ensembl.org/Homo_sapiens/Info/Index) and perform UMI counting. From filtered counts HTODemux was used to demultiplex hash-tagged samples and Seurat1 version 3.1.3 was used to process the single cell data including dimension reduction, UMAP representation and differential expression to identify cell type specific markers determined by wilcox test.

treatment_protocol: To stimulate HAEC with IFN-⍺, 500 U/ml IFN-ß were added to the basolateral chamber media for 6 hours.

value: PBS (control)


title: HTO library

source_name: Basal-like human airway progenitor cells (Bci-NS1.1)

value: HTO library


title: Caco-2_CoCl2_mRNA_rep1

description:
mRNA_counts.tsv
mRNA_RPKM.tsv


title: Mixture_C4_24_T.1

description: whole zebrafish embryo, exposed to Mixture, 24hpf-48hpf, 102.93 micromol per liter

source_name: whole embryo, exposed to Mixture, 24hpf-48hpf, 102.93 micromol per liter


title: Caco-2_Control_mRNA_rep2

description:
mRNA_counts.tsv
mRNA_RPKM.tsv


title: human induced pluripotent stem cell-derived Muller Glial cells_1


title: SLE less active_CDR-45_IGF0005603

source_name: SLE Less Active_Peripheral blood


title: Mixture_C3_24_T.1

description: whole zebrafish embryo, exposed to Mixture, 24hpf-48hpf, 86.49 micromol per liter

source_name: whole embryo, exposed to Mixture, 24hpf-48hpf, 86.49 micromol per liter


title: human Primary Muller Glial cells_3

value: primary cells


title: Mixture_C2_24_T

description: whole zebrafish embryo, exposed to Mixture, 24hpf-48hpf, 61.06 micromol per liter

source_name: whole embryo, exposed to Mixture, 24hpf-48hpf, 61.06 micromol per liter


title: Mixture_C4_24_T


title: Mixture_C3_24_T


title: SLE active_CDR-23_IGF0005599

source_name: SLE Active_Peripheral blood