title: C. elegans-hsf-1 OE;ubiquilin-1-Rep3

city: London

first: John

last: Labbadia

address: Darwin Building, Gower Street

department: GEE

country: United Kingdom

institute: UCL

description: hsf-1 OE;ubiquilin-1(tm1574)-Rep3

data_processing:
Sequenced reads were trimmed for adaptor sequences and polyN and low quality reads were removed before mapping reads to the WBcel235 reference genome using  Hisat2 v2.0.5
featureCounts v1.5.0-p3 was used to count the number of reads mapped to each gene and FPKM for each gene was then calculated
DESeq2 was then used for differential expression analysis
Assembly: WBcel235
Supplementary files format and content: Table with raw gene counts for every gene and every sample

organism: Caenorhabditis elegans

source_name: Whole animals

growth_protocol: Worms were grown on standard NGM plates with OP50 at 20degC

extract_protocol:
Worms were lysed in Trizol by vortexing at 4degC for 20 minutes. RNA was then purified using a Qiagen Rneasy Minelute kit as per manufacturers instructions
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Worms were collected at Day1 of adulthood as young adults and immediately snap frozen before RNA was extracted using an RNeasy kit (Qiagen).

value: Whole animals

tag: genotype

value: uthIs235 [sur-5p::hsf-1::unc-54 3'UTR + myo-2p::tdTomato::unc-54 3' UTR];ubql-1(tm1574)

tag: time point

value: Young adult (d1 of adulthood)


title: NZBWF_28_seven_(miRNA-4_0)

status: Public on Sep 01 2023

type: RNA

city: beijng

first: shipeng

last: Li

address: Nan Li Shi Road No. 56,Beijing

country: China

institute: Beijing children's hospital

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Human Transcriptome Array 2.0 were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Hewlett-Packard GeneArray Scanner G3000 7G.

data_processing: The data were analyzed with RMA using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100

label: total RNA

molecule: total RNA

organism: Mus musculus

source_name: 28-week-old NZBWF1 kidney

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 ug total RNA

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

tag: strain

tag: age

tag: tissue

value: kidney


title: C. elegans-hsf-1 OE;ubiquilin-1-Rep4

type: SRA

description: hsf-1 OE;ubiquilin-1(tm1574)-Rep4

library_source: transcriptomic


title: pdac_18_after

city: Rotterdam

first: Willem

last: de Koning

state: Zuid-Holland

address: Doctor Molewaterplein 40

country: Netherlands

institute: Erasmus University Medical Center

hyb_protocol: For each sample, a total of 200 ng RNA, in a maximum volume of 7 μL, was subjected to hybridization with the two panels for a duration of 17 h at 65 °C, following the protocol provided by the manufacturer (NanoString Technologies Inc., Seattle, WA, USA).

scan_protocol: The nCounter® FLEX platform was utilized to wash away the unbound probes and to count the genes by scanning 490 fields of view (FOV).

data_processing: Data analysis was performed using the advanced analysis module (version 2.0) of nSolver software (version 4.0, NanoString Technology).

organism: Homo sapiens

source_name: pancreatic ductal adenocarcinoma, blood

extract_protocol: The whole-blood samples intended for targeted gene expression analysis were collected in Tempus tubes (Applied Biosystems, Foster City, CA, USA) and subsequently stored at −80 °C. Tempus tubes are designed to contain an RNA-stabilizing reagent, which effectively preserves RNA quality, enabling the measurement of gene expression profiles without the need to isolate peripheral blood mononuclear cells. To extract total RNA from the blood in Tempus tubes, a Tempus Spin RNA Isolation Kit from Thermo Fisher Scientific (Waltham, MA, USA) was employed, following the manufac-turer’s instructions. Subsequently, RNA quality was assessed using an Agilent 2100 Bi-oAnalyzer (Santa Clara, CA, USA). Samples with RNA concentrations below 35 mg/mL were excluded from further analysis. Corrected RNA concentrations were calculated based on the percentage of fragments within the 300–4000 nucleotide range to account for RNA degradation. An nCounter® PanCancer Immune Profiling (IP) Panel and nCounter® Myeloid Innate Immunity (MII) Panel, each consisting of 730 genes and 40 housekeeping genes, were used for NanoString targeted gene expression analysis of the 88 whole-blood samples

value: blood

tag: patient diagnosis

value: Pancreatic Ductal Adenocarcinoma

tag: gender

value: Female

tag: smoking status

value: Current

tag: alcohol status

tag: baseline ca19-9 (u/ml)

tag: baseline cea (µg/l)

tag: baseline sii

tag: baseline nlr

tag: baseline bilirubin (micromol/l)

tag: baseline crp (mg/l)

tag: disease stage

value: LAPC

tag: total cycles of folfirinox

tag: progression after 4 cycles (recist 1.1)

value: Disease control

tag: overall survival


title: NZBWF_8_two_(miRNA-4_0)

source_name: 8-week-old NZBWF1 kidney

tag: strain


title: NZBWF_8_three_(miRNA-4_0)

tag: age


title: NZBWF_28_eight_(miRNA-4_0)

tag: tissue


title: NZBWF_8_one_(miRNA-4_0)


title: C. elegans-hsf-1 OE;ubiquilin-1-Rep2

description: hsf-1 OE;ubiquilin-1(tm1574)-Rep2

tag: genotype

tag: time point


title: HeLa Cas9 WT SRA_siRNA_ER l (Sample 17)

city: Durham

first: Christopher

middle: Vincent

last: Nicchitta

state: NC

department: Department of Cell Biology

country: USA

institute: Duke University School of Medicine

description:
Sample 17
Sample 17 provides an additional reference transcriptome control for SRA knockdown in the parental cell line.

data_processing:
Run Type: 51PE, Application Name: Ilumina NovaSeq 6000 Control Software, Application Version 1.6.0, RTA Version 3.4.4, Flow Cell: NovaSeq 6000 S-Prime
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm8 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
RNAseq reads were analyzed using Kallisto. A Kallisto index was built from all RefSeq genes (https://ftp.ncbi.nlm.nih.gov/refseq/H_sapiens/mRNA_Prot/ on 04.06.2018).  Illumina read files were mapped to the RefSeq index at default settings (single end mapping; parameters of -1 300 -s20). Mapped reads were transformed to transcript per million (TPM), including only annotated mRNAs (NM prefix) and using total transcript length (5’UTR, CDS, 3’UTR) and summed to generate a TPM/gene metric.
Genome_build: https://ftp.ncbi.nlm.nih.gov/refseq/H_sapiens/mRNA_Prot/
Supplementary_files_format_and_content: RNA-Seq Analysis_rawTPM_Total.xlsx (Excel file include TPM values for each sample and experimental condition)

molecule: polyA RNA

source_name: HeLa cells

growth_protocol: HeLa cell cultures were maintained in DMEM, 10% FCS, 5% CO2, and all experiments conducted with cultures at 70-80% confluence

extract_protocol:
HeLa cell fractions were extracted in guanidinium thiocyanate-phenol-chloroform and total RNA was isolated.
Following  oligo-dT selection for poly(A) mRNA, mRNAs was processed for deep sequencing library construction using the NEBNext® Ultra™ II RNA Library Prep Kit for Illumina® (New England Biolabs, E7770).  NEBNext® Poly(A) mRNA Magnetic Isolation Module (New England Biolabs, E7490) was used for poly(A) selection. NEBNext® Multiplex Oligos for Illumina® (Index Primers Set 1 and Set 2) adapter/primers were used to enable multiplexing.

treatment_protocol: Parental HeLa/Cas9 cells (non-trasnsfected), parental HeLa/Cas9 cells transfected with a non-targeting siRNA, parental,HeLa/Cas9 cells transfected with siRNA targeting SRPRA, HeLa/Cas9 SRB knockout cells (non-transfected), HeLa/Cas9 SRB knockout cells transfected with a non-targeting siRNA, and HeLa/Cas9 SRB knockout cells transfected with siRNA targeting SRPRA, were cultured for 96 hrs in DMEM, 10% FCS, 5% CO2 and at the 96 hour time point fractionated by sequential detergent treatments to yield cytosol and ER fractions.

tag: cell line

value: HeLa

tag: fraction

value: endoplasmic reticulum RNA fraction

tag: treatment

value: parental Cas9 cells, transfected with SRA targeting siRNA


title: C. elegans-hsf-1 OE;ubiquilin-1-Rep1

description: hsf-1 OE;ubiquilin-1(tm1574)-Rep1


title: HeLa Cas9 SRB-3-12 non-targeting siRNA_ER l (Sample 16)

description:
Sample 16
Sample 16 provides an additional reference transcriptome control for CRISPR SRB KO and siRNA transfection.

value: Cas9 SRB KO cells, transfected with a non-targeting siRNA


title: HeLa Cas9 SRB-3-12 untransfected_ER l (Sample 14)

description:
Sample 14
Sample 14 provides a transcriptome for CRISPR SRB KO with siRNA transfection control.

value: parental HeLa Cas9 SRB KO cells, untransfected


title: S842 BiSulfite-seq

city: ROCHESTER

first: ZHIFU

last: SUN

state: Minnesota

address: 200 1st St SW

department: Quantitative Health Sciences

institute: Mayo Clinic

library_source: genomic

data_processing:
Illumina’s RTA version 1.13.48.
RRBS reads were aligned to the hg19 genome assembly using the internal SAAP-RRBS pipeline
RRBS was performed at the Mayo Clinic Genotyping Shared Resource facility as previously described.  Briefly, DNA (250ng) was digested with Msp1 (New England Biolabs, Catalog Number:  R0106M) and purified using Qiaquick Nucleotide Removal Kit (Qiagen, Catalog Number: 28004).  End-repair A tailing was performed (New England Biolabs, Catalog Numbers:  M0212L) and TruSeq methylated indexed adaptors (Illumina, Catalog Number:  15025064) were ligated with T4 DNA ligase (New England Biolabs, Catalog Number: M0202L). Size selection was performed with Agencourt AMPure XP beads (Beckman Coulter, Catalog Number:  A63882). Bisulfite conversion was performed using EZ-DNA Methylation Kit (Zymo Research, Catalog Number:  D5001) as recommended by the manufacturer with the exception that incubation was performed using 55 cycles of 95 ̊C for 30 sec and 50°C for 15 min.  Following bisulfite treatment, the DNA was purified as directed and amplified using Pfu Turbo C Hotstart DNA Polymerase (Agilent Technologies, Catalog Number: 600414). Library quantification was performed using Qubits dsDNA HS Assay Kit (Life Technologies, Catalog Number:  Q32854) and the Bioanalyzer DNA 1000 Kit (Agilent Technologies, Catalog Number:  5067-1504).
Genome_build: hg19
Supplementary_files_format_and_content: methylation ratio file (text)

molecule: genomic DNA

source_name: Isolated CD4+ cells

extract_protocol: Resection or mucosal biopsies of the terminal ileum and CD4+ cells were isoloated for RNA-seq and RRBS

tag: Sex

value: M

tag: case control

value: Dis


title: C. elegans-hsf-1 OE-Rep4

description: hsf-1 OE-Rep4

value: Whole animals

value: uthIs235 [sur-5p::hsf-1::unc-54 3'UTR + myo-2p::tdTomato::unc-54 3' UTR]


title: C. elegans-hsf-1 OE-Rep3

description: hsf-1 OE-Rep3

value: Young adult (d1 of adulthood)


title: S831 BiSulfite-seq

value: F


title: pdac_18_before

value: blood

tag: patient diagnosis

tag: gender

tag: smoking status

tag: alcohol status

tag: baseline ca19-9 (u/ml)

tag: baseline cea (µg/l)

tag: baseline sii

tag: baseline nlr


title: S830 BiSulfite-seq

tag: age


title: S835 BiSulfite-seq


title: HeLa Cas9 WT untransfected_ER l (Sample 13)

description:
Sample 13
Sample 13 provides a reference transcriptome control for CRISPRSRB KO and siRNA transfection.

value: parental HeLa Cas9 cells, untransfected


title: pdac_17_after

tag: tissue

value: Pancreatic Ductal Adenocarcinoma

value: Female

tag: baseline bilirubin (micromol/l)

tag: baseline crp (mg/l)

tag: disease stage

tag: total cycles of folfirinox

tag: progression after 4 cycles (recist 1.1)

tag: overall survival


title: S833 BiSulfite-seq

tag: Sex

tag: case control


title: pdac_17_before

tag: patient diagnosis

tag: gender

value: Current

value: LAPC


title: C. elegans-hsf-1 OE-Rep2

description: hsf-1 OE-Rep2

tag: genotype

tag: time point


title: HeLa Cas9 SRB-3-12 SRA_siRNA_Cyt l (Sample 12)

description:
Sample 12
Sample 12 provides  a transcriptome for CRISPR SRB KO/SRA knockdown.

tag: cell line

value: HeLa

tag: fraction

value: cytosol RNA fraction

tag: treatment

value: Cas9 SRB KO cells, transfected with a SRA-targeting siRNA


title: C. elegans-hsf-1 OE-Rep1

description: hsf-1 OE-Rep1


title: S128 BiSulfite-seq

tag: age

value: Ctr


title: pdac_16_before

tag: tissue

tag: smoking status

value: Never

tag: alcohol status

tag: baseline ca19-9 (u/ml)

tag: baseline cea (µg/l)

tag: baseline sii

tag: baseline nlr

value: No CT-scan evaluation


title: pdac_16_after

tag: baseline bilirubin (micromol/l)

tag: baseline crp (mg/l)

tag: disease stage

tag: total cycles of folfirinox

tag: progression after 4 cycles (recist 1.1)

tag: overall survival


title: S129 BiSulfite-seq

tag: Sex

tag: case control


title: C. elegans-ubiquilin-1-Rep4

tag: genotype

tag: time point


title: pdac_15_after

tag: tissue

tag: patient diagnosis

tag: age

tag: gender

value: Former

value: Metastatic disease

value: Progressive disease


title: HeLa Cas9 WT non-targeting siRNA_ER l (Sample 15)

description:
Sample 15
Sample 15 provides a transcriptome control for CRISPR SRB KO and siRNA transfection.

tag: cell line

tag: fraction

value: endoplasmic reticulum RNA fraction

tag: treatment

value: parental HeLa Cas9 cells, transfected with a non-targeting siRNA


title: pdac_15_before

value: blood

tag: smoking status

tag: alcohol status

tag: baseline ca19-9 (u/ml)

tag: baseline cea (µg/l)

tag: baseline sii

tag: baseline nlr

tag: baseline bilirubin (micromol/l)


title: HeLa Cas9 WT non-targeting siRNA_Cyt l (Sample 9)

description:
Sample 9
Sample 9 provides a reference transcriptome control for the cytosol fraction of CRISPR SRB KO and siRNA transfection.


title: pdac_14_after

tag: baseline crp (mg/l)

tag: disease stage

tag: total cycles of folfirinox

tag: progression after 4 cycles (recist 1.1)

value: Disease control

tag: overall survival


title: C. elegans-ubiquilin-1-Rep1

tag: tissue

value: Whole animals

tag: genotype

tag: time point

value: Young adult (d1 of adulthood)


title: pdac_14_before

tag: patient diagnosis

value: Pancreatic Ductal Adenocarcinoma

tag: age

tag: gender

value: Female

value: Current


title: C. elegans-wildtype-Rep3

value: N2 - Wild-type


title: S122 BiSulfite-seq

tag: Sex

value: M

tag: case control


title: HeLa Cas9 SRB-3-12 SRA_siRNA_total (Sample 6)

description:
Sample 6
Sample 6 provides  a transcriptome for CRISPR SRB KO/SRA knockdown.

tag: cell line

value: HeLa

tag: fraction

value: total RNA fraction

tag: treatment

value: Cas9 SRB KO cells, transfected with a SRA-targeting siRNA


title: S127 BiSulfite-seq

value: F

value: Ctr


title: HeLa Cas9 WT SRA_siRNA_total (Sample 5)

description:
Sample 5
Sample 5 provides an additional reference transcriptome control for SRA knockdown in the parental cell line.

value: parental Cas9  cells, transfected with SRA targeting siRNA


title: S125 BiSulfite-seq


title: C. elegans-ubiquilin-1-Rep2


title: C. elegans-wildtype-Rep4


title: C. elegans-wildtype-Rep2


title: HeLa Cas9 WT untransfected_Cyt l (Sample 7)

description:
Sample 7
Sample 7 provides a reference transcriptome control for the cytosol fraction of parental HeLa Cas9 cells.

value: cytosol RNA fraction

value: parental HeLa Cas9 cells, untransfected


title: S126 BiSulfite-seq


title: HeLa Cas9 SRB-3-12 non-targeting siRNA_total (Sample 4)

description:
Sample 4
Sample 4 provides an additional reference transcriptome control for CRISPR SRB KO and siRNA transfection.

value: Cas9 SRB KO cells, transfected with a non-targeting siRNA


title: C. elegans-wildtype-Rep1


title: pdac_13_before

value: blood

value: Male

tag: smoking status

value: Former

tag: alcohol status

tag: baseline ca19-9 (u/ml)

tag: baseline cea (µg/l)

tag: baseline sii

tag: baseline nlr

tag: baseline bilirubin (micromol/l)

value: LAPC

value: Disease control


title: pdac_13_after

tag: tissue

value: Pancreatic Ductal Adenocarcinoma

value: Current

tag: baseline crp (mg/l)

tag: disease stage

tag: total cycles of folfirinox

tag: progression after 4 cycles (recist 1.1)

tag: overall survival


title: HeLa Cas9 SRB-3-12 non-targeting siRNA_Cyt l (Sample 10)

description:
Sample 10
Sample 10 provides a reference transcriptome control for CRISPR SRB KO and siRNA transfection.


title: HeLa Cas9 WT SRA_siRNA_Cyt l (Sample 11)

description:
Sample 11
Sample 11 provides a reference transcriptome control for SRA knockdown in the parental cell line.


title: C. elegans-ubiquilin-1-Rep3

value: Whole animals

tag: genotype

tag: time point

value: Young adult (d1 of adulthood)


title: pdac_11_after

tag: patient diagnosis

tag: age

tag: gender

value: Never

value: Metastatic disease


title: pdac_12_after

tag: smoking status

tag: alcohol status


title: S120 BiSulfite-seq

tag: Sex

value: M

tag: case control


title: pdac_12_before

tag: baseline ca19-9 (u/ml)

tag: baseline cea (µg/l)

tag: baseline sii

tag: baseline nlr


title: S116 BiSulfite-seq

value: Ctr


title: S117 BiSulfite-seq

value: F


title: HeLa Cas9 SRB-3-12 untransfected_Cyt l (Sample 8)

description:
Sample 8
Sample 8 provides a reference transcriptome control for the cytosol fraction of CRISPR SRB KO cells.

tag: cell line

value: HeLa

tag: fraction

value: cytosol RNA fraction

tag: treatment

value: Total cytosolic RNA from HeLa Cas9 SRB KO cells, untransfected


title: HeLa Cas9 WT non-targeting siRNA_total (Sample 3)

description:
Sample 3
Sample 3 provides an additional reference transcriptome control for CRISPRSRB KO and siRNA transfection.

value: total RNA fraction

value: parental HeLa Cas9 cells, transfected with a non-targeting siRNA


title: pdac_11_before

tag: tissue

value: blood

value: Male

tag: baseline bilirubin (micromol/l)

tag: baseline crp (mg/l)

tag: disease stage

tag: total cycles of folfirinox

tag: progression after 4 cycles (recist 1.1)

tag: overall survival


title: L20 ER HT 2

data_processing:
Run Type: 51 SR, Application Name: Ilumina HiSeq Control Software, Application Version HD 3.4.0.38, RTA Version 2.7.7, Flow Cell: HiSeq 3000/4000 SR
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm8 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
4SU-seq reads were analyzed using Kallisto. A Kallisto index was built from all RefSeq genes (https://ftp.ncbi.nlm.nih.gov/refseq/H_sapiens/mRNA_Prot/ on 04.06.2018).  Illumina read files were mapped to the RefSeq index and B. subtilis spike-in sequences at default settings (single end mapping; parameters of -1 300 -s20). Mapped reads were transformed to transcript per million (TPM), including only annotated mRNAs (NM prefix) and using total transcript length (5’UTR, CDS, 3’UTR) and the B. subtilis spike-in700 sequence,  and summed to generate a TPM/gene metric. TPM values were then normalized to B. subtilis spike-in700 abundance to correct for fractional recovery.
Genome_build: https://ftp.ncbi.nlm.nih.gov/refseq/H_sapiens/mRNA_Prot/
Supplementary_files_format_and_content: Excel file include TPM values for each sample and experimental condition

source_name: L20 ER HT 2

extract_protocol:
HeLa cell fractions were extracted in guanidinium thiocyanate-phenol-chloroform and total RNA was isolated. Following biotinylation, streptavidin affinity isolated of 4SU RNA, and oligo-dT selection for 4SU-poly(A) mRNA, mRNAs was processed for deep sequencing using NEBNext® Ultra™ II RNA Library Prep Kit for Illumina® (New England Biolabs, E7770).  NEBNext® Poly(A) mRNA Magnetic Isolation Module (New England Biolabs, E7490) was used for poly(A) selection.
libraries were constructed using NEBNext® Ultra™ II RNA Library Prep Kit for Illumina® (New England Biolabs, E7770)

treatment_protocol: In part I of the experiments (Samples 1-40), cells were pulse labeled with 4-thiouridine for 15 min, rinsed, and the media replaced with chase media containing 1 mM uridine. Cell cultures were sampled at the indicated times, and cytosol and ER fractions processed for 4SU RNA-seq. In Part II of th experiment (Samples 41-85) cells were treated with either vehicle (control), dithiothreitol (DTT), or harringtonine (HT) at the beginning of the pulse period and chased as in Part I, with inhibitors present in the chase media. Cells were sampled at 45 min of chase and processed for RNA-seq.


title: L19 ER DTT 2

source_name: L19 ER DTT 2


title: S114 BiSulfite-seq

tag: age


title: HeLa Cas9 SRB-3-12 untransfected_total (Sample 2)

description:
Sample 2
Sample 2 provides a transcriptome for CRISPR SRB KO with siRNA transfection control.

value: parental HeLa Cas9 SRB KO cells, untransfected


title: L17 ER Control 2

source_name: L17 ER Control 2


title: S131 BiSulfite-seq

tag: Sex


title: MS56_sh_CD10_2

city: Lyon

first: Véronique

last: Maguer-Satta

address: 28 Rue Laennec, Bat Cheney D, 4ème étage

country: France

institute: Centre de Recherche en Cancérologie de Lyon

data_processing:
Raw sequencing reads were aligned on the human genome (GRCh38) with STAR (v2.7.3a), with the annotation of known genes from gencode v33.
Gene expression was quantified using Salmon (1.1.0) and the annotation of protein coding genes from gencode v33.
Genome_build: GRCh38
Supplementary_files_format_and_content: Tab delimited file, Matrix table with raw gene counts for every gene and every sample

growth_protocol: MCF10A-derived cell lines used in this study were grown as recommended by thte American Type Culture Collection.

extract_protocol:
Total RNA were extracted using the Rneasy Mini kit from Qiagen
Poly-A RNA libraries were prepared for sequencing using standard Illumina protocols

tag: phenotype

value: CD10 knock-down


title: L16 ER Background 2

source_name: L16 ER Background 2


title: HeLa Cas9 WT untransfected_total (Sample 1)

description:
Sample 1
Sample 1 provides a reference transcriptome control for CRISPR SRB KO and siRNA transfection.

value: parental HeLa Cas9 cells, untransfected


title: L15 Cytosol HT 2

source_name: L15 Cytosol HT 2


title: MS55_sh_CD10_1


title: S863 RNA-seq

data_processing:
Illumina’s RTA version 1.13.48.
RNA-seq reads were aligned to the hg19 genome assembly using the internal MAPR-seq pipeline
The paired end reads were aligned by TopHat 2.0.6
Gene counts were generated using HTseq (http://www-huber.embl.de/users/anders/HTSeq/doc/overview.html)
QC was performed on the FASTQ files using RSeQC software (http://rseqc.sourceforge.net/)
Genome_build: hg19
Supplementary_files_format_and_content: gene expression count matrix (text)

extract_protocol:
Resection or mucosal biopsies of the terminal ileum and CD4+ cells were isoloated for RNA-seq and RRBS
total RNA was extracted from purified CD4+ cells using Exiqon’s miRCURY RNA Isolation Kit. Illumina TruSeq un-stranded RNA library preparation protocol was used for RNA-seq library preparation. The pair end sequencing was carried out using the Illumina HiSeq 2000 sequencer at 50bps (3-4 samples per lane), which generated 42-113 million pair-end reads for each sample. Raw data was processed using MAPR-Seq pipeline

tag: case control

value: Dis


title: pdac_10_after

tag: patient diagnosis

value: Pancreatic Ductal Adenocarcinoma

tag: gender

tag: smoking status

value: Former

tag: alcohol status

tag: baseline ca19-9 (u/ml)

tag: baseline cea (µg/l)

value: LAPC

value: Disease control


title: S861 RNA-seq


title: pdac_10_before

tag: tissue

value: Never

tag: baseline sii

tag: baseline nlr


title: pdac_9_after

value: Current

tag: baseline bilirubin (micromol/l)

tag: baseline crp (mg/l)

tag: disease stage

value: Metastatic disease


title: S857 RNA-seq

value: M


title: pdac_9_before

tag: total cycles of folfirinox

tag: progression after 4 cycles (recist 1.1)

tag: overall survival


title: L14 Cytosol DTT 2

source_name: L14 Cytosol DTT 2

tag: cell line

value: HeLa


title: S856 RNA-seq

tag: age

tag: Sex

value: F

tag: case control


title: L12 Cytosol Control 2

source_name: L12 Cytosol Control 2


title: pdac_8_after

tag: patient diagnosis

tag: gender

tag: smoking status


title: S115 BiSulfite-seq

value: Ctr


title: MS54_sh_ctrl_3

tag: phenotype

value: WT


title: L10 ER HT 1

source_name: L10 ER HT 1


title: MS53_sh_ctrl_2


title: S855 RNA-seq


title: pdac_8_before

tag: tissue

value: blood

value: Male

tag: alcohol status

tag: baseline ca19-9 (u/ml)

tag: baseline cea (µg/l)


title: MS52_sh_ctrl_1


title: pdac_7_after

value: Female

tag: baseline sii

tag: baseline nlr

tag: baseline bilirubin (micromol/l)

tag: baseline crp (mg/l)


title: S854 RNA-seq


title: MS57_sh_CD10_3

value: CD10 knock-down


title: M1B26_3

growth_protocol: MCF10A used in this study were grown as recommended by thte American Type Culture Collection. For MC26 and M1B26 cells, culture medium was supplemented with 5 ng/microliter of recombinant human BMP2 and 10 ng/mucroliter of recombinant human IL6.

tag: culture supplementation

tag: transformation status

value: transformed


title: L9 ER DTT 1

source_name: L9 ER DTT 1

tag: cell line


title: S862 RNA-seq

tag: age

tag: Sex

value: Dis


title: L7 ER Control 1

source_name: L7 ER Control 1


title: S853 RNA-seq

tag: case control


title: M1B26_2


title: pdac_6_after

tag: patient diagnosis

value: Pancreatic Ductal Adenocarcinoma

tag: gender

value: Former

tag: disease stage

tag: total cycles of folfirinox

tag: progression after 4 cycles (recist 1.1)

tag: overall survival


title: S852 RNA-seq


title: L6 ER Background 1

source_name: L6 ER Background 1


title: MC26_3


title: L5 Cytosol HT 1

source_name: L5 Cytosol HT 1


title: L4 Cytosol DTT 1

source_name: L4 Cytosol DTT 1


title: S850 RNA-seq


title: M1B26_1


title: pdac_6_before

source_name: pancreatic ductal adenocarcinoma, blood

tag: tissue

tag: smoking status

tag: alcohol status

tag: baseline ca19-9 (u/ml)

tag: baseline cea (µg/l)

value: LAPC

value: Disease control


title: S849 RNA-seq


title: MC26_2

tag: culture supplementation


title: S846 RNA-seq


title: MC26_1

tag: transformation status


title: pdac_7_before

value: Never

tag: baseline sii

tag: baseline nlr

tag: baseline bilirubin (micromol/l)

tag: baseline crp (mg/l)


title: MCF10A_CT_2

value: not transformed

tag: cell line


title: S842 RNA-seq

tag: age

tag: Sex

value: M

tag: case control


title: MCF10A_CT_3


title: pdac_4_after

tag: patient diagnosis

tag: gender

tag: disease stage

value: Metastatic disease

tag: total cycles of folfirinox

tag: progression after 4 cycles (recist 1.1)

value: Progressive disease


title: S843 RNA-seq

value: F


title: pdac_4_before

tag: tissue

tag: smoking status

tag: alcohol status

tag: baseline ca19-9 (u/ml)

tag: overall survival


title: B10 ER 60 min

source_name: B10 ER 60 min

value: HeLa


title: B9 ER 45 min

source_name: B9 ER 45 min


title: L1 Cytosol Background 1

source_name: L1 Cytosol Background 1


title: S839 RNA-seq

source_name: Isolated CD4+ cells


title: pdac_3_after

value: blood

value: Current

tag: baseline cea (µg/l)

tag: baseline sii

tag: baseline nlr


title: MCF10A_CT_1

tag: culture supplementation

tag: transformation status

tag: cell line


title: B8 ER 30 min

source_name: B8 ER 30 min


title: pdac_5_after

tag: age

value: Male

tag: baseline bilirubin (micromol/l)

tag: baseline crp (mg/l)


title: pdac_3_before

tag: patient diagnosis

tag: gender

tag: disease stage


title: S838 RNA-seq

tag: Sex

tag: case control


title: BRCA2_3

source_name: Mammary gland

extract_protocol:
Epithelial mammary cells were purified from the mammary gland by proteolytic digestion and differential centrifugation and frozen in FCS 10% DMSO prior to RNA extraction using a Qiagen RNeasy Plus Mini kit.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: genotype

value: BRCA2 mutated

tag: origin

value: Preventive mastectomy


title: L2 Cytosol Control 1

source_name: L2 Cytosol Control 1


title: pdac_5_before

tag: tissue

tag: smoking status

tag: alcohol status

tag: baseline ca19-9 (u/ml)

tag: total cycles of folfirinox

tag: progression after 4 cycles (recist 1.1)

tag: overall survival


title: BRCA2_2


title: S837 RNA-seq

tag: age

value: Dis


title: B7 ER 15 min

source_name: B7 ER 15 min

tag: cell line


title: S835 RNA-seq


title: pdac_2_after

value: Pancreatic Ductal Adenocarcinoma

value: Female

tag: baseline cea (µg/l)

tag: baseline sii

tag: baseline nlr

tag: baseline bilirubin (micromol/l)

tag: baseline crp (mg/l)

value: No CT-scan evaluation


title: pdac_1_after

tag: patient diagnosis

tag: gender

tag: disease stage

value: Disease control


title: BRCA2_1

tag: genotype

tag: origin


title: B5 Cytosol 60 min

source_name: B5 Cytosol 60 min


title: S833 RNA-seq

tag: Sex

tag: case control


title: pdac_1_before

tag: tissue

tag: smoking status

value: Never

tag: alcohol status

tag: baseline ca19-9 (u/ml)

tag: total cycles of folfirinox


title: B4 Cytosol 45 min

source_name: B4 Cytosol 45 min

tag: cell line


title: Pg+Fa H2O2-3

city: Loma Linda

first: Yuetan

last: Dou

state: CA

address: 11021 Campus Street AH114

department: Microbiology and Molecular Genetics

institute: Loma Linda University

data_processing:
NextSeq 550 onboard basecalling, fastq files were generated using Illumina bcl2fastq package v1.8.4 with default settings.
RNA-seq fastq files were trimmed with trimmomatic, aligned to P. gingivalis W83 genome, and reads were qunatified with cutfflinks. Gene differential expression was analyzed using cuffdiff with FPKM threshold of 1.
Assembly: Porphyromonas gingivalis W83, Filifactor alocis ATCC 35896
Supplementary files format and content: original process to.csv file, with all genes reads in two files, P. gingivalis and F. alocis respectively.

organism:
Porphyromonas gingivalis W83
Filifactor alocis ATCC 35896

source_name: culture

growth_protocol: Anaerobic condotions (80% N2, 10% H2, 10%CO2)

extract_protocol:
Briefly, RNA were harvested by Qiagen RNA kit. ribosomal RNA was removed from 2 µg of total RNA by using RiboMinus Transcriptome Isolation Kit (Life Technologies, Carlsbad, CA).
The first- and the second- strand cDNA synthesis, the RNA-seq barcode ligation, and other steps of libraries construction were performed by using Nextflex RNA-Seq kit according to the protocol of manufacturer (Bioo Scientific, Austin, TX).
cDNA in library were taged by specific barcode sequence and exposed to sequencing.

treatment_protocol: Treated by 0.25 mM of hydrogen peroxide

tag: cell type

value: culture

tag: treatment

value: 0.25 mM H2O2 stress


title: BRCA1_3

value: BRCA1 mutated


title: Pg+Fa H2O2-2


title: BRCA1_2


title: B3 Cytosol 30 min

source_name: B3 Cytosol 30 min


title: S830 RNA-seq

tag: age


title: BRCA1_1


title: WT_3

value: WT

value: Reduction mammoplasty


title: Pg+Fa H2O2-1


title: WT_2


title: B6 ER Control

source_name: B6 ER Control

value: HeLa


title: S131 RNA-seq

value: M

value: Ctr


title: B2 Cytosol 15 min

source_name: B2 Cytosol 15 min


title: S128 RNA-seq


title: pdac_2_before

value: blood

tag: baseline cea (µg/l)

tag: baseline sii

tag: baseline nlr

tag: baseline bilirubin (micromol/l)

tag: baseline crp (mg/l)

value: LAPC

tag: progression after 4 cycles (recist 1.1)

tag: overall survival


title: WT_1

tag: genotype

tag: origin


title: A9 ER 45 min

source_name: A9 ER 45 min


title: S127 RNA-seq

tag: Sex

value: F

tag: case control


title: A10 ER 60 min

source_name: A10 ER 60 min


title: P-3

city: Hefei

first: Kan

last: He

state: Anhui

address: 111 Jiulong Road

institute: Anhui University

data_processing:
PE150 platform used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm9 whole genome using HISAT2 v2.0.5.
We used HTSeq(0.9.1) statistics to compare the Read Count values on each gene as the original expression of the gene, and then used FPKM to standardize the expression.
Difference expression of genes was analyzed by DESeq (1.30.0) with screened conditions as follows: expression difference multiple |log2FoldChange| > 1, significant P-value < 0.05.
Bidirectional clustering analysis was performed for all different genes in the samples using R language Pheatmap(1.0.8) software package.
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text files include the raw count expression values of this transcript for each Sample ..

growth_protocol: SCC-15 cells were cultured in DMEM/F-12  supplemented with 10% FBS , penicillin (100 U/ml), and streptomycin (100 µg/ml).

extract_protocol:
RNA was harvested using Trizol reagent. NEBNext Ultra II RNA Library Prep Kit for Illumina was used with total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: Plasmid (PB-IP-2flag and PB-IP-PPARG) was transferred to SCC-15 cells, respectively.

value: Oral squamous cell carcinoma

value: transfected with  PB-IP-PPARG


title: STAT4flox/floxLDLr-/- +DDC_12

city: Valhalla

first: Patric

middle: K

last: Stanton

state: New York

address: 15 Dana Road Basic Sciences Bldg Room 217

department: Cell Biology & Anatomy

institute: New York Medical College

hyb_protocol: Standard Nanostring™ hybridization protocol was used, available at: https://nanostring.com/wp-content/uploads/MAN-10056-05-Gene-Expression-Hybridization-Protocol.pdf

scan_protocol: Standard Nanostring™ scan protocol was used, available at: https://jp.nanostring.com/wp-content/uploads/MAN-10147-03-nCounter-Pro-Analysis-System-User-Manual.pdf

data_processing: The raw counts from Nanostring™ of each desired comparison were placed together and normalized. The p-values, adjusted p-values, log2Fold-change, and baseMean were then calculated. Utilizing the clusterprofiler package in R, over-representation analysis was conducted to identify important gene set changes. Setting the p-value cutoff to 0.05, genes that showed significant differences (for example, in Chow_LysMcre_Vs_Control or DDC_LysMcre_Vs_Control) were extracted and cross-referenced with publically available databases, such as WikiPathways, Reactome, KEGG, or GeneOntology, via their log2Fold-changes. The pathway changes observed in each group were then ranked by -log (P.adj).

label: Qubit

source_name: Hippocampus

label_protocol: Standard Nanostring™ label protocol was used, available at: https://jp.nanostring.com/wp-content/uploads/MAN-10147-03-nCounter-Pro-Analysis-System-User-Manual.pdf

extract_protocol: Standard Nanostring™ extraction protocol was used, available at: https://tools.thermofisher.com/content/sfs/manuals/trizol_reagent.pdf

tag: diet

value: DDC

tag: duration

value: 16 weeks

value: 24 weeks

value: Male

tag: tissue

value: Hippocampus


title: STAT4flox/floxLDLr-/- +chow_10

value: chow


title: STAT4flox/floxLDLr-/- +chow_11


title: A8 ER 30 min

source_name: A8 ER 30 min

tag: cell line


title: S126 RNA-seq


title: S831 RNA-seq

value: Dis


title: STAT4flox/floxLDLr-/- +chow_9


title: P-2

tag: cell type

tag: treatment


title: B1 Cytosol Control

source_name: B1 Cytosol Control


title: A7 ER 15 min

source_name: A7 ER 15 min


title: P-1


title: S129 RNA-seq

source_name: Isolated CD4+ cells

tag: age


title: CK-3

value: transfected with  PB-IP-2flag


title: STAT4flox/floxLDLr-/- +DDC_8


title: S125 RNA-seq


title: A6 ER Control

source_name: A6 ER Control


title: S122 RNA-seq


title: A4 Cytosol 45 min

source_name: A4 Cytosol 45 min


title: A5 Cytosol 60 min

source_name: A5 Cytosol 60 min


title: S117 RNA-seq


title: CK-2


title: S120 RNA-seq


title: A3 Cytosol 30 min

source_name: A3 Cytosol 30 min


title: STAT4floxLysMCreLDLr-/- +DDC_5


title: STAT4floxLysMCreLDLr-/- +DDC_6


title: STAT4flox/floxLDLr-/- +DDC_7


title: STAT4floxLysMCreLDLr-/- +DDC_4


title: S115 RNA-seq


title: A2 Cytosol 15 min

source_name: A2 Cytosol 15 min


title: S116 RNA-seq


title: S114 RNA-seq


title: Met_s1 [MULTI-seq barcodes]

city: Irvine

first: Devon

last: Lawson

address: 839 Health Science Road, Sprague Hall 140

institute: University of California, Irvine

description:
MULTI-seq barcodes
nR003-L1-P2-CGATGTAT

data_processing:
Sequencing reads were aligned utilizing 10x Genomics Cell Ranger Count 3.1.0 to the dual indexed mm10/GRCh38 genome provided by Cell Ranger
All libraries were aggregated using 10x Genomics Cell Ranger Aggr 3.1.0, to normalize the number of mean reads per cells. MULTI-seq reads were processed according to McGinnis et al. 2019 MULTI-seq protocol (https://github.com/chris-mcginnis-ucsf/MULTI-seq).
Cells in dataset were subsequently trimmed and analyzed in Seurat v3, with assigned cell type labels and quality control metrics for each cell passing initial quality filtering included in the metadata sheets.
Genome_build: mm10/GRCh38
Supplementary_files_format_and_content: tab seperated barcode list for each mouse from MULTI-seq protocol is provided for demultiplexing

source_name: Metastatic brain with MDA-MB-231BR2

extract_protocol:
At 10 weeks old, MITRG mice were injected intracardially with 500,000 mCherry labeled 231BR cells as previously described. 25 days after intracardiac injection and following perfusion with ice cold PBS containing 5μg/ml actinomycin D (act D), whole metastatic brains were briefly imaged on a dissection microscope (Leica Biosystems, DMC 2900) for mCherry and GFP intensity.  Half brains were then dissected, fixing the left hemisphere in 4% PFA for histology and the right hemisphere was prepped for dissociation as described in Hasselmann and Coburn et al. (2019) with  modifications. The cerebellum was removed and the whole right hemisphere was stored briefly in RPMI 1640 containing 5μg/mL act D, 10μM triptolide, and 27.1ug/mL anisomycin. Tissue dissociation was then performed using the Tumor Dissociation kit, human (Miltenyi Biotec) and the gentleMACS OctoDissociator with heaters (Miltenyi Biotec) according to manufacturer guidelines with modifications. Briefly, tissue was cut into ~1mm pieces and placed into the C-tubes with the kit’s enzymes, 5μg/mL act D, 10μM triptolide, and 27.1ug/mL anisomycin and samples were dissociated using the preprogrammed soft tumor protocol. Following enzymatic digestion, samples were strained through a 70μm filter and pelleted by centrifugation. Myelin and debris were removed by resuspending the pellet in 8mL 23% Percoll, overlaid with 2mL of 1X DPBS, spinning at 400xg for 25 minutes at 4°C, with acceleration and brake set to 0, and discarding the myelin band and supernatant.  For barcoding of cells from each individual mouse the MULTI-seq lipid- tagged indices for sample multiplexing for scRNAseq protocol was followed (McGinnis et al, 2019). Lipid anchor and co-anchor reagents were a generous gift from Zev Gartner, and barcode index oligos were purchased from Integrated DNA Technologies, Inc. Cells were resuspended and washed with 15 mL cold DPBS and pelleted by centrifugation (10 minutes, 400xg). The supernatant was discarded, and cells were resuspended in 180μL of DPBS. 20μL of 20μM Anchor:Barcode solution was added to a final concentration of 2μM, and incubated on ice for 5 minutes. Next 20μL of 20μM Co-Anchor solution was added, gently mixed and incubated for 5 minutes. After incubation 1mL 1% BSA in DPBS was added and cells were pelleted by centrifugation (5 minutes, 400xg). Finally, the supernatant was removed and washed a second time with 1mL 1% BSA in PBS and pelleted by centrifugation (5 minutes, 400xg). Next, mouse cell removal was performed by resuspending cell pellets in 160μL FACS buffer (0.5% BSA in 1X DPBS) + 40μL Mouse cell removal beads (Miltenyi Biotec) and incubated at 4°C for 15 minutes. Mouse and human cells were then separated using LS columns and the MidiMACs separator (Miltenyi Biotec) and the human cells were collected in the flow through. Human cells were pelleted via centrifugation (10 minutes, 400xg) and control samples and metastatic samples were then pooled separately. Cells were resuspended to ~1,000 cells per microliter in FACS buffer, according to counts performed on a hemocytometer.
MULTI-seq tagged isolated human cells were pelleted via centrifugation for 10 minutes at 400xg and resuspended to approximately 1,000 cells per microliter in FACS buffer. Replicate cell pools were counted by hemocytometer and pooled for further single cell sequencing. Final cell suspensions were counted on the Countess II automated cell counter to determine actual concentration for droplet generation. Cells were loaded onto the 10x Genomics Chromium Single Cell Gene Expression 3’ v3 Chemistry kits for GEMs generation. Following the Chromium Single Cell 3′ Reagents Kits version 3 user guide (CG000183 Rev C), cells were loaded to achieve approximately 10,000 cells for capture. MULTI-seq barcode libraries were prepared according to McGinnis et al. 2019 MULTI-seq protocol.  Libraries were sequenced on the Illumina NovaSeq 6000 platform to achieve an average read depth of 50,000 mean reads per cell for 3’ gene expression libraries. MULTI-seq barcode libraries were sequenced to achieve at least 5,000 reads per cell.

tag: pooled mouse barcodes

tag: batch

value: group 2

tag: mouse host strain genotype

value: C:129S2- Rag2tm1.1Flv Csf1tm1(CSF1)Flv CSF2/IL3tm1.1(CSF2,IL3)Flv Thpotm1.1(TPO)Flv Il2rgtm1.1Flv/J

tag: mouse host strain common name

value: MITRG


title: STAT4floxLysMCreLDLr-/- +chow_3


title: A1 Cytosol Control

source_name: A1 Cytosol Control

value: HeLa


title: Control [MULTI-seq barcodes]

description:
MULTI-seq barcodes
nR003-L1-P1-ATCACGAT

source_name: Control brain

value: group 1


title: STAT4floxLysMCreLDLr-/- +chow_2


title: SUGP1,seqrun2,rep2

status: Public on Aug 31 2023

city: New York

first: Jahan

last: Rahman

address: 417 E 68th St

department: Center for Hematologic Malignancies

institute: Memorial Sloan Kettering

description: SF3B1WT_SUGP1-ADAR_replicate2_IGO_13990_B_4

data_processing:
reads from the sequencing libraries are trimmed (Trimmomatic) and aligned (STAR) to the hg19 human reference genome. The aligned BAM file is converted to a SAM file and the nucleotide frequency at each position in the transcriptome is recorded from aligned reads and placed into a SQL table. For each nucleotide in the transcriptome, the TRIBE RNA nucleotide frequency is compared with the wild-type mRNA library (WT RNA) nucleotide frequency to identify RNA editing sites. For a legitimate edit site, the frequency of A is greater than 80% and the frequency of G is 0.5% in the WT RNA and the frequency of G is greater than 0 in the TRIBE RNA (using the reverse complement if annotated gene is in the reverse strand). Modifying the nucleotide frequency of G in WT RNA from 0 to 0.5% allows very low-level sequence heterogeneity in WT RNA and does not disrupt the identification of legitimate editing sites in deeply sequenced libraries. We used an editing threshold of at least 5% in each replicate. The TRIBE edit sites are required to be present in both replicates and any sites that overlap with catalytic Adar alone edit sites with at least 1% editing are removed. Finally, a list of transcripts is created by tabulating all transcript that contain edit sites.
Assembly: hg19
Supplementary files format and content: tab-delimited text-files summarizing the number of editing sites per gene in the samples: gpatch8.txt, sugp1.txt
Library strategy: TRIBE-seq

extract_protocol:
293T were transfected with GPATCH8-ADAR, ADAR-SUGP1, or respective MCP/ADAR non-targeting control, fusion expression plasmids using a 3:1 ratio of Polyethylenimine (PEI):DNA. 24 hours after transfections cells were suspended in sorting buffer (DPBS, 1% BSA supplemented with DAPI) and passed through a 35μm strainer mesh. FACS was performed by selecting for GFP positive DAPI negative single cells. One million GFP positive cells were sorted on a BD FACSymphony S6 or BD FACSAria III Cell Sorter, and RNA was isolated using RNeasy Plus Mini Kit. A minimum of 500 ng of high-quality RNA (as determined by Agilent Bioanalyzer) per replicate was used as input for library preparation.
Ribo-depleted Illumina libraries were prepared by the Integrated Genomics Operation (IGO) at Memorial Sloan Kettering with a modified TruSeq protocol and sequenced on the Illumina HiSeq 2000 to obtain ∼60-80M paired-end 100 bp reads per sample.


title: K700E,sgGPATCH8,seqrun2,rep2

data_processing:
A genome annotation (UCSC hg19/GRCh37) was created by combining the UCSC knownGene (PMID: 24270787), Ensembl 71 (PMID: 23203987), and MISO v2.0 (PMID: 21057496) annotations. Transcriptome mapping was accomplished using RSEM v1.2.4 (PMID: 21816040) with the argument ‘‘-v 2’’ which indicates Bowtie invocation (PMID: 19261174). Unaligned reads were mapped to the genome with TopHat v2.0.8b (PMID: 19289445), and to a custom annotation which includes all gene-level pairwise combinations of annotated 5’ and 3’ splice sites. The combined RSEM/Bowtie and TopHat alignments were inputted to MISO v2.0 (PMID: 21057496) to quantify isoform expression levels.
Assembly: hg19
Supplementary files format and content: tab-delimited text-file includes raw isoform counts for each sample: isoform.expression.txt

extract_protocol:
For cell line RNA sequencing (RNA-seq), RNA was extracted from K562 cells using the Qiagen RNeasy extraction kit, according to the manufacturer’s instructions. A minimum of 500 ng of high-quality RNA (as determined by Agilent Bioanalyzer) per replicate was used as input for library preparation.
Poly(A)-selected, strand-specific (dUTP method) Illumina libraries were prepared by the Integrated Genomics Operation (IGO) at Memorial Sloan Kettering with a modified TruSeq protocol and sequenced on the Illumina HiSeq 2000 to obtain ∼60-80M paired-end 100 bp reads per sample.


title: control,seqrun2,rep2

description: SF3B1WT_control-ADAR_replicate2_IGO_13990_B_2


title: control,seqrun1,rep2

description: SF3B1WT_control-ADAR_replicate2_IGO_13990_2


title: Gut_scRNA_Tcf7fVavCre

city: Morgantown

first: Gangqing

last: Hu

state: West Virginia

address: 64 Medical Center Drive

department: MicroBiology, Immunology, and Cell Biology

institute: West Virginia University

library_source: transcriptomic single cell

data_processing:
Cell Ranger v.3.0.2 were used to process scRNA-seq fastq files which performed alignment filtering barcode counting and unique molecular identifier counting.
Assembly: mm10
Supplementary files format and content: UMI versus gene counting matrix for scRNA-Seq

source_name: Gut

extract_protocol:
Cells were isolated from bone marrows or gut. Isolated cells were further sorted based on their surface markers.
The scRNA-seq libraries were generated using Chromium Single Cell 3’ Library & Gel Bead Kit v3 (10X Genomic) according to manufacturer’s protocol. Briefly, 15,000 live cells were FACS-sorted and used to generate single-cell gel-bead in emulsion (GEM). After reverse transcription, GEMs were disrupted. Barcoded cDNA was isolated and amplified by PCR (12 cycles). Following fragmentation, end repair, and A-tailing, sample indexes were added during index PCR (8 cycles).
Indexed libraries were multiplexed and sequenced on an Illumina NOVO Seq instruments according to the manufacturer's instructions (26 cycles of Read 1, 8 cycles of i7 Index, and 98 cycles of Read2).

tag: strain

value: Bone Marrow

tag: sorting marker


title: GPATCH8,seqrun1,rep2

description: SF3B1WT_GPATCH8-ADAR_replicate2_IGO_13990_4


title: untransfected,seqrun2,rep1


title: K700E,sgGPATCH8,seqrun1,rep2


title: STAT4floxLysMCreLDLr-/- +chow_1

tag: genotype


title: control,seqrun1,rep1

description: SF3B1WT_control-ADAR_replicate1_IGO_13990_1


title: CK-1


title: K700E,sgGPATCH8,seqrun2,rep1


title: Met_s2 [MULTI-seq barcodes]

description:
MULTI-seq barcodes
nR003-L1-P3-TTAGGCAT


title: K700E,sgSUGP1,seqrun1,rep2


title: Gut_scRNA_Tcf7flox


title: K700E,sgGPATCH8,seqrun1,rep1


title: control,seqrun2,rep1

description: SF3B1WT_control-ADAR_replicate1_IGO_13990_B_1


title: K700E,sgSUGP1,seqrun2,rep2


title: K700E,sgRenilla,seqrun1,rep1


title: K700E,sgRenilla,seqrun2,rep1


title: K700E,sgSUGP1,seqrun1,rep1


title: SUGP1,seqrun2,rep1

description: SF3B1WT_SUGP1-ADAR_replicate1_IGO_13990_B_3


title: GPATCH8,seqrun1,rep1

description: SF3B1WT_GPATCH8-ADAR_replicate1_IGO_13990_3


title: K700E,sgSUGP1,seqrun2,rep1


title: WT,sgGPATCH8,seqrun2,rep2


title: WT,sgGPATCH8,seqrun2,rep1


title: WT,sgGPATCH8,seqrun1,rep1


title: WT,sgGPATCH8,seqrun1,rep2


title: WT,sgSUGP1,seqrun2,rep2


title: WT,sgSUGP1,seqrun2,rep1


title: WT,sgSUGP1,seqrun1,rep2


title: WT,sgRenilla,seqrun2,rep1


title: WT,sgRenilla,seqrun1,rep1


title: RNA-seq of NMP differentiation - D7 WT rep2

city: Melbourne

first: Gabriel

middle: Markus

last: Hauswirth

state: Victoria

address: 15 Innovation Walk, Clayton Campus

department: Australian Regenerative Medicine Institute / EMBL Australia

country: Australia

institute: Monash University

data_processing:
Data were analysed twice with similar methods. Once for looking at RNA-seq alone and a second time for integration with ATAC-seq data.
1. [RNA_seq_Raw_Count_table.txt, AllDays_RNAseq_Log2FoldchangeFDR0point1.csv] Raw fastq files have been analysed with RNAsik pipeline (Tsyganov et al. 2018) to produce raw genes count matrix and various quality control metrics. For this analysis RNAsik pipeline (Tsyganov et al. 2018) ran with STAR aligner option (Dobin et al. 2013) and reads were quantified with featureCounts (Liao, Smyth, and Shi 2014). The reference GTF and FASTA files were downloaded from Ensembl database.
1. [RNA_seq_Raw_Count_table.txt, AllDays_RNAseq_Log2FoldchangeFDR0point1.csv]  Raw counts were then analysed with Degust (Powell 2015) web tool to do differential expression analysis to produce list of differentially expressed genes and several quality plots including classical multidimensional scaling (MDS) and MA plots. In this analysis limma voom (Law et al. 2014) was used for differential expression analysis. Degust (Powell 2015) largely follows limma voom workflow with typical conts per million (CPM) library size normalisation and trimmed mean of M values (TMM) normalisation (Robinson and Oshlack 2010) for RNA composition normalisation.
2. [all.counts.txt] Illumina RTA 2.0 software used for basecalling.
2. [all.counts.txt] Sequenced reads were  mapped to mm10 whole genome using Hisat2 (version 2.1.0) with default parameters
2. [all.counts.txt] Reads Per Gene were calculated with the featureCount software (version 1.6.3) usingth gencode M19 annoation as reference
genome build: mm10
processed data files format and content: CSV file includes Log2FC normalised to D2, CPM, p-values values for each sampling day with an FDR cut-off of 0.1.
processed data files format and content: Matrix table with raw gene counts for every gene and every sample

source_name: ES-derived neuromesodermal progenitor

growth_protocol: Mouse ESCs were differentiated according to published protocols (Gouti et al. 2014; Gouti et al. 2017) with minor modifications. Briefly, ESCs were routinely maintained in ES media (Composition: 81.8% Knockout DMEM (Gibco, 10829-018); 15% fetal bovine serum; 1% Pen Strep (Gibco, 15140-122); 1% GlutaMAX-I (Gibco, 35050-061); 1% MEM NEAA (Gibco, 11140-040), 0.2% 1000x 2-Mercaptoethanol (Gibco, 21985-023)) supplied with LIF (1000x, made in-house) on mitotically inactive primary mouse embryo fibroblasts. In preparation for differentiation, cells were detached in 0.25% Trypsin-EDTA (Gibco, 25200-056), feeder depleted once for 45 mins and plated on gelatin coated (0.1% Gelatin Sigma, G1890-100G) 6-wells (Falcon, 353046) at a density of 8x103 cells/cm2 in ES media. Cells were given 24-48 hours to settle. To start differentiation (Day (D) 0), ES media was changed to N2B27 media (1:1 medium of Advanced Dulbecco’s Modified Medium F-12  (Gibco, 12634028) supplemented with 1x N2 (Gibco, 17502001), and Neurobasal medium (Gibco, 21103049) supplemented with 1x B27 with or without Vitamin A, 1x Glutamax (Gibco, 17504044 or 12587010), 40 µg/ml BSA Fraction V (Gibco, 15260037) and 100 mM Beta-mercaptoethanol. For ESC differentiation, N2B27 was supplemented as follows: D0 - 10 ng/ml bFgf (human, Miltenyi Biotec), refreshed at 24 hours; D2 - 5µM CHIR99021 (StemMACS, 130-103-926); D6 - 50 ng/ml Gdf11 (human, Miltenyi Biotec). Cells were mechanically dissociated and split at a ratio 1:3 on D3 of  differentiation.

extract_protocol:
ESC in vitro differentiation samples for RNA-seq were collected on D2, D3, D6 and D7 +/- Gdf11. Approximately 2-4 million cells were detached from plates with 0.25% Trypsin, washed in PBS, lysed directly in RA1 lysis buffer (Macherey-Nagel GmbH & Co) and immediately frozen on dry ice. After all samples were collected RNA was further extracted using Nucleospin RNA (Macherey-Nagel GmbH & Co) kit.
RNA libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: Two replicates were Gdf11 treated for 24h

value: untreated

tag: differentiation day


title: RNA-seq of NMP differentiation - D6 WT rep2


title: RNA-seq of NMP differentiation - D3 WT rep2


title: RNA-seq of NMP differentiation - D7 WT rep1


title: RNA-seq of NMP differentiation - D7G WT rep1

value: treated with 50ng/ml Gdf11 (human, Miltenyi Biotec)


title: RNA-seq of NMP differentiation - D7G WT rep2


title: RNA-seq of NMP differentiation - D2 WT rep2

source_name: ES-derived epiblast stem cell


title: RNA-seq of NMP differentiation - D6 WT rep1


title: RNA-seq of NMP differentiation - D2 WT rep1


title: ATAC-seq of NMP differentiation - D7G WT rep2

data_processing:
Illumina RTA 2.0 software used for basecalling.
Sequenced reads were  mapped to mm10 whole genome using Hisat2 (version 2.1.0) with  parameters  --no-unal --no-mixed -X 2000
duplicated reads were removed with samtools rmdub command (version 1.3)
filtered bam files were converted to Bigwig files
peaks were called using MACS version 2.1.1.20160309 with the following paramaters -g mm --nomodel --extsize 100 --shift -45
insertions per peak was determined with the  intersectBed for all peaks and samples
Enriched DNA binding motifs were identified within the differential peaks with the findMotifsGenome.pl of the Homer package(Heinz et al. 2010) (v4.10) with parameters "-len 8,10,12 -size given -S 8 -p 6 -cache 1000 -fdr 0 -chopify".
genome build: mm10
processed data files format and content: bigwig files
processed data files format and content: peak text files as produced by MACS2
processed data files format and content: reads counts per peak file
processed data files format and content: 2 excel files containing differential peaks (up- or downregulated, opening or closing respectively) - multitabular format
processed data files format and content: 4 motif enrichment (tab delimited) files - (up- or downregulated, opening or closing respectively) and joined or unjoined with RNA-seq data in this study.

extract_protocol:
ESCs in vitro differentiation samples for ATACseq were collected on D2, D3, D6 and D7 +/- Gdf11. Cells were rinsed in PBS, dissociated at 37℃ for 5 mins using 0.25% Trypsin, pelleted and resuspended in fresh N2B27 supplemented with bFGF and CHIR99021, placed on ice and cell counting performed on a Countess Automated Cell Counter (ThermoFisher Scientific). 50,000 cells were used for ATAC library preparation as previously described (Buenrostro et al., 2014).
50,000 cells were used for ATAC library preparation as previously described (Buenrostro et al., 2014) and underwent double Bead clean-up prior to sequencing..


title: ATAC-seq of NMP differentiation - D7 WT rep2


title: RNA-seq of NMP differentiation - D3 WT rep1


title: ATAC-seq of NMP differentiation - D3 WT rep2


title: ATAC-seq of NMP differentiation - D2 WT rep1


title: ATAC-seq of NMP differentiation - D6 WT rep1


title: ATAC-seq of NMP differentiation - D2 WT rep2


title: ATAC-seq of NMP differentiation - D7G WT rep1


title: ATAC-seq of NMP differentiation - D6 WT rep2


title: ATAC-seq of NMP differentiation - D7 WT rep1


title: ATAC-seq of NMP differentiation - D3 WT rep1


title: WT,sgSUGP1,seqrun1,rep1


title: i706_i503

status: Public on Aug 28 2023

city: cambridge

first: Kendig

last: Sham

state: england

address: Jeffrey Cheah Biomedical Centre, Puddicombe Way

department: MRC Cambridge Stem Cell Institute

institute: University of Cambridge

data_processing:
STAR alignment parameters: --outFilterMultimapNmax 1 –outSAMstrandField intronMotif –outSAMattributes All –outSAMtype BAM SortedByCoordinate
Picard AddOrReplaceReadGroups with parameters: RGID=4 RGLB=lib1 RGPL=illumina RGPU=unit1 RGSM=20
Picard ValidateSamFile with parameters: MODE=SUMMARY
Picard MarDuplicates -REMOVE_DUPLICATES true
HTSeq was used to ount reads mapped to each gene with parameters: -s no -f bam
Assembly: GRCh38
Supplementary files format and content: raw_counts.txt.gz

source_name: mobilized peripheral blood

growth_protocol: single HSC/MPPs (CD19-/CD33-/CD34+/CD45dim/CD38-/CD45RA-) and single GMPs (CD19-, CD33-, CD34+, CD45dim, CD38+, CD7/CD10-, CD45RA+)  were cultured for 21 days in media promoting HSC/MPP differentiation: StemPro base media supplemented with Nutrients , Pen/Strep (1%), L-Glu (1%), human LDL (50ng/ml)  in addition to the following cytokines: SCF (100ng/ml), Flt-3L (20ng/ml), TPO (100ng/ml), EPO (3 units/ml), IL-6 (50ng/ml), IL-3 (10ng/ml) and GM-CSF (20ng/ml), IL-11 (50ng/ml), IL-2 (10ng/ml), IL-7 (20ng/ml).

extract_protocol:
Qiagen RNA extraction kit
Library preparation was performed based on the protocol from Picelli et al. (doi: 10.1038/nprot.2014.006) modified as follows: 1) using a set input of 500pg for each sample in 2uL volume 2) starting protocol at reverse transcription step 3) number of preamplification cycles changed from 21 to 16 4) cDNA input amount for library prep step with Illumina Nextera XT kit was 0.2ng 5) library pooling and clean up step modified by quantifying each sample individually and making an equimolar pool for sequencing.

value: mobilized peripheral blood

value: Single haematopoietic stem cell derived colonies

value: DNMT3A R882H

value: 21 day culture in MEM medium


title: i706_i502


title: i705_i503


title: i705_i510

value: DNMT3A WT


title: i705_i505


title: i705_i502


title: i704_i502


title: i704_i510


title: i703_i511


title: i704_i508


title: i704_i511


title: i704_i505


title: i704_i506


title: i703_i510


title: i703_i508


title: i702_i506


title: i703_i503


title: i702_i511


title: i702_i503


title: i702_i505


title: i702_i510


title: i703_i506


title: i702_i502


title: i705_i508


title: i701_i506


title: i701_i511


title: i703_i505


title: i701_i503


title: i701_i505


title: i701_i507


title: Tumor_D_MC38_KOICB_CD8

status: Public on Aug 24 2023

first: Luca

last: Biasco

address: 30 Guilford St, Holborn

description: 10x Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: mm10
Supplementary files format and content: Cell Ranger output files (barcodes.tsv, features.tsv, matrix.mtx)

source_name: Tumor

extract_protocol:
scRNA-seq on tumor-infiltrating CD8+ TILs:Tcf7fl/fl (wildtype) and E8i-CRE+ x Tcf7fl/fl (TCF1 KO) mice were injected with 3.75x105 B16-OVA or 1x106 MC38-OVA cells subcutaneously in the right flank. On day 6 and 9, mice were randomized and treated intraperitoneally with a combination of anti-PD-L1 (10F.9G2, 200g per mouse) and anti-Tim-3 (RMT3-23, 200g per mouse) antibodies or control immunoglobulins (Rat IgG2a and Rat IgG2b). Two (for MC38-OVA tumors) or three (for B16-OVA tumors) days after the second dose, tumors were harvested (n=3-5 per group) dissociated to single cell suspensions prior to fluorescence-activated cell sorting. An equal amount of CD45+ TCRb+ CD8+ T cells were sorted from each mouse (10,000 cells/mouse) within each experimental group and then pooled together prior to scRNA sequencing. scRNA-seq on adoptively transferred OTI T cells from the TDLN: CD45.1 C57Bl/6 were injected with 3.75x105 B16-OVA or 1x106 MC38-OVA cells subcutaneously in the right flank. On day 5 post tumor implantation, mice were randomized by tumor size and given 1x106 TCF7 KO or WT OT-1 naïve T cells resuspended in PBS via tail vein injections. Mice were then treated on day 6 post tumor injection with one dose of ICB (PDL1 + Tim3, 200ug each) or control antibodies (Rat IgG2a and Rat IgG2b). On day 8 post tumor injection the inguinal tumor-draining lymph nodes (TDLN) were dissected and dissociated to single cell suspensions by passing tissue through a 70M filter prior to centrifugation and fluorescence-activated cell sorting. CD45.2+CD8+TCRVa2+ OTI T cells were purified from the TDLN of n=4-5 mice per group.
For the generation of single cell transcriptomes, 10^3 to 16x10^3 -  target cells from each sorted population were run using the Chromium Controller (10x Genomics) using Chromium Next GEM Single Cell 3' Reagent Kits (10x Genomics). The libraries generated were then run on the NextSeq 550 Sequencing System (Illumina) using NextSeq 500/550 High Output v2.5 (150 cycles) Kit (Illumina).

value: CD8 T cells

value: Tumor

value: TCF1 KO (E8i-CRE+ x Tcf7fl/fl) and WT (E8i-CREneg x Tcf7fl/fl) mice, previously generated in our lab ( DOI:10.1016/j.immuni.2018.11.014).

value: 8-11 weeks

value: TCF1 KO

tag: challenge

value: ICB


title: i701_i508


title: Tumor_C_MC38_WTICB_CD8

description: 10x Genomics

value: WT


title: Tumor_B_MC38_KOISO_CD8

description: 10x Genomics

value: ISO


title: i703_i502


title: i701_i502


title: 41107_6_9_EV_32

status: Public on Aug 23 2023

city: Kilifi

first: Abdirahman

last: Abdi

state: Not US or Canada

address: Mombasa-Malindi Road

department: Bioscience

country: Kenya

institute: KEMRI-Wellcome Trust Research Programme

data_processing:
Transcript quantification was done using Kallisto and imported into R using tximport
R/bioconductor was used to normalize read counts for sequencing depth, gene length and unwanted variation
normalized counts were smoothed using loess and Fourier transformed
Assembly: Plasmodium falciparum 3D7
Supplementary files format and content: supplementary file containing Fourier transformed normalized TPM

organism: Plasmodium falciparum

source_name: Blood

extract_protocol:
RNA was extracted using Isolate II RNA kit (Bioline) following Manufacturer’s instructions
RNA preparation was performed using

value: Blood

value: Asexual Plasmodium falciparum isolates


title: 41107_6_23_EV_20


title: 41107_6_7_WP_32


title: 41107_6_3_WP_12


title: 41107_6_4_WP_16


title: 41107_6_24_WP_28


title: 41107_6_21_EV_28


title: 41107_6_16_EV_4


title: 41107_6_17_EV_8


title: 41107_6_19_EV_16


title: 41107_6_2_WP_8


title: 41107_6_20_EV_24


title: 41107_6_18_EV_12


title: 41107_6_22_EV_48


title: 41107_6_15_WP_44


title: 41107_6_11_EV_40


title: 41107_6_8_WP_48


title: 41107_6_10_EV_36


title: 41107_6_1_WP_4


title: 41107_6_6_WP_24


title: 41107_5_7_WP_32


title: 41107_5_9_EV_32


title: 41107_5_8_WP_48


title: 41107_5_6_WP_24


title: 41107_5_5_WP_20


title: 41107_5_3_WP_12


title: 41107_5_4_WP_16


title: 41107_5_23_EV_20


title: 41107_5_21_EV_28


title: 41107_5_24_WP_28


title: 41107_5_22_EV_48


title: 41107_5_2_WP_8


title: 41107_5_19_EV_16


title: 41107_5_20_EV_24


title: 41107_6_12_EV_44


title: 41107_5_16_EV_4


title: 41107_5_18_EV_12


title: 41107_5_10_EV_36


title: 41107_5_15_WP_44


title: 41107_5_17_EV_8


title: 41107_5_1_WP_4


title: 41107_5_11_EV_40


title: 41107_4_9_EV_40


title: 41107_5_12_EV_44


title: 41107_4_8_EV_36


title: 41107_4_7_WP_36


title: 41107_4_6_WP_28


title: 41107_4_5_WP_24


title: 41107_4_3_WP_16


title: 41107_4_4_WP_20


title: 41107_5_14_WP_40


title: 41107_4_22_WP_32


title: 41107_4_19_EV_28


title: 41107_4_2_WP_12


title: 41107_4_18_EV_20


title: 41107_4_20_EV_32


title: 41107_4_21_EV_24


title: 41107_5_13_WP_36


title: 41107_6_5_WP_20


title: 41107_4_15_EV_8


title: 41107_4_17_EV_16


title: 41107_4_14_WP_48


title: 41107_4_10_EV_44


title: 41107_3_6_WP_24


title: 41107_4_1_WP_8


title: 41107_4_11_EV_48


title: 41107_3_9_EV_32


title: 41107_3_8_WP_48


title: 41107_3_7_WP_32


title: 41107_3_5_WP_20


title: 41107_3_23_EV_20


title: 41107_3_4_WP_16


title: 41107_3_24_WP_28


title: 41107_3_3_WP_12


title: 41107_4_16_EV_12


title: 41107_4_12_WP_40


title: 41107_4_13_WP_44


title: 41107_3_18_EV_12


title: 41107_3_20_EV_24


title: 41107_3_21_EV_28


title: 41107_3_2_WP_8


title: 41107_3_19_EV_16


title: 41107_3_12_EV_44


title: 41107_3_17_EV_8


title: 41107_3_16_EV_4


title: 41107_3_10_EV_36


title: 41107_3_11_EV_40


title: 41107_3_15_WP_44


title: 41107_2_9_EV_40


title: 41107_3_1_WP_4


title: 41107_3_14_WP_40


title: 41107_3_22_EV_48


title: 41107_2_5_WP_24


title: 41107_2_8_EV_36


title: 41107_2_21_EV_24


title: 41107_2_7_WP_36


title: 41107_2_6_WP_28


title: 41107_2_3_WP_16


title: 41107_2_20_EV_32


title: 41107_2_4_WP_20


title: 41107_2_2_WP_12


title: 41107_2_14_WP_48


title: 41107_2_19_EV_28


title: 41107_2_15_EV_8


title: 41107_2_18_EV_20


title: 41107_2_16_EV_12


title: 41107_2_17_EV_16


title: 41107_2_22_WP_32


title: 41107_1_8_WP_48


title: 41107_2_11_EV_48


title: 41107_2_13_WP_44


title: 41107_3_13_WP_36


title: 41107_1_6_WP_24


title: 41107_2_12_WP_40


title: 41107_1_5_WP_20


title: 41107_1_9_EV_32


title: 41107_2_10_EV_44


title: 41107_1_7_WP_32


title: 41107_2_1_WP_8


title: 41107_1_3_WP_12


title: 41107_1_4_WP_16


title: 41107_1_2_WP_8


title: 41107_1_19_EV_16


title: 41107_1_18_EV_12


title: 41107_1_24_WP_28


title: 41107_1_20_EV_24


title: 41107_1_23_EV_20


title: 41107_1_17_EV_8


title: 41107_1_14_WP_40


title: 41107_1_13_WP_36


title: 41107_1_16_EV_4


title: 41107_1_15_WP_44


title: 41107_1_12_EV_44


title: 41107_1_11_EV_40


title: 41107_1_1_WP_4


title: 41107_1_10_EV_36


title: 41107_1_22_EV_48


title: 41107_1_21_EV_28


title: APP/PS1:APOE4-KI, female, biol rep 9

status: Public on Jul 31 2023

city: Bonn

first: Rayk

last: Behrendt

address: Venusberg-Campus 1

department: Institute for Clinical Chemistry and Clinical Pharmacology

country: Germany

institute: University Bonn

data_processing:
Samples were processed according to Smart-Seq2 protocol and sequenced on Illumina sequencers.
Used Combat for debatching of samples due to plate batch effect
Reads in FASTQ were quantified at the transcript level using Salmon (v1.4) against the M. musculus Ensembl gene catalog (May 2020).
Differential expression analysis was conducted using R (v4.1.1) and DESeq2 (v1.34.0). Hypothesis testing was performed by using either DESeq2’s Wald test on appropriate variable contrasts or with a Likelihood Ratio Test (LRT) for models with greater than two variable conditions being tested.
Assembly: mm10
Supplementary files format and content: tar file of salmon outputs including plaint text  quantification file (quant.sf), transcripts used for quantification, parameter settings, version of Salmon, and estimated bias parameters

source_name: Microglia

extract_protocol:
1,000 isolated Ly6C–CD11b+Fcrls+ microglia were lysed in 5 ul TCL buffer +1% beta-mercaptoethanol.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Microglia

tag: Sex

value: Female

value: 4 months


title: APP/PS1:APOE4-KI, biol rep 2

description: 10x Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Salmon Alevin tool v.4.0.0  (https://salmon.readthedocs.io/en/latest/alevin.html)
Assembly: mm10
Supplementary files format and content: tar.gz folder containing Alevin outputs

source_name: Brain

extract_protocol:
The left hemisphere of the mouse brain was homogenized to form a single cell suspension, then resuspended and centrifuged in a 37%/70% Percoll Plus gradient at 800G, 23˚C, for 25 min with an acceleration of 3 and a deceleration of 1. Mononuclear cells were taken from the interface layer. The cells were stained with anti-CD11b PECy7 and CD45 PerCP. After staining cells were washed and sorted using BD FACSAriaTM II.
GEMs were generated according to the manufacturer’s protocol by combining barcoded Single Cell 3’ v3.1 Gel Beads, a Master Mix containing cells, and Partitioning Oil onto Chromium Next GEM Chip G (10X Genomics, USA) with targeted capture of 5000 cells per sample. Reverse transcription immediately followed GEM generation, producing barcoded, full-length cDNA from poly-adenylated mRNA. After incubation, GEMs were broken and pooled fractions of cDNA were recovered. Barcoded, full-length cDNA was amplified via PCR to generate sufficient mass for library construction.

value: Brain

value: female

value: 4 Months


title: APP/PS1:APOE4-cKO, biol rep 2

description: 10x Genomics


title: APP/PS1:APOE4-KI, female, biol rep 8


title: APP/PS1:APOE4-cKO, biol rep 1

description: 10x Genomics


title: APP/PS1:APOE4-KI, biol rep 1

description: 10x Genomics


title: APP/PS1:APOE4-cKO, male, biol rep 8

value: Male


title: APP/PS1:APOE4-KI, female, biol rep 6


title: 41107_6_13_WP_36


title: APP/PS1:APOE4-cKO, male, biol rep 7


title: APP/PS1:APOE4-KI, male, biol rep 9


title: APP/PS1:APOE4-cKO, male, biol rep 6


title: APP/PS1:APOE4-KI, male, biol rep 8


title: APP/PS1:APOE4-cKO, female, biol rep 4


title: APP/PS1:APOE4-cKO, male, biol rep 4


title: APP/PS1:APOE4-cKO, female, biol rep 3


title: APP/PS1:APOE-KI, female, biol rep 5


title: APP/PS1:APOE4-cKO, female, biol rep 2


title: APP/PS1:APOE4-cKO, male, biol rep 3


title: APP/PS1:APOE4-cKO, female, biol rep 1


title: APP/PS1:APOE4-cKO, female, biol rep 5


title: APP/PS1:APOE4-KI, female, biol rep 7


title: APP/PS1:APOE4-KI, male, biol rep 6


title: APP/PS1:APOE4-KI, female, biol rep 3


title: 41107_6_14_WP_40


title: APP/PS1:APOE4-KI, female, biol rep 1


title: APP/PS1:APOE4-KI, female, biol rep 2


title: APP/PS1:APOE4-KI, male, biol rep 2


title: APP/PS1:APOE4-KI, male, biol rep 4


title: APP/PS1:APOE4-KI, male, biol rep 3


title: APP/PS1:APOE4-KI, male, biol rep 1


title: APP/PS1:APOE4-KI, male, biol rep 5


title: APP/PS1:APOE4-KI, male, biol rep 7


title: APP/PS1:APOE4-cKO, male, biol rep 5


title: WT, Non-phagocytic microlia, biol rep 5

data_processing:
Samples were processed according to Smart-Seq2 protocol and sequenced on Illumina sequencers.
Reads in FASTQ were quantified at the transcript level using Salmon (v1.4) against the M. musculus Ensembl gene catalog (May 2020).
Differential expression analysis was conducted using R (v4.1.1) and DESeq2 (v1.34.0). Hypothesis testing was performed by using either DESeq2’s Wald test on appropriate variable contrasts or with a Likelihood Ratio Test (LRT) for models with greater than two variable conditions being tested.
Assembly: mm10
Supplementary files format and content: tar file of salmon outputs including plaint text  quantification file (quant.sf), transcripts used for quantification, parameter settings, version of Salmon, and estimated bias parameters

extract_protocol:
Isolated Dead neuron+Ly6C-CD11b+Fcrls+ and Dead neuron-Ly6C-CD11b+Fcrls+ microglia were lysed in 5 ul TCL buffer +1% beta-mercaptoethanol.
RNA libraries were prepared for sequencing using standard Illumina protocols.

value: Non-phagocytic Microglia

value: f

value: 62 days


title: Itgb8-cKO, Non-phagocytic microlia, biol rep 6


title: WT, Non-phagocytic microlia, biol rep 4


title: Itgb8-cKO, Non-phagocytic microlia, biol rep 5


title: Itgb8-cKO, Non-phagocytic microlia, biol rep 3


title: WT, Non-phagocytic microlia, biol rep 3


title: WT, Non-phagocytic microlia, biol rep 2

value: m


title: APP/PS1:APOE4-KI, female, biol rep 4


title: WT, Non-phagocytic microlia, biol rep 1


title: Itgb8-cKO, Non-phagocytic microlia, biol rep 1


title: Itgb8-cKO, Phagocytic microglia, biol rep 6

value: Phagocytic Microglia


title: Itgb8-cKO, Phagocytic microglia, biol rep 5


title: WT, Phagocytic microglia, biol rep 5


title: APP/PS1:APOE4-cKO, male, biol rep 1


title: Itgb8-cKO, Phagocytic microglia, biol rep 3


title: APP/PS1:APOE4-cKO, male, biol rep 2


title: Itgb8-cKO, Phagocytic microglia, biol rep 2


title: WT, Phagocytic microglia, biol rep 3


title: WT, Phagocytic microglia, biol rep 2


title: WT, Phagocytic microglia, biol rep 1


title: APP/PS1: IgG, biol rep 4


title: Itgb8-cKO, Phagocytic microglia, biol rep 4


title: Itgb8-cKO, Non-phagocytic microlia, biol rep 4


title: Itgb8-cKO, Phagocytic microglia, biol rep 1


title: APP/PS1: IgG, biol rep 2


title: APP/PS1: IgG, biol rep 3


title: APP/PS1:Itgb8 blocker, biol rep 4

value: APP/PS1:Itgb8 blocker


title: APP/PS1:Itgb8 blocker, biol rep 5


title: APP/PS1: IgG, biol rep 5


title: Itgb8-cKO, Non-phagocytic microlia, biol rep 2


title: APP/PS1: IgG, biol rep 1


title: APP/PS1:Itgb8 blocker, biol rep 2


title: APP/PS1:Itgb8 blocker, biol rep 1


title: WT, biol rep 2

source_name: Brain, Cortex

value: Brain, Cortex

value: WT

value: 36 days


title: WT, Phagocytic microglia, biol rep 4


title: Itgb8-cKO, biol rep 5


title: Itgb8-cKO, biol rep 2


title: Itgb8-cKO, biol rep 4


title: P301S_APOE4_KI, biol rep 5

data_processing:
Samples were processed according to Smart-Seq2 protocol and sequenced on Illumina sequencers.
Reads in FASTQ were quantified at the transcript level using Salmon (v1.4) against the M. musculus Ensembl gene catalog (May 2020).
Used Combat for debatching of samples due to plate batch effect
Differential expression analysis was conducted using R (v4.1.1) and DESeq2 (v1.34.0). Hypothesis testing was performed by using either DESeq2’s Wald test on appropriate variable contrasts or with a Likelihood Ratio Test (LRT) for models with greater than two variable conditions being tested.
Assembly: mm10
Supplementary files format and content: tar file of salmon outputs including plaint text  quantification file (quant.sf), transcripts used for quantification, parameter settings, version of Salmon, and estimated bias parameters

source_name: brain

extract_protocol:
1,000 isolated ACSA-2+/O1-/CD11b-/Cd45-/Olig4- astrocytes were lysed in 5 ul TCL buffer +1% beta-mercaptoethanol.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: brain

value: Astrocyte


title: WT, biol rep 3

value: Microglia

value: Female


title: Itgb8-cKO, biol rep 1


title: WT, biol rep 4


title: P301S_APOE4_KI, biol rep 6


title: WT, biol rep 1


title: P301S_APOE4_KI, biol rep 3


title: P301S_APOE4_KI, biol rep 2

value: male


title: P301S_APOE4_cKO, biol rep 2

value: female


title: WT:APOE4 cKO, biol rep 3

source_name: Astrocytes

value: Astrocytes

value: WT:APOE4 cKO


title: P301S_APOE4_cKO, biol rep 1

value: 4 Months


title: P301S_APOE4_cKO, biol rep 4


title: P301S_APOE4_cKO, biol rep 3


title: WT:APOE4 cKO, biol rep 2

value: Male


title: WT:APOE4, biol rep 4


title: WT:APOE4, biol rep 2


title: WT:APOE4, biol rep 3


title: APP/PS1:Itgb8 blocker, biol rep 3

value: Brain


title: APP/PS1:Lgals3(100ng)_injected, biol rep 2

extract_protocol:
1,000 isolated ACSA+/O1-/CD11b-/Cd45-/Olig4- astrocytes were lysed in 5 ul TCL buffer +1% beta-mercaptoethanol.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: 4 months


title: WT:APOE4, biol rep 1


title: APP/PS1:Lgals3(100ng)_injected, biol rep 3


title: APP/PS1:Lgals3(100ng)_injected, biol rep 4


title: Itgb8-cKO, biol rep 3


title: APP/PS1:Lgals3(20ng)_injected, biol rep 2


title: APP/PS1:Lgals3(20ng)_injected, biol rep 3


title: P301S_APOE4_KI, biol rep 1


title: APP/PS1:PBS_treated, biol rep 3


title: APP/PS1:PBS_treated, biol rep 2


title: APP/PS1:Lgals3(20ng)_injected, biol rep 1


title: APP/PS1:PBS_treated, biol rep 1


title: WT:APOE4-cKO, biol rep 3

extract_protocol:
Alexa 405+GFP+ phagocytic microglia were injected into the cortex and hippocampus (x = +1.5 mm, y = 2 mm, z = -1 and -2 mm; 2 ml per injection site) of WT mice. After 16 hours, astrocytes were isolated from the brain regions restricted to the injection sites. 1,000 isolated ACSA-2+/O1-/CD11b-/Cd45-/Olig4- astrocytes were lysed in 5 ul TCL buffer +1% beta-mercaptoethanol.
RNA libraries were prepared for sequencing using standard Illumina protocols


title: WT:APOE4-cKO, biol rep 2


title: WT:APOE4 cKO, biol rep 1


title: WT:APOE4-cKO, biol rep 1


title: WT:APOE4, biol rep 5


title: WT:APOE3-KI, biol rep 3


title: WT:APOE4-KI, biol rep 3


title: WT:APOE4-KI, biol rep 1


title: APP/PS1:Lgals3(100ng)_injected, biol rep 1


title: WT:APOE4-KI, biol rep 2


title: P301S_APOE4_KI, biol rep 7


title: APOE4-cKO, biol rep 6

value: 9 Months


title: APOE4-cKO, biol rep 7


title: APOE4-KI, biol rep 11


title: APOE4-KI, biol rep 8


title: WT:APOE3-KI, biol rep 1


title: APOE4-KI, biol rep 10


title: APOE3-cKO, biol rep 6


title: APOE3-cKO, biol rep 7


title: APOE3-cKO, biol rep 8


title: P301S:APOE4-KI, biol rep 5


title: APOE4-cKO, biol rep 5


title: APOE3-KI, biol rep 8


title: P301S:APOE4-KI, biol rep 4


title: APOE3-cKO, biol rep 5


title: P301S:APOE3-cKO, biol rep 5


title: APOE3-KI, biol rep 4


title: P301S:APOE4-cKO, biol rep 3


title: APOE4-KI, biol rep 9


title: P301S:APOE3-KI, biol rep 3


title: APOE3-KI, biol rep 7


title: APOE4-cKO, biol rep 8


title: APOE3-KI, biol rep 6


title: APOE3-KI, biol rep 5


title: P301S:APOE4-KI, biol rep 6


title: WT:APOE3-KI, biol rep 2


title: APOE4-KI, biol rep 7


title: APOE3-cKO, biol rep 4


title: P301S:APOE3-cKO, biol rep 6


title: P301S:APOE3-KI, biol rep 2


title: P301S:APOE4-cKO, biol rep 2


title: APOE4-KI, biol rep 6


title: P301S:APOE3-cKO, biol rep 4


title: APOE4-KI, biol rep 5


title: APOE3-KI, biol rep 3


title: APOE4-KI, biol rep 4


title: APOE4-cKO, biol rep 4


title: APOE4-cKO, biol rep 3


title: P301S:APOE4-KI, biol rep 1


title: P301S:APOE4-KI, biol rep 2


title: APOE4-KI, biol rep 1


title: APOE3-KI, biol rep 2


title: P301S:APOE4-cKO, biol rep 1


title: APOE4-cKO, biol rep 1


title: APOE4-KI, biol rep 2


title: APOE3-cKO, biol rep 2


title: APOE4-KI, biol rep 3


title: APOE4-cKO, biol rep 2


title: APOE3-KI, biol rep 1


title: APOE3-cKO, biol rep 3


title: APOE3-cKO, biol rep 1


title: P301S:APOE3-KI, bio rep 1


title: P301S:APOE3-cKO, biol rep 3


title: P301S:APOE4-KI, biol rep 3


title: APP/PS1:APOE4-KI:PU.1-Inhibitor, biol rep 4


title: P301S:APOE3-cKO, biol rep 2


title: APP/PS1:APOE4-KI:PU.1-Inhibitor, biol rep 2


title: APP/PS1:APOE4-KI:PU.1-Inhibitor, biol rep 1


title: APP/PS1:APOE4-KI:PU.1-Inhibitor, biol rep 3


title: APP/PS1:APOE4-KI:IgG_control, biol rep 5


title: APP/PS1:APOE4-KI:IgG_control, biol rep 4


title: APP/PS1:APOE4-KI:PU.1-Inhibitor, rep 4


title: APP/PS1:APOE4-KI:IgG_control, biol rep 2


title: APP/PS1:APOE4-KI:IgG_control, biol rep 1


title: APP/PS1:APOE4-KI:PU.1-Inhibitor, rep 3


title: APP/PS1:APOE4-KI:IgG_control, rep 5


title: APP/PS1:APOE4-KI:PU.1-Inhibitor, rep 2


title: APP/PS1:APOE4-KI:PU.1-Inhibitor, rep 1


title: APP/PS1:APOE4-KI:IgG_control, rep 1


title: APP/PS1:APOE4-KI:IgG_control, biol rep 3


title: Control, biol rep 3

extract_protocol:
Isolated dead neuron+/Ly6C–CD11b+Fcrls+ microglia were lysed in 5 ul TCL buffer +1% beta-mercaptoethanol.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Phagocytic microglia

value: Control

value: 2 months


title: Control, biol rep 2


title: APP/PS1:APOE4-KI:IgG_control, rep 3


title: APP/PS1:APOE4-KI:IgG_control, rep 2


title: Control, biol rep 4


title: APP/PS1:APOE4-KI:IgG_control, rep 4


title: Spi1-cKO, biol rep 4


title: Spi1-cKO, biol rep 3


title: P301S:APOE3-cKO, biol rep 1


title: Spi1-cKO, biol rep 2


title: APOE3-cKO, Non-phagocytic microglia, biol rep 3

extract_protocol:
Isolated Dead neuron+Ly6C–CD11b+Fcrls+ and Dead neuron-Ly6C–CD11b+Fcrls+ microglia were lysed in 5 ul TCL buffer +1% beta-mercaptoethanol.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Non-phagocytic microglia

value: 8 Months


title: Spi1-cKO, biol rep 1

value: brain


title: APOE3-cKO, Non-phagocytic microglia, biol rep 2


title: APOE3-cKO, Phagocytic microglia, biol rep 3


title: APOE3-cKO, Phagocytic microglia, biol rep 2


title: APOE3-cKO, Phagocytic microglia, biol rep 1


title: APOE3-cKO, Non-phagocytic microglia, biol rep 1


title: APOE3-KI, Phagocytic microglia, biol rep 3


title: APOE3-KI, Phagocytic microglia, biol rep 4


title: APOE3-KI, Phagocytic microglia, biol rep 2


title: APOE3-KI, Non-phagocytic microglia, biol rep 1


title: APOE3-KI, Non-phagocytic microglia, biol rep 4


title: APOE3-KI, Phagocytic microglia, biol rep 1


title: APOE3-KI, Non-phagocytic microglia, biol rep 2


title: APOE4-cKO, Non-phagocytic microglia, biol rep 4


title: Control, biol rep 1


title: APOE4-cKO, Phagocytic microglia, biol rep 4


title: APOE4-cKO, Non-phagocytic microglia, biol rep 1


title: APOE4-cKO, Non-phagocytic microglia, biol rep 2


title: APOE3-KI, Non-phagocytic microglia, biol rep 3


title: APOE4-cKO, Phagocytic microglia, biol rep 1


title: APOE4-KI, Phagocytic microglia, biol rep 6


title: APOE4-cKO, Phagocytic microglia, biol rep 2


title: APOE4-KI, Non-phagocytic microglia, biol rep 4


title: APOE4-cKO, Non-phagocytic microglia, biol rep 3


title: APOE4-cKO, Phagocytic microglia, biol rep 3


title: APOE4-KI, Non-phagocytic microglia, biol rep 5


title: APOE4-KI, Phagocytic microglia, biol rep 5


title: APOE4-KI, Phagocytic microglia, biol rep 4


title: APOE4-KI, Phagocytic microglia, biol rep 3


title: APOE4-KI, Phagocytic microglia, biol rep 2


value: 8 months


title: APOE4-KI, Non-phagocytic microglia, biol rep 3


title: APOE4-KI, Non-phagocytic microglia, biol rep 1

value: Female


title: APOE4-KI, Phagocytic microglia, biol rep 1


title: APOE3-KI, Non-phagocytic microglia, biol rep 5


title: APOE3-KI, Non-phagocytic microglia, biol rep 2


title: APOE4-KI, Non-phagocytic microglia, biol rep 2


title: APOE3-KI, Phagocytic microglia, biol rep 4


title: Control, APOE3-KI

data_processing:
Raw fastq files were first checked for quality using Multiqc sequence analysis
Cutadapt (v.4.0) was used to cut adaptors (-a AGATCGGAAGAGCACACGTCTGAACTCCAGTC -A AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT)
ChIP-seq reads were aligned to the UCSC mm10 genome using Bowtie version 1.1.2. Only uniquely mapping reads with at most two mismatches were retained.
To create ChIP-seq coverage plots, the locations of the mapped ChIP-seq reads were normalized (to size of mouse genome, 2652783500, RPGC) and reformatted in the bigWig file format.
Peaks were called uing MACS v2.1.0 with the significance cut-off q-value <=0.001
BigWig files were created using deeptools and counts were extracted using bedtools multicov command from Bam files. Extracted counts were summarized as matrix file and imported in DESeq2 for normalization and differential analysis.
Motifs were determined using HOMER findMotifsGenome.pl
Assembly: mm10
Supplementary files format and content: BigWig

extract_protocol:
The sonication program was 20 cycles (30 seconds “ON”, 30 seconds “OFF”) each at High power setting. Two ul of anti-H3K9ac antibody (Millipore, 07-352) was added per IP reaction.
The DNA libraries were prepared using NEBNext® UltraTM II DNA Library Prep Kit for Illumina® (NEB, E7103S) following the manufacturer’s instruction. The DNA libraries were analyzed using Qubit 4 Fluorometer (Invitrogen, Q33238) and 2100 Bioanalyzer DNA system (Agilent). The pooled libraries were sent to Genewiz, lnc and sequenced 2x150 bp in Illumina HiSeq platform.

value: Microglia

tag: chip antibody


title: APOE3-KI, Phagocytic microglia, biol rep 1

value: female


title: anti-H3K9ac, APOE3-KI

value: anti-H3K9ac antibody (Millipore, 07-352)


title: APOE3-KI, Non-phagocytic microglia, biol rep 1


title: APOE3-KI, Non-phagocytic microglia, biol rep 6


title: APOE3-KI, Phagocytic microglia, biol rep 2


title: Control, APOE4-KI


title: AD:APOEε3/ε4, female, rep 6

data_processing:
Samples were processed according to Smart-Seq2 protocol and sequenced on Illumina sequencers.
Reads in FASTQ were quantified at the transcript level using Salmon (v1.4) against the Homo_sapiens Ensembl gene catalog (May 2020).
Differential expression analysis was conducted using R (v4.1.1) and DESeq2 (v1.34.0). Hypothesis testing was performed by using either DESeq2’s Wald test on appropriate variable contrasts or with a Likelihood Ratio Test (LRT) for models with greater than two variable conditions being tested.
Assembly: hg38
Supplementary files format and content: tar file of salmon outputs including plaint text  quantification file (quant.sf), transcripts used for quantification, parameter settings, version of Salmon, and estimated bias parameters

extract_protocol:
mRNA were isolated using mirVana miRNA isolation kit and 10ng total RNA in 5ul Rnase-free water
RNA libraries were prepared for sequencing using standard Illumina protocols

value: whole tissue


title: APOE4-KI, Non-phagocytic microglia, biol rep 4


title: APOE3-KI, Phagocytic microglia, biol rep 3


title: AD:APOEε3/ε4, female, rep 5


title: APOE3-KI, Non-phagocytic microglia, biol rep 4


title: AD:APOEε3/ε4, female, rep 3


title: P301S_APOE4_KI, biol rep 4

value: Astrocyte

value: 4 Months


title: AD:APOEε3/ε4, female, rep 2


title: AD:APOEε3/ε4, male, rep 7

value: Male


title: AD:APOEε3/ε4, male, rep 2


title: AD:APOEε3/ε4, male, rep 6


title: AD:APOEε3/ε4, male, rep 3


title: AD:APOEε3/ε4, male, rep 5


title: AD:APOEε3/ε4, male, rep 4


title: AD:APOEε3/ε4, male, rep 1


title: AD:APOEε3/ε3, female, rep 4


title: AD:APOEε3/ε3, female, rep 5


title: AD:APOEε3/ε3, female, rep 6


title: AD:APOEε3/ε3, female, rep 2


title: AD:APOEε3/ε3, female, rep 3


title: AD:APOEε3/ε3, female, rep 7


title: AD:APOEε3/ε3, male, rep 1


title: AD:APOEε3/ε4, female, rep 1


title: AD:APOEε3/ε3, male, rep 2


title: AD:APOEε3/ε3, male, rep 5


title: APP;ST2KO_Microglia, IL33, 3hours, rep3 [BulkRNA_ST2KO_IL33_3]

status: Public on Jul 18 2023

city: Hong Kong

first: Nancy

last: Ip

address: Room 6313, Academic Building The Hong Kong University of Science and Technology Clear Water Bay, Kowloon

description:
BulkRNA_ST2KO_IL33_3
BulkRNA_ST2KO_IL33_3
NextSeq 500/NovaSeq 6000
bulkRNA_IL33_ST2KO_DESeq2_normalized_count.csv

data_processing:
We aligned the sequencing data to the mm10 mouse reference genome using STAR and quantified the data using the Rsubread package in R. We also performed differential expression analysis using the DESeq2 package in R. Genes were considered differentially regulated if the adjusted p value was < 0.1. We visualized the gene expression of differentially expressed genes (DEGs) under different conditions using Morpheus online software. We functionally annotated the DEGs by GO enrichment analysis and the STRING database.
assembly: mm10
csv file include DESeq2 normalized count for each sample

extract_protocol:
In brief, we deeply anesthetized adult mice using isoflurane and then perfused them with ice-cold PBS. We isolated the forebrain, minced them into small pieces, then mechanically dissociated them with a Dounce homogenizer on ice. We used a Percoll gradient (30%; Sigma-Aldrich) to remove myelin. We blocked the resultant mononuclear cell suspensions with an FcR blocker for 10 min on ice, then incubated them with antibody in the dark for 30 min on ice. Next, we performed flow cytometry analysis and cell sorting with a BD Influx Cell Sorter. We used unstained controls to identify cell populations and visualized clear subpopulations of living microglia on scatter plots; the purity of microglial isolation was routinely >90% according to a reanalysis of the sorted cells.
We sorted approximately 10,000 living microglia directly into RA1 Lysis Buffer and stored them at −80 °C until RNA extraction. We then extracted RNA from the microglia using a NucleoSpin RNA XS Kit (Macherey-Nagel) according to the manufacturer’s instructions. We immediately converted the extracted RNA into full-length complementary DNA (cDNA) using a SMART-Seq v4 kit (Takara Bio). Next, we quantified the concentrations of the cDNA libraries with Qubit (Thermo Fisher Scientific) and fragment lengths with Fragment Analyzer (Advanced Analytical). For library construction, we tagmented 1 ng cDNA by incubation with Tn5 transposase (Illumina) for 30 min at 55 °C and then amplified the tagmented cDNA by PCR for 12 cycles. We size-selected the libraries (100–600 bp) with AMPure XP beads (Beckman Coulter). We quantified the concentrations of the final libraries with Qubit (Thermo Fisher Scientific) and fragment lengths with Fragment Analyzer (Advanced Analytical). We performed paired-end sequencing using a NextSeq 500 or NovaSeq 6000 instrument (Novogene) according to the manufacturer’s instructions.

value: IL33, 3hours


title: MUC26097

status: Public on Jul 20 2023

city: Munich

first: Karin

middle: A.

last: Ziegler

address: Biedersteiner Str. 29

institute: Technical University of Munich

description: 10x Genomics

data_processing:
bcl2fastq for basecalling, fastq conversion and demultiplexing
cellranger v5.0.0 for alignment, filtering, barcode counting, UMI counting
Assembly: mm10
Supplementary files format and content: Feature-Barcode Matrices from cellranger (10x Genomics)

source_name: Sympathetic ganglion

extract_protocol:
After harvest and cleaning, ganglionic tissue was incubated in artificial cerebrospinal fluid (ACSF) oxygenated by Carbogen with a stabile pH of 7.4 at 37°C for 2 hours. SCGs were then dissociated to single cells with collagenase II and proceeded for single cell capture, barcoding and library preparation (10x genomics).
Barcoding and library preparation was done using Chromium single cell 3’ (v3, 10x Genomics).

value: Sympathetic ganglion

value: 8-12 weeks old

value: male

tag: disease state

value: late stage heart disease (18d)


title: APP;ST2KO_Microglia, IL33, 3hours, rep2 [BulkRNA_ST2KO_IL33_2]

institute: Hong Kong University of Science and Technology

description:
BulkRNA_ST2KO_IL33_2
BulkRNA_ST2KO_IL33_2
NextSeq 500/NovaSeq 6000
bulkRNA_IL33_ST2KO_DESeq2_normalized_count.csv

tag: tissue


title: MUC13694

description: 10x Genomics

value: early stage heart disease (5d)


title: MUC13693

description: 10x Genomics


title: MUC26096

description: 10x Genomics


title: AD:APOEε3/ε3, female, rep 1


title: APP;ST2KO_Microglia, IL33, 3hours, rep4 [BulkRNA_ST2KO_IL33_4]

description:
BulkRNA_ST2KO_IL33_4
BulkRNA_ST2KO_IL33_4
NextSeq 500/NovaSeq 6000
bulkRNA_IL33_ST2KO_DESeq2_normalized_count.csv


title: APP;ST2WT_Microglia, IL33, 3hours, rep4 [BulkRNA_ST2WT_IL33_4]

description:
BulkRNA_ST2WT_IL33_4
BulkRNA_ST2WT_IL33_4
NextSeq 500/NovaSeq 6000
bulkRNA_IL33_ST2KO_DESeq2_normalized_count.csv


title: APP;ST2WT_Microglia, IL33, 3hours, rep3 [BulkRNA_ST2WT_IL33_3]

description:
BulkRNA_ST2WT_IL33_3
BulkRNA_ST2WT_IL33_3
NextSeq 500/NovaSeq 6000
bulkRNA_IL33_ST2KO_DESeq2_normalized_count.csv


title: AD:APOEε3/ε3, male, rep 3


title: AD:APOEε3/ε3, male, rep 4


title: APP;ST2WT_Microglia, IL33, 3hours, rep1 [BulkRNA_ST2WT_IL33_1]

description:
BulkRNA_ST2WT_IL33_1
BulkRNA_ST2WT_IL33_1
NextSeq 500/NovaSeq 6000
bulkRNA_IL33_ST2KO_DESeq2_normalized_count.csv


title: APP;ST2WT_Microglia, PBS, 3hours, rep3 [BulkRNA_ST2WT_Con_3]

description:
BulkRNA_ST2WT_Con_3
BulkRNA_ST2WT_Con_3
NextSeq 500/NovaSeq 6000
bulkRNA_IL33_ST2KO_DESeq2_normalized_count.csv

value: PBS, 3hours


title: APP;ST2WT_Microglia, PBS, 3hours, rep4 [BulkRNA_ST2WT_Con_4]

description:
BulkRNA_ST2WT_Con_4
BulkRNA_ST2WT_Con_4
NextSeq 500/NovaSeq 6000
bulkRNA_IL33_ST2KO_DESeq2_normalized_count.csv

value: brain


title: APP;ST2KO_Microglia, IL33, 3hours, rep1 [BulkRNA_ST2KO_IL33_1]

description:
BulkRNA_ST2KO_IL33_1
BulkRNA_ST2KO_IL33_1
NextSeq 500/NovaSeq 6000
bulkRNA_IL33_ST2KO_DESeq2_normalized_count.csv


title: APP_Microglia, IL33, 8hours, rep1 [scRNAseq_IL33_8h_1]

description:
scRNA_IL33_8h
scRNA_IL33_8h
NextSeq 500/NovaSeq 6000

data_processing:
We aligned the demultiplexed FASTQ files from Novogene to the mm10 mouse reference genome using Cell Ranger (v3.0.1) with the default settings 70. After alignment, we performed the initial quality control (QC) step using the default QC settings in Cell Ranger, which retained only the barcodes with unique molecular identifier counts within the top 10% of the 99th percentile of unique molecular identifier values among all barcodes and sorted them into cell-associated matrixes; the remaining barcodes were treated as background barcodes and excluded. We used these cell-associated matrices as inputs for the second round of QC and downstream analysis in Seurat (v3.0). For the second round of QC, we removed microglia with £200 genes, ³20,000 unique molecular identifiers, and ³20% mitochondrial genes. A total of 8,893 microglia passed QC and were retained in the matrix.
assembly: mm10
filtered count matrix from Seurat

extract_protocol:
In brief, we deeply anesthetized adult mice using isoflurane and then perfused them with ice-cold PBS. We isolated the forebrain, minced them into small pieces, then mechanically dissociated them with a Dounce homogenizer on ice. We used a Percoll gradient (30%; Sigma-Aldrich) to remove myelin. We blocked the resultant mononuclear cell suspensions with an FcR blocker for 10 min on ice, then incubated them with antibody in the dark for 30 min on ice. Next, we performed flow cytometry analysis and cell sorting with a BD Influx Cell Sorter. We used unstained controls to identify cell populations and visualized clear subpopulations of living microglia on scatter plots; the purity of microglial isolation was routinely >90% according to a reanalysis of the sorted cells.
We generated scRNA-seq libraries using the Chromium Next GEM Single Cell 3′ Library Kit (v3.1 Chemistry; 10x Genomics) according to the manufacturer’s instructions. In brief, we counted sorted living CD11b+ cells on a hemocytometer. We mixed single-cell suspensions (400 cells/µL) with reverse-transcription reagent mix and loaded them into the chip for single-cell encapsulation. We immediately incubated the encapsulated cells in a thermocycler for reverse transcription. We obtained barcoded cDNA and used it for library construction according to the manufacturer’s instructions. We quantified the concentrations of the final libraries with Qubit (Thermo Fisher Scientific) and fragment lengths with Fragment Analyzer (Advanced Analytical). We performed paired-end sequencing of the libraries on a NovaSeq 6000 instrument (Novogene) according to the manufacturer’s instructions.

value: IL33, 8hours


title: APP_Microglia, IL33, 3hours, rep1 [scRNAseq_IL33_3h_1]

description:
scRNA_IL33_3h
scRNA_IL33_3h
NextSeq 500/NovaSeq 6000


title: APP_Microglia, IL33, 24hours, rep3 [BulkRNA_IL33_24h_3]

description:
BulkRNA_IL33_24h_3
BulkRNA_IL33_24h_3
NextSeq 500/NovaSeq 6000
bulkRNA_IL33_timecourse_DESeq2_normalized_count.csv

value: IL33, 24hours


title: APP_Microglia, IL33, 24hours, rep2 [BulkRNA_IL33_24h_2]

description:
BulkRNA_IL33_24h_2
BulkRNA_IL33_24h_2
NextSeq 500/NovaSeq 6000
bulkRNA_IL33_timecourse_DESeq2_normalized_count.csv

value: Microglia


title: APP_Microglia, IL33, 24hours, rep1 [BulkRNA_IL33_24h_1]

description:
BulkRNA_IL33_24h_1
BulkRNA_IL33_24h_1
NextSeq 500/NovaSeq 6000
bulkRNA_IL33_timecourse_DESeq2_normalized_count.csv


title: APP_Microglia, IL33, 8hours, rep4 [BulkRNA_IL33_8h_4]

description:
BulkRNA_IL33_8h_4
BulkRNA_IL33_8h_4
NextSeq 500/NovaSeq 6000
bulkRNA_IL33_timecourse_DESeq2_normalized_count.csv


title: APP_Microglia, IL33, 8hours, rep2 [BulkRNA_IL33_8h_2]

description:
BulkRNA_IL33_8h_2
BulkRNA_IL33_8h_2
NextSeq 500/NovaSeq 6000
bulkRNA_IL33_timecourse_DESeq2_normalized_count.csv


title: APP_Microglia, IL33, 8hours, rep1 [BulkRNA_IL33_8h_1]

description:
BulkRNA_IL33_8h_1
BulkRNA_IL33_8h_1
NextSeq 500/NovaSeq 6000
bulkRNA_IL33_timecourse_DESeq2_normalized_count.csv


title: APP_Microglia, IL33, 8hours, rep3 [BulkRNA_IL33_8h_3]

description:
BulkRNA_IL33_8h_3
BulkRNA_IL33_8h_3
NextSeq 500/NovaSeq 6000
bulkRNA_IL33_timecourse_DESeq2_normalized_count.csv


title: APP_Microglia, IL33, 3hours, rep4 [BulkRNA_IL33_3h_4]

description:
BulkRNA_IL33_3h_4
BulkRNA_IL33_3h_4
NextSeq 500/NovaSeq 6000
bulkRNA_IL33_timecourse_DESeq2_normalized_count.csv


title: APP_Microglia, IL33, 3hours, rep3 [BulkRNA_IL33_3h_3]

description:
BulkRNA_IL33_3h_3
BulkRNA_IL33_3h_3
NextSeq 500/NovaSeq 6000
bulkRNA_IL33_timecourse_DESeq2_normalized_count.csv


title: APP_Microglia, IL33, 3hours, rep1 [BulkRNA_IL33_3h_1]

description:
BulkRNA_IL33_3h_1
BulkRNA_IL33_3h_1
NextSeq 500/NovaSeq 6000
bulkRNA_IL33_timecourse_DESeq2_normalized_count.csv


title: APP_Microglia, PBS, 24hours, rep2 [BulkRNA_Con_2]

description:
BulkRNA_Con_2
BulkRNA_Con_2
NextSeq 500/NovaSeq 6000
bulkRNA_IL33_timecourse_DESeq2_normalized_count.csv

value: PBS, 24hours


title: APP_Microglia, IL33, 3hours, rep2 [BulkRNA_IL33_3h_2]

description:
BulkRNA_IL33_3h_2
BulkRNA_IL33_3h_2
NextSeq 500/NovaSeq 6000
bulkRNA_IL33_timecourse_DESeq2_normalized_count.csv


title: APP;ST2WT_Microglia, IL33, 3hours, rep2 [BulkRNA_ST2WT_IL33_2]

description:
BulkRNA_ST2WT_IL33_2
BulkRNA_ST2WT_IL33_2
NextSeq 500/NovaSeq 6000
bulkRNA_IL33_ST2KO_DESeq2_normalized_count.csv


title: APP_Microglia, PBS, 24hours, rep1 [BulkRNA_Con_1]

description:
BulkRNA_Con_1
BulkRNA_Con_1
NextSeq 500/NovaSeq 6000
bulkRNA_IL33_timecourse_DESeq2_normalized_count.csv