title: ZAPS-KO1_untreated_rep3

city: Singapore

first: Phuong Thao

last: Ly

address: SBS-02S-88D, 60 Nanyang Drive

department: School of Biological Sciences

country: Singapore

institute: Nanyang Technological University

description: 101 bp PE

data_processing:
We inspected the quality of the RNA-seq datasets using FastQC. We used STAR (2.7.0a) to align reads to the GRCh38 and GENCODE v34.
We used RSEM with default settings for transcript abundance quantification.
Assembly: hg38
Supplementary files format and content: tab-delimited text files include TPM and FPKM values for each Sample

growth_protocol: We cultured the HEK293T (ATCC CRL-3216) cell lines in DMEM/Hi-Glucose supplemented with 10% FBS (Hyclone, United States), 100units/ml penicillin, and 100μg/ml streptomycin (Gibco, United States), 370C with 5% CO2.

extract_protocol:
We extracted the total RNA with RNeasy Mini Kit (Qiagen, #774104) and QIAshredder (Qiagen #79654), and removed the residual genomic DNA with TURBO DNase. Next, we concentrated the total DNase-treated RNA using the RNA Clean & Concentrator™-5 kit (Zymo Research #SKUR1015)
We prepared cDNA libraries using the TruSeq Stranded mRNA Library Prep Kit (Illumina).

treatment_protocol: Only in drug treatment groups, we added IFN-β (Peprotech #300-02BC) to a final concentration of 100ng/ml to complete medium for 24 hours.

tag: cell line

value: human embryonic kidney cells

value: untreated

tag: time

value: 24 hours


title: ctrl_yhp1_13A_20_rep3

status: Public on Jul 25 2022

type: SRA

city: Worcester

first: Jennifer

last: Benanti

state: MA

address: 364 Plantation St., LRB 525

department: Molecular, Cell and Cancer Biology

country: USA

institute: University of Massachusetts Medical School

description:
MATa ura3∆0 his3∆1 lyp∆0 can1∆::STE2pr-SpHIS5 URA3::Z4pr-HO HAP1+::NatMX::pACT1-Z3EV-ENO2term yhp1-13A-3V5-KanMx
TPM.inducible.yhp1.xlsx

library_source: transcriptomic

data_processing:
aligned to Saccharomyces_cerevisiae R64-1-1 genome, with R64-1-1.90 annotation, by STAR(v2.5.3a) aligner.
Gene expression were quantified with featureCounts v1.5.2, measuring exon reads for each gene_id.
TPM was calculated
Genome_build: R64-1-1
Supplementary_files_format_and_content: TPM was calculated

molecule: total RNA

organism: Saccharomyces cerevisiae

growth_protocol: RNA was purified from asynchronous cells growing in rich medium (YM-1 with 2% dextrose) without estradiol addition (0 minutes), and 20 or 60 minutes following the addition of estradiol.

extract_protocol:
Total RNA was purified using an acid-phenol extraction protocol.
polyA depletion and library construction were performed by BGI Americas.

treatment_protocol: 1μM estradiol was added for 20 or 60 minutes, as indicated.

tag: strain

tag: genotype

value: MATa ura3delta0 his3delta1 lypdelta0 can1delta::STE2pr-SpHIS5 URA3::Z4pr-HO HAP1+::NatMX::pACT1-Z3EV-ENO2term yhp1-13A-3V5-KanMx


title: NFF2_AMBO2_7

city: Grand Rapids

first: Peter

middle: W

last: Laird

state: MI

address: 333 Bostwick Ave NE

department: Epigenetics

institute: Van Andel Institute

data_processing:
Pooled lbraries were sequenced using 2x50 bp sequencing on the Illumina NovaSeq 6000 sequencer at the Van Andel Research Institute. Data were demultplexed using Bcl2fastq v1.9.0.
Adapter removal performed using Trimgalore v0.6.0 with options --paired -q 20
Alignment to hg38 performed using STAR v2.7.8a with options --twopassMode Basic --quantMode GeneCounts
Data were filtered in R for a minimum of 0.36 counts per million in >6 samples to generate the filtered expression matrix
RNAseq differential expression analysis was performed in R (v4.1.1) using standard edgeR and DESeq2 workflow
Genome_build: GRCh38

organism: Homo sapiens

source_name: Foreskin

extract_protocol:
RNA was isolated from frozen cell pellets using the AllPrep DNA/RNA Mini Kit (Qiagen 80204), then stored at -80°C before analysis.
RNA Libraries were prepared from 100 ng of total RNA with the KAPA Stranded mRNA-Seq Kit (Kapa Biosystems KK8401).

tag: subexperiment

value: Reduced oxygen

value: 0 years

value: male

value: ambient

tag: subculture

value: a

tag: growth protocol

value: Fibroblasts were maintained in Ham’s F12/DMEM 1:1 media supplemented with 10% v/v fetal bovine serum. Triplicate cultures derived from the same parent plate or vial obtained from Coriell were maintained in parallel through replicative senescence, which was defined in this study as drastically slowed growth (inability to reach near-confluence at 14 days after previous passage) or viable fraction of cells falling below 60%. Passaging occurred as cells became approximately 90% confluent.


title: CM_sham_2

city: Tokyo

first: Shintaro

last: Yamada

address: 7-3-1, Hongo, Bunkyo-ku

department: Department of Cardiovascular Medicine

country: Japan

institute: The University of Tokyo

description: Chromium (10X Genomics)

data_processing:
Raw data was processed using Cell Ranger (version 4.1.1)
Each barcode.tsv.gz, features.tsv.gz and matrix.mtx.gz files genereted using Cell Ranger.

organism: Mus musculus

source_name: cardiomyocyte

growth_protocol: All the animal experiments were approved by the University of Tokyo Ethics Committee for Animal Experiments and strictly adhered to the guidelines for animal experiments of the University of Tokyo (Approved Number P14-106). All of wild type C57BL/6 male mice were purchased from CLEA JAPAN. All mouse were housed in separate cages at a maximum of 6 mice per cage in a specific-pathogen–free, temperature-controlled vivarium under a 12-h light/dark cycle with ad libitum access to food and water.

extract_protocol:
Cardiomyocytes were isolated using Langendorff perfusion from the left ventricle as previously described. Enzymatic dissociation using Langendorff perfusion was performed with 35 mL enzyme solution (type 2 collagenase 1 mg/mL [Worthington], protease type XIV 0.05 mg/mL [Sigma-Aldrich], NaCl 130 mM, KCl 5.4 mM, MgCl2 0.5 mM, NaH2PO4 0.33 mM, D-glucose 22 mM, HEPES 25 mM; pH 7.4) pre-heated to 37 °C, at a rate of 3 mL/min. To neutralize enzymatic activity, fetal bovine serum (FBS) was added to the solution to a final concentration of 0.2% (v/v). After perfusion of digestion buffer, left ventricle was cut according to each sectional region (IZ+BZ vs RZ) and cardiomyocytes were subsequently isolated. Cell suspensions were filtered through a 100-μm nylon mesh cell strainer and centrifuged at 100 g for 2 min, after which the supernatant was discarded. To prevent hypercontraction, the cardiomyocytes were resuspended in medium (NaCl 130 mM, KCl 5.4 mM, MgCl2 0.5 mM, NaH2PO4 0.33 mM, D-glucose 22 mM, HEPES 25 mM, FBS 0.2%; pH 7.4) containing a low concentration of calcium (0.1 mM). Nuclei were isolated immediately after the collection of cardiomyocytes using Minute™ Detergent-Free Single Nuclei Isolation Kit (NI-024, Invent Biotechnologies, USA) according to the manufacturer’s instruction.
Single-nucleus cDNA libraries were generated using 5,000 isolated nuclei by the Chromium 3′ v3 chemistry kit (10x Genomics) according to the manufacturer’s instruction.

treatment_protocol: Myocardial infarction (MI) was induced as previously described. Mice were anaesthetized by inhalation of 2% isoflurane. MI was induced by ligation of the left anterior descending artery. Mice that failed to develop MI or died within one week after the operation were excluded from the analysis.

tag: operation

value: sham

tag: region

tag: tissue

value: cardiomyocyte

tag: name in supplementary file

tag: genome build

value: The reference transcript data and the gene annotation file for mouse was downloaded from  https://cf.10xgenomics.com/supp/cell-exp/refdata-gex-mm10-2021-A.tar.gz.


title: CM_sham_1

description: Chromium (10X Genomics)

value: The reference transcript data and the gene annotation file for mouse was downloaded from  https://cf.10xgenomics.com/supp/cell-exp/refdata-gex-mm10-2020-A.tar.gz.


title: ctrl_yhp1_13A_60_rep1


title: NFF2_AMBO2_6


title: ctrl_yhp1_13A_20_rep2


title: NFF2_AMBO2_5


title: ctrl_yhp1_13A_20_rep1


title: ctrl_yhp1_13A_60_rep3


title: ZAPL-KO2_IFNB_rep3

description: 101 bp PE

tag: cell type

tag: treatment

value: 100ng/ml IFN--beta


title: Mouse_50MII_b

city: beijing

first: Wenqi

last: Hu

state: beijing

address: Room D110, Medical Science Building, School of Medicine, Tsinghua University

country: China

institute: Tsinghua University

description:
ribosome proteched RNA fragment
miniRibo-seq

data_processing:
For T&T-seq data,  sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence by Trim galore (v0.6.4) with parameters  -q 20 --phred33 --stringency 3 -j 32 --length 50 -e 0.1. For miniRibo-seq  sequenced reads were treated by Cutadapt (v1.18) with parameters -j 16  -a AAAAAAAAAA -u 3 --discard-untrimmed -m 25 -M 40
For T&T-seq data,reads were mapped to hg38 or mm10 whole genome using Hisat2 (v2.1.0) with default parameters. For miniRibo-seq, reads were mapped to  mm10 whole genome using STAR (v2.7.1a) with parameters --outFilterType BySJout --runThreadN 16 --outFilterMismatchNmax 2  --outSAMtype BAM SortedByCoordinate --quantMode TranscriptomeSAM GeneCounts --outFilterMultimapNmax1 --outFilterMatchNmin 16 --alignEndsType EndToEnd --outSAMattrIHstart 0
gene count was calculated using Featurecounts (v1.6.5) with parameters -T 32 -O -t exon -M --extraAttributes gene_name
transcripts per million(TPM) was calculated by customize R script
Genome_build: hg38 or mm10
Supplementary_files_format_and_content: tab-delimited text files include TPM values for each Sample ...

source_name: oocyte

growth_protocol: oocytes were collect from 4-6 weeks C57BL/6 female mice, human oocytes were collected form donors underwent ART treatment.

extract_protocol:
For miniRibo-seq,total RNAs were digested by Rnase cocktail. Ribosome protected RNA fragment are separated by PAGE-gel and recovered by isopropanol precipitation. For the transcriptome of T&T-seq mRNAs were directly reverse transcribed after lysing . For the translatome of T&T-seq, ribosome binding RNAs are purifed by RiboLace beads.
For T&T-seq, RNA libraries were prepared for sequencing using Single Cell Full Length mRNA-Amplification Kit (N712, Vazyme) ,TruePrep DNA Library Prep Kit V2 for Illumina (TD502, Vazyme) and TruePrep® Index Kit V2 for Illumina (TD202, Vazyme). For miniRibo-seq, RNA libraries were prepared for sequencing using SMARTer® smRNA-Seq Kit for Illumina (635030, TAKARA)

treatment_protocol: One replicate was OOSP2 protein or  OOSP2 antibody treated for 90 minutes

tag: Stage

value: MII

tag: type

value: translatiome

tag: cell number


title: ZAPL-KO1_untreated_rep3

description: 101 bp PE

tag: cell line

value: human embryonic kidney cells


title: ctrl_yhp1_13A_0_rep3


title: NFF2_AMBO2_4


title: ZAPS-KO1_IFNB_rep3

description: 101 bp PE

tag: time


title: NFF2_AMBO2_3


title: ctrl_yhp1_13A_0_rep1

tag: strain


title: ZAPL-KO2_untreated_rep3

description: 101 bp PE

tag: genotype

value: untreated


title: Mouse_50GV_a

value: GV


title: Mouse_50GV_b


title: ctrl_yhp1_13A_0_rep2

value: MATa ura3delta0 his3delta1 lypdelta0 can1delta::STE2pr-SpHIS5 URA3::Z4pr-HO HAP1+::NatMX::pACT1-Z3EV-ENO2term yhp1-13A-3V5-KanMx


title: ZAPL-KO1_IFNB_rep3

description: 101 bp PE

value: 24 hours


title: WT_untreated_rep3

description: 101 bp PE

value: wildtype


title: NFF2_AMBO2_2

tag: subexperiment

value: Reduced oxygen

value: 0 years

value: male


title: WT_IFNB_rep3

description: 101 bp PE


title: ZAPS-KO2_untreated_rep2

description: 101 bp PE


title: ctrl_YHP1_0_rep3

description:
MATa ura3∆0 his3∆1 lyp∆0 can1∆::STE2pr-SpHIS5 URA3::Z4pr-HO HAP1+::NatMX::pACT1-Z3EV-ENO2term YHP1-3V5-KanMx
TPM.inducible.yhp1.xlsx

value: MATa ura3delta0 his3delta1 lypdelta0 can1delta::STE2pr-SpHIS5 URA3::Z4pr-HO HAP1+::NatMX::pACT1-Z3EV-ENO2term YHP1-3V5-KanMx


title: ctrl_YHP1_0_rep2


title: Mouse_1MII_a_Ribo

description:
ribosome-binding RNA
T&T-seq


title: Mouse_50MII_a


title: Mouse_1MII_b_Ribo

description:
ribosome-binding RNA
T&T-seq


title: NFF2_6

value: Baseline profiling

value: ambient

tag: subculture

value: a

value: Fibroblasts were maintained in Ham’s F12/DMEM 1:1 media supplemented with 10% v/v fetal bovine serum. Triplicate cultures derived from the same parent plate or vial obtained from Coriell were maintained in parallel through replicative senescence, which was defined in this study as drastically slowed growth (inability to reach near-confluence at 14 days after previous passage) or viable fraction of cells falling below 60%. Passaging occurred as cells became approximately 90% confluent.


title: Mouse_10MII_c_Ribo

description:
ribosome-binding RNA
T&T-seq


title: NFF2_7

tag: growth protocol


title: yox1_del_yhp1_del_B_rep3

description:
MATa ura3∆0 leu2∆0 his3∆0 met15∆0 yox1∆::NatMX yhp1∆::LEU2
tpm.constitutive.del.0818.csv

growth_protocol: RNA was purified from asynchronous cells growing in rich medium (YM-1 with 2% dextrose).

value: MATa ura3delta0 leu2delta0 his3delta0 met15delta0 yox1delta::NatMX yhp1delta::LEU2


title: WT_IFNB_rep2

description: 101 bp PE

value: 100ng/ml IFN--beta


title: Mouse_10MII_b_Ribo

description:
ribosome-binding RNA
T&T-seq

value: MII

value: translatiome


title: WT_untreated_rep2

description: 101 bp PE

value: human embryonic kidney cells

value: untreated


title: ctrl_YHP1_0_rep1


title: Mouse_1MII_b_RNA

description:
ployA RNA
T&T-seq

value: transcriptome


title: yox1_del_yhp1_del_B_rep2


title: ZAPS-KO1_untreated_rep1

description: 101 bp PE

value: 24 hours


title: ZAPS-KO1_IFNB_rep1

description: 101 bp PE


title: NFF2_AMBO2_1


title: yox1_del_B_rep3

description:
MATa ura3∆0 leu2∆0 his3∆0 met15∆0 yox1∆::KanMX
tpm.constitutive.del.0818.csv

value: MATa ura3delta0 leu2delta0 his3delta0 met15delta0 yox1delta::KanMX


title: NFF2_8


title: yox1_del_yhp1_del_B_rep1


title: ZAPL-KO1_untreated_rep1

description: 101 bp PE


title: NFF2_4


title: Mouse_1MII_a_RNA

description:
ployA RNA
T&T-seq


title: NFF2_2


title: WT_untreated_rep1

description: 101 bp PE

value: wildtype


title: ZAPL-KO1_IFNB_rep1

description: 101 bp PE


title: Mouse_10MII_a_Ribo

description:
ribosome-binding RNA
T&T-seq


title: NFF2_3

value: 0 years


title: yox1_del_B_rep1


title: yox1_9A_yhp1_13A_A_rep3

description:
MATa ura3∆0 leu2∆0 his3∆0 met15∆0 yox1-9A-3V5-KanMx yhp1-13A-13MYC-LEU2
tpm.constitutive.phos.0718.csv

value: MATa ura3delta0 leu2delta0 his3delta0 met15delta0 yox1-9A-3V5-KanMx yhp1-13A-13MYC-LEU2


title: ZAPS-KO2_IFNB_rep2

description: 101 bp PE


title: Mouse_10MII_b_RNA

description:
ployA RNA
T&T-seq


title: Mouse_10MII_a_RNA

description:
ployA RNA
T&T-seq


title: Mouse_1GV_b_Ribo

description:
ribosome-binding RNA
T&T-seq

value: GV


title: NFF1_8

value: Baseline profiling

value: male

value: b


title: Mouse_1GV_a_Ribo

description:
ribosome-binding RNA
T&T-seq


title: WT_IFNB_rep1

description: 101 bp PE


title: NFF2_5

value: ambient

value: a

value: Fibroblasts were maintained in Ham’s F12/DMEM 1:1 media supplemented with 10% v/v fetal bovine serum. Triplicate cultures derived from the same parent plate or vial obtained from Coriell were maintained in parallel through replicative senescence, which was defined in this study as drastically slowed growth (inability to reach near-confluence at 14 days after previous passage) or viable fraction of cells falling below 60%. Passaging occurred as cells became approximately 90% confluent.


title: Mouse_10MII_c_RNA

description:
ployA RNA
T&T-seq

value: MII


title: yox1_9A_yhp1_13A_A_rep2


title: NFF1_7


title: Mouse_10GV_c_Ribo

description:
ribosome-binding RNA
T&T-seq

value: translatiome


title: yox1_9A_A_rep3

description:
MATa ura3∆0 leu2∆0 his3∆0 met15∆0 yox1-9A-3V5-KanMx
tpm.constitutive.phos.0718.csv

value: MATa ura3delta0 leu2delta0 his3delta0 met15delta0 yox1-9A-3V5-KanMx


title: NFF1_6


title: yox1_del_B_rep2


title: yox1_9A_A_rep2


title: NFF2_1


title: Mouse_10GV_b_Ribo

description:
ribosome-binding RNA
T&T-seq


title: NFF1_5


title: Adjacent Normal 5

type: RNA

city: SHENYANG

first: ZHIDONG

last: YANG

state: LIAONING

address: 155, nanjingbei str.

department: Department of Laboratory Medicine

institute: The First Affiliated Hospital of China Medical University

description: lncRNA and mRNA expression

hyb_protocol: DNA in hybridization solution was denatured at 95℃ for 3 min prior to loading onto a microarray. Arrays were hybridized was preformed in a Agilent Hybridization Oven overnight at a rotation speed of 20 rpm at 42℃ and washed with two consecutive solutions (0.2% SDS, 2× SSC at 42℃ for 5 min, and 0.2× SSC for 5 min at room temperature).

scan_protocol: Scanned on an Agilent G2565CA scanner.

data_processing: Feature Extraction v10.7 (Agilent Technologies, CA) software was used to extract all features of the data obtained from the scanned images and genespring software was used to analyze the raw data, which are normalized by percentile normalization.

source_name: Adjacent Normal

label_protocol: cDNA labeled with a fluorescent dye (Cy3-dCTP) was produced by Eberwine’s linear RNA amplification method and subsequent enzymatic reaction. This procedure has been previously described, and the procedure has been improved by using CapitalBio cRNA Amplification and Labeling Kit (CapitalBio) for producing higher yields of labeled cDNA.

extract_protocol: RNA was prepared using the TRIzol reagent following the manufacturer's recommendations.  RNA was quantified using a NanoDrop-1000 spectrophotometer.

value: colon

tag: gender


title: yox1_9A_A_rep1


title: Cancer 5

description: lncRNA and mRNA expression

source_name: Cancer


title: Mouse_1GV_b_RNA

description:
ployA RNA
T&T-seq

value: transcriptome


title: NFF1_3


title: yox1_9A_yhp1_13A_A_rep1


title: NFF1_2


title: Mouse_10GV_a_Ribo

description:
ribosome-binding RNA
T&T-seq


title: NFF1_1


title: yhp1_del_B_rep1

description:
MATa ura3∆0 leu2∆0 his3∆0 lys2∆0 yhp1∆::LEU2
tpm.constitutive.del.0818.csv

value: MATa ura3delta0 leu2delta0 his3delta0 lys2delta0 yhp1delta::LEU2


title: Mouse_1GV_a_RNA

description:
ployA RNA
T&T-seq


title: Adjacent Normal 4

description: lncRNA and mRNA expression

value: rectum

value: female


title: ASF1_8

source_name: Skin, arm

value: 31 years

value: Fibroblasts were maintained in Eagle’s MEM with Earle’s salts with 10% v/v fetal bovine serum. Triplicate cultures derived from the same parent plate or vial obtained from Coriell were maintained in parallel through replicative senescence, which was defined in this study as drastically slowed growth (inability to reach near-confluence at 14 days after previous passage) or viable fraction of cells falling below 60%. Passaging occurred as cells became approximately 90% confluent.


title: Mouse_10GV_c_RNA

description:
ployA RNA
T&T-seq

value: GV


title: yhp1_13A_A_rep3

description:
MATa ura3∆0 leu2∆0 his3∆0 met15∆0 yhp1-13A-13MYC-LEU2
tpm.constitutive.phos.0718.csv

value: MATa ura3delta0 leu2delta0 his3delta0 met15delta0 yhp1-13A-13MYC-LEU2


title: NFF1_4

value: Baseline profiling

value: 0 years

value: male


title: Adjacent Normal 3

description: lncRNA and mRNA expression


title: yhp1_del_B_rep2


title: ASF1_7

value: ambient

value: b


title: Mouse_10GV_a_RNA

description:
ployA RNA
T&T-seq


title: yhp1_del_B_rep3


title: Mouse_10GV_b_RNA

description:
ployA RNA
T&T-seq


title: ASF1_6


title: ASF1_5


title: yhp1_13A_A_rep1


title: WT_B_rep3

description:
MATa ura3∆0 leu2∆0 his3∆0 met15∆0 YOX1-3V5-KanMx YHP1-13MYC-LEU2
tpm.constitutive.del.0818.csv

value: MATa ura3delta0 leu2delta0 his3delta0 met15delta0 YOX1-3V5-KanMx YHP1-13MYC-LEU2


title: ASF1_4


title: WT_B_rep2


title: Adjacent Normal 2

description: lncRNA and mRNA expression


title: gtl1_WS_Exp_R3

city: WEST LAFAYETTE

first: Noel

middle: Anthony

last: Mano

state: IN

address: 170 S University Street

institute: Purdue University

description: S4 300 cycle chemistry

data_processing:
fastq files generated with Illumina bcl2fastq software
fastq files trimmed with trimmomatic: PE LEADING:20 TRAILING:20 MINLEN:30 ILLUMINACLIP:our_vector_file:2:40:10
FastQC to check sequence quality
TrimGalore removed low quality (phred <33) reads
STAR-Aligner aligned genome to Araport 11 Arabidopsis genome.
RSEM abundance estimataion function generated transcript counts/million and expected counts
EBSeq filtered low expressed genes and normalized expected count data.
Assembly: Arabidopsis thaliana Araport 11 release, TAIR10 annotation
Supplementary files format and content: csv files with normalized expected count data; 1 file for emerging leaves and 1 file for expanding leaves.

organism: Arabidopsis thaliana

source_name: 50% fully expanded leaves

growth_protocol: Arabidopsis plants of both genotypes grown in a growth chamber with 8h photoperiod, 150 μmol m-2 s-1 light intensity and day night temperature and VPD of 23/18˚C and 1.2/0.8 kPa.

extract_protocol:
RNA extracted following manufacturer's protocol for the QIAGEN PowerPlant RNA Kit. gDNA removed using QIAGEN Dnase Max Kit. 2µg of RNA used for RNA-Seq.
Illumina mRNA-Seq Kit

treatment_protocol: Well-watered plants maintained between 65 and 100% media water content, water-stressed plants at 30% MWC. All plants weighed every 2 days and watered to bring plants to target MWC as necessary.

value: 50% fully expanded leaves

value: Water-stressed post-differentiation expanding leaf tissue

value: Water-stressed (30% media water content)


title: gtl1_WS_Exp_R1

description: S4 300 cycle chemistry


title: Cancer 3

description: lncRNA and mRNA expression


title: Adjacent Normal 1

description: lncRNA and mRNA expression


title: Cancer 4

description: lncRNA and mRNA expression


title: Col-0_WS_Exp_R3

description: S4 300 cycle chemistry


title: WT_B_rep1


title: ASF1_3


title: yhp1_13A_A_rep2


title: ASF1_2


title: ASF1_1


title: Col-0_WS_Exp_R2

description: S4 300 cycle chemistry


title: WT_A_rep3

description:
MATa ura3∆0 leu2∆0 his3∆0 met15∆0 YOX1-3V5-KanMx YHP1-13MYC-LEU2
tpm.constitutive.phos.0718.csv


title: Col-0_WS_Exp_R1

description: S4 300 cycle chemistry


title: WT_A_rep1


title: WT_A_rep2


title: AVSMC1_7

source_name: Iliac vein

value: 19 years

value: Vascular smooth muscle cells were maintained in Medium 199 with 1X GlutaMAX, 0.02mg/ml endothelial cell growth supplement, 0.05 mg/ml sodium heparin, and 10% v/v fetal bovine serum on plates pre-coated with gelatin. Triplicate cultures derived from the same parent plate or vial obtained from Coriell were maintained in parallel through replicative senescence, which was defined in this study as drastically slowed growth (inability to reach near-confluence at 14 days after previous passage) or viable fraction of cells falling below 60%. Passaging occurred as cells became approximately 90% confluent.


title: gtl1_WW_Exp_R3

description: S4 300 cycle chemistry

value: Well-watered post-differentiation expanding leaf tissue

value: Well-watered (65-100% media water coontent)


title: gtl1_WS_Exp_R2

description: S4 300 cycle chemistry


title: elmo3-/- knockout rep6

city: Mannheim

first: Carsten

last: Sticht

address: Theodor-Kutzer-Ufer

department: ZMF

country: Germany

institute: University Heidelberg

data_processing:
trimmed with trim_galore version 0.6.4. Parameters: --length 26 --phred33
Get raw counts with kallisto quant version 0.4.6.
TPM abundance estimates, generated with kallisto quant 0.4.6
Genome_build: GRCz11
Supplementary_files_format_and_content: TPM abundance estimates and raw counts generated with kallisto.

organism: Danio rerio

source_name: 30 zebrafish larvae

extract_protocol:
30 larvae per sample were snap frozen. Then total RNA was isolated using the RNeasy Kit (Qiagen) following the manufacturer's protocol
RNA libraries were prepared for sequencing using standard BGISeq-500 protocols

tag: genotype/variation

value: 30 zebrafish larvae


title: elmo3-/- knockout rep5

tag: tissue


title: AVSMC1_5


title: Cancer 2

description: lncRNA and mRNA expression

value: rectum


title: AVSMC1_6


title: gtl1_WW_Exp_R1

description: S4 300 cycle chemistry


title: Col-0_WW_Exp_R3

description: S4 300 cycle chemistry


title: elmo3-/- knockout rep4


title: AVSMC1_4


title: Cancer 1

description: lncRNA and mRNA expression


title: AVSMC1_8


title: elmo3-/- knockout rep2


title: elmo3-/- knockout rep3


title: AVSMC1_3


title: elmo3-/- knockout rep1


title: Col-0_WW_Exp_R2

description: S4 300 cycle chemistry


title: gtl1_WS_Em_R3

description: S4 300 cycle chemistry

source_name: Day old emerging leaves

value: Day old emerging leaves

value: Water-stressed proliferating leaf tissue


title: gtl1_WS_Em_R2

description: S4 300 cycle chemistry


title: AVEC1_8

value: Baseline profiling

value: 15 years

value: c

value: Vascular endothelial cells were maintained in Medium 199 with 1X GlutaMAX, 0.02mg/ml endothelial cell growth supplement, 0.05 mg/ml sodium heparin, and 15% v/v fetal bovine serum on plates pre-coated with gelatin. Triplicate cultures derived from the same parent plate or vial obtained from Coriell were maintained in parallel through replicative senescence, which was defined in this study as drastically slowed growth (inability to reach near-confluence at 14 days after previous passage) or viable fraction of cells falling below 60%. Passaging occurred as cells became approximately 90% confluent.


title: AVSMC1_2

value: male

value: ambient

value: b


title: elmo3+/+ wildtype rep6

value: WT


title: AVEC1_7


title: gtl1_WW_Exp_R2

description: S4 300 cycle chemistry

value: 50% fully expanded leaves


title: elmo3+/+ wildtype rep4


title: Col-0_WS_Em_R3

description: S4 300 cycle chemistry

value: Water-stressed (30% media water content)


title: AVEC1_6


title: gtl1_WS_Em_R1

description: S4 300 cycle chemistry


title: Col-0_WS_Em_R2

description: S4 300 cycle chemistry


title: AVEC1_5


title: elmo3+/+ wildtype rep3


title: elmo3+/+ wildtype rep2


title: Spleen_Chronic_D8_CD8_TetPos_gex

city: Stanford

first: Ansuman

middle: T

last: Satpathy

state: CA

address: 300 Pasteur Drive

department: Pathology

institute: Stanford University

description: 5' gene expression library (10X Genomics)

data_processing:
Processed with cellranger pipeline, version 3.1.0.
Genome_build: mm10
Supplementary_files_format_and_content: scRNA_LCMV.mtx, scRNA_LCMV_barcodes.tsv, scRNA_LCMV_features.tsv, scRNA_LCMV_metadata.tsv.

molecule: polyA RNA

source_name: CD8+ gp33+ T cells from spleen 8 dpi with LCMV-c13

extract_protocol: 10X Genomics Single Cell 5' Library & Gel Bead Kit (v1.1 Chemistry).

value: CD8+ gp33+ T cells


title: gtl1_WW_Em_R3

description: S4 300 cycle chemistry

value: Well-watered proliferating leaf tissue


title: elmo2+/+ wildtype rep6

value: Rplus


title: Spleen_Chronic_D8_CD8_TetNeg_gex

source_name: CD8+ gp33- T cells from spleen 8 dpi with LCMV-c13

value: CD8+ gp33- T cells


title: AVSMC1_1

value: 19 years

value: Vascular smooth muscle cells were maintained in Medium 199 with 1X GlutaMAX, 0.02mg/ml endothelial cell growth supplement, 0.05 mg/ml sodium heparin, and 10% v/v fetal bovine serum on plates pre-coated with gelatin. Triplicate cultures derived from the same parent plate or vial obtained from Coriell were maintained in parallel through replicative senescence, which was defined in this study as drastically slowed growth (inability to reach near-confluence at 14 days after previous passage) or viable fraction of cells falling below 60%. Passaging occurred as cells became approximately 90% confluent.


title: AVEC1_4


title: AVEC1_3


title: Spleen_Chronic_D21_CD8_TetPos_gex

source_name: CD8+ gp33+ T cells from spleen 21 dpi with LCMV-c13


title: elmo3+/+ wildtype rep1

value: 30 zebrafish larvae


title: gtl1_WW_Em_R2

description: S4 300 cycle chemistry

value: Day old emerging leaves

value: Well-watered (65-100% media water coontent)


title: Spleen_Chronic_D21_CD8_TetNeg_gex

source_name: CD8+ gp33- T cells from spleen 21 dpi with LCMV-c13


title: AVEC1_2

value: Baseline profiling

value: 15 years

value: c


title: elmo2+/+ wildtype rep5


title: AVEC1_1

value: male

value: ambient

value: Vascular endothelial cells were maintained in Medium 199 with 1X GlutaMAX, 0.02mg/ml endothelial cell growth supplement, 0.05 mg/ml sodium heparin, and 15% v/v fetal bovine serum on plates pre-coated with gelatin. Triplicate cultures derived from the same parent plate or vial obtained from Coriell were maintained in parallel through replicative senescence, which was defined in this study as drastically slowed growth (inability to reach near-confluence at 14 days after previous passage) or viable fraction of cells falling below 60%. Passaging occurred as cells became approximately 90% confluent.


title: gtl1_WW_Em_R1

description: S4 300 cycle chemistry


title: Col-0_WW_Exp_R1

description: S4 300 cycle chemistry

value: 50% fully expanded leaves

value: Well-watered post-differentiation expanding leaf tissue


title: Spleen_Chronic_D21_CD8_TetMid_gex

source_name: CD8+ gp33 mid T cells from spleen 21 dpi with LCMV-c13

value: CD8+ gp33 mid T cells


title: FSF1_8

source_name: Skin, sacrum

value: 16 fetal weeks

value: female

value: b

value: Fibroblasts were maintained in Eagle’s MEM with Earle’s salts and non-essential amino acids with 15% v/v fetal bovine serum. Triplicate cultures derived from the same parent plate or vial obtained from Coriell were maintained in parallel through replicative senescence, which was defined in this study as drastically slowed growth (inability to reach near-confluence at 14 days after previous passage) or viable fraction of cells falling below 60%. Passaging occurred as cells became approximately 90% confluent.


title: elmo2+/+ wildtype rep3

value: Rplus


title: elmo2+/+ wildtype rep4

value: 30 zebrafish larvae


title: Spleen_Acute_D8_CD8_TetPos_gex

source_name: CD8+ gp33+ T cells from spleen 8 dpi with LCMV-Armstrong

value: CD8+ gp33+ T cells


title: Col-0_WS_Em_R1

description: S4 300 cycle chemistry

value: Day old emerging leaves

value: Water-stressed proliferating leaf tissue

value: Water-stressed (30% media water content)


title: Col-0_WW_Em_R3

description: S4 300 cycle chemistry

value: Well-watered proliferating leaf tissue

value: Well-watered (65-100% media water coontent)


title: Spleen_Acute_D8_CD8_TetNeg_gex

source_name: CD8+ gp33- T cells from spleen 8 dpi with LCMV-Armstrong

value: CD8+ gp33- T cells


title: elmo2+/+ wildtype rep2


title: Col-0_WW_Em_R1

description: S4 300 cycle chemistry


title: elmo3+/+ wildtype rep5

value: WT


title: FSF1_7

value: Baseline profiling

value: ambient


title: elmo2+/+ wildtype rep1


title: Myoblast-EID-N2

city: Montréal

first: Sophie

last: Ehresmann

state: Quebec

address: 110 Avenue des pins

country: Canada

institute: IRCM

data_processing:
FASTQ Validation FastQC 0.11.5
Alignment STAR 2.5.1b
Gene quantification with featureCounts 1.4.6 (reverse stranded)
Differential analysis with DESeq2 1.34.0
Assembly: GRCm38
Supplementary files format and content: EIDvsWT_DESeq2NormCounts.tsv: Normalized counts were obtained with DESeq2.

source_name: Myoblast

growth_protocol: Primary myoblasts were isolated from leg muscles of mice. Muscles were minced mechanically and digested with trypsin and collagenase D in F12 media for 1h-3h at 37°C. Cells were resuspended with PBS and incubate 1 min at RT in Red Blood Cell Lysis Solution (Sigma, cat#R7757). Isolation of myoblasts was performed using magnetic beads from Miltenyl Biotec (MACS Satellite Cell Isolation Kit (cat#130-104-268) and anti-Integrin -7 MicroBeads (cat#130-104-261)), where cells were incubated on ice for 15 min prior to selection on columns (LS columns; Miltenyi Biotec, cat#130-042-401). Primary myoblasts were cultured on gelatin-coated dishes (Sigma, cat#G9382) in the following media: 39% DMEM with glutamax, 39% F12 with glutamax, 20% fetal bovin serum (Wisent) and 2% UltroserG (Pall Life Sciences, cat#15950-017). Myoblast differentiation was induced, by changing media for 2% horse serum in DMEM/F12 (with glutamax) for 72h.

extract_protocol:
RNA was extracted using RNeasy columns following the kit protocol (QIAGEN).
Poly-A RNAs were enriched from 1ug total RNA using the NEBNext® Poly(A) mRNA Magnetic Isolation Module and libraries were prepared using the KAPA Stranded mRNA-Seq Kit. Libraries were sequenced on a HiSeq4000 in Paired-End 50bp fragments with an average of 52M fragments per library.

value: Myoblast

value: EID


title: FSF1_6

value: 16 fetal weeks

value: female


title: Myoblast-EID-N1


title: FSF1_5

value: b

value: Fibroblasts were maintained in Eagle’s MEM with Earle’s salts and non-essential amino acids with 15% v/v fetal bovine serum. Triplicate cultures derived from the same parent plate or vial obtained from Coriell were maintained in parallel through replicative senescence, which was defined in this study as drastically slowed growth (inability to reach near-confluence at 14 days after previous passage) or viable fraction of cells falling below 60%. Passaging occurred as cells became approximately 90% confluent.


title: Spleen_Acute_D21_CD8_TetNeg_gex

source_name: CD8+ gp33- T cells from spleen 21 dpi with LCMV-Armstrong


title: Lung_Chronic_D21_CD8_TetPos_gex

source_name: CD8+ gp33+ T cells from lung 21 dpi with LCMV-c13


title: elmo2-/- knockout rep6

value: Rmin

value: 30 zebrafish larvae


title: Col-0_WW_Em_R2

description: S4 300 cycle chemistry

value: Day old emerging leaves


title: Myoblast-WT-N3


title: elmo2-/- knockout rep5


title: FSF1_3


title: Lung_Chronic_D21_CD8_TetNeg_gex

source_name: CD8+ gp33- T cells from lung 21 dpi with LCMV-c13


title: elmo2-/- knockout rep3


title: Myoblast-WT-N1


title: elmo2-/- knockout rep4


title: Myoblast-WT-N2


title: FSF1_4


title: FSF1_1


title: Liver_Chronic_D21_CD8_TetNeg_gex

source_name: CD8+ gp33- T cells from liver 21 dpi with LCMV-c13


title: elmo2-/- knockout rep2


title: elmo2-/- knockout rep1


title: RBMS3_ACTD_6hr_REP3

city: Detroit

first: Guojun

last: Wu

address: 4100 John R

department: Oncology

institute: Karmanos Cancer Institute

data_processing:
FASTQ files trimmed using Trim Galore (v0.6.6) with default parameters, except: --three_prime_clip_R1 12
Trimmed FASTQ files were quantified using Salmon (v1.4.0) with default parameters, except: --validateMappings -l A
Transcripts were mapped to genes using biomaRT (v2.48.1) and tximport (v1.20.0)
Normalized gene counts were computed using DESeq2 (v1.32.0) counts(normalized=TRUE)
Differential expression was computed using DESeq2 (v1.32.0) DESeq()
Genome_build: Gencode v36
Supplementary_files_format_and_content: tab-delimited quant.sf text files generated by Salmon for each sample
Supplementary_files_format_and_content: comma-delimited text file of normalized gene counts for all samples

growth_protocol: HMLE cells were cultured in 1:1 Dulbecco's Modified Eagle's Medium (DMEM)/HAMF12 medium (Invitrogen) complemented with 10% FBS (Cambrex), 100 U/ml penicillin-streptomycin (Invitrogen), 2 mM L glutamine (Invitrogen), 10 ng/ml human epidermal growth factor (EGF) (PromoCell), 0.5 µg/ml hydrocortisone (Sigma) and 10 µg/ml insulin (Sigma)

extract_protocol:
RNA was extracted with the RNeasy Plus mini kit (Qiagen)
Library preparation using Lexogen's QuantSeq 3'mRNA-seq method.  75bp single reads with dual indexing.

treatment_protocol: the HMLE/LacZ and HMLE/RBMS3 cells were treated with 10 µg/mL of Actinomycin D for 4 different time points (0, 90, 180 and 360 mins).

tag: cell line background

value: HMLE

value: Immortalized mammary epithelial cells

value: RbMS3 expression

tag: treament

value: treated with ACTD at 360 minutes


title: Liver_Chronic_D21_CD8_TetPos_gex

source_name: CD8+ gp33+ T cells from liver 21 dpi with LCMV-c13

tag: cell type

value: CD8+ gp33+ T cells


title: RBMS3_ACTD_6hr_REP2


title: Spatial_MI_day14_1

description: Visium (10X Genomics)

data_processing:
Raw sequencing reads from single-cardiomyocyte RNA sequencing libraries were trimmed to remove adapter sequences and low-quality bases using fastp-0.20.027 with the parameters “--cut_tail --cut_tail_window_size 1 --cut_tail_mean_quality 30 --length_required 30”
The clean reads were aligned to the mouse genome (mm10) using STAR (version 2.7.2b)
The reads aligned to exon were counted using featureCounts
For nonCM RNA-seq, raw data was processed using Cell Ranger (version 4.0.0)
For spatial transcriptome, raw data was processed using Space Ranger (version 1.2.1)
Genome_build: For single-cardiomyocyte RNA-seq, the reference transcript data and the gene annotation file for mouse was downloaded from GENCODE (release 23, https://www.gencodegenes.org/)
Genome_build: For nonCM RNA-seq, the reference transcript data and the gene annotation file for mouse was downloaded from  https://cf.10xgenomics.com/supp/cell-exp/refdata-gex-mm10-2020-A.tar.gz.
Genome_build: For spatial transcrptome, the reference transcript data and the gene annotation file for mouse was downloaded from https://cf.10xgenomics.com/supp/spatial-exp/refdata-gex-mm10-2020-A.tar.gz.
Supplementary_files_format_and_content: ReadCounts file generated using featureCounts.
Supplementary_files_format_and_content: Each barcode.tsv.gz, features.tsv.gz and matrix.mtx.gz files genereted using Cell Ranger or Space Ranger.

source_name: Heart

extract_protocol:
Cardiomyocytes were isolated using Langendorff perfusion from the left ventricle as previously described7. Enzymatic dissociation using Langendorff perfusion was performed with 35 mL enzyme solution (type 2 collagenase 1 mg/mL [Worthington], protease type XIV 0.05 mg/mL [Sigma-Aldrich], NaCl 130 mM, KCl 5.4 mM, MgCl2 0.5 mM, NaH2PO4 0.33 mM, D-glucose 22 mM, HEPES 25 mM; pH 7.4) pre-heated to 37 °C, at a rate of 3 mL/min. To neutralize enzymatic activity, fetal bovine serum (FBS) was added to the solution to a final concentration of 0.2% (v/v). After perfusion of digestion buffer, left ventricle was cut according to each sectional region (IR, RR) and cardiomyocytes were subsequently isolated. Cell suspensions were filtered through a 100-μm nylon mesh cell strainer and centrifuged at 100 g for 2 min, after which the supernatant was discarded. To prevent hypercontraction, the cardiomyocytes were resuspended in medium (NaCl 130 mM, KCl 5.4 mM, MgCl2 0.5 mM, NaH2PO4 0.33 mM, D-glucose 22 mM, HEPES 25 mM, FBS 0.2%; pH 7.4) containing a low concentration of calcium (0.1 mM). Rod-shaped live cardiomyocytes (viability of cardiomyocytes was ≥80% for all time points) were collected immediately with a 0.2–2-µL pipette (sample volume, 0.5 µL) and incubated in lysis buffer.
Single-cardiomyocyte cDNA libraries were generated using the Smart-seq2 protocol26 and the efﬁciency of reverse transcription was assessed by examining the cycle threshold (Ct) values of control genes (Tnnt2) from quantitative real-time polymerase chain reaction (qRT-PCR) using a CFX96 Real-Time PCR Detection System (Bio-Rad), and the distribution of cDNA fragment lengths was assessed using LabChip GX (Perkin Elmer) and/or TapeStation 2200 (Agilent Technologies). The following primer sets were used for qRT-PCR: Tnnt2 mRNA forward: TCCTGGCAGA GAGGAGGAAG; Tnnt2 mRNA reverse: TGCAGGTCGA ACTTCTCAGC. A Ct value of 25 was set as the threshold. The sequencing libraries were subjected to paired-end 51-bp RNA sequencing on a HiSeq 2500 (Illumina) in rapid mode

treatment_protocol: Myocardial infarction (MI) was induced as previously described25. Mice were anaesthetized by inhalation of 2% isoflurane. MI was induced by ligation of the left anterior descending artery. Mice that failed to develop MI or died within one week after the operation were excluded from the analysis.

tag: operation

value: MI day14

tag: region

value: heart

tag: name in supplementary file


title: RBMS3_ACTD_6hr_REP1


title: Spleen_Acute_D21_CD8_TetPos_gex

source_name: CD8+ gp33+ T cells from spleen 21 dpi with LCMV-Armstrong


title: Spatial_MI_day7_1

description: Visium (10X Genomics)

value: MI day7


title: elmo1-/- knockout rep5

source_name: 30 zebrafish larvae

value: hz


title: elmo1-/- knockout rep6


title: Spatial_Sham

description: Visium (10X Genomics)

value: sham


title: FSF1_2

value: Baseline profiling

value: 16 fetal weeks

value: ambient


title: RBMS3_ACTD_3hr_REP2

value: treated with ACTD at 180 minutes


title: RBMS3_ACTD_3hr_REP1


title: RBMS3_ACTD_3hr_REP3


title: B6B6_4

city: Aurora

first: Kent

middle: Augustus

last: Riemondy

state: Colorado

department: Biochemistry and Molecular Genetics

institute: University of Colorado School of Medicine

description:
count_matrix.tsv.gz
meta-data.tsv.gz

data_processing:
Sequencing data was processed using the cellranger pipeline from 10x Genomics with the mm10 genome assembly to generate unique molecular identifier (UMI) count matrices for each sample. Seurat was used to perform normalization, clustering, and to generate UMAP projections. The R package SoupX was used to remove free RNA contamination. Principal component analysis was performed on z-score transformed data using 30 dimensions for the full dataset and 20 dimensions for the structural lung cells and B-cell subsets. Graph-based clustering was performed using a resolution of 0.1, 0.3, and 0.1 for the full dataset, structural cells, and B-cell subsets respectively. The R package clustifyr was used to aid in assigning cell types to clusters.
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: count_matrix.tsv.gz, meta-data.tsv.gz: UMI count matrix and metadata table indicating cell types for each cell.

source_name: lung

extract_protocol: Single cells were captured using the 10x Genomics Chromium platform. 10,000 cells were loaded and single cell libraries were generated using the 10x Genomics 3’ end single cell gene expression kit.

treatment_protocol: Male C57BL/6 (B6), and HLA (C57BL/6-Tg(HLA-A2.1)1Enge/J) mice were purchased from The Jackson Laboratory. Orthotopic left lung transplantations (LTx) were performed as described previously (Smirnova et al., JCI Insight, 2019) with minor modifications. No immunosuppression was applied to any of the transplanted mice. B6 and HLA mice were used as donors, and B6 as recipients, resulting respectively in non-rejecting controls and BOS development. The mice were sacrificed at one month post-LTx, during the progression phase of BOS. All animal experimentations were approved by the IACUC of the University of Colorado (protocol 115517(04)2D).

tag: treatment

value: B6 lung graft into B6 mouse (non-rejected control)

value: lung


title: elmo1-/- knockout rep3

value: 30 zebrafish larvae


title: elmo1-/- knockout rep2


title: HLAB6_1

description:
count_matrix.tsv.gz
meta-data.tsv.gz

value: HLA lung graft into B6 mouse (BOS)


title: RBMS3_ACTD_1p5hr_REP2

value: HMLE

value: Immortalized mammary epithelial cells

value: treated with ACTD at 90 minutes


title: RBMS3_ACTD_1p5hr_REP3

value: RbMS3 expression


title: elmo1-/- knockout rep1


title: HLAB6_3

description:
count_matrix.tsv.gz
meta-data.tsv.gz


title: RBMS3_ACTD_1p5hr_REP1


title: B6B6_3

description:
count_matrix.tsv.gz
meta-data.tsv.gz


title: elmo1+/+ wildtype rep6

value: wt


title: B6B6_2

description:
count_matrix.tsv.gz
meta-data.tsv.gz


title: B6B6_1

description:
count_matrix.tsv.gz
meta-data.tsv.gz


title: B6B6_5

description:
count_matrix.tsv.gz
meta-data.tsv.gz


title: elmo1+/+ wildtype rep5


title: HMLE-RBMS3_REP3

value: treated with ACTD at 0 minutes


title: elmo1+/+ wildtype rep4


title: HMLE-RBMS3_REP1


title: elmo1-/- knockout rep4


title: HLAB6_2

description:
count_matrix.tsv.gz
meta-data.tsv.gz


title: HMLE-RBMS3_REP2


title: elmo1+/+ wildtype rep2


title: Liver_scRNASeq_LSL_7d_rep3

city: milano

first: stefano

last: campaner

address: via adamello 16

department: Center for Genomic Science

country: Italy

institute: fondazione Istituto italiano di tecnologia

data_processing:
Reads alignment and the gene-barcode matrices were obtained using cellranger 10X v. 2.1.1 and mm10 genome assembly
Replicates aggregation and downstream analyses were carried out using Seurat v.2 R package
Cell type identification was carried out using scMCA (single-cell mouse cell atlas) R package
Genome_build: mm10
Supplementary_files_format_and_content: raw_counts_scRNASeq

extract_protocol:
Liver cells from collagenease treated whole livers were processed with the GemCode Single Cell Platform loaded into Chromium microfluidic chips.
RNA from the barcoded cells was subsequently reverse-transcribed and sequencing libraries were prepared with Chromium Single Cell v2 and v3 reagent kit

tag: strain background

value: ROSA26-rtTA-IRES-EGFP; tetYAP

value: doxycycline food for 7 days

value: Liver


title: Liver_scRNASeq_LSL_7d_rep2


title: elmo1+/+ wildtype rep1


title: elmo1+/+ wildtype rep3


title: Spleen_Chronic_D21_CD8_TetPos_rep1_gex

value: CD8+ gp33+ T cells


title: LACZ_ACTD_6hr_REP2

value: LacZ expression

value: treated with ACTD at 360 minutes


title: Rescue biol rep 3

city: Frederick

first: Jairaj

middle: K

last: Acharya

state: MD

address: 1050 Boyle Street

department: Cancer and Developmental Biology Laboratory

institute: National Cancer Institute, NIH

data_processing:
Data filtering to discard reads with adaptor contamination, uncertain nucleotides constitute >10% and low quality nucleotides constitutes more than 50% of the reads
Mapping to genome using HiSAT2
Transcript abundance measurements using HTSeq software
GSEA analysis using vst transformed read counts
Supplementary files format and content: read counts.xls, vst transfored counts, fpkm.xls and fpkm.stat.xls

organism: Drosophila melanogaster

source_name: testis

growth_protocol: Flies were grown under ambient temperature (18-22 ºC) with 75% humidit and 12 hours light and 12 hours dark cycles

extract_protocol:
200 pairs of testes for each replicate from wild type, cpes mutant and Rescue (Bam-Gal4 and UAS-CPES) Drosophila males were dissected and total RNA was extracted using Trizol and RNA-Clean and concentrater column. About 1ug of RNA in 20ul was submitted for bulk RNAseq using Illumina machine (HWI-ST1276).
Total RNA sample quality was measured using Nanodrop (OD260/280), gel electrophoresis and Agilent 2100 to measure RNA integrity. Susequently mRNA was enriched using oligo(dT) beads, fragmented, cDNA was synthesized using random hexamers and reverse transcriptase. After first strand synthesis a custom second strand Synthesis was performed using nick translation method. the final cDNA library was processed via a series of steps including purification, terminal repair, A-tailing, ligation of seequencing adaptors , size selection and PCR enrichment.After quality check libraries were fed into Illumina machines accroding to a activity (>2nM) and expected data volume.

treatment_protocol: 1-2 days old male flies were used for testis dissection

value: testis

value: Rescue (Bam>UAS CPES)


title: Liver_scRNASeq_LSL_3d_rep4

value: doxycycline food for 3 days


title: Rescue biol rep 2


title: LACZ_ACTD_6hr_REP3


title: Spleen_Chronic_D21_CD8_TetNeg_rep1_gex

value: CD8+ gp33- T cells


title: Rescue biol rep 1


title: Liver_scRNASeq_LSL_3d_rep2


title: LACZ_ACTD_3hr_REP3

value: treated with ACTD at 180 minutes


title: Liver_scRNASeq_LSL_3d_rep3


title: Spleen_Chronic_D21_CD8_CX3CR1Pos_gex

source_name: CD8+ CX3CR1+ T cells from spleen 21 dpi with LCMV-c13

value: CD8+ CX3CR1+ T cells


title: Liver_scRNASeq_LSL_7d_rep1


title: LACZ_ACTD_3hr_REP2

value: HMLE

value: Immortalized mammary epithelial cells


title: cpes biol rep 3

value: cpes mutant


title: Spleen_Chronic_D21_CD8_PD1Pos_gex

source_name: CD8+ PD1+ T cells from spleen 21 dpi with LCMV-c13

value: CD8+ PD1+ T cells


title: LACZ_ACTD_6hr_REP1


title: Liver_scRNASeq_LSL_3d_rep1


title: cpes biol rep 2


title: LACZ_ACTD_3hr_REP1


title: Spleen_Chronic_D21_CD8_CX3CR1Neg_gex

source_name: CD8+ CX3CR1- T cells from spleen 21 dpi with LCMV-c13

value: CD8+ CX3CR1- T cells


title: LACZ_ACTD_1p5hr_REP3

value: treated with ACTD at 90 minutes


title: Liver_scRNASeq_LSL_WT_rep2

value: ROSA26-rtTA-IRES-EGFP; WT

value: doxycycline food for 7 days


title: LACZ_ACTD_1p5hr_REP2


title: w1118 biol rep 3

value: wild type


title: murine kidney_non-pathogenic Leptospira spp.-infected_7day_biological rep3

city: Taoyuan

first: Li-Fang

last: Chou

address: 5 Fu-Shing St., Kueishan

department: Department of Medical Research and Development

country: Taiwan

institute: Chang Gung Memorial Hospital, Linkou

description:
P662
Expression data from infected mice kidney tissue.
Non-pathogenic L. biflexa serovar Patoc (ATCC number 23582).
After infection at day 7

data_processing:
Primary sequencing data was produced by Illumina Hiseq 2000 and 4000 Sequencing System (Flowcell ID: 0416 and HL2F3BBXX).
Fastq files are quality checked with FastQC, v0.11.5 (Babraham Bioinformatics, Cambridge, UK).
Sequenced reads were trimmed using the CLC Genomics Workbench V9.5 on the basis of the per base sequence quality score (Q) >= 20.
After this trimming step, sequenced reads were mapped to Mus_musculus GRCM38 using the CLC Genomics Workbench V9.5.
RPKM, Reads Per Kilobase of exon model per Million mapped reads, values for estimating transcript expression levels were done using the CLC Genomics Workbench V9.5.
Genome_build: Mus_musculus GRCm38
Supplementary_files_format_and_content: Tab-delimited text files contain gene name, ID, reads and RPKM values.

source_name: Kidney from mice infected with non-pathogenic L. biflexa after 7 days

growth_protocol: C57BL/6 female mice aged 6–8 weeks were used for this study. All animal experiments were handled under Animal Biosafety Level 2 conditions and followed all appropriate guidelines for the use of infected animals.

extract_protocol:
Total RNA was extracted from kidney tissues using the TRIzol reagent (Invitrogen, Carlsbad, CA) with DNaseI digestion. The quantity and integrity of extracted RNA were verified using a Nano-Drop spectrophotometer (Thermo Fisher Scientific, Waltham, MA) and an Agilent 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA, USA).
Total RNA samples were converted to cDNA using the Ovation RNA-seq System V2 (NuGEN). Library construction was performed using the Ovation Ultralow Library System V2 1-96 (NuGEN).

treatment_protocol: Bacteria were propagated at 28 °C under aerobic conditions in medium containing 10% Leptospira enrichment Elinghausen-McCullough-Johnson-Harris (EMJH) medium (BD Diagnostics) and 90% Leptospira medium base EMJM medium (Difco, Sparks, MD). The number of motile leptospires was counted using dark-field microscopy and a Petroff-Hausser counting chamber for experimental infections. Mice were inoculated using intraperitoneal challenge with 10^9 Leptospira spp. in 0.1 ml EMJH medium and the control groups were inoculated with sterile EMJH medium.

value: WT

value: Female

tag: age

value: 6-8 weeks

value: Kidney

tag: infection

value: L. biflexa serovar Patoc

tag: infection time

value: 7 days


title: LACZ_ACTD_1p5hr_REP1

value: LacZ expression


title: w1118 biol rep 2

value: testis

tag: genotype


title: murine kidney_non-pathogenic Leptospira spp.-infected_7day_biological rep2

description:
P106
Expression data from infected mice kidney tissue.
Non-pathogenic L. biflexa serovar Patoc (ATCC number 23582).
After infection at day 7

tag: strain


title: Liver_scRNASeq_LSL_WT_rep1

value: Liver


title: Liver_ATACSeq_LapTTA_4W_rep2

description: processed data file: Liver_ATACSeq_LapTTA_4W.bw.gz

library_source: genomic

data_processing:
Read filtering with fastx toolkit version 0.0.13.2: fastq_masker -Q33 -q 20 -r -N -v
Alignment to mm9 with bwa version 0.6.2; bwa aln -t 16 reffile fastqfile| bwa samse -n 1 reffile - fastqfile | samtools view -q 1 -ut reffile - |samtools sort - bamfile
Replicates of the same condition were merged after alignment to a single BAM file for the analyses
Transcription factors Yap and Tead at 4W: peak calling with MACS version 1.4;  --mfold=7,30 -g mm -p 0.00001
Other trancription factor (Hnf4a,Brd4,Pol2): peak calling with MACS version 2.0.9; macs2 -t samplebam -c inputbam  --mfold=7,30 -g mm -p 0.00001
Histone marks (H3K4me1, H3K27Ac, H3K122Ac, H3K4me3): peak calling with MACS version 2.0.9; macs2 -t samplebam -c inputbam  --auto-bimodal --broad -g mm -p 0.00000001
the input alignment file was randomly downsampled to the size of the ChIP sample alignment file
Input for peak calling was taken from GSE83863 published data
Genome_build: mm9
Supplementary_files_format_and_content: *_peaks.txt.gz files: bed files of transcription factors ChIP-Seq;  *_broad_peaks.bed.gz files: bed files of histone marks ChIP-Seq; *bw.gz: compreed bigWig files

molecule: genomic DNA

extract_protocol:
For ChIP experiments, whole cell extracts were sonicated to solubilize the chromatin. The chromatin extracts containing DNA fragments with an average size of 250 bp were immunoprecipitated using different antibodies. For TEAD, HNF4a, BRD4, Histone Marks, RNAPol2 ChIP dissected liver/tumors were fixed with 1% formaldehyde. For YAP ChIP, fixation was performed by a double step approach with 0.5 M DSG (Di-(N-succinimidyl)-glutarate)  and 1% formaldehyde (FA).                           For ATAC seq experiments, 100,000 cells obtained from liver perfused mice were lysed to obtain nuclei. Transposition reaction and DNA purification were then performed.
For ChIP seq, libraries were prepared for Illumina sequencing using a standard protocol consisting in blunting, addition of dA overhangs, ligation of Illumina adapters, selection on gel and PCR with index primers. For ATAC seq, libraries were prepared for Illumina sequencing with index primers.

value: tetYAP


title: Liver_ATACSeq_LapTTA_4W_rep1


title: w1118 biol rep 1


title: HMLE-LACZ_REP3

source_name: HMLE-LACZ

value: HMLE

value: Immortalized mammary epithelial cells

value: treated with ACTD at 0 minutes


title: murine kidney_pathogenic Leptospira spp.-infected_7day_biological rep1

description:
C407
Expression data from infected mice kidney tissue.
Pathogenic L. interrogans serovar Copenhageni Fiocruz L1-130 (ATCC number BAA-1198) isolate recovered from kidneys of hamsters.
After infection at day 7

source_name: Kidney from mice infected with pathogenic L. interrogans after 7 days


title: Spleen_Chronic_D21_CD8_CX3CR1Neg_Slamf6Pos_gex

source_name: CD8+ CX3CR1- SLAMF6+ T cells from spleen 21 dpi with LCMV-c13

value: CD8+ CX3CR1- SLAMF6+ T cells


title: Liver_scRNASeq_perfused_LapTTA_4W

data_processing:
Reads alignment and the gene-barcode matrices were obtained using cellranger 10X v. 3.0.0 and mm10 genome assembly
Downstream analyses were carried out using Seurat v.3 R package. Cells were downsampled to obtain 3000 cells/condition and cells with n UMI>7500 were excluded from the analyses
Cell type identification was carried out using scMCA (single-cell mouse cell atlas) R package
Genome_build: mm10
Supplementary_files_format_and_content: raw_counts_scRNASeq

source_name: Liver

extract_protocol:
Hepatocytes isolated by liver perfusion were processed with the GemCode Single Cell Platform loaded into Chromium microfluidic chips.
RNA from the barcoded cells was subsequently reverse-transcribed and sequencing libraries were prepared with Chromium Single Cell v2 and v3 reagent kit

value: LaptTA; tetYAP

value: hepatocytes


title: Liver_ATACSeq_LapTTA_WT_rep2

description: processed data file: Liver_ATACSeq_LapTTA_WT.bw.gz


title: HMLE-LACZ_REP2


title: HMLE-LACZ_REP1


title: murine kidney_non-infected_7day_biological rep3

description:
E678
Expression data from non-infected mice kidney tissue.
Sterilized Ellinghausen-McCullough-Johnson-Harris (EMJH) medium.
After inoculation at day 7

source_name: Kidney from mice inoculated with sterile EMJH medium after 7 days


title: Liver_scRNASeq_perfused_LapTTA_WT

value: LaptTA;WT


title: Liver_ATACSeq_LapTTA_WT_rep1

value: WT


title: cpes biol rep 1

value: cpes mutant


title: murine kidney_pathogenic Leptospira spp.-infected_7day_biological rep3

description:
C646
Expression data from infected mice kidney tissue.
Pathogenic L. interrogans serovar Copenhageni Fiocruz L1-130 (ATCC number BAA-1198) isolate recovered from kidneys of hamsters.
After infection at day 7

value: Female

value: 6-8 weeks


title: QuantSeq_RNAseq_AT3_3hours_A485+IFNy_Replicate_3

status: Public on Jul 24 2022

city: South San Francisco

first: Simon

middle: J

last: Hogg

state: California

address: 1000 Gateway Boulevard

department: Oncology Discovery Research

institute: AbbVie

data_processing:
Sequencing files were demultiplexed using Bcl2fastq (v2.17.1.14) to generate FASTQ files on which QC was performed using FASTQC (v0.11.5). Sequencing reads were trimmed using cutadapt (v1.7) and aligned to the mouse reference genome (Mm10) using HISAT2 (v2.1.0).
Read counting across genomic features was performed using featureCounts prior to differential gene expression analysis using limma voom.
Gene set enrichment analyses were performed using GSEA software (Broad Institute) and enrichment plots were plotted using replotGSEA.R.
Assembly: Mm10
Supplementary files format and content: CSV file of raw (non-normalized) gene expression counts

source_name: Mammary Carcinoma

growth_protocol: AT3 cells were grown in vitro under standard culture conditions

extract_protocol:
Cells were collected and washed once with ice-cold PBS prior to resuspension in TRIzol™ (ThermoFisher Scientific, 15596026). RNA was isolated using the Direct-zol RNA MiniPrep kit (Zymo Research, R2052) according to the manufacturers instructions. Sequencing libraries were prepared from 500ng RNA using the QuantSeq 3’-mRNA Seq Library Prep Kit for Ilumina (Lexogen, Vienna, Austria). Libraries were sequenced on the Illumina NextSeq 500 to obtain 75 b.p. single-end reads.
Sequencing libraries were prepared from 500ng RNA using the QuantSeq 3’-mRNA Seq Library Prep Kit for Ilumina (Lexogen, Vienna, Austria). Libraries were sequenced on the Illumina NextSeq 500 to obtain 75 b.p. single-end reads.

treatment_protocol: Samples were treated in biological triplicate in the presence of catalytic P300/CBP inhibitors, A-241 or A-485, or DMSO vehicle control, for 1 hour prior to the addition of recombinant murine IFNy for an additional 2 hours (total incubation time of 3 hours).

tag: cell line

tag: timepoint

value: 3 hours


title: 80ng NA12878, EM-seq, Rep1

city: Cambridge

first: Páidí

last: Creed

address: B400, The Trinity Building Chesterford Business Park, Saffron Walden

country: United Kingdom

institute: biomodal limited

data_processing:
Downsampling to 275M PE reads: seqtk v1.3  Adapter and quality trimming: trim galore v0.6.7  Alignment:  bwa-meth v0.2.4  Sorting and Indexing: samtools v1.15  Merging BAMs across lanes: bamtools v2.5  Duplicate Marking: Picard MarkDuplicates v2.23.8  BAM splitting: samtools v1.15  Methylation quantification: MethylDackel v0.6.1
supplementary_files_format_and_content: bedGraph.gz: BED file with methylation quantification data, generated by MethylDackel
Assembly: GRCh38
Library strategy: Enzymatic Methyl-seq

source_name: Blood

extract_protocol:
Genomic DNA was obtained from the Coriell Institute (https://www.coriell.org/0/Sections/Search/Sample_Detail.aspx?Ref=NA12878)
80ng of sonicated genomic DNA was processed by either 5-Letter Seq (Cambridge Epigenetix), EM-Seq (Cat#E7120, New England Biolabs) or EpiTect Plus DNA Bisulphite kit (Cat#59124, Qiagen). 5-Letter seq and 6-Letter seq was performed with kits available from Cambridge Epigenetix.

value: Blood

value: B-Lymphocyte


title: 80ng NA12878, WGBS, Rep2

data_processing:
Downsampling to 275M PE reads: seqtk v1.3  Adapter and quality trimming: trim galore v0.6.7  Alignment:  bwa-meth v0.2.4  Sorting and Indexing: samtools v1.15  Merging BAMs across lanes: bamtools v2.5  Duplicate Marking: Picard MarkDuplicates v2.23.8  BAM splitting: samtools v1.15  Methylation quantification: MethylDackel v0.6.1
supplementary_files_format_and_content: bedGraph.gz: BED file with methylation quantification data, generated by MethylDackel
Assembly: GRCh38


title: 80ng NA12878, WGBS, Rep1


title: 80ng NA12878, EM-seq, Rep2


title: QuantSeq_RNAseq_AT3_3hours_A241+IFNy_Replicate_2


title: QuantSeq_RNAseq_AT3_3hours_A241+IFNy_Replicate_3


title: QuantSeq_RNAseq_AT3_3hours_A241+IFNy_Replicate_1


title: QuantSeq_RNAseq_AT3_3hours_IFNy_Replicate_1

value: IFNy


title: QuantSeq_RNAseq_AT3_3hours_IFNy_Replicate_3


title: QuantSeq_RNAseq_AT3_3hours_A485_Replicate_3


title: QuantSeq_RNAseq_AT3_3hours_A485_Replicate_2


title: QuantSeq_RNAseq_AT3_3hours_A241_Replicate_1


title: QuantSeq_RNAseq_AT3_3hours_DMSO_Replicate_1

value: DMSO


title: ChIPseq_AT3_Input_3hours

data_processing:
Sequencing files were demultiplexed using Bcl2fastq (v2.17.1.14) to generate Fastq files on which QC was performed using FASTQC (v0.11.5).
Sequencing reads were then aligned to custom reference genome consisting the mouse genome (Mm10) and the Drosophila melanogaster genome (Dm3) using Bowtie2 (v2.3.3).
The resulting SAM files were converted to BAM files using Samtools (v1.4.1) using the view command, which were subsequently sorted, indexed, and potential PCR duplicates removed using the rmdup function.
BAM files were converted into BigWig files using the bamCoverage function (Deeptools, v3.0.0) using the following settings (--normalizeUsing CPM --smoothLength 150 --binSize 50 -e 200 scaleFactor 1).
For experiments with external normalization, the reads mapping to either Mm10 or Dm3 genomes were quantified using FeatureCounts (Subread package, v1.5.0) and the percentage of mapped Dm3 reads as a total of total mapped Dm3+Mm10 reads was calculated. A scale factor was then calculated as the ratio of Dm3 reads in the control treatment condition and the treatment sample, which was then applied as the scaleFactor in the bamCoverage function.
Assembly: Mm10
Supplementary files format and content: bigWig

growth_protocol: AT3 cells were grown in vitro under standard culture conditions.

extract_protocol:
Cells were washed once in ice-cold PBS prior to crosslinking. For crosslinking, 1/10th volume of fresh formaldehyde solution (11% formaldehyde, 0.05mM EGTA, 1mM EDTA, 100mM NaCl, 50mM Hepes-KOH pH 7.5) was added and incubated for 20 minutes at room temperature with rotation. Crosslinking was quenched by addition of 1/20th volume of 2.5M glycine and incubated for 5 minutes at room temperature with rotation. For isolation of nuclei, cell pellets were washed once in ice-cold PBS and then resuspended in ice-cold nuclear extraction buffer (0.5% NP-40, 2mM EDTA, 10mM NaCl, 20mM Tris-HCl pH 8) and incubated for 5 minutes on ice. Following three sequential incubations in nuclear extraction buffer, cell nuclei were pelleted and resuspended in sonication buffer (0.3% SDS, 1% NP-40, 2mM EDTA, 150mM NaCl, 20mM Tris-HCl pH 7.5) at a concentration equivalent to 50e6 cells per mL. Samples were sonicated in 12x24mm Covaris tubes using the Covaris S2 instrument for 18 minutes using the following settings: 20% Duty Cycle, 1000 cycles/burst, and 10 Intensity. Prior to immunoprecipitation, sheared chromatin was diluted 1:1 in ChIP dilution buffer (1% Triton X-100, 2mM EDTA, 150mM NaCl, 20mM Tris-HCl pH 8) and quantified using Qubit dsDNA HS assay kit. For ChIP-Rx (for H3K27ac IPs), sheared Drosophila chromatin from S2 cells was spiked into immunoprecipitations at 1:40 ratio of Drosophila:human and processed as a single sample until ChIP-Rx normalization following DNA sequencing. Immunoprecipitations were performed overnight (12-16 hours, 4°C, with rotation) using Protein A and Protein G Dyna beads (Invitrogen) and the indicated antibody. Samples were washed once with ChIP dilution buffer, wash buffer 1 (0.1% SDS, 1% Triton X-100, 2mM EDTA, 500mM NaCl, 20mM Tris-HCl pH 8), wash buffer 2 (0.5% deoxycholate, 0.5% NP-40, 2mM EDTA, 250mM LiCl, 20mM Tris-HCl pH 8), and TE buffer (1mM EDTA, 10mM Tris-HCl pH 7.5) prior to incubation in reverse crosslinking buffer (200mM NaCl, 100mM NaHCO3, 1% SDS, 300μg/mL Proteinase-K) for 4 hours at 55°C with shaking. Finally, the supernatant was reverse-crosslinked overnight (12-16 hours) at 65°C prior to ChIP DNA isolation using Zymogen ChIP DNA Clean and Concentrator Kit (Zymo Research, D5205).
Libraries were generated from ChIP DNA using the NEBNext Ultra II DNA Library Prep Kit (NEB, E7645) and sequenced on an Ilumina NextSeq 500 with 75 b.p. single-end reads.

treatment_protocol: Cells were treated with A-241 alone or in combination with recombinant murine IFNy, or DMSO vehicle, for 3 hours.

tag: antibody


title: murine kidney_non-infected_7day_biological rep2

description:
E676
Expression data from non-infected mice kidney tissue.
Sterilized Ellinghausen-McCullough-Johnson-Harris (EMJH) medium.
After inoculation at day 7

tag: gender

tag: tissue

value: Kidney


title: QuantSeq_RNAseq_AT3_3hours_A485_Replicate_1


title: QuantSeq_RNAseq_AT3_3hours_A241_Replicate_3


title: ChIPseq_AT3_H3K27ac_A241+IFNy_3hours

value: H3K27ac (Abcam, ab4729)


title: QuantSeq_RNAseq_AT3_3hours_DMSO_Replicate_3


title: QuantSeq_RNAseq_AT3_3hours_DMSO_Replicate_2


title: QuantSeq_RNAseq_AT3_3hours_A485+IFNy_Replicate_2


title: ChIPseq_AT3_H3K27ac_IFNy_3hours


title: ChIPseq_AT3_IRF1_IFNy_3hours

value: IRF1 (sc-497, Santa Cruz Biotechnology, Inc)


title: ChIPseq_AT3_H3K27ac_A241_3hours


title: QuantSeq_RNAseq_AT3_3hours_IFNy_Replicate_2


title: 80ng NA12878, 6-letter seq

description: Whole genome 6-letter sequencing

data_processing:
Downsampling to 550M PE reads: seqtk v1.3  Adapter and quality trimming: fastp v0.20.1  Read resolution: proprietary Python package  Alignment:  bwa v0.7.17  Sorting and Indexing: samtools v1.15  Merging BAMs across lanes: bamtools v2.5  Duplicate Marking: Picard MarkDuplicates v2.23.8  BAM splitting: samtools v1.15  Methylation quantification: proprietary Python package
supplementary_files_format_and_content: quant.tsv.gz: TSV file with methylation quantification data
Assembly: GRCh38
Library strategy: 6-letter sequencing


title: ChIPseq_AT3_H3K27ac_DMSO_3hours


title: QuantSeq_RNAseq_AT3_3hours_A485+IFNy_Replicate_1


title: ATACseq_AT3_A241+IFNy_Replicate1

data_processing:
Sequencing files were demultiplexed using Bcl2fastq (v2.17.1.14) to generate Fastq files on which QC was performed using FASTQC (v0.11.5).
Sequencing reads were then aligned to custom reference genome consisting the mouse genome (Mm10) and the Drosophila melanogaster genome (Dm3) using Bowtie2 (v2.3.3).
The resulting SAM files were converted to BAM files using Samtools (v1.4.1) using the view command, which were subsequently sorted, indexed, and potential PCR duplicates removed using the rmdup function.
BAM files were converted into BigWig files using the bamCoverage function (Deeptools, v3.0.0) using the following settings (--normalizeUsing CPM --smoothLength 150 --binSize 50 -e 200 scaleFactor 1)
For experiments with external normalization, the reads mapping to either Mm10 or Dm3 genomes were quantified using FeatureCounts (Subread package, v1.5.0) and the percentage of mapped Dm3 reads as a total of total mapped Dm3+Mm10 reads was calculated. A scale factor was then calculated as the ratio of Dm3 reads in the control treatment condition and the treatment sample, which was then applied as the scaleFactor in the bamCoverage function.
Assembly: Mm10
Supplementary files format and content: bigWig

extract_protocol:
Cells were washed once in ice-cold PBS and lysed in ATAC lysis buffer (0.1% Tween-20, 0.1% NP-40, 3mM MgCl2, 10mM NaCl, 10mM Tris HCl pH 7.4). Tagmentation was performed with Tn5 transposase and 2x TD Buffer (Nextera DNA Library Prep Kit, Ilumina) for 30 minutes at 37°C.
Tagmented DNA was purified using a MinElute colum (Qiagen, 28004) and amplified for 12 cycles using 2x KAPA HiFi HotStart ReadyMix (Kapa Biosystems, KK2602). The amplified libraries were purified using MinElute columns (Qiagen) and sequenced on an Ilumina NextSeq 500.

tag: treatment+dose


title: ChIPseq_AT3_IRF1_A241_3hours


title: ATACseq_AT3_A241+IFNy_Replicate2


title: ATACseq_AT3_IFNy_Replicate2


title: ChIPseq_AT3_IRF1_DMSO_3hours


title: ATACseq_AT3_IFNy_Replicate1


title: ATACseq_AT3_DMSO_Replicate1


title: QuantSeq_RNAseq_AT3_3hours_A241_Replicate_2


title: ATAC_DoxTreated_rep1

city: VILLEJUIF

first: Christel

last: GUILLOUF

address: 114 rue Edouard vaillant

country: France

institute: Gustave Roussy

data_processing:
Image analysis and base calling were performed using RTA 2.7.3 and bcl2fastq 2.17.1.14.
ATAC-seq reads were aligned to the mm10 genome assembly using BWA with the following configurations :
Peaks were called using HMCan with a specific option dedicated to ATAC-seq data.
Normalization between density files of different conditions (bigWig) for each experiment was performed using CHIPIN.
Genome_build: mm10
Supplementary_files_format_and_content: bigWig files generated using HMCan and normalized using CHIPIN.

source_name: Bone marrow leukemic cells

growth_protocol: Cells were maintained in culture with EPO, in exponential growth before treatment with Dox

extract_protocol:
Cell pellets were lysed and tagmented using the Nextera Library Prep Kit (Illumina). Tagmented DNA was then purified using the MinElute PCR purification kit (Qiagen).
Tagmented DNA was amplified with 10 cycles of PCR, and purified using Agencourt AMPure SPRI beads (Beckman Coulter). Resulting material was quantified using the KAPA Library Quantification Kit for Illumina platforms (KAPA Biosystems).

treatment_protocol: Dox treated or not for 54 hours

tag: cell type

value: Leukemic erythroid cells

tag: molecule subtype

value: tagmented DNA


title: ATACseq_AT3_DMSO_Replicate2


title: ATACseq_AT3_A241_Replicate2


title: ChIPseq_AT3_IRF1_A241+IFNy_3hours


title: ATAC_DoxUntreated_rep2


title: FAT_16: ganglia fat of animal 16

city: Baton Rouge

first: Rui

last: Zhang

state: Louisiana

address: 6400 Perkins Road

institute: Pennington Biomedical Research Center

data_processing:
Lexogen Quantseq pipeline V1.8.8 on the Bluebee platform, quality control, mapping, and read count tables
Annotation and preparation for analysis, R V3.4.3, Rstudio V1.1.423 and biomaRt V2.24.1
DESeq2  V1.18.1 differential gene expression
JMP Genomics V9 quality control, principal components, ANOVA, hierarchical clustering
Genome_build: mouse- GRCm38.84
Supplementary_files_format_and_content: DESeq2 analysis: DESeq_Normalized_counts.xlsx
Supplementary_files_format_and_content: DESeq2 analysis: raw counts.xlsx
Supplementary_files_format_and_content: JMP analysis: RawCts_GT_60.xlsx
Supplementary_files_format_and_content: JMP analysis: log2_rawcts_gt_60_meanNormalized.xlsx

source_name: RNA extracted from ganglia fat of animal 16

growth_protocol: All mice were fed with chow (LabDiet Rodent 5001) at room temperature.

extract_protocol:
Trizol method was used for extracting RNA.
Lexogen Quant-Seq
indexed and pooled samples, 50bp forward read

tag: date of birth

value: Ganglion fat

tag: animal id

value: Animal 16


title: FAT_13: ganglia fat of animal 13

source_name: RNA extracted from ganglia fat of animal 13

value: Animal 13


title: ATACseq_AT3_A241_Replicate1


title: FAT_04: ganglia fat of animal 4

source_name: RNA extracted from ganglia fat of animal 4

value: Male

value: Animal 4


title: FAT_01: ganglia fat of animal 1

source_name: RNA extracted from ganglia fat of animal 1

value: Animal 1


title: ATAC_DoxTreated_rep2

tag: treatment


title: FAT_11: ganglia fat of animal 11

source_name: RNA extracted from ganglia fat of animal 11

value: Female

value: Animal 11


title: FAT_06: ganglia fat of animal 6

source_name: RNA extracted from ganglia fat of animal 6

value: Animal 6


title: L2_13: L2 of animal 13

source_name: RNA extracted from L2 of animal 13

value: Lumbar ganglion L2 (both sides)


title: L2_14: L2 of animal 14

source_name: RNA extracted from L2 of animal 14

value: Animal 14


title: FAT_14: ganglia fat of animal 14

source_name: RNA extracted from ganglia fat of animal 14


title: L2_16: L2 of animal 16

source_name: RNA extracted from L2 of animal 16


title: ATAC_DoxUntreated_rep1


title: L2_04: L2 of animal 4

source_name: RNA extracted from L2 of animal 4


title: T13_L1_14: T13/L1 of animal 14

source_name: RNA extracted from T13/L1 of animal 14

value: Thoracolumbar ganglion T13/L1 (both sides)


title: L2_06: L2 of animal 6

source_name: RNA extracted from L2 of animal 6


title: T13_L1_07: T13/L1 of animal 7

source_name: RNA extracted from T13/L1 of animal 7

value: Animal 7


title: L2_11: L2 of animal 11

source_name: RNA extracted from L2 of animal 11


title: L2_07: L2 of animal 7

source_name: RNA extracted from L2 of animal 7


title: L2_01: L2 of animal 1

source_name: RNA extracted from L2 of animal 1


title: T13_L1_13: T13/L1 of animal 13

source_name: RNA extracted from T13/L1 of animal 13


title: FAT_07: ganglia fat of animal 7

source_name: RNA extracted from ganglia fat of animal 7


title: T13_L1_11: T13/L1 of animal 11

source_name: RNA extracted from T13/L1 of animal 11


title: T13_L1_06: T13/L1 of animal 6

source_name: RNA extracted from T13/L1 of animal 6


title: RNAseq_Dox_Treated_Entinostat_Treated_rep1

description:
CLGF66
processed data file: rawCounts_DMSO_Treated__Entinostat_treated.txt

data_processing:
Image analysis and base calling were performed using RTA 2.7.3 and bcl2fastq 2.17.1.14.
RNA-seq reads were aligned to the mm10 genome assembly using STAR with the following configurations :
Read counts have been normalized across samples with the median-of-ratios method.
Differential gene expression analysis was performed using DESeq2.
Genome_build: mm10
Supplementary_files_format_and_content: Raw Counts tbale (txt file)

source_name: Bone marrow leukemic cells

growth_protocol: Cells were maintained in culture with EPO, in exponential growth  before treatment with Dox and or Entinostat

extract_protocol:
Total RNA was isolated from cells using RNeasy Plus Mini Kit (Qiagen).
RNA quality was evaluated using an Agilent Fragment Analyzer apparatus as described in the manufacturer’s procedure (Agilent Technologies, Basel, Switzerland). RNA-seq libraries were generated from 300ng of total RNA Illumina TruSeq RNA Sample Preparation Kit v2 (Part Number RS-122-2001).

treatment_protocol: Two different conditions have been used: a) treatment or not with doxycycline for 48h to induce the expression of an shRNA against Spi1; b) treatment or not with doxycycline for 48h additionally to treatment of cells with 3μM Entinostat (HDAC1/3 inhibitor) for 6h or with DMSO as control. Three biological replicates have been generated for all conditions.


title: T3_14: T3 of animal 14

source_name: RNA extracted from T3 of animal 14

value: Thoracic ganglion T3 (both sides)


title: T13_L1_01: T13/L1 of animal 1

source_name: RNA extracted from T13/L1 of animal 1


title: T13_L1_04: T13/L1 of animal 4

source_name: RNA extracted from T13/L1 of animal 4


title: RNAseq_Dox_Treated_DMSO_Treated_rep1

description:
CLGF65
processed data file: rawCounts_DMSO_Treated__Entinostat_treated.txt


title: T3_11: T3 of animal 11

source_name: RNA extracted from T3 of animal 11


title: T3_07: T3 of animal 7

source_name: RNA extracted from T3 of animal 7


title: SG_16: stellate ganglion of animal 16

source_name: RNA extracted from stellate ganglion of animal 16

value: Stellate ganglion (both sides)


title: T3_16: T3 of animal 16

source_name: RNA extracted from T3 of animal 16


title: RNAseq_Dox_Untreated_Entinostat_Treated_rep2

description:
CLGF68
processed data file: rawCounts_DMSO_Treated__Entinostat_treated.txt

value: Leukemic erythroid cells


title: RNAseq_Dox_Treated_Entinostat_Treated_rep2

description:
CLGF70
processed data file: rawCounts_DMSO_Treated__Entinostat_treated.txt


title: RNAseq_Dox_Treated_Entinostat_Treated_rep3

description:
CLGF74
processed data file: rawCounts_DMSO_Treated__Entinostat_treated.txt


title: SG_11: stellate ganglion of animal 11

source_name: RNA extracted from stellate ganglion of animal 11


title: T3_13: T3 of animal 13

source_name: RNA extracted from T3 of animal 13


title: SG_07: stellate ganglion of animal 7

source_name: RNA extracted from stellate ganglion of animal 7


title: RNAseq_Dox_Treated_DMSO_Treated_rep2

description:
CLGF69
processed data file: rawCounts_DMSO_Treated__Entinostat_treated.txt


title: T13_L1_16: T13/L1 of animal 16

source_name: RNA extracted from T13/L1 of animal 16


title: RNAseq_Dox_Untreated_Entinostat_Treated_rep3

description:
CLGF72
processed data file: rawCounts_DMSO_Treated__Entinostat_treated.txt


title: RNAseq_Dox_Treated_DMSO_Treated_rep3

description:
CLGF73
processed data file: rawCounts_DMSO_Treated__Entinostat_treated.txt


title: T3_06: T3 of animal 6

source_name: RNA extracted from T3 of animal 6


title: SG_04: stellate ganglion of animal 4

source_name: RNA extracted from stellate ganglion of animal 4

value: Stellate ganglion  (both sides)


title: InputDNA_ChIP3_Entinostat_Treated_rep1-2

data_processing:
Image analysis and base calling were performed using RTA 2.7.3 and bcl2fastq 2.17.1.14.
ChIP-seq reads were aligned to the mm10 genome assembly using mem algorithm from Burrow Wheeler Aligner (BWA) with the following configurations: option -t equal to 7 paired-end mode used when necessary
Reads were filtered by applying a threshold of 20 on the MAPQ field of bam files. PCR duplicates were removed.
Peaks were called using HMCan with the following settings: minLength=150, medLength=350, maxLength=600, smallBinLength=50bp, largeBin- Length=100000, pvalueThreshold=0.05, blackListFile supplied. The mergeDistance parameter was different according the analyzed protein.
Normalization between density files of different conditions (bigWig) for each experiment was performed using CHIPIN.
Genome_build: mm10
Supplementary_files_format_and_content: bigWig files generated using HMCan and normalized using CHIPIN.
Supplementary_files_format_and_content: bed files (peaks files) generated using HMCan.

extract_protocol:
ChIP assays were performed using the ChIP assay kit (Millipore) following the manufacturer’s protocol as previously described (Ridinger-Saison et al., NAR, 2012). ChIP samples were sonicated  for 17min using the Covaris S220 sonicator (peak power 220, duty factor 20 and cycle Burst 200) was used for sonication.
ChIP samples were purified using Agencourt AMPure XP beads (Beckman Coulter). ChIP-seq libraries were prepared from 5ng of double-stranded purified DNA using the MicroPlex Library Preparation kit v2 (C05010014, Diagenode s.a.).

treatment_protocol: Two different conditions have been used: a) treatment or not with doxycycline for 48h to induce the expression of an shRNA against Spi1; b) treatment or not with with 3μM Entinostat (HDAC1/3 inhibitor) for 6h or with DMSO as control. Three biological replicates have been generated for all conditions.

tag: chip antibody

value: InputDNA


title: SG_01: stellate ganglion of animal 1

source_name: RNA extracted from stellate ganglion of animal 1


title: RNAseq_Dox_Untreated_DMSO_Treated_rep2

description:
CLGF67
processed data file: rawCounts_DMSO_Treated__Entinostat_treated.txt


title: SG_14: stellate ganglion of animal 14

source_name: RNA extracted from stellate ganglion of animal 14


title: H3K27ac_ChIP3_DMSO_Treated_rep1


title: InputDNA_ChIP2_Dox_Treated_rep1-2


title: S2, Hlc#3, KD, rep2

city: Chongqing

first: jin

last: you

address: Huxi Campus

institute: Chongqing University

data_processing:
Low quality bases and adapter sequences were removed by trimmomatic(version 0.36).The remaining highly quality reads were then aligned to the Drosophila melanogaster genome (BDGP6) from Ensembl using Tophat(version 2.1.0). StringTie(version 2.1.7) was used to estimate the gene expressing level of each sample based on Ensembl annotation(BDGP6.32,version 104).
Assembly: dme6
Supplementary files format and content: tab-delimited text file includes counts values for each Sample

extract_protocol:
total RNA extracted from Drosophila S2 cells by using RNAiso Plus(Takara, 9109).
Library preparation was performed using the TruSeqTM RNA Sample Preparation Kit (Illumina,15008136 ) following the manufacturer’s instructions.

value: embryo-derived embryonic stem cells

value: Hlc knockdown

tag: time

value: 3 days


title: RNAseq_Dox_Untreated_DMSO_Treated_rep1

description:
CLGF63
processed data file: rawCounts_DMSO_Treated__Entinostat_treated.txt


title: copMG_3

city: Oxford

first: Kevin

last: Talbot

address: John Radcliffe Hospital, Headley Way

department: Nuffield Department of Clinical Neurosciences

institute: University of Oxford

data_processing:
Paired end sequencing was performed using a NovaSeq6000 platform (Illumina, NovaSeq 6000 S2/S4 reagent kit, v1.5, 300 cycles), generating a raw read count of a minimum of 34M reads per sample
Paired-end reads were mapped to the human GRCh38.p13 reference genome (https://www.gencodegenes.org) using HISAT2 v2.2.1 (Kim et al., 2019).
The counts table was obtained using FeatureCounts v2.0.1 (Liao et al., 2014)
Normalization of counts and differential expression analysis for the comparison of pMGl and co-pMG was performed using DESeq2 v1.28.1 (Love et al., 2014)
Assembly: GRCh38.p13
Supplementary files format and content: csv file includes normalized DESeq2 counts for all samples

extract_protocol:
Co-cultures were first dissociated by 15 min incubation with papain (P4762, Sigma-Aldrich) diluted in accutase (20 U/mL) and gentle trituration based on a previously published protocol (Thiry et al., 2020). The cell suspension was then passed through a cell strainer (70 μm, Falcon) to remove cell clumps. To extract co-pMG, magnetic-activated cell sorting (MACS) was then performed using CD11b-MACS beads (130-093-634, Miltenyi Biotec) according to the manufacturer’s instructions. The panned cell population was lysed using an RNAeasy Micro kit (Qiagen) according to the manufacturer’s instructions
Material was quantified using RiboGreen (Invitrogen) on the FLUOstar OPTIMA plate reader (BMG Labtech) and the size profile and integrity analysed on the 2200 or 4200 TapeStation (Agilent, RNA ScreenTape). RIN estimates for all samples were between 9.2 and 9.9. Input material was normalised to 100 ng prior to library preparation. Polyadenylated transcript enrichment and strand specific library preparation was completed using NEBNext Ultra II mRNA kit (NEB) following manufacturer’s instructions. Libraries were amplified (14 cycles) on a Tetrad (Bio-Rad) using in-house unique dual indexing primers (based on (Lamble et al., 2013)). Individual libraries were normalised using Qubit, and the size profile was analysed on the 2200 or 4200 TapeStation. Individual libraries were normalised and pooled together accordingly. The pooled library was diluted to ~10 nM for storage. The 10 nM library was denatured and further diluted prior to loading on the sequencer

value: iPSC microglia extracted from co-culture with motor neurons

value: WT

tag: Sex

value: female

value: differentiation in co-culture with motor neurons for 14 days


title: T3_04: T3 of animal 4

source_name: RNA extracted from T3 of animal 4

value: Male

value: Animal 4


title: RNAseq_Dox_Untreated_DMSO_Treated_rep3

description:
CLGF71
processed data file: rawCounts_DMSO_Treated__Entinostat_treated.txt

source_name: Bone marrow leukemic cells


title: H3K27ac_ChIP3_Entinostat_Treated_rep2


title: InputDNA_ChIP3_DMSO_Treated_rep1-2


title: S2, Hlc#2, KD, rep1


title: T3_01: T3 of animal 1

source_name: RNA extracted from T3 of animal 1

value: Animal 1


title: RNAseq_Dox_Untreated_Entinostat_Treated_rep1

description:
CLGF64
processed data file: rawCounts_DMSO_Treated__Entinostat_treated.txt


title: SG_06: stellate ganglion of animal 6

source_name: RNA extracted from stellate ganglion of animal 6

value: Animal 6


title: H3K27ac_ChIP3_Entinostat_Treated_rep1


title: copMG_2

value: male


title: pMGl_2

extract_protocol:
RNA was extracted using an RNAeasy Mini Plus kit (Qiagen) according to the manufacturer’s instructions
Material was quantified using RiboGreen (Invitrogen) on the FLUOstar OPTIMA plate reader (BMG Labtech) and the size profile and integrity analysed on the 2200 or 4200 TapeStation (Agilent, RNA ScreenTape). RIN estimates for all samples were between 9.2 and 9.9. Input material was normalised to 100 ng prior to library preparation. Polyadenylated transcript enrichment and strand specific library preparation was completed using NEBNext Ultra II mRNA kit (NEB) following manufacturer’s instructions. Libraries were amplified (14 cycles) on a Tetrad (Bio-Rad) using in-house unique dual indexing primers (based on (Lamble et al., 2013)). Individual libraries were normalised using Qubit, and the size profile was analysed on the 2200 or 4200 TapeStation. Individual libraries were normalised and pooled together accordingly. The pooled library was diluted to ~10 nM for storage. The 10 nM library was denatured and further diluted prior to loading on the sequencer

value: iPSC microglia in monoculture

value: differentiation in monoculture for 14 days


title: S2, Hlc#2, KD, rep2


title: H3K4me1_ChIP2_Dox_Treated_rep1

value: Leukemic erythroid cells


title: pMGl_3


title: S2, Hlc#3, KD, rep1


title: pMGl_4


title: S2, Control, beta-gal, rep1

value: beta-gal knockdown


title: pMacpre_3

value: iPSC macrophage precursors

value: directly lysed after harvest from differentiation factories


title: copMG_1


title: H3K27ac_ChIP3_DMSO_Treated_rep2


title: InputDNA_ChIP2_Dox_Untreated_rep1-2

value: InputDNA


title: pMGl_1


title: copMG_4


title: S2, Control, beta-gal, rep2

value: embryo-derived embryonic stem cells

value: 3 days


title: pMacpre_2

value: WT


title: pMacpre_4


title: RNAseq_Dox_Untreated_rep2 [722]

data_processing:
Image analysis and base calling were performed using RTA 2.7.3 and bcl2fastq 2.17.1.14.
Raw data fastq composed of R1 + R2.
RNA-seq reads were aligned to the mm10 genome assembly using STAR.
Read counts have been normalized across samples with the median-of-ratios method.
Differential gene expression analysis was performed using DESeq2.
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: rawCounts_Dox_Untreated__Dox_Treated.txt: Raw Counts table (tab-delimited text file).

growth_protocol: Cells were maintained in culture with EPO, in exponential growth before treatment with Dox.

treatment_protocol: Cells have been treated or not with doxycycline for 48h to induce the expression of an shRNA against Spi1. Three biological replicates have been generated for all conditions.


title: RNAseq_Dox_Treated_rep2 [722]


title: RNAseq_Dox_Untreated_rep3 [722]


title: H3K4me1_ChIP2_Dox_Untreated_rep1


title: SG_13: stellate ganglion of animal 13

source_name: RNA extracted from stellate ganglion of animal 13

value: Female

value: Stellate ganglion (both sides)

value: Animal 13


title: RNAseq_Dox_Untreated_rep1 [722]


title: pMacpre_1

value: female


title: RNAseq_Dox_Treated_rep1 [722]


title: RNAseq_Dox_Treated_rep3 [722]


title: H3K27me3_ChIP2_Dox_Untreated_rep1

value: H3K27me3 (Cell Signaling, 9733, lot8)


title: H3K27me3_ChIP2_Dox_Treated_rep2


title: H3K27me3_ChIP2_Dox_Untreated_rep2


title: H3K27ac_ChIP2_Dox_Untreated_rep1


title: H3K27ac_ChIP2_Dox_Treated_rep1


title: YL-NBS1-TEV-ChIP-CTCF-R2

city: Worcester

first: Yu

last: Liu

address: 368 Plantation Street

department: Program in Systems Biology

institute: University of Massachusetts Medical School

description: HAP1 is a near-haploid human cell line that was derived from the male chronic myelogenous leukemia (CML) cell line KBM-7. HAP1 cells are adherent with fibroblast-like morphology.

data_processing:
Fastq files of Hi-C were mapped and parsed to generate cooler files using Distiller
Cooler files were directly processed for compartment and insulation pileup analysis using cooltools
Cooler files were transfer to cWord matrix files to generate contact heatmaps and analyze insulation and loop pileup
Fastq files of ChIPseq were mapped using Bowtie to generate sam files
HOMER (PMID 20513432) was used to generate tag and bigwig files and call peaks from sam files
DeepTools was used for ChIP signal stacking up
Genome_build: hg19
Supplementary_files_format_and_content: cooler for Hi-C and BigWig files for ChIPseq

source_name: HAP1-RAD21-TEV cells

growth_protocol:
HAP1-RAD21-TEV are grown in IMDM medium, with GlutaMAX, 10% FBS and 1% penicillin-streptomycin at 37C in 5% CO2
HCT116-RAD21-mAC cells are grown in McCoy's 5A medium, with GlutaMAX, 10% FBS and 1% penicillin-streptomycin at 37C in 5% CO2.

extract_protocol:
Nuclei were purified using hytonic buffer and after treatments, nuclei were fixed for Hi-C protocol
Hi-C 2.0 (PMID28435001)
After cells were fixed, cells or G1 sorted cells were used for Hi-C protocol
Hi-C 2.0 (PMID28435001)

treatment_protocol:
TEV protease treatment: 15U/ml at 4C for overnight; NB contains 10mM PIPES pH 7.4, 2mM MgCl2 and 10mM KCl; NBS1 and NBS2 buffers are NB with 132mM and 200mM NaCl, respectively. NBS1 is physical conditional buffer.
500mM 3-indole acetic acid in DMSO was added to culture to obtain final concentration of 500uM

tag: protocol

value: ChIPseq

value: HAP1-RAD21-TEV cells


title: H3K27ac_ChIP2_Dox_Treated_rep2


title: YL-NB-TEV-ChIP-IgG-R2


title: YL-NB-TEV-ChIP-CTCF-R2


title: YL-NB-ChIP-IgG-R2


title: YL-NB-ChIP-CTCF-R2


title: YL-NBS1-TEV-ChIP-IgG-R2


title: YL-NBS1-ChIP-CTCF-R2


title: YL-NuExp4hr-R3-T1

tag: enzyme

value: HindIII


title: YL-NBS1-TEV-ChIP-nRAD21-R2


title: H3K27ac_ChIP2_Dox_Untreated_rep2


title: YL-NuExp4hr-shrink1hr-R3-T1


title: YL-NuExp4hr-Tev-R3-T1


title: YL-NB-ChIP-nRAD21-R2


title: YL-NBS1-ChIP-nRAD21-R2


title: YL-NBS1-ChIP-IgG-R2


title: YL-NuCTL4hr-Tev-R3-T1


title: YL-NB-TEV-ChIP-nRAD21-R2


title: heart, Actr5 overexpression, rep1

city: Wakayama

first: Tsuyoshi

last: Morita

address: Mikazura 580

department: Department of Biology

institute: Wakayama Medical University

description: heart injected with Actr5 expression vector

hyb_protocol: 0.6ug of Cy3-labelled cRNA was fragmented at 60°C for 30 minutes in a reaction volume of 25 ul containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturer’s instructions. On completion of the fragmentation reaction, 25 ul of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to SurePrint G3 mouse GE 8x60K Microarray Ver2.0 (Agilent) for 17 hours at 65°C in a rotating Agilent hybridization oven. After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent).

scan_protocol: Slides were scanned immediately after washing on the Agilent SureScan Microarray Scanner (G2600D) using one color scan setting for 8x60k array slides (Scan Area 61x21.6 mm, Scan resolution 3um, Dye channel is set to Green PMT is set to 100%).

data_processing:
The scanned images were analyzed with Feature Extraction Software 12.0.3.1 (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities.
Normalized signal values were calculated by the following method using the Feature Extraction Software: (1) control probes were excluted by setting control type to 0 (2) averaged signal intensity values were calculated after excluding the top and bottom 2% of Processed Signal(3) scaling factors (SF) were calculated using the formula SF=target signal constant (2500) / the trimmed mean values. (4) normalized singal intensities Scale Signal were obtained by multiplying the SF value by the individula probe signal values

source_name: Actr5, replicant1

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.1ug Total RNA using the Low Input Quick Amp Labeling Kit(Agilent) according to the manufacturer's instructions, followed by RNeasy column purification (QIAGEN, Valencia, CA). Dye incorporation and cRNA yield were checked with the NanoDrop ND-2000 Spectrophotometer.

growth_protocol: C57BL/6 mice were bred under specific-pathogen-free conditions

extract_protocol: Total RNAs were extracted using  RNAiso plus, and purified using NucleoSpin RNA Plus.

treatment_protocol: Empty or Actr5-containing AAV6 vecters were intraperitoneally injected into 3-week-old mice, and the hearts were harvested 3 weeks after injection

tag: strain

tag: age

tag: genotype

value: Actr5 overexpression

value: heart


title: YL-NuExp4hr-shrink-Tev-R1-T1

tag: cell line


title: heart, control, rep1

description: heart injected with control vector

source_name: control, replicant1

value: heart injected with control vector

value: control


title: YL-NuExp4hr-shrink1hr-Tev-R3-T1


title: H3K27me3_ChIP2_Dox_Treated_rep1

value: Leukemic erythroid cells


title: YL-NuCTL4hr-R1-T1


title: YL-NuExp4hr-R1-T1


title: YL-NuTEVON-DpnII-R5-T1

value: DpnII


title: YL-NuCTL4hr-Tev-R1-T1


title: YL-NuCTL-DpnII-R4-T1


title: YL-NuExp4hr-shrink-R1-T1


title: YL-NuCTL-DpnII-R5-T1


title: YL-G1-NB-salt-TEV-R2-T1


title: YL-NuTEVON-DpnII-R4-T1


title: YL-G1-NB-R2-T1


title: YL-G1-NB-TEV-R2-T1


title: YL-NBS2-TEV-R10-T1


title: YL-G1-NB-salt-R2-T1


title: YL-G1-NB-TEV-R1-T1


title: YL-NuExp4hr-Tev-R1-T1


title: YL-G1-NB-R1-T1


title: YL-NB-R10-T1


title: YL-NBS2-R10-T1


title: YL-G1-NB-salt-TEV-R1-T1


title: RNAseq_Dox_Treated_rep3

description:
A140T6
raw data fastq composed of R1 + R2
processed data file: rawCounts_Dox_Untreated__Dox_Treated.txt


title: YL-NB-TEV-R10-T1


title: YL-NuCTL4hr-R3-T1


title: RNAseq_Dox_Treated_rep1

description:
A140T2
raw data fastq composed of R1 + R2
processed data file: rawCounts_Dox_Untreated__Dox_Treated.txt


title: YL-NB-salt-TEV-R8-T1


title: RNAseq_Dox_Treated_rep2

description:
A140T4
raw data fastq composed of R1 + R2
processed data file: rawCounts_Dox_Untreated__Dox_Treated.txt


title: YL-G1-NB-salt-R1-T1


title: RNAseq_Dox_Untreated_rep3

description:
A140T5
raw data fastq composed of R1 + R2
processed data file: rawCounts_Dox_Untreated__Dox_Treated.txt


title: YL-NB-salt-R8-T1


title: YL-NB-R8-T1


title: RNAseq_Dox_Untreated_rep2

description:
A140T3
raw data fastq composed of R1 + R2
processed data file: rawCounts_Dox_Untreated__Dox_Treated.txt


title: YL-TEVON-NaCl-R3-T1


title: InputDNA_ChIP1_Dox_Treated_rep1

value: InputDNA


title: YL-CTL-NB-NaCl-R3-T1


title: SPI1_ChIP1_Dox_Treated_rep1

value: SPI1/PU.1 (Santa Cruz, sc-352 X, D1113)


title: InputDNA_ChIP1_Dox_Untreated_rep1


title: YL-CTL-NB-R5-T1


title: YL-TEVON-NaCl-R6-T1


title: SPI1_ChIP1_Dox_Untreated_rep1


title: YL-NB-TEV-R8-T1


title: YL-TEVON-NB-R6-T1


title: RNAPolII_ChIP1_Dox_Treated_rep1

value: RNAPolII (N-20; Santa Cruz, sc-899X)


title: RNAPolII_ChIP1_Dox_Untreated_rep1


title: YL-TEVON-NB-R2-T1


title: PD1_R3

city: Belvaux

first: Enrico

last: Glaab

state: Capellen

address: 6, avenue du Swing

country: Luxembourg

institute: University of Luxembourg

data_processing:
The raw RNA-seq fastq files were quality-checked using the FastQC software and the data was pre-processed using the software package Rsubread
Assembly: GRCh38
Supplementary files format and content: tab-delimited text files include count values derived from Rsubread processing for each sample

growth_protocol: Smits et al., npj Parkinson's Disease, 2019

extract_protocol:
RNA was extracted using Allprep DNA/RNA mini kit (QIAGEN #80204). 1 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries were prepared using NEBNext Ultra Directional RNA Library Prep Kit for Illumina (E7420L).

value: Midbrain organoids

value: wt/ GBA-N370S

value: Male

tag: disease

value: Parkinson's disease (PD)


title: YL-CTL-NB-R1-T1


title: YL-CTL-NB-R6-T1


title: YL-TEVON-NB-R1-T1


title: YL-CTL-NB-R2-T1


title: PD1_R2


title: CTRL2_R3

value: wt/wt

value: Female

value: Healthy


title: YL-CTL-NB-NaCl-R6-T1

value: HAP1-RAD21-TEV cells


title: RNAseq_Dox_Untreated_rep1

description:
A140T1
raw data fastq composed of R1 + R2
processed data file: rawCounts_Dox_Untreated__Dox_Treated.txt


title: YL-RAD21mAC-6hrIAA-G1-R3-T1

description: Human colon carcinoma cell line; established from the primary colon carcinoma of an adult man.

source_name: HCT116-RAD21-mAC cells

value: HindIII

value: HCT116-RAD21-mAC cells


title: YL-RAD21mAC-6hrIAA-G1-R4-T1


title: PD1_R1


title: CTRL2_R2


title: YL-TEVON-NB-R5-T1


title: YL-RAD21mAC-2hrIAA-G1-R4-T1


title: CTRL2_R1


title: YL-RAD21mAC-2hrIAA-G1-R3-T1


title: PD2_R2

data_processing:
The raw RNA-seq fastq files were quality-checked using the FastQC software and the data was pre-processed using the software package Rsubread
Assembly: GRCh38
Supplementary files format and content: tab-delimited text file includes count values derived from Rsubread processing for each sample

value: PD


title: PD2_R3


title: YL-RAD21mAC-2hrIAA-G1-R2-T1


title: CCI14-IPSI

city: Chengdu

first: Yali

last: Chen

address: No.37 Guoxue Alley, Wuhou District

department: Anesthesiology

institute: West China Hospital of Sichuan University

library_source: transcriptomic single cell

data_processing:
The single cell suspension was loaded into Chromium microfluidic chips with 30 (v2 or v3, depends on project) chemistry and barcoded with a 10 Chromium Controller (10X Genomics).
RNA from the barcoded cells was subsequently reverse-transcribed and sequencing libraries constructed with reagents from a Chromium Single Cell 30 v2 (v2 or v3, depends on project) reagent kit (10X Genomics) according to the manufacturer’s instructions.
Sequencing was performed with Illumina (HiSeq 2000 or NovaSeq) according to the manufacturer’s instructions (Illumina).
Raw reads were demultiplexed and mapped to the reference genome by a 10X Genomics Cell Ranger pipeline using the default parameters.
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: spinal cord

extract_protocol:
Neuropathic pain was induced by CCI of the left sciatic nerve.  The right side was used as the CCI-contralateral side: the sciatic nerve was only exposed but not ligated.  The spinal lumbar enlargements of mice were minced and then digested using the Adult Brain Dissociation Kit (Miltenyi Biotec, Shanghai, China) and gentleMACS Octo Dissociator with Heaters (Miltenyi Biotec, Shanghai, China).
Library was performed according to the manufacter’s instructions (single cell 3’ v2 protocol, 10x Genomics).

value: C57BL/6 J

tag: tissue

value: spinal cord

value: chronic constriction injury of sciatic nerve

tag: timepoint

value: 14 days post-injury


title: CCI14-CONTRA


title: CTRL1_R2

tag: cell type


title: YL-RAD21mAC-0IAA-G1-R3-T1


title: CCI7-CONTRA

value: 7 days post-injury


title: CCI7-IPSI


title: CTRL1_R1


title: YL-RAD21mAC-0IAA-G1-R4-T1


title: YL-RAD21mAC-6hrIAA-G1-R2-T1