title: RNA_25_JEMV

description: Condition: JEMV


title: VCaP-DMSO 24hr-n=2

status: Public on Jul 08 2021

type: SRA

city: Ann Arbor

first: Pushpinder

middle: Singh

last: Bawa

state: Michigan

address: 1500 East Medical Center Drive

department: Pathology

country: USA

institute: University of Michigan

description: Time point: 24 hours of treatment

library_source: transcriptomic

data_processing:
RNA-seq
Align to GRCh38 using version STAR 2.4.1
Count reads using featureCounts (default settings, strand specific mode)
FPKM - upper quartile normalized using edgeR
Genome_build: Genome_build: GRCh38
Supplementary_files_format_and_content: Supplementary_files_format_and_content: raw read count

molecule: total RNA

organism: Homo sapiens

source_name: VCaP

extract_protocol:
polyA RNA
cDNA samples were converted to blunt-ended fragments using T4 DNA polymerase, E.coli DNA polymerase I large fragment (Klenow polymerase) and T4 polynuleotide kinase (New England BioLabs, NEB). A single A-base was added to fragment ends by Klenow fragment (3’ to 5’ exo minus; NEB) followed by ligation of Illumina adaptors (Quick ligase, NEB). The adaptor-modified DNA fragments were enriched by PCR using the Illumina Barcode primers and Phusion DNA polymerase (NEB). PCR products were size selected using 3% NuSieve agarose gels (Lonza) followed by gel extraction using QIAEX II reagents (QIAGEN). Libraries were quantified with the Bioanalyzer 2100 (Agilent) and sequenced on the Illumina HiSeq 2000 Sequencer (100 nucleotide read length).
RNA-seq using cDNA based on manufacturer's instructions (Illumina)

tag: cell line

value: VCaP

tag: cell type

value: Prostate Adenocarcinoma

tag: passage

value: Passage 30-70

tag: treatment

value: DMSO


title: RNA_27_JEMV

city: Oxford

first: Adam

last: Mead

address: Headley Way

department: Radcliffe Department of Medicine

country: United Kingdom

institute: University of Oxford

description: Condition: JEMV

data_processing:
Raw sequencing reads were aligned to the reference genome using STAR v2.4.2a.
Aligned reads were sorted using samtools v0.1.19.
Raw counts were generated using subread v1.5.0.
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: Final_rpkm_table_2_Mar2021.txt: Tab-delimited text file includes RPKM values.

organism: Mus musculus

source_name: Hematopoietic stem cells

extract_protocol:
Bone marrow cells were retrieved and stained for FACS-purification of HSCs, followed by Smart-Seq2 protocol.
RNA libraries were prepared for sequencing using Illumina protocols and adapted for Smart-Seq2 (Picelli et al., 2014).

value: Hematopoietic stem cells

tag: genotype

value: JAK2V17F + Ezh2 loss


title: A45

type: RNA

city: Saint-Pée-sur-Nivelle

first: Thérèse

last: Callet

country: France

institute: INRA

description: Gene expression in HN offspring

hyb_protocol: 600ng of Cy3-cRNA was then fragmented with a specific buffer (30 minutes at 60°C) and hybridized on a sub-array. Hybridization was performed in a microarray hybridization oven (Agilent) for 17h at 65°C.

scan_protocol: After a washing step, slides were scanned (Agilent DNA Microarray Scanner, Agilent Technologies, Massy, France) using the standard parameters for a gene expression 8x60K oligoarray (3μm and 20bits). Data were then obtained with the Agilent Feature Extraction software (10.7.1.1).

data_processing: Data from microarray analysis were transformed with a logarithmic transformation, scale-normalized and analyzed using the package limma from R.

organism: Oncorhynchus mykiss

source_name: Whole fry_condition HN

label_protocol: For each sample, 150 ng of total RNA was amplified and labelled using Cy3-CTP according to the manufacturer’s instructions (Agilent). cRNA were obtained by first reverse transcribed RNA, using a polyDT T7 primer (denaturation step: 10min at 65°C, reaction step: 2hr at 40°C, inactivation step: 5min at 70°C). cRNA were then labeled with Cy3-dye (2hr at 40°C). Excess dye was removed using a RNeasy kit (Qiagen). The level of dye incorporation was evaluated using a spectrophotometer (Nanodrop ND1000, LabTech)

extract_protocol: Total RNA was extracted from liver from 12 whole fry per condition, using the TRIzol reagent method (Invitrogen, Carlsbad, CA, USA), according to the manufacturer’s recommendations. The concentration of extracted RNA was analysed using a spectrophotometer (ND-1000, NanoDrop) by measuring absorbance at 260 nm. Quality of RNAs was checked with Bioanalyzer (Agilent Technologies, Kista, Sweden).

treatment_protocol: Whole fry from 4 different conditions : NN (offspring from both males and females fed the control NC diet); HN (offspring from only females fed the high carbohydrate/low protein (HC/LP) diet and males fed the control NC diet); NH (offspring from only males fed the HC/LP diet and females fed the NC diet); and HH (offspring from both parents fed the HC/LP diet) were sampled before the first feeding.

tag: FISH identification

tag: tissue

value: Whole fry

tag: female nutritional history

value: HC/LP

tag: male nutritional history

value: NC

tag: offspring condition

value: HN

tag: Sex

value: female


title: VCaP-ZBC11 3hr-150nM-n=2

description: Time point: 3 hours of treatment

value: ZBC-11 Inhibitor 150nM


title: A43

description: Gene expression in HN offspring


title: A53

description: Gene expression in NH offspring

source_name: Whole fry_condition NH

value: NH

value: male


title: RNA_13_JEMV

description: Condition: JEMV


title: VCaP-ZBX 246 3hr-10nM-n=2

description: Time point: 3 hours of treatment

value: ZBC-246 Degrader 10nM


title: RNA_2_JEMV

description: Condition: JEMV


title: A41

description: Gene expression in NN offspring

source_name: Whole fry_condition NN

value: NN


title: A42

description: Gene expression in HH offspring

source_name: Whole fry_condition HH

value: HH


title: A44

description: Gene expression in HH offspring


title: A37

description: Gene expression in HN offspring


title: A36

description: Gene expression in HH offspring


title: A35

description: Gene expression in NH offspring


title: A47

description: Gene expression in NH offspring


title: A38

description: Gene expression in HH offspring


title: RNA_CTR2

description: Condition: WT

value: CTR


title: VCaP-Thalido 3hr-10nM-n=2

description: Time point: 3 hours of treatment

value: VCaP

value: Prostate Adenocarcinoma

value: Thalidomide 10nM


title: A39

description: Gene expression in NH offspring


title: A34

description: Gene expression in NH offspring


title: A31

description: Gene expression in NN offspring


title: VCaP-DMSO 3hr-n=2

description: Time point: 3 hours of treatment

value: Passage 30-70

value: DMSO


title: A30

description: Gene expression in HH offspring

value: Whole fry


title: A29

description: Gene expression in HN offspring

value: HC/LP


title: A27

description: Gene expression in HN offspring

value: NC


title: VCaP-ZBC11 24hr-150nM-n=1

description: Time point: 24 hours of treatment


title: A28

description: Gene expression in NN offspring


title: RNA_3_CTR

description: Condition: WT

value: Hematopoietic stem cells


title: A33

description: Gene expression in NN offspring

value: female


title: RNA_5_CTR

description: Condition: WT


title: RNA_15_CTR

description: Condition: WT


title: VCaP-ZBX 246 24hr-10nM-n=1

description: Time point: 24 hours of treatment


title: VCaP-Thalido 24hr-10nM-n=1

description: Time point: 24 hours of treatment


title: A25

description: Gene expression in NN offspring


title: VCaP-DMSO 24hr-n=1

description: Time point: 24 hours of treatment


title: A26

description: Gene expression in NH offspring


title: A24

description: Gene expression in HH offspring


title: A22

description: Gene expression in HH offspring


title: KO_MPP_RNA_rep_4

city: Houston

first: Rebecca

last: Murdaugh

state: Texas

address: One Baylor Plaza

institute: Baylor College of Medicine

data_processing:
Reads were aligned to mm10 genome assembly using STAR aligner.
Differentially expressed genes were identified using DeSeq2.
Promoter motif analysis was done using HOMER.
Genome_build: mm10

molecule: polyA RNA

source_name: Bone marrow

growth_protocol: Mice were housed in AAALAC-accredited, specific-pathogen-free animal care facilities at Baylor College of Medicine (BCM) with 12-hour light-dark cycle and received standard chow ad libitum. All procedures were approved by the BCM (protocol #AN-5858) Institutional Animal Care and Use Committees.

extract_protocol:
HSCs and MPPs were sorted into Trizol and RNA purified according to the manufacturer's instructions. DNase I-treated RNA samples were purified using the QIAGEN MinElute kit before cDNA was made and amplified with a SMART-Seq2 kit.
The cDNA was then fragmented and barcoded for sequencing using a Nextera XT kit.

treatment_protocol: Conditional deletion of Hira in the hematopoietic system was induced by treating mice with 2 doses of 20𝝁g of polyinosinic:polycytidylic acid (poly(I:C)) by intraperitoneal injection skipping one day between each dose. Mice were sacrificed 1 week after the first dose of poly (I:C) and 2500 HSCs and MPPs were sorted into Trizol. To sort HSCs and MPPs based on cell division history following Hira deletion, we used a pulse of H2B-GFP expression  induced in Mx1-Cre; Hirafl/fl; Rosa26-M2rtTA; TetOP-H2B-GFP mice with Doxycycline dissolved in drinking water at 2 mg/ml with 10 mg/ml sucrose to counteract the bitter flavor of Doxycycline and encourage consumption. Doxycycline-treated water was changed every 7-10 days. After a 6-week pulse period, doxycycline treatment was stopped and 2 doses of Poly I:C were administered intraperitoneally with 20 μg every other day for 2 days to induce Hira deletion. These mice were sacrificed after 15 days after the last Poly I:C injection and 17 days after stopping doxycycline treatment (17 day chase period). HSCs and MPPs were then sorted based on their H2B-GFP expression levels.

tag: strain

value: HIRA KO

value: Bone marrow multipotent progenitors

tag: h2b-gfp expression


title: KO_MPP_RNA_rep_3


title: A18

description: Gene expression in NH offspring

value: NH

value: male


title: A16

description: Gene expression in HN offspring

value: HN


title: A19

description: Gene expression in NN offspring

value: NN


title: A20

description: Gene expression in HN offspring


title: A17

description: Gene expression in NN offspring


title: A21

description: Gene expression in HN offspring


title: VCaP-ZBC11 3hr-150nM-n=1

description: Time point: 3 hours of treatment

value: ZBC-11 Inhibitor 150nM


title: A15

description: Gene expression in HH offspring

value: HH


title: RNA_1_CTR

description: Condition: WT

value: CTR


title: VCaP-ZBX 246 3hr-10nM-n=1

description: Time point: 3 hours of treatment

value: VCaP

value: Prostate Adenocarcinoma

value: ZBC-246 Degrader 10nM


title: KO_MPP_RNA_rep_2


title: STF19_2

city: New York

first: Angad

last: Garg

state: New York

department: Molecular Biology

institute: Memorial Sloan Kettering Cancer Center

data_processing:
Base calls from Illumina NovaSeq 6000 (FASTQ files)
Each replicate processed separately
The FASTQ files were mapped to the S. pombe genome (current version, source: Pombase) using HISAT2_2.1.0
resulting SAM files were converted to BAM files using Samtools
Count files for individual replicates were generated with HTSeq-0.10.0 using exon annotations from Pombase (GFF annotations, genome-version ASM294v2; source ‘ensembl’)
Differential gene expression and fold change analysis was performed in DESeq2
Genome_build: Schizosaccharomyces_pombe_all_chromosomes.fa (Reference sequence, ftp://ftp.pombase.org/pombe/genome_sequence_and_features/genome_sequence/Schizosaccharomyces_pombe_all_chromosomes.fa.gz)
Supplementary_files_format_and_content: Matrix file for raw HTSeq counts

organism: Schizosaccharomyces pombe

source_name: h+ STF19 (seb1-G476S) rpb1-CTD-WT29::KanMX

growth_protocol: log phase cultures, 30ºC, YES medium

extract_protocol:
hot acid phenol RNA purification protocol
RNA-seq libraries were prepared from polyA+ RNA using the Illumina TruSeq stranded mRNA Kit according to the manufacturers protocol. Indexed libraries were normalized and pooled for paired-end sequencing performed using an Illumina NovaSeq 6000 instrument at the Weill Cornell Medical College Genome Core Facility (in New York).

tag: lab strain number

tag: growth conditions

value: log phase culture, YES medium

tag: developmental stage

value: vegetative growth


title: STF19_1


title: VCaP-Thalido 3hr-10nM-n=1

description: Time point: 3 hours of treatment

value: Passage 30-70

value: Thalidomide 10nM


title: wildtype3

source_name: h+ rpb1-CTD-WT29::NatMX


title: A14

description: Gene expression in HN offspring

value: Whole fry

value: HC/LP

value: NC


title: STF19_3


title: WT_MPP_RNA_rep_4

value: WT

value: Bone marrow multipotent progenitors


title: VCaP-DMSO 3hr-n=1

description: Time point: 3 hours of treatment

value: DMSO


title: A11

description: Gene expression in NN offspring

value: NN

value: female


title: KO_MPP_RNA_rep_1

value: HIRA KO


title: A12

description: Gene expression in NH offspring

value: NH


title: A13

description: Gene expression in NH offspring

value: male


title: ExpLBM_S3_rep2

city: okayama

first: Takeshi

last: Takarada

state: okayama

address: 2-5-1 Shikata-cho

department: Graduate School of Medicine, Dentistry and Pharmaceutical Sciences

country: Japan

institute: Okayama university

description:
ExpLBM PRRX1 high 3DCI Step 3: 6wks #2
A12-ExpLBM-S3-6wks

data_processing:
All sequence reads were extracted in FASTQ format using the CASAVA 1.8.4 pipeline.
Trimmomatic (version 0.36) was used to remove adapters and filter raw reads <36 bases as well as leading and trailing bases < quality 20.
Genome_build: Filtered reads were mapped to hg19 using HISAT2 (v2.1.0).
Supplementary_files_format_and_content: raw count

source_name: Stably expanded PRRX1 low LBM cells derived from hiPSC

growth_protocol: hPSCs were cultured or maintained with StemFit (Ajinomoto). Before reaching subconfluency, cells were stripped with TrypLE Select / 0.25 mM EDTA and suspended in StemFit containing 10 µM Y27632. Then 1x104 cells were suspended with StemFit containing 10 µM Y27632 and 8 µl iMatrix511-silk to seed them onto 6 cm dish. Next day culture media were replaced with fresh StemFit w/o 10 µM Y27632. Until next passage, culture media were changed every 2 days. LBM cells were stripped with Accutase and 2x105 cells were suspended with ExpLBM medium (CDM2 medium, 1 µM A-83-01, 0.5 µM LDN-193189, 3 µM CHIR99021, 150 nM Vismodegib, 10 µM Y27632) containing 16 µl iMatrix511-silk and seeded onto 6 cm culture dish. Culture media were replaced with fresh ExpLBM medium every 2 days. Before reaching subconfluency, cells were passaged as described.

extract_protocol:
Total RNA was extracted using RNeasy Mini Kit (QIAGEN).
Sequencing libraries were KAPA RNA HyperPrep Kit with RiboErase (HMR) (Kapa Biosystems) and SeqCap Adapter Kit (Set A or Set B, Roche) following manufacture`s instruction. The initial amount of total RNA was 1000 ng.

treatment_protocol: 3x10~4 hPSCs were suspended in 1 ml of StemFit (Ajinomoto) containing 10 µM Y27632 (Fujifilm wako) and 4 µl iMatrix511-silk (Nippi) and seeded to 3.5 cm culture dish. Next day culture medium was replaced with fresh StemFit w/o 10 µM Y27632. After culturing for 2 days, cells were washed with PBS and differentiation was induced by changing culture media at each time point. CDM2 medium26 was used as basal culture medium and cytokines or chemicals were added to prepare each differentiation medium. The composition of chemicals or cytokines used in this study was as follows: mid primitive streak (30 ng/ml ACTIVIN A, 40 ng/ml BMP4, 6 µM CHIR99021, 100 nM PIK90, 10 µM Y27632), lateral plate mesoderm (1 µM A-83-01, 30 ng/ml BMP4, 1 µM C59, 10 µM Y27632), limb bud mesenchyme (1 µM A-83-01, 0.5 µM LDN-193189, 3 µM CHIR99021, 150 nM Vismodegib, 10 µM Y27632)

value: PRRX1 3`tomato reporter established with 414C2

value: iPSC

tag: days after induction


title: WT_MPP_RNA_rep_3


title: wildtype2

value: log phase culture, YES medium


title: ExpLBM_S3_rep1

description:
ExpLBM PRRX1 high 3DCI Step 3: 6wks #1
A7-ExpLBM-S3-6wks

tag: cell line


title: wildtype1

value: vegetative growth


title: ExpLBM_S2_rep1

description:
ExpLBM PRRX1 high 3DCI Step 2 #1
A5-ExpLBM-S2

tag: cell type


title: WT_MPP_RNA_rep_1


title: WT_MPP_RNA_rep_2


title: ExpLBM_S1_rep2

description:
ExpLBM PRRX1 high 3DCI Step 1 #2
A4-ExpLBM-S1


title: ExpLBM_S2_rep2

description:
ExpLBM PRRX1 high 3DCI Step 2 #2
A6-ExpLBM-S2


title: ExpLBM_ABTGF_rep2

description:
ExpLBM PRRX1 high 2DCI Step 2 #2
A14-ExpLBM-ABTGF


title: ExpLBM_S1_rep1

description:
ExpLBM PRRX1 high 3DCI Step 1 #1
A2-ExpLBM-S1


title: KO_HSC_RNA_rep_4

value: Bone marrow hematopoietic stem cells


title: ExpLBM_ABTGF_rep1

description:
ExpLBM PRRX1 high 2DCI Step 2 #1
A13-ExpLBM-ABTGF


title: KO_HSC_RNA_rep_3


title: ExpLBM_PRRX1_low_rep1

data_processing:
All sequence reads were extracted in FASTQ format using the CASAVA 1.8.4 pipeline.
Trimmomatic (version 0.36) was used to remove adapters and filter raw reads <36 bases as well as leading and trailing bases < quality 20.
Genome_build: Filtered reads were mapped to hg19 using HISAT2 (v2.1.0).


title: WT_HSC_RNA_rep_3


title: KO_HSC_RNA_rep_2


title: KO_HSC_RNA_rep_1


title: WT_HSC_RNA_rep_2


title: WT_HSC_RNA_rep_4


title: WT_HSC_RNA_rep_1


title: A10

description: Gene expression in NN offspring


title: WT rep3

library_source: genomic

data_processing:
Reads alligned to mm10 genome assembly using Bowtie2.
Data were filtered using deepTools.
Peaks were called using MACS2 and PePr.
Genome_build: mm10
Supplementary_files_format_and_content: bigwig files

molecule: genomic DNA

extract_protocol:
ATAC-seq library generation was performed essentially as described in Buenrostro et al. (2013), with some modifications. 5000 HSCs were sorted and incubated in 100 μl lysis buffer (10 mM Tris-Cl, pH 7.4, 10 mM NaCl, 3 mM MgCl2 and 0.1% NP-40) for 3 minutes on ice. Immediately after lysis, the lysis buffer was removed by spinning at 500 x g for 5 minutes with 4oC table-top centrifuge.
The nuclei pellet was then resuspended in 10 μl of transposase reaction mix (2 μl 5X TAPS buffer (50 mM TAPS-NaOH, 25 mM MgCl2 (pH8.5)), 0.5 μl Tn5 (0.885 mg/mL), 7.5 μl of nuclear free water). The transposase reaction was incubated at 37oC for 30 minutes and then stopped by adding 5 μl of 0.2% SDS for 5 minutes at room temperature. The transposase reaction was then purified by a ZYMO DNA purification kit. Tagmentated DNA was eluted in 10μl nuclease free water, and a half of the elution volume was then used for PCR enrichment reaction with NEBNext Q5 Hot Start HiFi PCR Master Mix (NEB M0543S). The library amplification reaction included 25μl of 2x Q5 master mix, 5 μl of tagmentaed DNA template, 2.5μl of 25uM PCR primer 1 (final conc. 1.25μM), 2.5μl of 25μM barcoded PCR primer (final conc. 1.25μM) (all primers from SIGMA), and 15μl of nuclear free water. PCR protocol was 5 min at 72oC, 30 sec at 98oC, and then n cycles of 10 sec at 98oC, 30 seconds at 63oC, 1 minute at 72oC, where “n” cycles was determined by qPCR with SYBRGreen to reduce GC and size bias. After that, the library was purified using SPRI beads and eluted in 20 μl of nuclease-free water (the final concentration ~ 30 nM).

treatment_protocol: Conditional deletion of Hira in the hematopoietic system was induced by treating mice with 2 doses of 20 ug of polyinosinic:polycytidylic acid (poly(I:C)) by intraperitoneal injection skipping one day between each dose. Mice were sacrificed 1 week after the first dose of poly (I:C) and HSCs were sorted.


title: HIRA KO rep2


title: HIRA KO rep3


title: HIRA KO rep1


title: Day2_rep2

source_name: LPM cells derived from hiPSC

value: Day 2


title: Day4_rep1

source_name: LBM cells derived from hiPSC

value: Day 4


title: WT rep2


title: ExpLBM_PRRX1_low_rep2


title: Day0_rep2

source_name: hiPSC

value: Day 0


title: WT rep1


title: Day0_rep1


title: T21-FL1

city: Toronto

first: Elvin

last: Wagenblast

state: ON

address: 101 College Street

department: Princess Margaret Cancer Centre

country: Canada

institute: UHN

data_processing:
cutadapt v.1.18
removing all sequences below 15nt and trimming sequences by adapter TGGAATTCTCGGGTGCCAAGGAACTCCAG
cutadapt -m 15 -b TGGAATTCTCGGGTGCCAAGGAACTCCAG -o [output] -i [input]
bwa v.0.7.17
fastq genome alignment, sam file generation
bwa aln ./hg38.fa [fastq] > [sai]
bwa v.0.7.17
sam file indexing, one isoform can map 10 times to genome
bwa samse -n 10 ./hg38.fa [sai] [fastq] > [sam]
perl5
annotating using mirbase v22b and hg38
perl <BASEDIR>/v0.2.8/code/annotation/annotate.pl -m <mirbase> -u <ucsc_database> -o <species_code> -p <PROJECT>
perl5
Creating count table files and generating matrix files for full form and 3p/5p
perl <BASEDIR>/v0.2.8/code/custom\_output/tcga.pl -p <PROJECT>, perl <BASEDIR>/v0.2.8/code/library\_stats/expression\_matrix.pl -m <mirbase> -o <mirbase\_species\_code> -p <PROJECT>, perl <BASEDIR>/v0.2.8/code/library\_stats/tcga/expression\_matrix\_mimat.pl -m <mirbase> -o <mirbase\_species\_code> -p <PROJECT>
Genome_build: hg38, mirbase v22b
Supplementary_files_format_and_content: mirnas.txt, isoforms.txt

source_name: CD34+ cells

growth_protocol: CD34+ cells from N-FL and T21-FL were sorted by flow cytometry.

extract_protocol:
Total RNA was isolated from sorted 2-3x10^5 CD34+ cells using the mirVANA miRNA isolation kit (Thermo Fisher).
Samples were processed using the Small RNA Library Prep kit (Norgen Biotek). Libraries were size excised at 130-177bp using the Pippin Prep.

value: Fetal-liver derived hematopoietic stem and progenitor cells

tag: karyotype

value: trisomic fetal liver


title: T21-FL2


title: T21-FL3


title: N-FL3

value: disomic fetal liver


title: N-FL2


title: Day4_rep2


title: N-FL1


title: Day2_rep1


title: 083_Lgate_CD3PosCD14Pos

city: La Jolla

first: Bjoern

last: Peters

state: California

address: 9420 Athena Cir

institute: La Jolla Institute for Immunology

description: Whole Transcriptome Amplification (SmartSeq2 - Picelli et al.2014)

data_processing:
Single-cell RNA-seq data were mapped against the human hg19 reference genome using TopHat (v1.4.1., - -library-type fr-secondstrand -C) and Gencode version 19 (GRCh37.p13) as gene model reference for alignment. Sequencing read coverage per gene was counted using HTSeq-count (-m union -s yes -t exon -i gene_id, http://www huber.embl.de/users/anders/HTSeq/). Counts per gene are obtained by counting all the transcripts mapping to a gene and is together referred to as transcript. To normalize for sequencing depth and varying transcript length counts were TPM (Transcripts Per Million reads) transformed.
Genome_build: hg19
Supplementary_files_format_and_content: raw counts of sequencing reads obtained from HTSeq-count

source_name: Cryopreserved PBMC

growth_protocol: Cells were directly isolated post thawing of cryopreserved PBMC samples and lysed, no culture were involved.

extract_protocol:
Cryopreserved PBMC were thawed, stained with live/dead stain, anti-human CD14 and CD3 antibodies, and single cell sorted using BD Aria 3 cell sorter direclty in cell lysis buffer. Monocyte gate (Mgate) and lymphocyte gate (Lgate) were defined from FSC and SSC parameters. Monocytes were defined as live Mgate CD14+CD3- cells, T cells were defined as live Lgate CD14-CD3+ cells, CD14+CD3+ Mgate were defined as live Mgate CD14+CD3+ cells and CD14+CD3+ Lgate were defined as live Lgate CD14+CD3+ cells. Total RNA was extracted using Smart-seq2 method as previously described (Picelli et al., 2013).
Single cell RNAseq was performed as described in Picelli et al.Nat Protoc. 2014, PMID:24385147. 0.3 to 0.5 ng of pre-amplified cDNA was used to generate barcoded Illumina sequencing libraries (Nextera XT library preparation kit, Illumina) in an 8µL reaction volume.

tag: cell subset

value: CD3+CD14+ cells, Lgate

tag: patient diagnosis

value: infected with latent tuberculosis


title: 085_Lgate_CD3PosCD14Pos


title: 084_Lgate_CD3PosCD14Pos


title: 082_Lgate_CD3PosCD14Pos


title: 081_Lgate_CD3PosCD14Pos


title: 080_Lgate_CD3PosCD14Pos


title: Stable PDX Nevus recipient (mouse) 3

city: Charleston

first: Heehwa

last: Son

state: MA

address: 149 13 street

institute: MASSACHUSETTS GENERAL HOSPITAL

description:
Read counts estimated by using RSEM
stableM_3

data_processing:
The FASTQ files were analyzed by using FastQ Screen-0.14.0. Any sequences specifically matched to mouse genome from PDX samples were removed using FastQ Screen with --filter 03 –inverse options.
The trimmed sequences were aligned to human genome/GRCh38 and transcriptome/ensGene98 by using STAR-2.7.0e.
Sequences located at transcripts were quantified by using RSEM-1.3.1.
Differentially expressed genes (DEG) analysis was performed using DESeq2-1.24.0.
Genome_build: Human genome/GRCh38
Supplementary_files_format_and_content: Read counts estimated by using RSEM

source_name: Skin

growth_protocol: RNA extracted from Human/Mouse Tissue

extract_protocol:
Lysis buffer
Modified SMART-Seq2 cDNA and Illumina NexteraXT library construction. Protocol based on preparation of Single-Cell RNA-Seq libraries for next generation sequencing -Trombetta et al 2017

tag: harvest stage

value: Stable (>100 days)

tag: strain/genotpe

value: Human skin transplanted into NSG -/-

tag: vendor

value: Cox 7:Partners Research Core


title: 079_Lgate_CD3PosCD14Pos


title: Stable PDX Nevus recipient (mouse) 2

description:
Read counts estimated by using RSEM
stableM_2


title: Stable PDX Nevus recipient (mouse) 1

description:
Read counts estimated by using RSEM
stableM_1


title: 078_Lgate_CD3PosCD14Pos


title: genomic DNA from OPSCC - T23

type: genomic

city: Rio de Janeiro

first: Sheila

middle: Coelho

last: Soares-Lima

state: Rio de Janeiro

address: Rua André Cavalcanti 37

department: Molecular Carcinogenesis Program

country: Brazil

institute: Brazilian National Cancer Institute

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation450k Beadchip using standard Illumina protocol.

scan_protocol: iScan was used to scan the slides

data_processing: Illumina Infinium Human Methylation450k (HM450K) Bead-Chips (Illumina, San Diego, CA) were used for establishing genome-wide DNA methylation profiling. Raw data were subject to quality control, prefiltering, signal normalization across samples, and normalization using the funnorm function (R packages minfi)

label: cy3 and cy13

source_name: OPSCC - T23

label_protocol: Standard Illumina Protocol

extract_protocol: DNeasy Blood and Tissue Kit for snap-frozen samples and QIAamp DNA FFPE Tissue Kit for FFPE samples. In the case of FFPE samples, DNA quality was assessed by the Infinium FFPE DNA QC Kit (Illumina) and only samples that passed the established threshold were used in the fol-lowing experiments. After sodium bisulfite treatment, restoration was performed using the Infinium FFPE DNA Restoration Kit (Illumina).

tag: tissue

value: tumor

tag: sample type

value: FFPE


title: Reject PDX Nevus recipient (mouse) 3

description:
Read counts estimated by using RSEM
rejectM_3

value: Post-Rejection


title: genomic DNA from Tonsil 7

label: cy3 and cy12

source_name: Tonsil 7

value: normal tonsil


title: 076_Lgate_CD3PosCD14Pos


title: genomic DNA from Tonsil 3

label: cy3 and cy5

source_name: Tonsil 3


title: genomic DNA from Tonsil 4

source_name: Tonsil 4


title: genomic DNA from OPSCC - T16

source_name: OPSCC - T16


title: genomic DNA from OPSCC - T13

source_name: OPSCC - T13

value: snap-frozen


title: genomic DNA from OPSCC - T21

label: cy3 and cy9

source_name: OPSCC - T21


title: genomic DNA from OPSCC - T19

label: cy3 and cy6

source_name: OPSCC - T19


title: genomic DNA from OPSCC - T14

source_name: OPSCC - T14


title: genomic DNA from OPSCC - T18

source_name: OPSCC - T18


title: Reject PDX Nevus recipient (mouse) 2

description:
Read counts estimated by using RSEM
rejectM_2


title: genomic DNA from OPSCC - T20

label: cy3 and cy7

source_name: OPSCC - T20


title: genomic DNA from Tonsil 2

source_name: Tonsil 2


title: genomic DNA from Tonsil 1

source_name: Tonsil 1


title: genomic DNA from Tonsil 8

label: cy3 and cy14

source_name: Tonsil 8


title: genomic DNA from OPSCC - T22

label: cy3 and cy11

source_name: OPSCC - T22


title: genomic DNA from Tonsil 5

label: cy3 and cy8

source_name: Tonsil 5


title: genomic DNA from OPSCC - T15

source_name: OPSCC - T15


title: genomic DNA from Tonsil 9

label: cy3 and cy15

source_name: Tonsil 9


title: genomic DNA from OPSCC - T17

source_name: OPSCC - T17


title: genomic DNA from OPSCC - T7

source_name: OPSCC - T7


title: genomic DNA from Tonsil 6

label: cy3 and cy10

source_name: Tonsil 6


title: 074_Lgate_CD3PosCD14Pos

source_name: Cryopreserved PBMC


title: genomic DNA from OPSCC - T10

source_name: OPSCC - T10


title: genomic DNA from OPSCC - T8

source_name: OPSCC - T8


title: KO rep5

city: Singapore

first: Yusuf

last: Ali

address: Lee Kong Chian School of Medicine

country: Singapore

institute: Nanyang Technological University

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequenced reads were mapped to mm10 mouse genome using STAR v2.5.2a with parameters --outSAMtype BAM   SortedByCoordinate --outSAMstrandField intronMotif  --outSAMattributes NH   HI   AS   nM   NM   MD --outSAMmapqUnique 50 --outBAMsortingThreadN 16 --outWigType wiggle --outWigStrand Stranded --outWigNorm RPM --outFilterType BySJout --outFilterMultimapNmax 1 --outFilterMismatchNmax 999 --outFilterMismatchNoverLmax 0.04 --outFilterIntronMotifs RemoveNoncanonical --alignIntronMin 20 --alignIntronMax 1000000 --alignMatesGapMax 1000000 --alignSJoverhangMin 8 --alignSJDBoverhangMin 1 --alignEndsType EndToEnd --quantMode TranscriptomeSAM   GeneCounts
Cuffnorm v2.2.1 used to obtain quartile normalized FPKM expression matrix of genes across all replicates.
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: Cuffnorm output with quartile normalised FPKM expression value of each sample replicate.

source_name: Pancreatic islet

growth_protocol: Pancreatic islets were isolated and cultured in the complete CMRL medium overnight for recovery.

extract_protocol:
Total RNA was harvested using Rneasy Plus Mini Kit (74136, Qiagen).
PolyA-tail specific mRNA libraries were prepared from 1 ug of total RNA with the Illumina TruSeq stranded mRNA library preparation protocol, followed by single-end 1x75bp sequencing with the Illumina NextSeq.

value: Pancreatic islet

tag: age

value: 12 week

tag: genotype


title: 073_Lgate_CD3PosCD14Pos


title: genomic DNA from OPSCC - T9

source_name: OPSCC - T9


title: KO rep4


title: genomic DNA from OPSCC - T12

source_name: OPSCC - T12


title: KO rep3


title: genomic DNA from OPSCC - T11

source_name: OPSCC - T11


title: 075_Lgate_CD3PosCD14Pos


title: 072_Lgate_CD3PosCD14Pos


title: 077_Lgate_CD3PosCD14Pos


title: 071_Lgate_CD3PosCD14Pos


title: KO rep2


title: 070_Lgate_CD3PosCD14Pos


title: KO rep1


title: Flox rep3

value: wild type


title: 069_Lgate_CD3PosCD14Pos


title: 068_Lgate_CD3PosCD14Pos


title: Flox rep5


title: genomic DNA from OPSCC - T6

source_name: OPSCC - T6


title: Flox rep4


title: 067_Lgate_CD3PosCD14Pos


title: 065_Mgate_CD3PosCD14Pos

value: CD3+CD14+ cells, Mgate


title: 066_Lgate_CD3PosCD14Pos


title: Flox rep2


title: genomic DNA from LSCC - T20

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation450k Beadchip using standard Illumina protocol

source_name: LSCC - T20

extract_protocol: DNeasy Blood and Tissue Kit


title: genomic DNA from OPSCC - T2

source_name: OPSCC - T2


title: genomic DNA from LSCC - T21

source_name: LSCC - T21


title: genomic DNA from OPSCC - T3

source_name: OPSCC - T3


title: genomic DNA from OPSCC - T1

source_name: OPSCC - T1


title: genomic DNA from LSCC - N14

source_name: LSCC - N14

value: adjacent non-tumor


title: 063_Mgate_CD3PosCD14Pos


title: Flox rep1


title: 064_Mgate_CD3PosCD14Pos


title: genomic DNA from OPSCC - T4

source_name: OPSCC - T4


title: genomic DNA from LSCC - N15

source_name: LSCC - N15


title: genomic DNA from LSCC - N20

source_name: LSCC - N20


title: genomic DNA from LSCC - T19

source_name: LSCC - T19


title: genomic DNA from LSCC - T15

source_name: LSCC - T15


title: genomic DNA from OPSCC - T5

source_name: OPSCC - T5


title: 8-cell mouse embryos - plate 3

city: Santa Barbara

first: Siddharth

last: Dey

state: CA

address: 3357 Engrg II UCSB

department: Chemical Engineering

institute: UCSB

data_processing:
library strategy: scAba-seq (single-cell, genome-wide and strand-specific 5hmC sequencing technology, based on 5hmC glucosylation and glucosylation-dependent digestion of DNA)
Fastq files are parsed for library barcodes. Read 1 was mapped to the mm10 build using the Burrows-Wheeler Aligner (BWA), filtered for unique mapping full-length reads and demultiplexed. 5hmCG positions are obtained from the sequencing data using custom scripts in R and Perl identifying CG dinucleotides in the mm10 genome at the expected distance from the mapped read position. Finally, all PCR duplicates are removed. Computer codes will be made available upon request.
Genome_build: mm10
Supplementary_files_format_and_content: Text files with 4 columns: Single Cell ID, chromosome, coordinate and strand

source_name: 8-cell mouse preimplantation embryos

extract_protocol:
Embryos were gently flushed out of the infidubulum of E2.5 pregnant mice using warm M2 medium. Embryos were then manipulated in 4-ring IVF dishes coated with RNase-free BSA because, once dissociated, cells stick to plastic. Embryos were washed in PBS-0 and in Tyrode’s acid to remove the zone pellucida, then placed in a 1/3 dilution of Tryple select GIBCO A12177-01 (stock solution is referred by Gibco as x10 concentrated) and placed on the warm plate for 2 minutes. We then used glass capillaries of different diameters to dissociate the embryo into 2-3 clusters. Cells were then progressively extracted from each cluster, one after the other, using glass capillaries. Every single cell that is released from the clusters is immediately placed into a well of a 384-well plate containing lysis buffer.
4 μL Vapor-Lock (Qiagen) is dispensed manually into each well of a 384 well plate using a multichannel pipet. 0.2 μL of lysis buffer (1x NEB buffer 4, 0.1 μg Qiagen protease) is dispensed at 12 psi pressure into each well using the NanoDrop II liquid-handling robot. Single cells are deposited  into each well and the plate is incubated at 50°C for 3 hours, 75°C for 20 min and 80°C for 5 min. 0.2 μL of Glucosylation mix (1x NEB buffer 4, 2 U NEB T4-BGT, 1x NEB UDP-Glucose) is added and the plate is incubated at 37°C for 18 hours. Next, 0.2 μL of lysis buffer is added and the plate is incubated at 50°C for 3 hours, 75°C for 20 min and 80°C for 5 min. 0.2 μL of AbaSI (1x NEB buffer 4, 2 U NEB AbaSI) is added and the plate is incubated at 25°C for 1 hour and 65°C for 20 min. 0.2 μL of 0.01 μM adapter is added, followed by 0.2 μL of ligation mix (80 U T4-Ligase, 2X T4-ligase buffer, 0.6 mM ATP) and the plate is incubated for 16 hours at 16°C. Contents of all the wells with different adapters are pooled and incubated with 0.8x Agencourt Ampure XP beads for 30 min, washed twice with 80% ethanol and resuspended in 6.4 μL nuclease free water. 9.6 μL of in vitro transcription mix is added (1.6 μL of each ribonucleotide, 1.6 μL T7 buffer, 1.6 μL T7 enzyme mix) and incubated at 37°C for 14 hours. After in vitro transcription, the aRNA  (amplified RNA) is size selected by incubating with 0.8x Agencourt RNAClean beads for 30 min, washed twice with 70% ethanol and resuspended in 16 μL nuclease-free water. Next, the aRNA is fragmented using fragmentation buffer (200mM Tris-acetate, pH 8.1, 500 mM KOAc, 150 mM MgOAc) at 94°C for 1.5 min and quenched by putting the reaction on ice and adding 2 μL 0.5 M EDTA. Fragmented aRNA is then purified using 1x Agencourt RNAClean beads as mentioned before and eluted in 16 uL nuclease-free water. After these steps, library preparation is performed as described in the scAba-seq protocol.
scAba-seq [Mooijman et al. 2016 Nature Biotechnology]

tag: strain

value: 8-cell preimplantation embryos

tag: molecule subtype


title: genomic DNA from LSCC - T12

source_name: LSCC - T12


title: genomic DNA from LSCC - T13

source_name: LSCC - T13


title: genomic DNA from LSCC - T16

source_name: LSCC - T16


title: 062_Mgate_CD3PosCD14Pos

source_name: Cryopreserved PBMC


title: genomic DNA from LSCC - N16

source_name: LSCC - N16


title: genomic DNA from LSCC - N10

source_name: LSCC - N10


title: Reject PDX Nevus recipient (mouse) 1

description:
Read counts estimated by using RSEM
rejectM_1

source_name: Skin


title: genomic DNA from LSCC - T18

source_name: LSCC - T18


title: 061_Mgate_CD3PosCD14Pos


title: 8-cell mouse embryos - plate 2


title: genomic DNA from LSCC - T17

source_name: LSCC - T17


title: genomic DNA from LSCC - T8

source_name: LSCC - T8


title: 060_Mgate_CD3PosCD14Pos


title: 8-cell mouse embryos - plate 1


title: genomic DNA from LSCC - T11

source_name: LSCC - T11


title: genomic DNA from LSCC - T9

source_name: LSCC - T9


title: genomic DNA from LSCC - N11

source_name: LSCC - N11


title: 059_Mgate_CD3PosCD14Pos


title: 058_Mgate_CD3PosCD14Pos


title: genomic DNA from LSCC - T10

source_name: LSCC - T10


title: genomic DNA from LSCC - T7

source_name: LSCC - T7


title: Newly formed oligodendrocyte - Olig2 RIP-seq input

first: Haichao

last: Wei

state: TX

address: 1825 Pressler St., SRB 637.C

institute: UTHealth

data_processing:
ChIP-Seq of OLIG2, H3K4me3 and H3K27me3 in NSCs, OPCs and NFOs were performed on the Illumina platform. All reads were mapped to the mm10 reference genome using Bowtie2, and only unique mapped reads were used for subsequent analysis.
OLIG2 ChIP-Seq data were analyzed using the transcription factor pipeline from ENCODE (https://github.com/kundajelab/chipseq_pipeline). Peaks for OLIG2 were called using SPP and filtered to exclude regions blacklisted by ENCODE, and peaks with FDR > 0.05 and fold-enrichment < 5.
ChIP-Seq for H3K4me3 and H3K27me3 were analyzed using MACS2 (broad peak) and filtered to exclude the ENCODE blacklist regions, and peaks with FDR > 0.05 and fold-enrichment < 3.5.
ASPeak is a peak detection algorithm that is sensitive to differential expression levels of target transcripts. We ran ASPeak with default parameters and used NSC RNA-Seq data to estimate parameters p and r for the negative binomial distributions. We used NSC IgG RIP-Seq as a control library. Gene annotations were performed with mm10 GENCODE file (release GRCm38).
Genome_build: Mm10
Supplementary_files_format_and_content: peaks

source_name: Newly formed oligodendrocyte

growth_protocol: Mouse neural stem cells (NSCs) from the cortices of embryonic (E14.5) CD-1 mice were purchased from R&D Systems. Briefly, cells were cultured on poly-d-lysine-coated flasks and passaged every 2 d in MEM/F12 medium (Gibco) containing 20 ng/ml EGF, 20 ng/ml FGF, B27 and N2 supplement (Invitrogen). When passaging, cells were dissociated using Accutase (Invitrogen). Mouse embryo fibroblast cell NIH3T3 line was purchased from ATCC. Cells were cultured in DMEM (Gibco) medium with 10% FBS (Fisher) and passaged every 2-3 d.

extract_protocol:
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody.
RNA was extracted using TRIzol (15596026, Invitrogen) and was used for library construction with the TruSeq RNA Library Prep Kit (RS-122-2001, Illumina) following the manufacturer’s protocols.

value: Newly formed oligodendrocyte

tag: rip antibody

value: Anti-rabbit IgG (Cell Signaling, 2729S, lot 6)

tag: treatment

value: untreated


title: wm3

city: Bothell

first: Thelma

middle: F

last: Madzima

state: WA

address: 18115 Campus Way NE

department: Division of Biological Sciences

institute: University of Washington Bothell

data_processing:
Illumina base-calling
FASTQ adapters were trimmed and read quality control was assessed using fastp (0.21.0). Reads were mapped to the B73 maize genome (AGP B73v4) (Jiao et al. 2017) by HISAT2 v2.2.1 (Pertea et al. 2016).
Transcripts were assembled de novo to allow for inclusion of transcripts that are not included in the reference genome annotation and quantified using StringTie v2.1.4 (Pertea et al. 2016). Gene count matrices were generated from this data using the prepDE.py python script available in the StringTie website.
Genome_build: AGPv.4 B73
Supplementary_files_format_and_content: comma separated values files include gene counts for each Sample

organism: Zea mays

source_name: Seedling

growth_protocol: Maize plants were grown in greenhouse conditions (16 h light period, 25°C, 50% humidity) until V3 stage was reached.

extract_protocol:
Seedling shoots were flash frozen and RNA was harvested using Trizol reagent. NEBNext Ultra RNA Library Prep Kit from Illumina (NEB #E7770) was used with 1 µg of RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols.
Paired-end 150 bp (PE 150) RNA-sequencing.

treatment_protocol: Maize seedlings at the V3 stage were removed from the soil, roots were rinsed in water, dried and then submerged in a 1 L beaker with 250 mL of liquid Murashige and Skoog (MS) media (Sigma Aldrich, M6899) with 50 μM ABA (ABA; (Sigma Aldrich, (+/-) Abscisic Acid, A1049)) or without ABA (MS)  for 1 hour.

tag: develpmental stage and tissue

value: V3 seedling shoots

value: Treated with MS for 1 h

value: Mop1 homozygous wildtype


title: 057_Mgate_CD3PosCD14Pos

value: infected with latent tuberculosis


title: wm2


title: 2a3_PLN_MoGene

city: Chapel Hill

first: Matthew

last: Clark

state: NC

address: 125 Mason Farm Road

department: Microbiology and Immunology

institute: University of North Carolina at Chapel Hill

hyb_protocol: Affymetrix protocol

scan_protocol: Affymetrix protocol

data_processing: Expression Console

label: biotin

source_name: PLN CD4+ T cells

label_protocol: Affymetrix protocol

growth_protocol: 8 week old BDC2.4 mice

extract_protocol: PLN was removed and homginized. Live CD3+ CD4+ T cells were sorted by flow cytometry for microarray.

treatment_protocol: 48hr in vivo treatment with 1mg isotype control (2a3) or anti-CD4 (YTS177) antbodies

tag: agent

value: 8 week old

value: 1mg isotype control (2a3)

value: PLN CD4+ T cells


title: YTS_PLN_MoGene

value: anti-CD4 (YTS177) antbodies

tag: cell type


title: wm1


title: Newly formed oligodendrocyte - Olig2 RIP-seq

value: Olig2 (EMD Millipore AB9610, lot 3474051)


title: genomic DNA from LSCC - N9

source_name: LSCC - N9


title: 056_Mgate_CD3PosCD14Pos


title: Newly formed oligodendrocyte - Olig2

tag: chip antibody


title: wa1

value: Treated with ABA 50 microM for 1 h


title: 055_Mgate_CD3PosCD14Pos

tag: cell subset


title: genomic DNA from LSCC - N8

source_name: LSCC - N8


title: Oligodendrocyte precursor cells - Olig2

source_name: Oligodendrocyte precursor cells

value: Oligodendrocyte precursor cells


title: ma3

value: mop1-1 homozygous mutant


title: 054_Mgate_CD3PosCD14Pos

source_name: Cryopreserved PBMC

value: CD3+CD14+ cells, Mgate

tag: patient diagnosis


title: ma2


title: genomic DNA from LSCC - N7

source_name: LSCC - N7

value: adjacent non-tumor


title: Newly formed oligodendrocyte - input DNA

value: Newly formed oligodendrocyte


title: ma1


title: 052_Mgate_CD3PosCD14Pos


title: genomic DNA from LSCC - T6

source_name: LSCC - T6

value: tumor


title: genomic DNA from LSCC - T4

source_name: LSCC - T4


title: wa2


title: mm3


title: Newly formed oligodendrocyte - H3K4me3

value: untreated


title: 053_Mgate_CD3PosCD14Pos


title: wa3

value: V3 seedling shoots


title: Oligodendrocyte precursor cells - input DNA


title: 051_Mgate_CD3PosCD14Pos


title: genomic DNA from LSCC - N3

source_name: LSCC - N3


title: Newly formed oligodendrocyte - H3K27me3


title: 050_Mgate_CD3PosCD14Pos


title: mm1

value: Treated with MS for 1 h


title: mm2


title: genomic DNA from LSCC - T3

source_name: LSCC - T3


title: Oligodendrocyte precursor cells - H3K27me3


title: genomic DNA from LSCC - T5

source_name: LSCC - T5


title: genomic DNA from LSCC - N2

source_name: LSCC - N2


title: 049_Mgate_CD3PosCD14Pos


title: genomic DNA from LSCC - T1

source_name: LSCC - T1


title: Oligodendrocyte precursor cells - H3K4me3


title: genomic DNA from LSCC - T2

source_name: LSCC - T2


title: 047_Mgate_CD3PosCD14Pos


title: Neural stem cells - input DNA

source_name: Neural stem cells

value: Neural stem cells


title: WT_LIF_d0

city: Freiburg

first: Pierre

middle: Daniel

last: Cauchy

state: Baden-Württemberg

address: Breisacher Str. 115

department: Zentrum für Translationale Zellforschung

country: Germany

institute: University Medical Center Freiburg

data_processing:
base calling: HiSeq Analysis Software (2.2.58)
alignment: bwa (0.7.16a) mem -A1 -B4  -E50 -L0
interaction matrix creation: hicBuildMatrix (2.1.4) --binSize 40000 --restrictionSequence GATC --threads 4 --inputBufferSize 400000
filter threshold estimation: hicCorrectMatrix diagnostic_plot (2.1.4)
matrix correction: hicCorrectMatrix correct –filterThreshold (2.1.4)
Genome_build: mm9
Supplementary_files_format_and_content: h5 interaction matrix

source_name: mouse embryonic stem cells

growth_protocol: All mouse embryonic stem cell lines were routinely cultured and passaged on irradiated mouse embryonic fibroblasts in ES cell medium containing serum+LIF: 15% PANSera ES (PAN Biotech), 1xSodium Pyruvate (Gibco), 1×penicillin/streptomycin/glutamine (Gibco), 1×non-essential amino acids (Gibco), 0.1mM β-mercaptoethanol (Sigma), and 1,000 U ml−1 ESGRO LIF (Millipore) in DMEM High glucose (ThermoFisher). For differentiation experiments as well as RNA/DNA/protein extraction, ESCs were cultured on dishes covered with 0.1% Gelatine.

extract_protocol:
Cells were crosslinked for 10 mins at room temperature in 1% methanol-free formaldehyde at a density of 106 cells/ml, quenched for 5 mins with 125mM glycine at room temperature. Cells were split 1.5 107 crosslinked cells were resuspended in 500 μL Hi-C Lysis Buffer (10 mM Tris-HCl pH 8.0, 10 mM NaCl, 0.2% NP40, 1X protease inhibitors) for 30 mins at 4°C on a rotating wheel, then centrifuged 5 mins at 2500g, and subsequently washed with 500 μL Hi-C Lysis Buffer and resuspended in 100 μL 0.5% SDS. Cells were then incubated  at 62°C for 10 minutes, after which 285 μL of H2O and 50 μL of 10% Triton X-100 were added to quench the SDS, and incubated at 37°C for 15 mins.  50 μL 10X NEB Buffer 2 and 375 U of MboI restriction enzyme (NEB, R0147) were added to digest chromatin for 2 hours at 37°C with rotation, followed by MboI inactivation at 62°C for 10 minutes. Restriction fragment overhang filling and biotin marking of DNA-ends was carried out in 52 μL Master Mix (0.4 mM biotin-dATP (Thermo 19524016), 10 mM dCTP/dGTP/dTTP, 5U/μL DNA Polymerase I, Large (Klenow) Fragment (NEB, M0210)), mixed and incubated at 37 for 1 hour with rotation. 948 μL ligation master mix was subsequently added  (10X NEB T4 DNA ligase buffer with 10 mM ATP (NEB, B0202), 10% Triton X-100, 50 mg/mL BSA, 400 U/μL T4 DNA Ligase (NEB, M0202)), incubated at room temperature for 4 hours with rotation. Nuclei were then centrifuged at 2500g for 5 mins .For sonication, pellets were resupspended in 880 μL in Nuclear Lysis Buffer (50 mM Tris-HCl pH 7.5, 10 mM EDTA, 1% SDS, 1X protease inhibitors), and sonicated in a Covaris militube using a Covaris E220 sonicator (fill level: 10, duty cycle: 5, PIP: 140, cycles/burst: 200, time: 4 mins). Biotin pull-down was carried out with 5 μL Streptavidin C-1 beads washed with Tween Wash Buffer (5 mM Tris-HCl pH 7.5, 0.5 mM EDTA, 1M NaCl, 0.05% Tween-20) in 10 μL 2X Biotin Binding Buffer (10 mM Tris-HCl pH 7.5, 1 mM EDTA, 2 M NaCl). Beads were incubated at room temperature with 50ng chromatin for 15 minutes with rotation, magnet-separated and washed twice with 500 μL Tween Wash Buffer at 55 °C for 2 minutes with shaking and subsequently washed in 100 μL of 1X TD Buffer (10 mM Tris-HCl pH 7.5, 5 mM MgCl2, 10% dimethylformamide), and resuspended in 25 μL 2X TD Buffer, to which 2.5 μL Tn5 transposase was added, and subsequently incubated at 55 °C with interval shaking for 10 minutes. Beads were magnet-separated and incubated in 50 mM EDTA at 50°C for 30 mins, washed twice in 50 mM EDTA at 50°C for 3 mins, and twice in Tween Wash Buffer at 55°C for 2 minutes, as well as once in 10 mM Tris
For PCR and Post-PCR Size Selection, beads were resuspended in 50 μL of PCR master mix (Phusion HF 2X, Nextera Ad1.1 (Universal) 12.5 uM, Nextera Ad2.x (Barcoded) 12.5 uM), with 15 cycles (98°C 15 s, 63°C 30 s, 72°C 1 min). Libraries were cleaned up with 1.8X and subsequently 0.6X Ampure XP beads, and finally eluted in 10 μL water. Sequencing was carried out on an Illumina HiSeq 2500 sequencer.

treatment_protocol: For differentiation into ectodermal precursors, mESCs were initially plated on 0.1% Gelatine-covered dishes in ES cell media. 24h later the media was switch to ES cell medium containing serum+5uM retinoic acid (Sigma). Cells were cultured 4 days upon treatment.

tag: satb2 mutational status

value: WT

tag: culture conditions

value: LIF


title: dm_RA_d4

value: 4 days RA


title: 046_Mgate_CD3PosCD14Pos

value: infected with latent tuberculosis


title: Neural stem cells - H3K27me3


title: Neural stem cells - H3K4me3


title: 045_Mgate_CD3PosCD14Pos


title: genomic DNA from OSCC - T16

source_name: OSCC - T16


title: genomic DNA from OSCC - T15

source_name: OSCC - T15


title: 048_Mgate_CD3PosCD14Pos


title: XT3

city: Longyan

first: Yanfa

last: Sun

state: Fujian

address: Dongxiao North Road No. 1, Xinluo District

department: College of Life Science

country: China

institute: Longyan University

data_processing:
Clean data were acquired from quality reads of raw data reads using SOAPnuke software (Chen et al., 2018).
The adapters, unknown bases and those of low quality were removed as following: reads containing adapters (adapter contamination), more than 5% unknown bases, and low quality (less than 15 bases, >20%).
After the above treatment, all clean reads were mapped onto the reference chicken genome (Gallus gallus 5.0) with TopHat v2.0.12 software with default parameters(Kim and Salzberg, 2011;Ghosh and Chan, 2016).
The raw reads mapped to each gene were quantified using easyRNASeq software (Delhomme et al., 2012).
The Ensembl Genes v67 (Larsson et al., 2005) was used for the genes annotation.
Genome_build: chicken genome (Gallus gallus 5.0)

organism: Gallus gallus

source_name: sample from 100 IU/kg VE

extract_protocol:
Three pectoralis major tissue samples from the control group and three from vitamin E supplement group were used for RNA extraction and sequencing. Total RNA was isolated from the samples using the RNAsimple Total RNA kit (Tiangen Biotech Inc., Beijing, China) in accordance with the manufacturer’s instructions.
Integrity and concentration of the RNA were evaluated using an Agilent 2100 Bio-analyzer (Agilent Technologies, Palo Alto, CA, USA) to meet subsequent quality requirements for sequencing. The mRNA was enriched from total RNA samples using oligo (DT) magnetic beads (Invitrogen, USA) after them treated with Ambion DNase I (Life Technologies Inc.). First-strand cDNA was synthesized after purified mRNA fragmented by RNA fragmentation kit (Ambion, USA), then the second-strand cDNA were synthesized according to the manufacturer’s instructions. Quality of the cDNA library was assessed using Agilent 2100 Bioanalyzer and ABI Step One Plus Real-Time PCR System.
Finally, the qualified cDNA libraries were sequenced using the Illumina HiSeq 2500 system.

treatment_protocol: The birds were fed basal diet supplemented with 0, 20, 50, 75 and 100 IU/kg vitamin E in the form of DL-α-tocopheryl acetate, respectively

value: 35 days of age

value: pectoral muscle

tag: Sex

value: female


title: WT_RA_d4


title: E12_Ascl1.4

city: Bethesda

middle: J

last: Brooks

state: MD

address: 6 Center Dr Bldg 6, Rm 303

department: NEI

institute: NIH

description: embryonic day 11.5 Ascl1-GFP+ dorsal telencephalic replicate 4

data_processing:
Fastq files were generated from reads passing chastity filter and used for further analysis. Illumina adapter, polyA, and polyT sequence trimming was performed with Trimmomatic v0.36.
Transcript level quantitation was performed using Kallisto v0.44.0 employing a merged transcript cDNA and ncRNA FASTA file downloaded from the Ensembl ftp site. Gene level quantification was generated by summarization of the transcript level quantitation using tximport v1.8.0 with the option “countFromAbundance=lengthScaledTPM”. The gene level count values were TMM normalized and converted to count per million (CPM) via edgeR v3.22.5.
Genome_build: GRCm38.p6 with Ensembl v95

source_name: dorsal telencephalic

growth_protocol: CD15+ GFP/mCherry negative, single, double positive cortical progenitors were dissociated from E14.5 Neurog2Flag-mcherryKI/+;Ascl1GFPKI/+ dorsal telencephalic tissue in Hank’s Balanced Salt Solution (HBSS; Life Technologies, NY, USA), followed by dissociation in Accutase (Life Technologies) at 37°C for 10 min with constant agitation. After removing cell clumps by filtration, 4 ml of PBS (GIBCO, Life Technologies) was added to dissociated cells. The cells were collected by centrifugation at 800g for 5 min and re-suspended in 1 ml of PBS. GFP-positive cells were isolated by fluorescence-activated cell sorting (FACS) using FACS Aria II (Becton Dickinson, CA, USA) with a stringent precision setting to maximize the purity of the sorted cells.

extract_protocol:
Total RNA was extracted by Trizol LS (Life Tech).
Each library was paired-end sequenced to a length of 2x125 bases. Fastq files were generated from reads passing chastity filter.

value: embryonic day 11.5

tag: replicate

value: replicate 4


title: E12_Neurog2.4

description: embryonic day 11.5 Neurog2-mCherry+ dorsal telencephalic replicate 4


title: 044_Mgate_CD3PosCD14Pos

value: CD3+CD14+ cells, Mgate


title: 043_Tcell

value: T cell (CD3+CD14-, Lgate)


title: XT1

tag: tissue


title: E12_Neg.4

description: embryonic day 11.5 GFP and mCherry negative dorsal telencephalic replicate 4

tag: age

value: GFP and mCherry negative


title: genomic DNA from OSCC - N13

source_name: OSCC - N13

value: adjacent non-tumor


title: 042_Tcell

source_name: Cryopreserved PBMC


title: genomic DNA from OSCC - T12

source_name: OSCC - T12

value: tumor


title: E12_Dbl.3

description: embryonic day 11.5 Neurog2-mCherry+;Ascl1-GFP+ dorsal telencephalic replicate 3

value: replicate 3


title: genomic DNA from OSCC - T13

source_name: OSCC - T13


title: genomic DNA from OSCC - T14

source_name: OSCC - T14


title: XC3

source_name: sample from control


title: XT2


title: genomic DNA from OSCC - T11

source_name: OSCC - T11


title: XC1


title: XC2


title: E12_Ascl1.3

description: embryonic day 11.5 Ascl1-GFP+ dorsal telencephalic replicate 3


title: 039_Tcell


title: E12_Neurog2.3

description: embryonic day 11.5 Neurog2-mCherry+ dorsal telencephalic replicate 3


title: 48h-8

city: Jinzhong

first: Jun-hong

state: Shanxi Province

address: 98 University Street, Yuci District, Jinzhong

department: School of Forensic Medicine

institute: Shanxi Medical University

data_processing:
The read quality was then inspected using FastQC and MultiQC
The clean paired-end RNA-seq data obtained with Trimmomatic were aligned to the rn6 rat genome (HISAT2 version 2.1.0),The clean paired-end RNA-seq data obtained with Trimmomatic were aligned to the rn6 rat genome (HISAT2 version 2.1.0)
determine gene-level counts using uniquely aligned unambiguous reads in HTSeq (version 0.6.1)
Genome_build: rn6
Supplementary_files_format_and_content: Original gene expression  matrix for each sample

organism: Rattus norvegicus

source_name: muscle

extract_protocol:
Retinas were removed, flash frozen on dry ice, and RNA was harvested using Trizol reagent. the integrity of total RNA was determined with an Agilent 2100 Nano 6000 Assay kit on an Agilent 2100 Bioanalyzer system.
Samples were submitted to Illumina for library preparation using a NEBNext Ultra RNA Library Prep Kit and fluorometer  to build and preliminarily quantify the library.pair-end 150-bp sequencing, on the HiSeq-2500 platform (Illumina).

treatment_protocol: Mechanical damage

value: Sprague-Dawley

value: skeletal muscle injury

tag: injury state

value: muscle


title: 040_Tcell


title: genomic DNA from OSCC - T10

source_name: OSCC - T10


title: 041_Tcell


title: genomic DNA from OSCC - N12

source_name: OSCC - N12


title: E12_Neg.3

description: embryonic day 11.5 GFP and mCherry negative dorsal telencephalic replicate 3


title: genomic DNA from OSCC - N11

source_name: OSCC - N11


title: 038_Tcell


title: E12_Dbl.4

description: embryonic day 11.5 Neurog2-mCherry+;Ascl1-GFP+ dorsal telencephalic replicate 4


title: 037_Tcell


title: E12_Dbl.2

description: embryonic day 11.5 Neurog2-mCherry+;Ascl1-GFP+ dorsal telencephalic replicate 2

value: replicate 2


title: genomic DNA from OSCC - T8

source_name: OSCC - T8


title: genomic DNA from OSCC - T7

source_name: OSCC - T7


title: E12_Ascl1.2

description: embryonic day 11.5 Ascl1-GFP+ dorsal telencephalic replicate 2


title: 035_Tcell

description: Whole Transcriptome Amplification (SmartSeq2 - Picelli et al.2014)


title: 48h-7

tag: strain


title: genomic DNA from OSCC - T9

source_name: OSCC - T9


title: E12_Neg.2

description: embryonic day 11.5 GFP and mCherry negative dorsal telencephalic replicate 2


title: 48h-6


title: 48h-5


title: 036_Tcell


title: genomic DNA from OSCC - N5

source_name: OSCC - N5


title: E12_Neurog2.2

description: embryonic day 11.5 Neurog2-mCherry+ dorsal telencephalic replicate 2


title: 48h-4


title: 034_Tcell


title: E12_Ascl1.1

description: embryonic day 11.5 Ascl1-GFP+ dorsal telencephalic replicate 1

value: replicate 1


title: E12_Dbl.1

description: embryonic day 11.5 Neurog2-mCherry+;Ascl1-GFP+ dorsal telencephalic replicate 1


title: 032_Tcell

value: infected with latent tuberculosis


title: genomic DNA from OSCC - T6

source_name: OSCC - T6


title: 48h-3


title: 033_Tcell


title: 48h-2


title: 48h-1


title: 031_Tcell


title: E12_Neurog2.1

description: embryonic day 11.5 Neurog2-mCherry+ dorsal telencephalic replicate 1

source_name: dorsal telencephalic


title: genomic DNA from OSCC - T4

source_name: OSCC - T4


title: E12_Neg.1

description: embryonic day 11.5 GFP and mCherry negative dorsal telencephalic replicate 1


title: Satb2_ZNFKO_RA_d4_rep2

data_processing:
base calling: HiSeq Analysis Software (2.2.58)
alignment: bowtie2 (2.2.8)
peak calling and Signal per Million Reads (SPMR) normalized depth coverage generation (bedGraph): macs2 (2.1.0)
Genome_build: mm9
Supplementary_files_format_and_content: SPMR normalized bedGraph format

source_name: mouse embryonic stem cells

extract_protocol:
Approximately 10x107 Cells were used per ChIP. Cells were trypsinized, resuspended in 40 ml of ES cell medium containing 1% Methanol-free Formaldehyde (Thermo/Pierce) and incubated for 10 min on a rotor at room temperature (RT). Then, Glycine solution was added to a final concentration of 125 mM and incubated for 5 min on a rotor at RT. Next, the cells were centrifuged at 2000 rpm for 10 min at 4°C and washed two times with 50 ml of cold PBS. The cell pellet was resuspended in 10 ml of lysis buffer 1 (50mM HEPES-KOH, pH 7.5, 140mM NaCl, 1mM EDTA, 10% glycerol, 0.5% NP-40, 0.25% Triton X-100, 1× protease inhibitors) and then incubated on a rotor for 10 min at 4 °C. The cells were then pelleted, resuspended in 10 ml of lysis buffer 2 (10 mM Tris-HCl, pH 8.0, 200 mM NaCl, 1 mM EDTA, 0.5 mM EGTA, 1× protease inhibitors) and incubated at RT for 10 min on a rotor. The cells were pelleted again and resuspended in 2ml of sonication buffer (20mM Tris-HCl pH8, 150mM NaCl, 2mM EDTA, 0.1% SDS, 1% Triton X-100, 1× protease inhibitors). The suspension was trasnfered to 1ml AFA tubes (Covaris) and sonicated with the following settings: 140 peak incidence, 5 duty factor, 200 cycles/burst, 1200 secs in a E220 Ultrasonicator (Covaris). The sonicated lysate was recovered into DNA LoBind tubes (Eppendorf) and centrifuged at 16,000 g for 10 mins at 4°C to eliminate debris. Meanwhile, 100ul of GammaBind G Sepharose (Sigma) beads were washed twice and equilibrated for 15h at 4°C in blocking solution (0.5% BSA in PBS). The sonicated lysate was pre-cleared for 3h at 4°C with 100 ul of blocked beads equilibrated in sonication buffer. The samples were centrifuged for 3 mins at 16,000 g to recover the precleared lysate, 10% of the total volume was set aside as input control. Each ChIP was set up by adding 10ug of antibody (Supplementary table) to the lysate and incubating it 15h at 4°C on a rotator. The beads were then washed once with the sonication buffer, once with washing buffer 1 (20mM Tris-HCl pH8, 500mM NaCl, 2mM EDTA, 0.1% SDS, 1%Triton X-100), once with washing buffer 2 (10mM Tris-HCl pH8, 250mM LiCl, 2mM EDTA, 1% NP40), once with TE buffer (10 mM Tris-HCl, pH 8.0, 1 mM EDTA) containing 50mM NaCl, and twice with TE buffer. Following washing, the beads were resuspended in 100 µl of elution buffer (50 mM Tris-HCl, pH 8.0, 10 mM EDTA, 1.0% SDS) and incubated at 65°C for 30min at 800rpm. The supernatant was transferred to a new tube and further 100ul of elution buffer were added to the beads to repeat the elution and recover any remaining complexes. The input and eluates were then incubated first with 0.1 mg/ml RNase A (Thermo) at 37°C for 2h, and then with 0.1 mg/ml of Proteinase K (NEB) at 55°C for 2h. Finally, the DNA was purified using the QIAquick PCR purification kit (Qiagen) according to the manufacturer instructions, the samples were eluted in 50 µl of milliQ water and stored at -20 °C until analysis.
To generate libraries, DNA was first subjected to 300-1000 bp size selection with Agencourt AMPure XP beads (Beckman Coulter). Libraries were generated using the ChIP-Seq Ultra DNA Library Prep Kit for Illumina (NEB). Uniquely indexed libraries were pooled in equimolar ratios and sequenced on an Illumina HiSeq2500. Library preparation and sequencing were performed by the Deep Sequencing Facility of the Max-Planck Institute of Immunobiology and Epigenetics.

value: mouse embryonic stem cells

value: WT

tag: zfp451 mutational status

value: KO

value: 4 days RA

tag: antibody

value: Ty1 Invitrogen  MA5-23513


title: 24h-7

tag: treatment


title: genomic DNA from OSCC - N4

source_name: OSCC - N4


title: 029_Tcell

source_name: Cryopreserved PBMC


title: genomic DNA from OSCC - T3

source_name: OSCC - T3


title: 24h-8


title: genomic DNA from OSCC - N2

source_name: OSCC - N2


title: Satb2_ZNFKO_RA_d4_rep1


title: 030_Tcell


title: 24h-6


title: 028_Tcell


title: ZNFKO_LIF_3

data_processing:
base calling: HiSeq Analysis Software (2.2.58)
alignment: tophat2 (2.0.14)
transcript assembly: cufflinks (2.2.1)
FPKM generation: cuffquant (2.2.1)
RPKM-normalized bedGraph generation: deeptools bamCoverage (2.4.2)
Genome_build: mm9
Supplementary_files_format_and_content: RPKM-normalized bedGraph format

extract_protocol:
RNA was purified using Trizol reagent (Life Technologies) according to the manufacturer´s instructions. For RNA-sequencing analysis, trizol-purified RNA was further cleaned with the RNeasy mini kit (Qiagen) according to the manufacturer´s instructions.
Libraries were prepared from 1ug of purified total RNA using the TruSeq stranded mRNA sample preparation kit (Illumina) and quantified with a Qubit fluorometer (Thermo). Uniquely indexed libraries were pooled in equimolar ratios and sequenced on an Illumina NextSeq500 with single-end 75 bp. Library preparation and sequencing were performed by the Deep Sequencing Facility of the Max-Planck Institute of Immunobiology and Epigenetics.

value: LIF


title: 24h-5


title: 027_Tcell

value: T cell (CD3+CD14-, Lgate)


title: 24h-4


title: ZNFKO_D4_3


title: 24h-3


title: WT_LIF_3


title: 025_Tcell


title: genomic DNA from OSCC - T1

source_name: OSCC - T1


title: WT_D4_3


title: genomic DNA from OSCC - N1

source_name: OSCC - N1


title: genomic DNA from ESCC - T24

source_name: ESCC - T24


title: 026_Tcell


title: dmut_LIF_3


title: 24h-2

source_name: muscle


title: 24h-1


title: 023_Tcell


title: 20h-8


title: genomic DNA from ESCC - T22

source_name: ESCC - T22


title: 022_Tcell


title: 024_Tcell


title: genomic DNA from ESCC - T23

source_name: ESCC - T23


title: genomic DNA from ESCC - N21

source_name: ESCC - N21


title: genomic DNA from ESCC - T21

source_name: ESCC - T21


title: 20h-7


title: dmut_D4_3


title: 021_Monocyte

value: Monocyte (CD3-CD14+, Mgate)


title: 20h-6


title: 019_Monocyte


title: 20h-5


title: 20h-4


title: 020_Monocyte


title: 017_Monocyte


title: genomic DNA from ESCC - T20

source_name: ESCC - T20


title: 018_Monocyte


title: 016_Monocyte


title: 20h-1


title: 16h-8


title: genomic DNA from OSCC - T2

source_name: OSCC - T2


title: 20h-3


title: 16h-7


title: 015_Monocyte


title: genomic DNA from ESCC - T18

source_name: ESCC - T18


title: genomic DNA from ESCC - T16

source_name: ESCC - T16


title: genomic DNA from ESCC - T19

source_name: ESCC - T19


title: 16h-6


title: genomic DNA from ESCC - N18

source_name: ESCC - N18

value: adjacent non-tumor


title: 014_Monocyte

source_name: Cryopreserved PBMC


title: 16h-5


title: 012_Monocyte


title: 013_Monocyte


title: genomic DNA from ESCC - T15

source_name: ESCC - T15

value: tumor


title: genomic DNA from ESCC - N16

source_name: ESCC - N16


title: 011_Monocyte


title: 16h-4


title: 16h-3


title: 010_Monocyte


title: 16h-2


title: genomic DNA from ESCC - T17

source_name: ESCC - T17


title: genomic DNA from ESCC - N17

source_name: ESCC - N17


title: 16h-1


title: 009_Monocyte


title: 008_Monocyte


title: 12h-8


title: 007_Monocyte


title: 12h-7


title: genomic DNA from ESCC - T14

source_name: ESCC - T14


title: 006_Monocyte


title: 005_Monocyte


title: ZNFKO_D4_1

source_name: mouse embryonic stem cells


title: ZNFKO_D4_2


title: 12h-5

source_name: muscle


title: 12h-6


title: 004_Monocyte


title: ZNFKO_LIF_2


title: 12h-4


title: 003_Monocyte


title: ZNFWT_D4_2


title: ZNFKO_LIF_1


title: 002_Monocyte


title: genomic DNA from ESCC - T11

source_name: ESCC - T11


title: 12h-2


title: genomic DNA from ESCC - N11

source_name: ESCC - N11


title: ZNFWT_D4_1


title: genomic DNA from ESCC - N12

source_name: ESCC - N12


title: 12h-3


title: genomic DNA from ESCC - T10

source_name: ESCC - T10


title: ZNFWT_LIF_2


title: 001_Monocyte


title: 12h-1


title: genomic DNA from ESCC - T12

source_name: ESCC - T12


title: genomic DNA from ESCC - T9

source_name: ESCC - T9


title: genomic DNA from ESCC - N9

source_name: ESCC - N9


title: ZNFWT_LIF_1


title: genomic DNA from ESCC - T8

source_name: ESCC - T8


title: 8h-12


title: genomic DNA from ESCC - T7

source_name: ESCC - T7


title: 8h-7


title: dmut_D4_1


title: genomic DNA from ESCC - N10

source_name: ESCC - N10


title: 8h-6


title: genomic DNA from ESCC - T13

source_name: ESCC - T13


title: Cell suspension_NS3_CD90+CD39+

city: Shanghai

first: Xin

last: Huang

state: China

address: zhizaoju Road 639

institute: Ninth People's Hospital affiliated to Shanghai Jiao Tong University School of Medicine

description:
NS_003
Gene expression of CD90+CD39+ fibroblast sorted from cell suspension of NS3

hyb_protocol: 1 μg of each labeled cRNA was fragmented by adding 11 μl 10 × Blocking Agent and 2.2 μl of 25×Fragmentation Buffer, then heated at 60°C for 30 min, and finally 55 μl 2 × GE Hybridization buffer was added to dilute the labeled cRNA. 100 μl of hybridization solution was dispensed into the gasket slide and assembled to the gene expression microarray slide. The slides were incubated for 17 hours at 65°C in an Agilent Hybridization Oven

scan_protocol: The hybridized arrays were washed, fixed and scanned with using the Agilent DNA Microarray Scanner (part number G2505C).

data_processing: Agilent Feature Extraction software (version 11.0.1.1) was used to analyze acquired array images. Quantile normalization and subsequent data processing were performed with using the GeneSpring GX v12.1 software package (Agilent Technologies). After quantile normalization of the raw data, genes that at least 4 out of 8 samples have flags in Detected (“All Targets Value”) were chosen for further data analysis. Differentially expressed genes with statistical significance between the two groups were identified through Volcano Plot filtering. Differentially expressed genes between the two samples were identified through Fold Change filtering. Hierarchical Clustering was performed using the R scripts. GO analysis and Pathway analysis were performed in the standard enrichment computation method.

source_name: Cell suspension, NS3, CD90+CD39+ fibroblast

label_protocol: Sample labeling and array hybridization were performed according to the Agilent One-Color Microarray-Based Gene Expression Analysis protocol (Agilent Technology). Briefly, total RNA from each sample was linearly amplified and labeled with Cy3-UTP. The Labeled cRNAs were purified by RNeasy Mini Kit (Qiagen). The concentration and specific activity of the labeled cRNAs (pmol Cy3/μg cRNA) were measured by NanoDrop ND-1000.

extract_protocol: Sorted cells were collected in TRIzol™ Reagent (Invitrogen, Carlsbad, CA, USA) for RNA isolation. RNA quantity and quality were measured by NanoDrop ND-1000. RNA integrity was assessed by standard denaturing agarose gel electrophoresis

treatment_protocol: Three 10 cm × 10 cm samples of hypertrophic scar and three 5 cm × 5 cm samples of normal skin were cut into small pieces and put into Dispase II (Gibco, 17105041, 0.3% in DMEM) for 30min at 37°C to allow the separation of the epidermis. Scar were then minced and digested with a modified protocol, namely, 2.5 mg/mL Collagenase I (Gibco, 17100017), 1 mg/mL Collagenase II (Gibco, 17101015), 1 mg/mL Collagenase IV (Gibco, 17104019), 0.2 mg/mL Hyaluronidase (Sigma, H3884) and 0.1 mg/mL DNase I (Sigma, D4263) in DMEM + 2% P/S (Gibco, 15070-063) for 4h shaking in a 37°C waterbath. Acquired cell suspension was filtered, lysed with ACK Lysis Buffer, stained with FVS780- APC-CY7 and Human Fc block. Afterwards, cells were stained with anti-human antibodies for 10min at 4°C: Lineage Cocktail-Pacific Blue (BD, 562722, 1:100), CD45- APC-CY7 (BD, 557833, 1:100), E-Cadherin-BV421 (BD, 743712, 1:100), CD31-PE-CY7 (BD, 563651, 1:100), CD49f/ITGA6-PE (BD, 555736, 1:50), CD90-BV510 (BD, 563070, 1:20), and CD39-PE-CF594 (BD, 563678, 1:100). After negative selection (singlets, FVS780-, CD49f-, E-Cadherin-, Lin-, CD45-, and CD31-), CD90+CD39+ and CD90+CD39- Fb from hypertrophic scar tissue and CD90+CD39+ Fb from normal skin were sorted using BD FACS Aria II. Sorted cells were collected in TRIzol™ Reagent (Invitrogen, Carlsbad, CA, USA) for RNA isolation and subjected to Agilent Human 4x44K Gene Expression Microarrays v2 according to Agilent One-Color Microarray-Based Gene Expression Analysis protocol (Agilent Technology).

value: Normal skin

tag: subject id

tag: gender

value: female

tag: vancouver scar scale

value: non applicable

tag: cell markers


title: genomic DNA from ESCC - T6

source_name: ESCC - T6


title: dmut_D4_2


title: genomic DNA from ESCC - N7

source_name: ESCC - N7


title: Cell suspension_NS1_CD90+CD39+

description:
NS_001
Gene expression of CD90+CD39+ fibroblast sorted from cell suspension of NS1

source_name: Cell suspension, NS1, CD90+CD39+ fibroblast


title: 8h-5

value: Sprague-Dawley

value: skeletal muscle injury

value: muscle


title: Cell suspension_NS2_CD90+CD39+

description:
NS_002
Gene expression of CD90+CD39+ fibroblast sorted from cell suspension of NS2

source_name: Cell suspension, NS2, CD90+CD39+ fibroblast


title: 8h-4

source_name: muscle


title: genomic DNA from ESCC - N5

source_name: ESCC - N5


title: dmut_LIF_1

source_name: mouse embryonic stem cells


title: Primary breast tissue #23pre_#24pre Sample #23pre_#24pre Cy5

city: Baltimore

first: leslie

last: cope

address: 550 N. Broadway

institute: leslie cope

description:
Primary breast tissue #23pre_#24pre
tissue from Tiple negative breast cancer patient

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

scan_protocol: Agilent Technologies Scanner G2505C US22502585 Images were quantified using Agilent Feature Extraction Software (version A.8.5.1.1).

data_processing: R language and limma package was used for within (Loess) and between array (Aquantile) normalization. Intensity of single color channel was obtained afterwards.

label_protocol: 400ng RNA was used for labeling by SKCCC microarry core facility

extract_protocol: Total RNA extracted using Trizol and Qiagen RNeasy purification kit following manufacturer's instructions

value: breast


title: genomic DNA from ESCC - T5

source_name: ESCC - T5


title: genomic DNA from ESCC - N6

source_name: ESCC - N6


title: genomic DNA from ESCC - N8

source_name: ESCC - N8


title: WT_D4_2

value: mouse embryonic stem cells


title: Hoxa10 scKO rep9

city: Fukuoka

first: Yasuyuki

last: Ohkawa

address: 3-1-1 Maidashi

institute: Medical Institute of Bioregulation

data_processing:
The raw sequence reads were aligned to the rat reference genome (Rnor_6.0) using HISAT2.
Read counting was performed with HTSeq and UMI duplicates were removed.
Genome_build: Rnor_6.0
Supplementary_files_format_and_content: Text file for UMI counts

source_name: Satellite cell

growth_protocol: Satellite cells derived from tibialis anerior muscle were  cultured on matrigel-corted dish with growth medium.

extract_protocol:
RNA was harvested using IsogenII reagent.  The RNA was further purified with the Qiagen RNeasy Mini Kit (Qiagen) following the manufacturer's instructions.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: scKO group were treated with 4-hydroxy tamoxifen (1 µM) for 2 days.

tag: genotype

value: scKO (Pax7-CreERT2/+;Hoxa10f/f)


title: 8h-3


title: Hoxa10 scKO rep8


title: Hoxa10 scKO rep7


title: Primary breast tissue #23pre_#24pre Sample #23pre_#24pre Cy3


title: WT_D4_1

value: WT


title: genomic DNA from ESCC - N4

source_name: ESCC - N4


title: Primary breast tissue #20pre_#26pre Sample #20pre_#26pre Cy5

description:
Primary breast tissue #20pre_#26pre
tissue from Tiple negative breast cancer patient


title: genomic DNA from ESCC - T3

source_name: ESCC - T3


title: WT_LIF_2


title: Primary breast tissue #20pre_#26pre Sample #20pre_#26pre Cy3


title: 8h-1


title: WT_LIF_1


title: Hoxa10 scKO rep6


title: 8h-2


title: 4h-8


title: genomic DNA from ESCC - T4

source_name: ESCC - T4


title: Hoxa10 scKO rep5


title: Primary breast tissue #19pre_#21pre Sample #19pre_#21pre Cy5

description:
Primary breast tissue #19pre_#21pre
tissue from Tiple negative breast cancer patient


title: Satb2_WT_RA_d4_rep2

value: 4 days RA


title: 4h-6


title: Hoxa10 scKO rep4


title: Primary breast tissue #19pre_#21pre Sample #19pre_#21pre Cy3


title: 4h-5


title: Hoxa10 scKO rep3


title: Primary breast tissue #19post_#18pre Sample #19post_#18pre Cy5

description:
Primary breast tissue #19post_#18pre
tissue from Tiple negative breast cancer patient


title: Satb2_WT_RA_d4_rep1

value: Ty1 Invitrogen  MA5-23513


title: Satb2_WT_LIF_d0_rep2

value: LIF


title: genomic DNA from ESCC - T1

source_name: ESCC - T1


title: genomic DNA from ESCC - T2

source_name: ESCC - T2


title: 4h-4


title: dmut_LIF_2


title: Hoxa10 scKO rep2


title: 4h-3


title: genomic DNA from ESCC - N3

source_name: ESCC - N3


title: genomic DNA from ESCC - N2

source_name: ESCC - N2


title: control rep9

value: CON (Hoxa10f/f)


title: 4h-1


title: Satb2_dm_RA_d4_rep2


title: Satb2_WT_LIF_d0_rep1


title: genomic DNA from ESCC - N1

source_name: ESCC - N1


title: Satb2_dm_RA_d4_rep1


title: Primary breast tissue #19post_#18pre Sample #19post_#18pre Cy3


title: control rep8


title: Primary breast tissue #18post_#17post Sample #18post_#17post Cy5

description:
Primary breast tissue #18post_#17post
tissue from Tiple negative breast cancer patient


title: Hoxa10 scKO rep1


title: N-6

value: normal


title: N-7


title: control rep7


title: Primary breast tissue #22pre_#17pre Sample #22pre_#17pre Cy5

description:
Primary breast tissue #22pre_#17pre
tissue from Tiple negative breast cancer patient


title: Primary breast tissue #22pre_#17pre Sample #22pre_#17pre Cy3


title: control rep6


title: Satb2_dm_LIF_d0_rep1


title: control rep5


title: Primary breast tissue #18post_#17post Sample #18post_#17post Cy3


title: N-5


title: Primary breast tissue #16pre Sample #16pre Cy5

description:
Primary breast tissue #16pre
tissue from Tiple negative breast cancer patient


title: 4h-2


title: Satb1_WT_RA_d4_rep1

value: Satb1 Abcam 92307


title: Satb1_WT_RA_d4_rep2


title: Satb2_dm_LIF_d0_rep2


title: Primary breast tissue #16pre Sample #16pre Cy3


title: N-2


title: control rep3


title: N-4


title: Satb1_WT_LIF_d0_rep2


title: control rep4


title: control rep2


title: control rep1


title: TCR_1_4_engineered_T_cells_scRNA-seq

city: Munich

first: Thomas

middle: R

last: Müller

state: Bavaria

address: Trogerstr. 30

department: MIH

institute: TUM

description: scRNA seq

data_processing:
Cell Ranger (version 3.0.2; 10x Genomics) was used for demultiplexing and alignment using default parameters
Python software package SCANPY (version 1.4.3) was used for downstream analysis
cells filtered out that express < 200 genes, > 20% mitochondrial genes, > 4000 genes, >15000 counts ; genes filtered out that are expressed in less than 3 cells
Gene counts were per-cell normalized and (log+1)-transformed
Genome_build: GRCh38, modified with fluorescent protein sequences (BFP, CFP, GFP) and TCR constructs
Supplementary_files_format_and_content: matrix file containing filtered gene counts per cell
Supplementary_files_format_and_content: features file contains gene annotation
Supplementary_files_format_and_content: barcodes file contains 10x barcodes for the individual cell
Supplementary_files_format_and_content: The three above named files can be used as input for analysis in SCANPY

source_name: engineered PBMCs

growth_protocol: Human T cells were stimulated with CD3/CD28 expamer for two days. Upon that, TCRs were genetically introduced via retroviral transduction or CRISPR/Cas9-mediated orthotopic TCR replacement. Cells were sorted 5 days post editing.

extract_protocol:
Chromium next GEM Single Cell VDJ V1.1, Rev D; In order to amplify transgenic TCR sequences, the cDNA was amplified in two steps in parallel to the VDJ enrichment by using the 10x forward outer and inner primers as well as TCR- and/or editing method-specific reverse primers (see Supplementary Table 2). In target enrichment 1 and 2 (protocol step 4.1 and 4.3) the elongation time was increased to 90 seconds in adaptation to the longer transduction products. In addition, the second amplification of the KI constructs was performed for 15 cycles instead of 10 in order to compensate for lower integration frequencies. The double-sided size selection (Step 4.4 of the 10x protocol) was adjusted to 0.4X and 0.8X for the transduction constructs and was kept at 0.5X and 0.8X for the KI constructs.
Chromium™ Next GEM Single Cell 5' Library & Gel Bead Kit

treatment_protocol: FACS sorted CD8+TCR+fluorochrome+ cells (8000 cells per editing method for each TCR) were centrifuged and the supernatant was carefully removed. Cells were resuspended in the mastermix plus 37.8 µl of water before 70 µl of the cell suspension was transferred to the chip

tag: engineered tcr

value: TCR 1-4

tag: cell type

value: CD8 T cells


title: Satb1_dm_RA_d4_rep2

tag: satb2 mutational status

tag: culture conditions


title: Satb1_dm_RA_d4_rep1


title: TCR_6_2_engineered_T_cells_scRNA-seq

description: scRNA seq

value: TCR 6-2


title: Satb1_WT_LIF_d0_rep1


title: Satb1_dm_LIF_d0_rep1


title: N-1


title: Satb1_dm_LIF_d0_rep2


title: B5-6

city: Nanning

first: Zhenxing

last: Wang

state: Guangxi

address: Zhongshan Street

department: Center for Genomic and Personalized Medicine

institute: Guangxi Medicla University

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to human genome (hg38) using the CLC Biomedical Genomics Workbench 4 (QIAGEN Bioinformatics).
The read numbers mapped of each gene was counted and Reads Per Kilobase of exon model per Million mapped reads,(RPKM) of each gene was calculated based on the length of the gene and reads count mapped to this gene by using the CLC Biomedical Genomics Workbench 4 (QIAGEN Bioinformatics).
Genome_build: Genome_build: hg38
Supplementary_files_format_and_content: RPKM values for each Sample.

source_name: Bladder canncer

extract_protocol:
Total RNA was extracted using Trizol reagent according to the manufacturer’s instructions.
The construction of RNA-seq library was based on the protocol of the IlluminaTruSeq RNA Sample Preparation Kit (illumina)

tag: developmental stage

value: muscle invasive bladder cancer

tag: tumor stage

value: human bladder cancer tissue


title: B5-7

tag: tissue


title: LSD1_WT_RA_d4_rep2

value: Lsd1 Abcam 17721


title: B5-5


title: Primary breast tissue #16post_#15pre Sample #16post_#15pre Cy3

description:
Primary breast tissue #16post_#15pre
tissue from Tiple negative breast cancer patient


title: bile c

city: shanghai

first: wentao

last: shao

address: 150, jimo road

department: Shanghai East Hospital

institute: Tongji University School of Medicine

data_processing:
the Cell Ranger Single Cell Software Suite was used to perform sample de-multiplexing, alignment, filtering, and UMI counting (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger). Clustering and gene expression were visualized with 10X Genomics Loupe R Cell Browser v.2.0.0 (https://support.10xgenomics.com/single-cell-gene-expression/software/visualization/latest/what-is-loupe-cell-browser). The mean and variance of the mean and variance of gene expression density, cluster identities and filtered gene matrices generated by Cell Ranger were used as input into R toolkit Seurat (http://satijalab.org/seurat/)(52) for generating violin plots.
Genome_build: mm10
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every cell

source_name: gallbladder

extract_protocol:
When sacrifice, mouse was anesthetized using phenobarbital. Upon opening the abdomen, the gallbladder was exposed and cystic duct was ligated. The gallbladder was soon removed avoiding liver tissues at the gallbladder bed. After aspiration of the bile, the gallbladder was washed with D-hanks solution. Thereafter, the gallbladder was cut into pieces and put in 1.5ml Trypsin-EDTA (0.25%) solution (No.25200-056, Gibco®) and incubated at 37°C for 20 minutes and then centrifuged at 1500rpm for 5 minutes. After removing the supernatant, the pellet was suspended in Trypsin-EDTA solution and repeated the digestion process additionally for twice. The collected cell pellets were then suspended in Gibco® RPMI 1640 medium. The living singles cells were then picked by a mouth pipette and transferred to cold scRNA-seq lysis buffer.For the quality check and counting of single cell suspension, the cell survival rate was > 80%. The cells that had passed the test were washed and re-suspended to prepare a suitable cell concentration of ~1,000 cells/ul for 10x Genomics ChromiumTM. The loaded Single Cell 3’ Chip was placed on a 10X Genomics Chromium Controller Instrument (10X Genomics, Pleasanton, CA, USA) to generate single cell gel beads in emulsion (GEMs). GEMs were constructed for single cell separation according to the number of cells to be harvested. After GEMs were normally formed, GEMs were collected for reverse transcription in a PCR machine for labeling. The GEMs were oil-treated, and the amplified cDNA was purified by magnetic beads, and then subjected to cDNA amplification and quality inspection.
The 3ʹ Gene Expression Library was constructed with the quality-qualified cDNA. After fragmentation, adaptor ligation, sample index PCR, etc., the library is finally quantitatively examined. Single cell RNA-seq libraries were prepared using the Chromium Single Cell 3’ Library & Cell Bead Kit (Cat. No. 120237, 120236, 120262; 10X Genomics) according to the manufacturer’s protocol. The final library pool was sequenced on the Illumina instrument using 150-base-pair paired-end reads.

value: gallbladder

tag: age

value: 84-day age

value: harvested at day-28 after fed with lithogenic diet


title: Bile d

tag: strain

value: harvested at day-28 after fed with lithogenic diet and Tauro-ursodeoxycholic acid


title: LSD1_WT_RA_d4_rep1

value: mouse embryonic stem cells

value: WT

tag: zfp451 mutational status


title: B5-4


title: Sample 2_Reprogrammed cells

city: seoul

first: Jaeyeaon

last: Cho

address: Yonsei-ro 50

country: South Korea

institute: Yonsei University College of Medicine

data_processing:
Conversion of preliminary result to FASTQ files (Cell Ranger v3.1)
Alignment of FASTQ files to the mouse reference genome (mm10)
Data analysis and generation of a file containing a barcode table, a gene table and a gene expression matrix
Generation of Cloupe files with Cell Ranger
Analysis of Cloupe files using Loupe Browser
Genome_build: mm10
Supplementary_files_format_and_content: cloupe files

source_name: mouse tail-tip fibroblast

extract_protocol:
MTTFs with of without MAB treatment for 6 days were dissociated with Accutase (STEMCELL) and filtered to remove aggregated cells or oversized cells.
RNA libraries were constructed for sequencing using standard Illumina protocols  (10X Chromium Single Cell 3' Reagent Kits v3.1)

value: mouse tail

value: fibroblast

tag: mouse age

value: 3-month old

value: MAB (miR-208b, ascorbic acid and BMP4) for 6 days


title: Sample 1_MTTF

tag: treatment

value: untreated


title: Primary breast tissue #15post_#17post6month Sample #15post_#17post6month Cy3

description:
Primary breast tissue #15post_#17post6month
tissue from Tiple negative breast cancer patient

value: breast


title: Primary breast tissue #15post_#17post6month Sample #15post_#17post6month Cy5


title: Primary breast tissue #14 Sample 14 Cy5

description:
Primary breast tissue #14
pre and post treatment tissue from luminal breast cancer patient


title: Primary breast tissue #13 Sample 13 Cy5

description:
Primary breast tissue #13
pre and post treatment tissue from luminal breast cancer patient


title: Primary breast tissue #14 Sample 14 Cy3


title: BILE2 b

value: 70-day age

value: harvested at day-10 after fed with lithogenic diet


title: Primary breast tissue #12 Sample 12 Cy5

description:
Primary breast tissue #12
pre and post treatment tissue from luminal breast cancer patient


title: Primary breast tissue #16post_#15pre Sample #16post_#15pre Cy5


title: Primary breast tissue #12 Sample 12 Cy3


title: B5-2

value: muscle invasive bladder cancer


title: LSD1_WT_LIF_d0_rep1

source_name: mouse embryonic stem cells

value: LIF

tag: antibody


title: LSD1_WT_LIF_d0_rep2

value: Lsd1 Abcam 17721


title: BILE a

value: gallbladder

value: 56-day age

value: the basal condition under chow diet


title: LSD1_dm_RA_d4_rep2

value: 4 days RA


title: B4-5

value: human bladder cancer tissue


title: Primary breast tissue #11 Sample 11 Cy5

description:
Primary breast tissue #11
pre and post treatment tissue from luminal breast cancer patient


title: LSD1_dm_LIF_d0_rep1

value: mouse embryonic stem cells

value: WT


title: B5-1


title: LSD1_dm_RA_d4_rep1


title: B4-2


title: Primary breast tissue #13 Sample 13 Cy3


title: B4-3


title: Input_WT_RA_d4


title: Input_WT_LIF_d0


title: B4-1


title: SmoWT_GDC0449 rep2

first: Jialin

last: Mo

address: South Chongqing Road, Shanghai 200025. P.R. China

institute: Shanghai Jiao Tong University School of Medicine

data_processing:
Trim galore was used to automatically detect and trim adapters
Reads were mapped to mm10 reference genome using Hisat2
Read count was generated using HTSeq (version 0.11.1). Differentially expressed genes (DEGs) were calculated using DESeq2 (version 1.26.0).
FPKM (Fragments per Kilobase Million) was calculated from the number of reads that mapped to each particular gene sequence and the gene length and the sequencing depth were taken into account
Genome_build: mm10
Supplementary_files_format_and_content: Matrix table with raw gene counts and FPKM for every expressed gene and every sample

source_name: SHH-subtype medulloblastoma cells

growth_protocol: SmoWT cells were cultured as neurospheres in Neurobasal(-A) media containing 1×B27(-A) and 1×Antibiotic-Antimycotic.

extract_protocol:
Total RNA was extracted with TRIzol Reagent (Thermo Fisher Scientific, 15596-026) according to the manufacturers’ protocols.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: DMSO or GDC0449 (0.1 μM) treatment for 24 h

value: mouse SHH-subtype medulloblastoma cells


title: Primary breast tissue #11 Sample 11 Cy3


title: Primary breast tissue #10 Sample 10 Cy3

description:
Primary breast tissue #10
pre and post treatment tissue from luminal breast cancer patient


title: Input_dm_RA_d4


title: Primary breast tissue #10 Sample 10 Cy5


title: R4 tumor peripheral tissue

city: Uppsala

first: L.

last: He

address: Dag Hammarskjölds Väg 20

country: Sweden

institute: Uppsala University

description: tumor core

data_processing:
The raw sequence reads were analyzed by Cell Ranger v.3.0.1 with default parameters
Genome_build: GRCh38
Supplementary_files_format_and_content: tab-delimited text files with read counts for each sample

source_name: Brain

extract_protocol:
CD31+ selection for endothelial cell enrichment was performed using Dynabeads (11155D, Invitrogen).
scRNAseq libraries were prepared using Chromium Single Cell 30 V2/3 Reagent Kit (10X Genomics) according to the manufacturer’s protocol.

value: Brain

value: adult


title: SmoWT_GDC0449 rep1


title: Primary breast tissue #9 Sample 9 Cy5

description:
Primary breast tissue #9
pre and post treatment tissue from luminal breast cancer patient


title: Primary breast tissue #8 Sample 8 Cy5

description:
Primary breast tissue #8
pre and post treatment tissue from luminal breast cancer patient


title: B4-6


title: R4 tumor core

description: tumor core


title: Input_dm_LIF_d0


title: Primary breast tissue #9 Sample 9 Cy3


title: Primary breast tissue #7 Sample 7 Cy5

description:
Primary breast tissue #7
pre and post treatment tissue from luminal breast cancer patient


title: B4-4


title: LSD1_dm_LIF_d0_rep2


title: R3 tumor peripheral tissue

description: tumor core


title: SmoWT_DMSO rep1

value: DMSO


title: R3 tumor core

description: tumor core


title: Primary breast tissue #7 Sample 7 Cy3

value: breast


title: SmoWT-CBL0137 rep2

treatment_protocol: DMSO or CBL0137 (1μM) treatment for 24 h


title: H3K4me2_dm_RA_d6

value: 6 days RA

value: H3K4me2 Millipore 07-030


title: SmoWT-CBL0137 rep1


title: R2 tumor core

description: tumor core


title: Individual #11, EtOH

city: Kuopio

first: Andrea

last: Hanel

address: Yliopistonranta 1E, POB 1627

department: Institute of Biomedicine

country: Finland

institute: University of Eastern Finland

description: H5F7YBGX9_CC-SET1_3_18s005575-1-1_Nurminen_lane1SET3LIB5

data_processing:
Quality control using "afterQC"
Read alignment using "kallisto"
Differential gene expression using "DESeq2"
Genome_build: hg38
Supplementary_files_format_and_content: relative abundance and statistical metrics in Excel table

growth_protocol: RPMI 1640 medium supplemented with 10% charcoal-depleted fetal calf serum, 2 mM L-glutamine, 0.1 mg/ml streptomycin and 100 U/ml penicillin and were at 37 °C in a humidified 95% air/5% CO2 incubator.

extract_protocol:
extraction of total RNA using High Pure RNA Isolation kit (Roche)
rRNA-deplete cDNA library following NEB protocols

treatment_protocol: treatment for 24 h with either 10 nM 1,25(OH)2D3 (Sigma-Aldrich) or solvent (0.1% EtOH)

value: peripheral blood mononuclear cells

value: 0.1% ethanol for 24 h


title: Individual #12, EtOH

description: H5F7YBGX9_CC-SET1_3_18s005575-1-1_Nurminen_lane1SET3LIB9


title: SmoWT-DMSO rep2


title: Individual #09, EtOH

description: HL2JVBGX9_ccSet78_18s006344-1-1_Malinen_lane1SET8LIB5


title: Primary breast tissue #8 Sample 8 Cy3


title: R1 tumor peripheral tissue

description: tumor core


title: Individual #10, EtOH

description: HL2JVBGX9_ccSet78_18s006344-1-1_Malinen_lane1SET8LIB9


title: SmoWT-DMSO rep1


title: SmoWT_DMSO rep2


title: R1 tumor core

description: tumor core


title: Primary breast tissue #6 Sample 6 Cy3

description:
Primary breast tissue #6
pre and post treatment tissue from luminal breast cancer patient


title: Primary breast tissue #5 Sample 5 Cy5

description:
Primary breast tissue #5
pre and post treatment tissue from luminal breast cancer patient


title: H3K4me2_WT_RA_d6


title: Individual #08, EtOH

description: H5F7YBGX9_CC-SET1_3_18s005575-1-1_Nurminen_lane1SET3LIB1


title: Primary breast tissue #4 Sample 4 Cy5

description:
Primary breast tissue #4
pre and post treatment tissue from luminal breast cancer patient


title: Primary breast tissue #6 Sample 6 Cy5