title: sample_3341

description: medium: DMEM, atmosphere: room air, temperature: 37C, cAMP: 20 mM, time: 1440 min, librarydate: 2021-06-08, biol rep: 3


title: Blood-Granul, Z000000UD reanalysis

status: Public on Aug 02 2023

type: SRA

city: Jerusalem

first: Benjamin

middle: P

last: Berman

address: Ein Kerem campus

department: Developmental Biology and Cancer Research

country: Israel

institute: The Hebrew University

description:
Blood-Granul, Z000000UD
GSM5652312

library_source: genomic

data_processing:
BAM files were re-processed with the nf-core/methylseq pipeline using the biscuit aligner (https://github.com/ekushele/methylseq/blob/master/main_bams.nf ). The quality of fastQ files was assessed using FastQC (v0.11.9). TrimGalore (v0.6.4_dev) was used to trim adapters from all samples with the following parameters: ‘clip_r1 = 10 clip_r2 = 15 three_prime_clip_r1 = 10 three_prime_clip_r2 = 10’. We aligned the trimmed samples to the hg19 genome assembly, using the biscuit aligner (v0.3.15.20200318), with ‘-b 1’ for directional library. Duplicates were marked using samblaster (v0.1.24) with ‘--addMateTags’. Then, BAM files were sorted and indexed using Samtools (v1.9). The sorted and indexed BAMs were given as an input to ‘biscuit pileup’, to generate VCF files. We implemented a custom approach to filtering SNPs and generating Biscuit epiread files which contained a merged version of the two ends of each paired-end read. The code is available at https://github.com/ekushele/methylseq
Assembly: hg19
Supplementary files format and content: tab delimited file with the following columns: chromosome, start position, end position, read name, pair (1/2), strand,  CpG positions, methylation pattern, SNP positions, SNP patterns

molecule: genomic DNA

organism: Homo sapiens

source_name: Blood

extract_protocol:
refer to GSE186458
refer to GSE186458

tag: tissue

value: Blood


title: O1_WT_B11_2.5hpf

city: Freiburg

first: Daria

last: Onichtchouk

address: Hauptstrasse 1

country: Germany

institute: University of Freiburg

library_source: transcriptomic

data_processing:
Clean raw data were uploaded into Galaxy EU (https://galaxy.uni-freiburg.de) and passed fastQC quality check. Following analysis are all performed on Galaxy server.
Clean raw data were trimmed on 5' end for 5bp by Trim Galore! according to the sequencing quality.
Trimmed reads were mapped to GRCz11/danRer11 ensGene using RNA STAR.
Number of reads for each gene was counted in Featurecount using GRCz11/danRer11 ensGene reference genome.
All Featurecount reads from each sample were normalized in Deseq2. We used genotypes as factor level 1. The rest parameters are default.
Data has been run in 2 groups: first one with WT/MZsox19b/MZspg/MZnanog/MZsox19bnanog/MZsox19bspg (WT/MZsox19b/MZspg/MZsox19bspg data is from Series GSE137424), second group include WT/Mznanogspg/triple mutants.
Genome_build: GRCz11/danRer11
Supplementary_files_format_and_content: text files with normalized reads for each Sample

molecule: total RNA

organism: Danio rerio

source_name: whole zebrafish embryos

extract_protocol:
40-45 zebrafish embryos were collected, sorted and fixed in liquid nitrogen for each time point. Total RNA was isolated with QIAGEN RNeasy kit following the user’s manual.  RNA was eluted in ddH2O.
Eukaryotic Poly-A enriched library preparation

tag: Stage

tag: genotype

value: wild-type

tag: biological replicates number


title: L3_ClampNull_F06

city: Providence

first: Erica

last: Larschan

state: RI

address: Sidney Frank Hall 367, 185 Meeting Street

department: MCB

country: USA

institute: Brown University

data_processing:
FastQC was used for quality control.
Trimmed adaptor sequences (trimgalore and cutadapt).
Used Bowtie2 to align trimmed sequences to dm6 genome and sorted output bam files.
Ran salmon to quantify transcript expression based on Fly Base genes creating quant.sf files.
Preliminary run using SUPPA to create iso_tmp.txt files that can be used to calculate dPSI (delta percent spliced in) values.
Assembly: dm6
Supplementary files format and content: iso_tmp.txt (percent spliced in values for FlyBase gene IDs)

organism: Drosophila melanogaster

source_name: Third Instar Larva

growth_protocol: Drosophila melanogaster fly stocks were maintained at 24C on standard corn flour sucrose media.

extract_protocol:
Total RNA extracted using Trizol (Invitrogen) from 3 third instar larvae each.
Messenger RNA was purified from total RNA using poly-T oligo-attached magnetic beads. After fragmentation, the first strand cDNA was synthesized using random hexamer primers followed by the second strand cDNA synthesis. The library was ready after end repair, A-tailing, adapter ligation, size selection, amplification, and purification.

value: Third Instar Larva

tag: Sex

value: male

value: CLAMP mutant (yw;Clampnull)


title: L3_ClampNull_F05


title: sample_3046

city: St Louis

first: Michael

last: Brent

state: Missouri

address: 4515 McKinley Ave

institute: Washington University

description: medium: DMEM, atmosphere: room air, temperature: 37C, cAMP: 20 mM, time: 1440 min, librarydate: 2021-04-07, biol rep: 2

data_processing:
Reads were aligned with Novoalign (version 4.03.02) and quantified with HTSeq (0.9.1) using the FungiDB KN99 alpha genome sequence. Quality control ensued in two phases. In Phase I, custom scripts were used to verify the Crypto C. neoformans strain in each sample by calculating CDS coverage over putatively deleted genes and the corresponding selectable deletion cassette, ensuring that the former were absent and the latter present. Strains that passed this step were labeled as ‘passing’ if they contained at least 1e6 reads aligned to protein coding regions and less than 7% of all reads failed to align.
In Phase 2, we evaluated replicate agreement using the Regularized Log Expression (RLE). First, we used DESeq2 (version 1.34.0) to estimate the effect of the library date (the known batch effect). We removed the batch effect using the DESeq coefficients for the library dates such that the data was standardized to a single date, resulting in adjusted expression levels on a log2 normalized scale. To compute the RLE value for a given gene, the median expression level of that gene, across all samples in a replicate set, was subtracted from the expression level of that the gene in each sample. For each sample, we then calculated the interquartile range of the distribution of these RLE values across genes. If the interquartile range of RLEs of a given sample was greater than 1, indicating that more than half of genes deviated from their respective medians by a factor of 2 in adjusted count, the sample was considered an outlier and failed for replicate agreement.
Assembly: ASM221672v1
Supplementary files format and content: Tab separated (tsv) raw counts and DESeq2 sizeFactor normalized counts

organism: Cryptococcus neoformans

growth_protocol: Strains were removed from -80C to YPD agar no more than 5 days before the experiment, grown at 30C for 2 nights , and a single colony was inoculated into 4 mL YPD and grown overnight  at 30C shaking at 230 rpm. One day before the experiment, 1 mL of the ON culture was inoculated into 100 mL YPD and grown as above. At the beginning of the experiment, this culture was spun down, washed in 25 mL PBS, and resuspended in 10 mL PBS. 2 x 10^8 cells were then inoculated into each of four T75 flasks containing preconditioned medium  and incubated under the conditions specified for the experiment. A single flask was harvested for each time point (30, 90, 180, and 1440 min after inoculation), with 1.5 mL of culture removed for imaging and the remaining 18.5 mL used for RNA-Seq. The latter was transferred into a tube on ice containing 2 mL RNA Stop solution (5% tris-saturated phenol in ethanol), the cells were sedimented (3000g, 5 min, 4C), supernatant fraction decanted, and the pellet was frozen in liquid nitrogen and stored at -80C. All flasks were prepared and then preconditioned for 24 hours at the designated temperature and pH concentration before use. Cultures were then inoculated as above and the T75 flasks (MIDSCI TP90076) incubated without rotation. DMEM (Sigma D6429) RPMI (Sigma R8758) was used as purchased except in “buffer” conditions, where sterile 1M HEPES pH 7.0 was added to a final concentration of 25 mM

extract_protocol:
Frozen cell pellets were thawed on ice and 875m  TRIzol (Ambion 15-596-018) was added. Cells were then lysed with 750 ml 0.5mm silica-zirconia beads for 3 min in a Minibeadbeater (Biospec Products) and RNA isolated following the Trizol manufacturer’s protocol. Residual DNA was removed with the Turbo DNA-free Kit (Life Technologies AM1907) and polyA+ RNA isolated from ~1 mg of total RNA using the NEBNext Poly(A) mRNA Magnetic Isolation Module.
Libraries were constructed using the NEBNext Ultra Directional RNA Library Prep Kit from Illumina and samples were pooled at 10 nM. The pools were sequenced on a NextSeq 500 using the High75v2 kit as a 1x75 with 7bp Index1 and 6bp Index2 with 1% PhiX.  Fastq files were demultiplexed using the Illumina bcl2fastq2 allowing 1 bp mismatch.

tag: cell line

tag: cell type

value: yeast cell

value: WT

tag: medium

value: DMEM

tag: atmosphere

value: room air

tag: temperature

tag: treatment

value: cAMP 20 mM

tag: time


title: O3_WT_B11_3.5hpf


title: Blood-Mono+Macro, Z0000044D reanalysis

description:
Blood-Mono+Macro, Z0000044D
GSM5652309

source_name: Lung interstitial

value: Lung interstitial


title: Blood-Mono+Macro, Z00000447 reanalysis

description:
Blood-Mono+Macro, Z00000447
GSM5652308


title: B7_triple_B10_6hpf


title: L3_ClampNull_F04


title: sample_411

description: medium: DMEM, atmosphere: room air, temperature: 37C, cAMP: 20 mM, time: 1440 min, librarydate: 2019-11-10, biol rep: 1


title: Blood-Mono+Macro, Z0000044C reanalysis

description:
Blood-Mono+Macro, Z0000044C
GSM5652307

source_name: Lung alveolar

value: Lung alveolar


title: B6_triple_B10_5.5hpf


title: L3_ClampNull_M06


title: Blood-Mono+Macro, Z00000448 reanalysis

description:
Blood-Mono+Macro, Z00000448
GSM5652306


title: sample_3303

description: medium: DMEM, atmosphere: room air, temperature: 30C, cAMP: none, time: 90 min, librarydate: 2021-06-04, biol rep: 5

value: cAMP none

value: 90 min


title: O8_WT_B11_6hpf


title: L3_ClampNull_M05


title: sample_3215

description: medium: DMEM, atmosphere: room air, temperature: 30C, cAMP: none, time: 90 min, librarydate: 2021-05-13, biol rep: 4


title: B5_triple_B10_5hpf


title: L3_ClampNull_M04


title: B4_triple_B10_4.5hpf


title: Blood-Mono+Macro, Z0000043P reanalysis

description:
Blood-Mono+Macro, Z0000043P
GSM5652305

source_name: Liver

value: Liver


title: L3_Control_F03

value: female

value: control (yw)


title: Blood-Mono+Macro, Z00000446 reanalysis

description:
Blood-Mono+Macro, Z00000446
GSM5652304

source_name: Colon

value: Colon


title: Blood-Mono+Macro, Z00000444 reanalysis

description:
Blood-Mono+Macro, Z00000444
GSM5652303


title: sample_1900

description: medium: DMEM, atmosphere: room air, temperature: 30C, cAMP: none, time: 90 min, librarydate: 2020-09-28, biol rep: 3


title: B3_triple_B10_4hpf


title: sample_1397

description: medium: DMEM, atmosphere: room air, temperature: 30C, cAMP: none, time: 90 min, librarydate: 2020-10-17, biol rep: 2


title: sample_458

description: medium: DMEM, atmosphere: room air, temperature: 30C, cAMP: none, time: 90 min, librarydate: 2020-10-15, biol rep: 1


title: Blood-Mono+Macro, Z000000UH reanalysis

description:
Blood-Mono+Macro, Z000000UH
GSM5652302

value: Blood


title: L3_Control_F02

value: Third Instar Larva


title: L3_Control_F01


title: B1_triple_B10_3hpf


title: Blood-Mono+Macro, Z000000U3 reanalysis

description:
Blood-Mono+Macro, Z000000U3
GSM5652301


title: Blood-Mono+Macro, Z000000TP reanalysis

description:
Blood-Mono+Macro, Z000000TP
GSM5652300


title: sample_3209

description: medium: DMEM, atmosphere: room air, temperature: 30C, cAMP: none, time: 30 min, librarydate: 2021-05-13, biol rep: 5

value: 30 min


title: L3_Control_M02


title: A6_WT_B10_5.5hpf

value: wild-type


title: sample_1888

description: medium: DMEM, atmosphere: room air, temperature: 30C, cAMP: none, time: 30 min, librarydate: 2020-09-28, biol rep: 4

value: yeast cell


title: Blood-NK, Z000000UF reanalysis

description:
Blood-NK, Z000000UF
GSM5652299


title: L3_Control_M01


title: sample_1637

description: medium: DMEM, atmosphere: room air, temperature: 30C, cAMP: none, time: 30 min, librarydate: 2020-09-21, biol rep: 3

value: WT


title: S2_GFP_3

source_name: Embryonic

growth_protocol: Kc and S2 cells were maintained at 25C in Schneider's media supplemented with 10% Fetal Bovine Serum and 1.4X Antibiotic-Antimycotic. Cells were passaged every 3 days to maintain an appropriate cell density.

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen). 2 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using Illumina TruSeq V2 mRNA-Seq Library Prep Kit following manufacturer's protocols.

treatment_protocol: 15ug of CLAMP dsRNA used for CLAMP RNAi per T25 flask. Cells incubated with dsRNA in FBS minus media for 45 minutes and allowed to grow in media supplemented with 10% FBS for 6 days before harvesting.

value: Embryonic

value: male

value: GFP RNAi


title: Blood-NK, Z000000U1 reanalysis

description:
Blood-NK, Z000000U1
GSM5652298


title: Blood-NK, Z000000TM reanalysis

description:
Blood-NK, Z000000TM
GSM5652297


title: A4_WT_B10_4.5hpf


title: sample_1385

description: medium: DMEM, atmosphere: room air, temperature: 30C, cAMP: none, time: 30 min, librarydate: 2020-10-17, biol rep: 2

value: DMEM

value: room air


title: A5_WT_B10_5hpf


title: B2_triple_B10_3.5hpf


title: S2_GFP_2


title: sample_3297

description: medium: DMEM, atmosphere: room air, temperature: 30C, cAMP: none, time: 30 min, librarydate: 2021-06-04, biol rep: 6

value: cAMP none


title: A3_WT_B10_4hpf


title: A2_WT_B10_3.5hpf


title: sample_446

description: medium: DMEM, atmosphere: room air, temperature: 30C, cAMP: none, time: 30 min, librarydate: 2020-10-15, biol rep: 1


title: sample_3309

description: medium: DMEM, atmosphere: room air, temperature: 30C, cAMP: none, time: 180 min, librarydate: 2021-06-04, biol rep: 5

value: 180 min


title: Blood-T, Z0000041B reanalysis

description:
Blood-T, Z0000041B
GSM5652295


title: sample_3221

description: medium: DMEM, atmosphere: room air, temperature: 30C, cAMP: none, time: 180 min, librarydate: 2021-05-13, biol rep: 4


title: Blood-T, Z0000041H reanalysis

description:
Blood-T, Z0000041H
GSM5652296


title: S2_CLAMP_3

value: CLAMP RNAi


title: A1_WT_B10_3hpf


title: S2_GFP_1


title: L3_Control_M03

value: female


title: A7_WT_B10_6hpf


title: S2_CLAMP_2


title: sample_1912

description: medium: DMEM, atmosphere: room air, temperature: 30C, cAMP: none, time: 180 min, librarydate: 2020-09-28, biol rep: 3


title: ACC100  (Agilent)

type: genomic

city: Gothenburg

first: Mattias

last: Andersson

address: Medicinaregatan 1F

department: Sahlgrenska Cancer Center

country: Sweden

institute: University of Gothenburg

hyb_protocol: Oligoarray control targets (Cot-1 DNA and Blocking agent) and hybridization buffer (Agilent oligo aCGH/ChIP-on-Chip Hybridization Kit) were added, the samples were denatured and applied to microarrays (Agilent SurePrint G3 Human CGH Microarray 4X180K and Human Genome CGH Microarray 244K) as recommended by the manufacturer. The arrays were enclosed in a rotating hybridization oven at 65°C for 40 h. After hybridization, the slides were sequentially washed and dried.

scan_protocol: The arrays were scanned on an Agilent Microarray Confocal Scanner (G2506B) and the images were quantified with Agilent Feature Extraction Software (v.12.0.1.1) using the intensity-dependent linear normalization method.

data_processing:
Data analysis was carried out using Nexus Copy Number software v.8.1 (BioDiscovery Inc., El Segundo, CA, USA), which uses the FASST2 segmentation algorithm to define non-random regions of CNAs across the genome. Sex chromosomes were excluded from the analysis. The significance threshold for segmentation was set to P=1.0E-8 for FFPE and P=10E-6 for FF and the Log2 ratio thresholds for gain/loss were set to 0.25/−0.2 for FF and 0.3/-0.3 for FFPE; the thresholds for high copy number gain/amplification and homozygous deletion were 1.0 and −1.0, respectively.
*TMA.txt processed data files report normalized log10 ratio (Cy5/Cy3) representing tumor DNA/normal DNA

source_name: adenoid cystic carcinoma

label_protocol: Genomic tumor DNA and sex-matched reference normal DNA (pooled peripheral blood cells from 5 normal female and male genomes) were labeled with Cy5-dUTP and Cy3-dUTP (Agilent).

extract_protocol: Genomic DNA was isolated from FF and FFPE tumor specimens using the Qiagen DNeasy Blood & Tissue Kit and QIAamp DNA FFPE Tissue Kit respectively (Qiagen GmbH, Hilden, Germany).

treatment_protocol: Fresh frozen (FF) tumor material from 58 ACCs and formalin-fixed paraffin-embedded (FFPE) tumor material from 42 ACCs were obtained  from Sahlgrenska university hospital, Gothenburg university, Sweden; MD Anderson Cancer Center, University of Texas, US; the University of Virginia Hospital, Virginia, US; Hamburg University Medical Centre, Hamburg, Deutschland, the Portuguese Institute of Oncology, Lisboa, Portugal; and Icahn School of Medicine at Mount Sinai, New York, US. Tumors were classified according to the WHO histological classification of salivary gland tumors and graded as tumors with no solid component (grade 1), <30% solid component (grade 2), and ≥30% solid component (grade 3).

value: adenoid cystic carcinoma

tag: obtained from

value: University of Virginia Health System

tag: tumor grade

tag: age

tag: gender

tag: tumor material

value: FF

source_name: normal tissue

value: normal tissue


title: Blood-T, Z0000041G reanalysis

description:
Blood-T, Z0000041G
GSM5652293

tag: tissue

value: Blood


title: sample_1661

description: medium: DMEM, atmosphere: room air, temperature: 30C, cAMP: none, time: 180 min, librarydate: 2020-09-21, biol rep: 2


title: S2_CLAMP_1


title: ACC99  (Agilent)


title: Blood-T, Z0000041A reanalysis

description:
Blood-T, Z0000041A
GSM5652292


title: sample_470

description: medium: DMEM, atmosphere: room air, temperature: 30C, cAMP: none, time: 180 min, librarydate: 2020-10-15, biol rep: 1


title: KC_GFP_2

value: KC


title: Blood-T, Z0000041M reanalysis

description:
Blood-T, Z0000041M
GSM5652291


title: KC_GFP_1


title: Blood-T, Z0000041C reanalysis

description:
Blood-T, Z0000041C
GSM5652290


title: KC_GFP_3


title: Blood-T, Z00000416 reanalysis

description:
Blood-T, Z00000416
GSM5652289


title: sample_3712

description: medium: DMEM, atmosphere: room air, temperature: 30C, cAMP: none, time: 1440 min, librarydate: 2021-09-15, biol rep: 4

value: yeast cell


title: KC_CLAMP_2


title: Blood-T, Z0000041Q reanalysis

description:
Blood-T, Z0000041Q
GSM5652288


title: sample_3443

description: medium: DMEM, atmosphere: room air, temperature: 30C, cAMP: none, time: 1440 min, librarydate: 2021-07-06, biol rep: 3

value: WT


title: Blood-T, Z0000041F reanalysis

description:
Blood-T, Z0000041F
GSM5652287


title: Blood-T, Z0000041E reanalysis

description:
Blood-T, Z0000041E
GSM5652294


title: sample_3315

description: medium: DMEM, atmosphere: room air, temperature: 30C, cAMP: none, time: 1440 min, librarydate: 2021-06-04, biol rep: 2


title: ACC96  (Agilent)


title: ACC94  (Agilent)


title: sample_3227

description: medium: DMEM, atmosphere: room air, temperature: 30C, cAMP: none, time: 1440 min, librarydate: 2021-05-13, biol rep: 1


title: ACC95  (Agilent)


title: ACC97  (Agilent)


title: ACC93  (Agilent)


title: sample_2247

description: medium: DMEM, atmosphere: room air, temperature: 30C, cAMP: none, HEPES buffer pH 7.0 25 mM, time: 90 min, librarydate: 2020-01-06, biol rep: 3

value: cAMP none; HEPES buffer pH 7.0 25 mM

value: 90 min


title: KC_CLAMP_1

value: Embryonic


title: Blood-T, Z00000419 reanalysis

description:
Blood-T, Z00000419
GSM5652286


title: ACC92  (Agilent)


title: sample_871

description: medium: DMEM, atmosphere: room air, temperature: 30C, cAMP: none, HEPES buffer pH 7.0 25 mM, time: 90 min, librarydate: 2019-12-19, biol rep: 2

value: DMEM


title: Blood-T, Z0000041N reanalysis

description:
Blood-T, Z0000041N
GSM5652285


title: ACC98  (Agilent)

value: male


title: sample_103

description: medium: DMEM, atmosphere: room air, temperature: 30C, cAMP: none, HEPES buffer pH 7.0 25 mM, time: 90 min, librarydate: 2020-01-10, biol rep: 1

value: room air


title: Blood-T, Z0000041D reanalysis

description:
Blood-T, Z0000041D
GSM5652284


title: KC_CLAMP_3


title: ACC90  (Agilent)


title: sample_2364

description: medium: DMEM, atmosphere: room air, temperature: 30C, cAMP: none, HEPES buffer pH 7.0 25 mM, time: 30 min, librarydate: 2020-01-16, biol rep: 4

value: 30 min


title: ACC91  (Agilent)


title: Blood-T, Z00000417 reanalysis

description:
Blood-T, Z00000417
GSM5652283


title: Blood-T, Z000000UK reanalysis

description:
Blood-T, Z000000UK
GSM5652282


title: ACC89  (Agilent)


title: sample_2241

description: medium: DMEM, atmosphere: room air, temperature: 30C, cAMP: none, HEPES buffer pH 7.0 25 mM, time: 30 min, librarydate: 2020-01-06, biol rep: 3


title: Blood-T, Z000000TR reanalysis

description:
Blood-T, Z000000TR
GSM5652280


title: Blood-T, Z000000U5 reanalysis

description:
Blood-T, Z000000U5
GSM5652281


title: ACC87  (Agilent)


title: sample_97

description: medium: DMEM, atmosphere: room air, temperature: 30C, cAMP: none, HEPES buffer pH 7.0 25 mM, time: 30 min, librarydate: 2020-01-10, biol rep: 1


title: ACC86  (Agilent)


title: Blood-T, Z000000UM reanalysis

description:
Blood-T, Z000000UM
GSM5652279


title: sample_2253

description: medium: DMEM, atmosphere: room air, temperature: 30C, cAMP: none, HEPES buffer pH 7.0 25 mM, time: 180 min, librarydate: 2020-01-06, biol rep: 3

value: 180 min


title: Blood-T, Z000000U7 reanalysis

description:
Blood-T, Z000000U7
GSM5652278


title: sample_865

description: medium: DMEM, atmosphere: room air, temperature: 30C, cAMP: none, HEPES buffer pH 7.0 25 mM, time: 30 min, librarydate: 2019-12-19, biol rep: 2


title: sample_877

description: medium: DMEM, atmosphere: room air, temperature: 30C, cAMP: none, HEPES buffer pH 7.0 25 mM, time: 180 min, librarydate: 2019-12-19, biol rep: 2


title: Blood-T, Z000000TT reanalysis

description:
Blood-T, Z000000TT
GSM5652277


title: female ovx_high fat diet_1

type: RNA

city: Seoul

first: Mi-Kyung

last: Sung

address: Cheongpa-ro 47 gil

country: South Korea

institute: Sookmyung Women's University

description:
gene expression of mouse colon tissue
F4

hyb_protocol: 600ng of each labeled cRNA was fragmented by adding 5 μl 10 x blocking agent and 1 μl of 25 x fragmentation buffer, and then heated at 60°C for 30 min. Finally 25 μl 2 x GE hybridization buffer was added to dilute the labeled cRNA. 40μl of hybridization solution was dispensed into the gasket slide and assembled to the Agilent SurePrint G3 Mouse GE 8X60K, V2 Microarrays (Agilent®). The slides were incubated for 17 h at 65°C in an Agilent hybridization oven. then washed at room temperature by using the Agilent One-Color Microarray-Based Gene Expression Analysis protocol (Agilent Technology, V 6.5, 2010).

scan_protocol: The hybridized array was immediately scanned with an Agilent Microarray Scanner D (Agilent Technologies, Inc.)

data_processing: Raw data were extracted using the Agilent Feature Extraction Software (v11.0.1.1) and were summarized for the same gene automatically using the Agilent feature extraction protocol to generate a raw data text file, providing expression data for each gene probed on the array. Array probes with Flag A in samples were filtered out. The selected gProcessedSignal value was logarithmically transformed and normalized using the quantile method. Statistical significance of the expression data was determined using fold change and independent t-test, in which the null hypothesis was that no difference existed among groups. Fold change ≥ 1.5 and p-value < 0.05 were regarded as the cut-off criteria to determine DEGs.

molecule: polyA RNA

organism: Mus musculus

source_name: mouse colon tissue

label_protocol: RNA labeling and hybridization were performed by using the Agilent One-Color Microarray-Based Gene Expression Analysis protocol (Agilent Technology, V 6.5, 2010). Briefly, 100ng of total RNA from each sample was linearly amplified and labeled with Cy3-dCTP. The labeled cRNAs were purified by RNAeasy Mini Kit (Qiagen). The concentration and specific activity of the labeled cRNAs (pmol Cy3/μg cRNA) were measured by NanoDrop ND-1000(NanoDrop, Wilmington, USA).

extract_protocol: Total RNA was extracted from colon tissues using TRIzol reagent (Thermo Fisher Scientific, Waltham, MA, USA). RNA purity was assessed from the ratio of absorbances at 260 and 280 nm using a ND-2000 NanoDrop (Thermo Fisher Scientific, USA), with values between 1.7–2 considered acceptable. Total RNA integrity was checked using an Agilent Technologies 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA), with an RNA Integrity Number value ≥ 7.

value: colon

value: female

value: ovariectomized

tag: diet

value: high fat diet


title: female ovx_low fat diet_4

description:
gene expression of mouse colon tissue
E10

value: low fat diet


title: female ovx_high fat diet_2

description:
gene expression of mouse colon tissue
F5


title: female ovx_high fat diet_4

description:
gene expression of mouse colon tissue
F10


title: female ovx_low fat diet_3

description:
gene expression of mouse colon tissue
E8


title: Blood-T, Z000000UP reanalysis

description:
Blood-T, Z000000UP
GSM5652276

value: Blood


title: female ovx_high fat diet_3

description:
gene expression of mouse colon tissue
F7


title: female ovx_low fat diet_2

description:
gene expression of mouse colon tissue
E5


title: ACC85  (Agilent)

value: adenoid cystic carcinoma

value: University of Virginia Health System

value: FF

value: normal tissue


title: Blood-T, Z000000TV reanalysis

description:
Blood-T, Z000000TV
GSM5652275


title: female ovx_low fat diet_1

description:
gene expression of mouse colon tissue
E3


title: female_high fat diet_4

description:
gene expression of mouse colon tissue
D9


title: sample_3435

description: medium: DMEM, atmosphere: room air, temperature: 30C, cAMP: none, HEPES buffer pH 7.0 25 mM, time: 1440 min, librarydate: 2021-07-06, biol rep: 3

value: yeast cell

tag: genotype

value: WT

value: cAMP none; HEPES buffer pH 7.0 25 mM


title: ACC83  (Agilent)

value: male


title: sample_3731

description: medium: DMEM, atmosphere: room air, temperature: 30C, cAMP: none, HEPES buffer pH 7.0 25 mM, time: 1440 min, librarydate: 2021-09-15, biol rep: 4

value: DMEM

value: room air


title: ACC82  (Agilent)


title: female_high fat diet_3

description:
gene expression of mouse colon tissue
D7


title: ACC80  (Agilent)


title: ACC84  (Agilent)


title: sample_3633

description: medium: DMEM, atmosphere: room air, temperature: 30C, cAMP: none, HEPES buffer pH 7.0 25 mM, time: 180 min, librarydate: 2021-09-08, biol rep: 4

value: 180 min


title: female_low fat diet_4

description:
gene expression of mouse colon tissue
C10

value: colon


title: sample_2259

description: medium: DMEM, atmosphere: room air, temperature: 30C, cAMP: none, HEPES buffer pH 7.0 25 mM, time: 1440 min, librarydate: 2020-01-06, biol rep: 2


title: Eryth-prog, Z000000RH reanalysis

description:
Eryth-prog, Z000000RH
GSM5652273

source_name: Bone marrow

value: Bone marrow


title: sample_883

description: medium: DMEM, atmosphere: room air, temperature: 30C, cAMP: none, HEPES buffer pH 7.0 25 mM, time: 1440 min, librarydate: 2019-12-19, biol rep: 1


title: Eryth-prog, Z000000RF reanalysis

description:
Eryth-prog, Z000000RF
GSM5652272


title: Ovary+Endom-Ep, Z0000043S reanalysis

description:
Ovary+Endom-Ep, Z0000043S
GSM5652271

source_name: Endometrium

value: Endometrium


title: ACC79  (Agilent)


title: sample_3328

description: medium: DMEM, atmosphere: room air, temperature: 30C, cAMP: 20 mM, time: 90 min, librarydate: 2021-06-08, biol rep: 7

value: cAMP 20 mM

value: 90 min


title: sample_109

description: medium: DMEM, atmosphere: room air, temperature: 30C, cAMP: none, HEPES buffer pH 7.0 25 mM, time: 180 min, librarydate: 2020-01-10, biol rep: 1


title: ACC81  (Agilent)


title: ACC77  (Agilent)

value: Sahlgrenska University Hospital


title: Ovary+Endom-Ep, Z00000434 reanalysis

description:
Ovary+Endom-Ep, Z00000434
GSM5652269


title: ACC76  (Agilent)

value: adenoid cystic carcinoma

value: female


title: sample_3033

description: medium: DMEM, atmosphere: room air, temperature: 30C, cAMP: 20 mM, time: 90 min, librarydate: 2021-04-07, biol rep: 6


title: sample_2605

description: medium: DMEM, atmosphere: room air, temperature: 30C, cAMP: 20 mM, time: 90 min, librarydate: 2020-12-22, biol rep: 5


title: ACC88  (Agilent)

value: University of Virginia Health System

value: FF


title: ACC75  (Agilent)

value: normal tissue


title: sample_1208

description: medium: DMEM, atmosphere: room air, temperature: 30C, cAMP: 20 mM, time: 90 min, librarydate: 2019-07-02, biol rep: 4

value: yeast cell

value: WT


title: Ovary+Endom-Ep, Z000000QT reanalysis

description:
Ovary+Endom-Ep, Z000000QT
GSM5652268

source_name: Ovary

value: Ovary


title: Eryth-prog, Z000000RK reanalysis

description:
Eryth-prog, Z000000RK
GSM5652274


title: Fallopian-Ep, Z000000UV reanalysis

description:
Fallopian-Ep, Z000000UV
GSM5652267

source_name: Fallopien tubes

value: Fallopien tubes


title: ACC74  (Agilent)

value: male


title: sample_1158

description: medium: DMEM, atmosphere: room air, temperature: 30C, cAMP: 20 mM, time: 90 min, librarydate: 2019-07-22, biol rep: 3

value: DMEM

value: room air


title: Ovary+Endom-Ep, Z00000435 reanalysis

description:
Ovary+Endom-Ep, Z00000435
GSM5652270


title: ACC73  (Agilent)


title: sample_424

description: medium: DMEM, atmosphere: room air, temperature: 30C, cAMP: 20 mM, time: 90 min, librarydate: 2019-08-09, biol rep: 2


title: Fallopian-Ep, Z000000S9 reanalysis

description:
Fallopian-Ep, Z000000S9
GSM5652266


title: female_high fat diet_1

description:
gene expression of mouse colon tissue
D4

value: colon

value: high fat diet


title: female_high fat diet_2

description:
gene expression of mouse colon tissue
D6


title: female_low fat diet_3

description:
gene expression of mouse colon tissue
C9

value: low fat diet


title: female_low fat diet_2

description:
gene expression of mouse colon tissue
C8


title: female_low fat diet_1

description:
gene expression of mouse colon tissue
C7


title: ACC72  (Agilent)


title: sample_396

description: medium: DMEM, atmosphere: room air, temperature: 30C, cAMP: 20 mM, time: 90 min, librarydate: 2019-06-20, biol rep: 1

value: cAMP 20 mM

value: 90 min


title: Fallopian-Ep, Z000000Q7 reanalysis

description:
Fallopian-Ep, Z000000Q7
GSM5652265


title: sample_3322

description: medium: DMEM, atmosphere: room air, temperature: 30C, cAMP: 20 mM, time: 30 min, librarydate: 2021-06-08, biol rep: 6

value: 30 min


title: male_high fat diet_3

description:
gene expression of mouse colon tissue
B11


title: male_high fat diet_2

description:
gene expression of mouse colon tissue
B10


title: Thyroid-Ep, Z0000042T reanalysis

description:
Thyroid-Ep, Z0000042T
GSM5652263

source_name: Thyroid

value: Thyroid


title: ACC70  (Agilent)

value: adenoid cystic carcinoma

value: Sahlgrenska University Hospital


title: male_high fat diet_1

description:
gene expression of mouse colon tissue
B3


title: male_high fat diet_4

description:
gene expression of mouse colon tissue
B12


title: male_low fat diet_4

description:
gene expression of mouse colon tissue
A8


title: sample_3027

description: medium: DMEM, atmosphere: room air, temperature: 30C, cAMP: 20 mM, time: 30 min, librarydate: 2021-04-07, biol rep: 5


title: ACC78  (Agilent)

value: University of Virginia Health System

value: female

value: FF

value: normal tissue


title: male_low fat diet_3

description:
gene expression of mouse colon tissue
A5


title: ACC69  (Agilent)


title: male_low fat diet_2

description:
gene expression of mouse colon tissue
A6


title: Thyroid-Ep, Z0000042S reanalysis

description:
Thyroid-Ep, Z0000042S
GSM5652262


title: male_low fat diet_1

description:
gene expression of mouse colon tissue
A4


title: sample_1152

description: medium: DMEM, atmosphere: room air, temperature: 30C, cAMP: 20 mM, time: 30 min, librarydate: 2019-07-22, biol rep: 3

value: yeast cell

value: WT


title: S9

city: Ithica

first: Praveen

last: Sethupathy

state: NY

address: Cornell University College of Veterinary Medicine, Box 17

institute: Cornell University

data_processing:
Reads aligned with STAR
Quantified by Salmon
Assembly: Sscrofa.11.1
Supplementary files format and content: Normalized counts from DESeq2 in a csv

organism: Sus scrofa

source_name: liver

extract_protocol:
Qiagen RNeasy
Illumina TruSeq Stranded mRNA kit

value: liver


title: ACC68  (Agilent)


title: ACC71  (Agilent)


title: S8


title: Kidney-Ep, Z00000442 reanalysis

description:
Kidney-Ep, Z00000442
GSM5652261

source_name: Kidney glomerular

value: Kidney glomerular


title: Thyroid-Ep, Z0000042U reanalysis

description:
Thyroid-Ep, Z0000042U
GSM5652264


title: ACC67  (Agilent)

value: male


title: sample_390

description: medium: DMEM, atmosphere: room air, temperature: 30C, cAMP: 20 mM, time: 30 min, librarydate: 2019-06-20, biol rep: 1

value: DMEM

value: room air


title: sample_418

description: medium: DMEM, atmosphere: room air, temperature: 30C, cAMP: 20 mM, time: 30 min, librarydate: 2019-08-09, biol rep: 2

value: cAMP 20 mM


title: ACC66  (Agilent)


title: Kidney-Ep, Z00000441 reanalysis

description:
Kidney-Ep, Z00000441
GSM5652260


title: Kidney-Ep, Z0000042W reanalysis

description:
Kidney-Ep, Z0000042W
GSM5652259


title: S7

source_name: gallbladder

value: gallbladder

value: pBTSCs


title: sample_3334

description: medium: DMEM, atmosphere: room air, temperature: 30C, cAMP: 20 mM, time: 180 min, librarydate: 2021-06-08, biol rep: 7

value: 180 min


title: S5


title: S4


title: ACC64  (Agilent)

value: adenoid cystic carcinoma


title: sample_3039

description: medium: DMEM, atmosphere: room air, temperature: 30C, cAMP: 20 mM, time: 180 min, librarydate: 2021-04-07, biol rep: 6


title: sample_1202

description: medium: DMEM, atmosphere: room air, temperature: 30C, cAMP: 20 mM, time: 30 min, librarydate: 2019-07-02, biol rep: 4

value: 30 min


title: Kidney-Ep, Z0000043Z reanalysis

description:
Kidney-Ep, Z0000043Z
GSM5652257

source_name: Kidney tubular

value: Kidney tubular


title: S3


title: sample_2611

description: medium: DMEM, atmosphere: room air, temperature: 30C, cAMP: 20 mM, time: 180 min, librarydate: 2020-12-22, biol rep: 5


title: ACC63  (Agilent)

value: Sahlgrenska University Hospital

value: female


title: Kidney-Ep, Z00000440 reanalysis

description:
Kidney-Ep, Z00000440
GSM5652258


title: Kidney-Ep, Z000000QH reanalysis

description:
Kidney-Ep, Z000000QH
GSM5652256


title: ACC62  (Agilent)

value: FF

value: normal tissue


title: sample_1215

description: medium: DMEM, atmosphere: room air, temperature: 30C, cAMP: 20 mM, time: 180 min, librarydate: 2019-07-02, biol rep: 4

value: yeast cell

value: WT


title: S23

value: liver


title: Kidney-Ep, Z0000045L reanalysis

description:
Kidney-Ep, Z0000045L
GSM5652255

value: Kidney glomerular


title: S22


title: Kidney-Ep, Z0000045K reanalysis

description:
Kidney-Ep, Z0000045K
GSM5652254


title: S21


title: ACC65  (Agilent)


title: sample_1164

description: medium: DMEM, atmosphere: room air, temperature: 30C, cAMP: 20 mM, time: 180 min, librarydate: 2019-07-22, biol rep: 3

value: DMEM


title: ACC61  (Agilent)


title: S20


title: sample_430

description: medium: DMEM, atmosphere: room air, temperature: 30C, cAMP: 20 mM, time: 180 min, librarydate: 2019-08-09, biol rep: 2

value: room air


title: sample_402

description: medium: DMEM, atmosphere: room air, temperature: 30C, cAMP: 20 mM, time: 180 min, librarydate: 2019-06-20, biol rep: 1

value: cAMP 20 mM


title: ACC8  (Agilent)

value: Instituto Português de Oncologia de Francisco Gentil

value: male

value: FFPE


title: ACC9  (Agilent)

value: adenoid cystic carcinoma

value: Gerhard-Seifert Reference Centre


title: Pancreas-Alpha, Z00000456 reanalysis

description:
Pancreas-Alpha, Z00000456
GSM5652252

source_name: Pancreas

value: Pancreas


title: S2

value: gallbladder

value: pBTSCs


title: ACC7  (Agilent)

value: female


title: Pancreas-Alpha, Z00000459 reanalysis

description:
Pancreas-Alpha, Z00000459
GSM5652253


title: sample_3614

description: medium: DMEM, atmosphere: room air, temperature: 30C, cAMP: 20 mM, time: 1440 min, librarydate: 2021-09-08, biol rep: 5


title: ACC6  (Agilent)

value: normal tissue


title: S19


title: Pancreas-Beta, Z00000458 reanalysis

description:
Pancreas-Beta, Z00000458
GSM5652250


title: S18


title: ACC5  (Agilent)


title: sample_3437

description: medium: DMEM, atmosphere: room air, temperature: 30C, cAMP: 20 mM, time: 1440 min, librarydate: 2021-07-06, biol rep: 3

value: yeast cell


title: sample_3438

description: medium: DMEM, atmosphere: room air, temperature: 30C, cAMP: 20 mM, time: 1440 min, librarydate: 2021-07-06, biol rep: 4

value: WT


title: Pancreas-Beta, Z00000455 reanalysis

description:
Pancreas-Beta, Z00000455
GSM5652249


title: S17

value: liver


title: S16


title: ACC4  (Agilent)


title: ACC3  (Agilent)


title: sample_3340

description: medium: DMEM, atmosphere: room air, temperature: 30C, cAMP: 20 mM, time: 1440 min, librarydate: 2021-06-08, biol rep: 2


title: sample_3045

description: medium: DMEM, atmosphere: room air, temperature: 30C, cAMP: 20 mM, time: 1440 min, librarydate: 2021-04-07, biol rep: 1


title: Pancreas-Beta, Z00000452 reanalysis

description:
Pancreas-Beta, Z00000452
GSM5652248


title: S15


title: ACC1  (Agilent)


title: sample_3106

description: medium: DMEM, atmosphere: CO2 5%, temperature: 37C, cAMP: none, time: 90 min, librarydate: 2021-04-23, biol rep: 6

value: cAMP none

value: 90 min


title: S14


title: Pancreas-Delta, Z00000457 reanalysis

description:
Pancreas-Delta, Z00000457
GSM5652247


title: S13


title: Pancreas-Delta, Z00000451 reanalysis

description:
Pancreas-Delta, Z00000451
GSM5652245


title: Pancreas-Alpha, Z00000453 reanalysis

description:
Pancreas-Alpha, Z00000453
GSM5652251


title: ACC2  (Agilent)


title: sample_1502

description: medium: DMEM, atmosphere: CO2 5%, temperature: 37C, cAMP: none, time: 90 min, librarydate: 2020-11-02, biol rep: 4

value: DMEM


title: sample_2706

description: medium: DMEM, atmosphere: CO2 5%, temperature: 37C, cAMP: none, time: 90 min, librarydate: 2021-01-26, biol rep: 5


title: S12


title: IKZF3 Homo, B cell, rep2

city: Yokohama

first: CHANG

last: JINGJIE

state: -- Choose State --

address: 横滨市鹤见区1Chome suehirocho

country: Japan

institute: RIKEN

data_processing:
Trimmomatic (version 0.38.1) performed a variety of useful trimming tasks for Fastq files.
RNA-seq sequences were aligned on mm10 using HISAT2 (version 2.2.1) using default parameters.
Read counts were culculated using HTseq (version 2.0.2) with refGene as the GTF file, using default parameters.
Assembly: mm10
Supplementary files format and content: Raw read count for each RNA-seq sample.

source_name: spleen

extract_protocol:
Total RNA was extracted by using Trizol reagent (Invitrogen).
RNA libraries for RNA-seq were prepared using NEBNext UltraⅡRNA Library Prep Kit for Illumina with following the manufacturer’s protocol.

value: spleen

tag: strain

value: B220+CD19+ B cell

value: Ikzf3 N159S/N159S

value: FACS purified


title: Pancreas-Acinar, Z0000043Y reanalysis

description:
Pancreas-Acinar, Z0000043Y
GSM5652244


title: sample_1239

description: medium: DMEM, atmosphere: CO2 5%, temperature: 37C, cAMP: none, time: 90 min, librarydate: 2019-08-19, biol rep: 3


title: S11


title: IKZF3 Homo, B cell, rep1


title: sample_805

description: medium: DMEM, atmosphere: CO2 5%, temperature: 37C, cAMP: none, time: 90 min, librarydate: 2019-08-22, biol rep: 2


title: IKZF3 Het, B cell, rep2

value: Ikzf3 +/N159S


title: Pancreas-Acinar, Z0000043W reanalysis

description:
Pancreas-Acinar, Z0000043W
GSM5652242


title: IKZF3 Het, B cell, rep1


title: Pancreas-Acinar, Z000000QX reanalysis

description:
Pancreas-Acinar, Z000000QX
GSM5652241


title: sample_579

description: medium: DMEM, atmosphere: CO2 5%, temperature: 37C, cAMP: none, time: 90 min, librarydate: 2019-08-15, biol rep: 1


title: Pancreas-Delta, Z00000454 reanalysis

description:
Pancreas-Delta, Z00000454
GSM5652246


title: Astrocyte-Stim-IFNb-BR3 [ATACAA]

city: Erlangen

first: Mathias

last: Linnerbauer

address: Schwabachanlage 6

department: Neurology

institute: University Hospital Erlangen

data_processing:
Data processing and analysis was performed by Thomas Engleitner
DropSeqTools v.1.12
Picard v.2.18.26
STAR v.2.7.5b
Bcl2Fastq
Assembly: GRCm38
Supplementary files format and content: tab-delimited file includes normalized count values

source_name: CNS

extract_protocol:
Astrocytes were isolated by enzymatic and mechanic digestion of mouse CNS tissue as previously described.
Library preparation was performed by Rupert Oellinger

value: CNS

value: astrocytes

value: wild type

value: interferon beta

tag: biologicalrep

tag: technicalrep


title: Astrocyte-Stim-IFNb-BR2 [TCGGGC]

tag: cell type


title: sample_3100

description: medium: DMEM, atmosphere: CO2 5%, temperature: 37C, cAMP: none, time: 30 min, librarydate: 2021-04-23, biol rep: 7

tag: cell line

tag: medium

value: 30 min


title: WT, B cell, rep4

value: Ikzf3 +/+


title: Pancreas-Duct, Z000000QZ reanalysis

description:
Pancreas-Duct, Z000000QZ
GSM5652240

value: Pancreas


title: Astrocyte-Stim-IFNb-BR1 [GCGCTG]


title: Pancreas-Duct, Z0000043V reanalysis

description:
Pancreas-Duct, Z0000043V
GSM5652239


title: WT, B cell, rep3


title: WT, B cell, rep2


title: Astrocyte-Stim-Ctrl-BR3 [TCTTAA]

value: vehicle


title: Astrocyte-Stim-Ctrl-BR2 [GATAAT]


title: Pancreas-Acinar, Z0000043X reanalysis

description:
Pancreas-Acinar, Z0000043X
GSM5652243


title: sample_2700

description: medium: DMEM, atmosphere: CO2 5%, temperature: 37C, cAMP: none, time: 30 min, librarydate: 2021-01-26, biol rep: 6

value: yeast cell

value: WT

tag: atmosphere

tag: temperature


title: sample_1543

description: medium: DMEM, atmosphere: CO2 5%, temperature: 37C, cAMP: none, time: 30 min, librarydate: 2020-12-18, biol rep: 5

tag: treatment

value: cAMP none

tag: time


title: WT, B cell, rep1


title: Astrocyte-Stim-Ctrl-BR1 [ATAAAC]


title: Pancreas-Duct, Z0000043U reanalysis

description:
Pancreas-Duct, Z0000043U
GSM5652238


title: sample_1490

description: medium: DMEM, atmosphere: CO2 5%, temperature: 37C, cAMP: none, time: 30 min, librarydate: 2020-11-02, biol rep: 4

value: DMEM


title: IKZF3 Homo, T cell, rep2

value: spleen

value: TCRb+CD4+CD44-CD127+ T cell


title: Liver-Hep, Z00000431 reanalysis

description:
Liver-Hep, Z00000431
GSM5652236

source_name: Liver

value: Liver


title: sample_1233

description: medium: DMEM, atmosphere: CO2 5%, temperature: 37C, cAMP: none, time: 30 min, librarydate: 2019-08-19, biol rep: 3


title: Microglia-EAE-BMS202-4 [TTATTG]

extract_protocol:
Mice were perfused with cold 1× PBS and the CNS was isolated and mechanically diced using sterile razors. Cortices were transferred into 5 ml of enzyme digestion solution consisting of 35.5 µl papain suspension (Worthington, #LS003126) diluted in enzyme stock solution (ESS) and equilibrated to 37 °C. ESS consisted of 10 ml 10× EBSS (Sigma-Aldrich, #E7510), 2.4 ml 30% D(+)-glucose (Sigma-Aldrich, #G8769), 5.2 ml 1 M NaHCO3 (VWR, #AAJ62495-AP), 200 µl 500 mM EDTA (Thermo Fisher Scientific, #15575020), and 168.2 ml ddH2O, filter-sterilized through a 0.22-µm filter. Samples were shaken at 80 rpm for 30–40 min at 37 °C. Enzymatic digestion was stopped with 1 ml of 10× hi ovomucoid inhibitor solution and 20 µl 0.4% DNase (Worthington, #LS002007) diluted in 10 ml inhibitor stock solution (ISS). 10× hi ovomucoid inhibitor stock solution contained 300 mg BSA (Sigma-Aldrich, #A8806) and 300 mg ovomucoid trypsin inhibitor (Worthington, #LS003086) diluted in 10 ml 1× PBS and filter sterilized using a 0.22-µm filter. ISS contained 50 ml 10× EBSS (Sigma-Aldrich, #E7510), 6 ml 30% D(+)-glucose (Sigma-Aldrich, #G8769), and 13 ml 1 M NaHCO3 (VWR, #AAJ62495-AP) diluted in 170.4 ml ddH2O and filter-sterilized through a 0.22-µm filter. Tissue was mechanically dissociated using a 5-ml serological pipette and filtered through a 70-µm cell strainer (Fisher Scientific, #22363548) into a fresh 50-ml conical tube. Tissue was centrifuged at 600g for 5 min and resuspended in 10 ml of 30% Percoll solution (9 ml Percoll (GE Healthcare Biosciences, #17-5445-01), 3 ml 10× PBS, 18 ml ddH2O). Percoll suspension was centrifuged at 600g for 25 min with no breaks. Supernatant was discarded and the cell pellet was washed once with 1× PBS, centrifuged at 500g for 5 min and prepared for downstream applications. Astrocytes were FACS-isolated using a negative gating strategy. Microglia were FACS-sorted by CD45hiCD11b+ staining.
Library preparation was performed by Rupert Oellinger

value: FACS-sorted microglia

value: NOD/ShitLtJ


title: sample_799

description: medium: DMEM, atmosphere: CO2 5%, temperature: 37C, cAMP: none, time: 30 min, librarydate: 2019-08-22, biol rep: 2


title: IKZF3 Homo, T cell, rep1

value: Ikzf3 N159S/N159S

value: FACS purified


title: Microglia-EAE-Control-4 [TTAGTT]

value: CNS


title: Liver-Hep, Z0000044H reanalysis

description:
Liver-Hep, Z0000044H
GSM5652234


title: Liver-Hep, Z0000044M reanalysis

description:
Liver-Hep, Z0000044M
GSM5652235


title: sample_573

description: medium: DMEM, atmosphere: CO2 5%, temperature: 37C, cAMP: none, time: 30 min, librarydate: 2019-08-15, biol rep: 1


title: IKZF3 Het, T cell, rep2

value: Ikzf3 +/N159S


title: IKZF3 Het, T cell, rep1


title: Astrocytes-EAE-BMS202-4 [TTAATC]

value: FACS-sorted astrocytes


title: sample_3112

description: medium: DMEM, atmosphere: CO2 5%, temperature: 37C, cAMP: none, time: 180 min, librarydate: 2021-04-23, biol rep: 6

value: 180 min


title: Astrocytes-EAE-control-4 [TGTTTA]


title: WT, T cell, rep2

value: Ikzf3 +/+


title: Pancreas-Duct, Z0000043T reanalysis

description:
Pancreas-Duct, Z0000043T
GSM5652237

value: Pancreas


title: Liver-Hep, Z000000T3 reanalysis

description:
Liver-Hep, Z000000T3
GSM5652232


title: sample_1567

description: medium: DMEM, atmosphere: CO2 5%, temperature: 37C, cAMP: none, time: 180 min, librarydate: 2020-12-18, biol rep: 5

value: yeast cell


title: Microglia-EAE-BMS202-5 [TCTGCA]


title: WT, T cell, rep1


title: sample_1514

description: medium: DMEM, atmosphere: CO2 5%, temperature: 37C, cAMP: none, time: 180 min, librarydate: 2020-11-02, biol rep: 4

value: WT


title: Liver-Hep, Z000000R3 reanalysis

description:
Liver-Hep, Z000000R3
GSM5652231


title: sample_1245

description: medium: DMEM, atmosphere: CO2 5%, temperature: 37C, cAMP: none, time: 180 min, librarydate: 2019-08-19, biol rep: 3

value: cAMP none


title: Microglia-EAE-BMS202-3 [TAATGA]


title: Microglia-EAE-Control-3 [TAAGAT]

value: vehicle


title: Let-7Tg, 5 Days activated, 3

city: Amherst

first: Leonid

last: Pobezinsky

state: MA

address: 661 N Pleasant St

department: Veterinary and Animal Sciences

institute: University of Massachusetts Amherst

data_processing:
Reference genome and genome annotation files were downloaded from genome website browser (NCBI/UCSC/Ensembl) and indexed using Bowtie v2.0.6.
Clean, paired-end reads were aligned to the reference genome with TopHat v2.0.9.
Read counts per gene and FPKM were determined using HTSeq v0.6.1.
Differential gene expression analysis between the WT, Let-7Tg, Lin28Tg sample groups (n=3 in each group) was performed using the DESeq2 R package (v2_1.6.3). Adjusted p-values were calculated with the Benjamini-Hochberg multiple test correction, and genes with an adjusted p-value < 0.05 were considered significantly differentially expressed between two groups.
Assembly: Mus Musculus(GRCm38/mm10)
Supplementary files format and content: CSV files contain FPKM counts for sample groups, sorted by individual samples (n=3 per group).

source_name: Lymph nodes

growth_protocol: Lymph nodes and spleens were harvested and gently tweezed to remove lymphocytes. Spleen cells were then lysed using ACK lysing buffer (KD Medical) to remove erythrocytes. For 12 hour activation, cells were stimulated with anti-CD3 mABs (2 μg/mL) and anti-CD28 mABs (5 μg/mL). For CTL generation, cells were stimulated with irradiated splenocytes and soluble anti-CD3 mAbs (2 μg/mL). Cells were cultured in RPMI supplemented with 10% fetal bovine serum, 1% HEPES, 1% sodium pyruvate, 1% penicillin/ streptomycin, 1% L-glutamine, 1% non-essential amino acids and 0.3% β-mercaptoethanol. 48h after activation IL-2 was added to culture media (100 U/mL) and cells were differentiated for additional 3 days; 2μg/mL doxycycline was added when necessary.

extract_protocol:
20x10^6 in vitro-generated CTLs and at least 4x10^6 naive and 12h-activated CD8+ T cells were lysed in TRIzol (Invitrogen) and sent to Novogene for RNA extraction, library preparation, sequencing and initial data processing. RNA quality was assessed by Nanodrop, Agarose gel electrophoresis, and by the Agilent 2100 Bioanalyzer.
RNA-Seq libraries were prepared using the HiSeq X Ten Reagent Kit following manufacturer's protocols.

value: Lymph nodes

value: 5 Days

value: T cells

value: Let-7Tg P14+

value: Activation by Anti-CD3 mAb and irridiated Splenocytes. 48h after activation, IL-2 was added to culture media (100 U/mL) and cells were differentiated for 3 more days; 2μg/mL doxycycline was added in culture media.


title: Neuron, Z000000TB reanalysis

description:
Neuron, Z000000TB
GSM5652229

source_name: Brain

value: Brain


title: Astrocytes-EAE-BMS202-3 [TAAAGT]

value: NOD/ShitLtJ


title: sample_811

description: medium: DMEM, atmosphere: CO2 5%, temperature: 37C, cAMP: none, time: 180 min, librarydate: 2019-08-22, biol rep: 2

value: DMEM


title: Neuron, Z0000042K reanalysis

description:
Neuron, Z0000042K
GSM5652228


title: Let-7Tg, 5 Days activated, 2


title: Let-7Tg, 5 Days activated, 1


title: Liver-Hep, Z0000043Q reanalysis

description:
Liver-Hep, Z0000043Q
GSM5652233

value: Liver


title: Astrocytes-EAE-control-3 [GTTTAT]

value: CNS

value: FACS-sorted astrocytes


title: Lin28bTg, 5 Days activated, 3

value: Lin28bTg P14+


title: Neuron, Z0000042P reanalysis

description:
Neuron, Z0000042P
GSM5652227


title: Microglia-EAE-Control-5 [GTTCGA]

value: FACS-sorted microglia


title: sample_3730

description: medium: DMEM, atmosphere: CO2 5%, temperature: 37C, cAMP: none, time: 1440 min, librarydate: 2021-09-15, biol rep: 4

value: yeast cell


title: Lin28bTg, 5 Days activated, 2


title: sample_3118

description: medium: DMEM, atmosphere: CO2 5%, temperature: 37C, cAMP: none, time: 1440 min, librarydate: 2021-04-23, biol rep: 3

value: WT


title: Neuron, Z0000042M reanalysis

description:
Neuron, Z0000042M
GSM5652226


title: Lin28bTg, 5 Days activated, 1


title: Astrocytes-EAE-BMS202-5 [GGGATT]


title: Neuron, Z0000042J reanalysis

description:
Neuron, Z0000042J
GSM5652225


title: Neuron, Z000000TD reanalysis

description:
Neuron, Z000000TD
GSM5652230


title: sample_2718

description: medium: DMEM, atmosphere: CO2 5%, temperature: 37C, cAMP: none, time: 1440 min, librarydate: 2021-01-26, biol rep: 2

value: cAMP none


title: WT, 5 Days activated, 3

value: WT P14+


title: Astrocytes-EAE-control-5 [GCTAGA]

value: vehicle


title: Microglia-EAE-BMS202-2 [ATTACT]


title: sample_1579

description: medium: DMEM, atmosphere: CO2 5%, temperature: 37C, cAMP: none, time: 1440 min, librarydate: 2020-12-18, biol rep: 1


title: Neuron, Z0000042H reanalysis

description:
Neuron, Z0000042H
GSM5652224


title: sample_585

description: medium: DMEM, atmosphere: CO2 5%, temperature: 37C, cAMP: none, time: 180 min, librarydate: 2019-08-15, biol rep: 1

value: 180 min


title: Neuron, Z0000042F reanalysis

description:
Neuron, Z0000042F
GSM5652223


title: sample_986

description: medium: DMEM, atmosphere: CO2 5%, temperature: 37C, cAMP: none, HEPES buffer pH 7.0 25 mM, time: 90 min, librarydate: 2020-02-20, biol rep: 4

value: cAMP none; HEPES buffer pH 7.0 25 mM

value: 90 min


title: WT, 5 Days activated, 2

value: Lymph nodes

value: 5 Days

value: T cells

value: Activation by Anti-CD3 mAb and irridiated Splenocytes. 48h after activation, IL-2 was added to culture media (100 U/mL) and cells were differentiated for 3 more days; 2μg/mL doxycycline was added in culture media.


title: WT, 5 Days activated, 1


title: sample_907

description: medium: DMEM, atmosphere: CO2 5%, temperature: 37C, cAMP: none, HEPES buffer pH 7.0 25 mM, time: 90 min, librarydate: 2020-06-01, biol rep: 3

value: DMEM


title: Microglia-EAE-Control-2 [ATGAAT]

value: CNS

value: NOD/ShitLtJ


title: Let-7Tg, 12 Hours activated, 3

value: 12 Hours

value: Let-7Tg P14+

value: 12 hour activation by Anti-CD3 mAb and Anti-CD28 mAB; 2μg/mL doxycycline was added in culture media.


title: sample_289

description: medium: DMEM, atmosphere: CO2 5%, temperature: 37C, cAMP: none, HEPES buffer pH 7.0 25 mM, time: 90 min, librarydate: 2020-02-25, biol rep: 2

value: yeast cell

value: WT


title: Neuron, Z000000TH reanalysis

description:
Neuron, Z000000TH
GSM5652222

value: Brain


title: sample_61

description: medium: DMEM, atmosphere: CO2 5%, temperature: 37C, cAMP: none, HEPES buffer pH 7.0 25 mM, time: 90 min, librarydate: 2020-05-25, biol rep: 1


title: Neuron, Z000000TF reanalysis

description:
Neuron, Z000000TF
GSM5652221


title: Let-7Tg, 12 Hours activated, 2


title: Oligodend, Z0000042N reanalysis

description:
Oligodend, Z0000042N
GSM5652220


title: Astrocytes-EAE-control-2 [ATATAG]

value: FACS-sorted astrocytes

value: vehicle


title: Astrocytes-EAE-BMS202-2 [ATCAAA]


title: Oligodend, Z0000042L reanalysis

description:
Oligodend, Z0000042L
GSM5652219


title: Microglia-EAE-BMS202-1 [AAGATT]

value: FACS-sorted microglia


title: Let-7Tg, 12 Hours activated, 1


title: Lin28bTg, 12 Hours activated, 3

value: Lin28bTg P14+


title: Lin28bTg, 12 Hours activated, 2

value: Lymph nodes


title: Microglia-EAE-Control-1 [AAATTG]


title: sample_895

description: medium: DMEM, atmosphere: CO2 5%, temperature: 37C, cAMP: none, HEPES buffer pH 7.0 25 mM, time: 30 min, librarydate: 2020-06-01, biol rep: 3

value: cAMP none; HEPES buffer pH 7.0 25 mM

value: 30 min


title: Oligodend, Z0000042E reanalysis

description:
Oligodend, Z0000042E
GSM5652218


title: sample_980

description: medium: DMEM, atmosphere: CO2 5%, temperature: 37C, cAMP: none, HEPES buffer pH 7.0 25 mM, time: 30 min, librarydate: 2020-02-20, biol rep: 4


title: sample_283

description: medium: DMEM, atmosphere: CO2 5%, temperature: 37C, cAMP: none, HEPES buffer pH 7.0 25 mM, time: 30 min, librarydate: 2020-02-25, biol rep: 2


title: Astrocytes-EAE-BMS202-1 [AAAGTT]


title: Lin28bTg, 12 Hours activated, 1

value: T cells


title: Oligodend, Z000000TK reanalysis

description:
Oligodend, Z000000TK
GSM5652217


title: Bone-Osteob, Z0000042Z reanalysis

description:
Bone-Osteob, Z0000042Z
GSM5652216

source_name: Bone

value: Bone


title: sample_49

description: medium: DMEM, atmosphere: CO2 5%, temperature: 37C, cAMP: none, HEPES buffer pH 7.0 25 mM, time: 30 min, librarydate: 2020-05-25, biol rep: 1

value: DMEM


title: WT, 12 Hours activated, 3

value: WT P14+


title: Vinorelbine replicate 2

city: LEBANON

first: Diwakar

middle: Pattabiraman

last: Pattabiraman

state: NH

address: 1 Medical Center Drive

department: Molecular and Systems Biology

institute: Geisel School of Medicine at Dartmouth

data_processing:
FASTQ files were generated using bcl2fastq v2.20.0.422 from Illumina Inc.
Raw reads were trimmed with Cutadapt (v2.4) and aligned to GRCm38 using STAR (2.7.2b) with parameters “--twopassMode Basic --outSAMattributes NH HI AS NM MD --outFilterMultimapNmax 10 --outFilterMismatchNmax 999 --outFilterMismatchNoverReadLmax 0.04 --alignIntronMin 20 –alignIntronMax 1000000 --alignMatesGapMax 1000000 --alignSJoverhangMin 8 --alignSJDBoverhangMin 1”
Gene-level abundance estimates were generated using RSEM (v1.3.2) using the rsem-calculate-expression command with the parameters “--paired-end --alignments --strandedness reverse”.
Assembly: GRCm38
Supplementary files format and content: txt files, RSEM output for each sample. Gene Identifers are from ENSEMBL v97

source_name: Breast Cancer Cells

growth_protocol: Cells Grown in DMEM/F12 media supplemented with 5% ABS, 100 I.U./mL penicillin,100 (μg/mL), and 1X MEM Non-Essential Amino Acids in a humidified incubatorns

extract_protocol:
RNA extracted using QIAGEN RNeasy Kits according to the manufacturing protocol.
Kapa mRNA Hyperprep, 200ng input
paired-end 76bp

treatment_protocol: To generate resistant clones cells treated with different concentration of drugs as follow:   -Eribulin- 300 nM-500 nM and 800 nM.   -Paclitaxel- 300 nM-500 nM and 800 nM.   -Vinorelbine 300 nM-500 nM and 800 nM.

value: Vinorelbine


title: Vinorelbine replicate 1


title: Heart-Cardio, Z0000044Q reanalysis

description:
Heart-Cardio, Z0000044Q
GSM5652214

source_name: Heart

value: Heart


title: sample_295

description: medium: DMEM, atmosphere: CO2 5%, temperature: 37C, cAMP: none, HEPES buffer pH 7.0 25 mM, time: 180 min, librarydate: 2020-02-25, biol rep: 2

value: 180 min


title: WT, 12 Hours activated, 1

value: 12 Hours

value: 12 hour activation by Anti-CD3 mAb and Anti-CD28 mAB; 2μg/mL doxycycline was added in culture media.


title: Heart-Cardio, Z0000044K reanalysis

description:
Heart-Cardio, Z0000044K
GSM5652213


title: sample_919

description: medium: DMEM, atmosphere: CO2 5%, temperature: 37C, cAMP: none, HEPES buffer pH 7.0 25 mM, time: 180 min, librarydate: 2020-06-01, biol rep: 3

value: yeast cell

value: WT


title: Let-7Tg, Naïve, 3

value: 0 Hours

value: Let-7Tg P14+


title: WT, 12 Hours activated, 2


title: sample_73

description: medium: DMEM, atmosphere: CO2 5%, temperature: 37C, cAMP: none, HEPES buffer pH 7.0 25 mM, time: 180 min, librarydate: 2020-05-25, biol rep: 1


title: Heart-Cardio, Z0000044G reanalysis

description:
Heart-Cardio, Z0000044G
GSM5652212


title: Astrocytes-EAE-control-1 [AAAACT]

value: CNS

value: FACS-sorted astrocytes

value: NOD/ShitLtJ

value: vehicle


title: Smooth-Musc, Z00000421 reanalysis

description:
Smooth-Musc, Z00000421
GSM5652211

source_name: Bronchial

value: Bronchial


title: sample_3434

description: medium: DMEM, atmosphere: CO2 5%, temperature: 37C, cAMP: none, HEPES buffer pH 7.0 25 mM, time: 1440 min, librarydate: 2021-07-06, biol rep: 4

value: cAMP none; HEPES buffer pH 7.0 25 mM


title: Smooth-Musc, Z0000041Y reanalysis

description:
Smooth-Musc, Z0000041Y
GSM5652210

source_name: Prostate

value: Prostate


title: sample_3433

description: medium: DMEM, atmosphere: CO2 5%, temperature: 37C, cAMP: none, HEPES buffer pH 7.0 25 mM, time: 1440 min, librarydate: 2021-07-06, biol rep: 3

value: DMEM


title: Paclitaxel replicate 1

value: Paclitaxel


title: Paclitaxel replicate 2


title: Let-7Tg, Naïve, 1

value: Lymph nodes

value: T cells


title: Vinorelbine replicate 3

value: Vinorelbine


title: Let-7Tg, Naïve, 2


title: Erubilin replicate 3

value: Erubilin


title: sample_998

description: medium: DMEM, atmosphere: CO2 5%, temperature: 37C, cAMP: none, HEPES buffer pH 7.0 25 mM, time: 1440 min, librarydate: 2020-02-20, biol rep: 2

value: yeast cell


title: Lin28bTg, Naïve, 3

value: Lin28bTg P14+


title: sample_992

description: medium: DMEM, atmosphere: CO2 5%, temperature: 37C, cAMP: none, HEPES buffer pH 7.0 25 mM, time: 180 min, librarydate: 2020-02-20, biol rep: 4

value: WT

value: 180 min


title: Heart-Cardio, Z0000044R reanalysis

description:
Heart-Cardio, Z0000044R
GSM5652215

value: Heart


title: Smooth-Musc, Z0000041Z reanalysis

description:
Smooth-Musc, Z0000041Z
GSM5652209

source_name: Bladder

value: Bladder


title: Erubilin replicate 2


title: sample_85

description: medium: DMEM, atmosphere: CO2 5%, temperature: 37C, cAMP: none, HEPES buffer pH 7.0 25 mM, time: 1440 min, librarydate: 2020-05-25, biol rep: 1


title: Paclitaxel replicate 3


title: Erubilin replicate 1


title: sample_1299

description: medium: DMEM, atmosphere: CO2 5%, temperature: 37C, cAMP: 20 mM, time: 90 min, librarydate: 2019-10-23, biol rep: 4

value: cAMP 20 mM

value: 90 min


title: sample_950

description: medium: DMEM, atmosphere: CO2 5%, temperature: 37C, cAMP: 20 mM, time: 90 min, librarydate: 2019-11-10, biol rep: 3


title: Control replicate 3

value: Untreated


title: WT, Naïve, 3

value: 0 Hours

value: WT P14+


title: Skeletal-Musc, Z00000429 reanalysis

description:
Skeletal-Musc, Z00000429
GSM5652206

source_name: Skeletal muscle

value: Skeletal muscle


title: Lin28bTg, Naïve, 1


title: WT, Naïve, 2


title: Control replicate 2


title: sample_251

description: medium: DMEM, atmosphere: CO2 5%, temperature: 37C, cAMP: 20 mM, time: 90 min, librarydate: 2019-11-04, biol rep: 1

value: DMEM


title: WT, Naïve, 1

value: Lymph nodes


title: Control replicate 1


title: Erubilin treatment 72hr replicate 2 (cutnrun-mouse)

description:
Tn5 fragmented genomic DNA
PB3-72.narrowPeak
PB3-72hr.merged.bw
PB3-72hr-2

data_processing:
FASTQ files were generated using bcl2fastq v2.20.0.422 from Illumina Inc.
Raw reads were trimmed with Cutadapt (v2.4) and aligned to mm10 using Bowtie (v2.2.6) in “--local” mode with parameters “--no-mixed --no-discordant”
Duplicate reads were identified and removed using MarkDuplicates (Picard Tools) to create filtered BAMs.
Peaks were called using MACS2 (v2.1.1) callpeak command with parameters ““-f BAMPE --keep-dup all -q 0.05 -g 2652783500 ”
Peaks were filtered against the ENCODE mm10 blacklist and those demonstrating 2-fold signal enrichment above background
Reproducible peak sets were identified for replicate pairs using BEDTools (v 2.30.0) command “intersect” with parameter “-a”.
A consensus peak set was generated by merging overlapping peaks called across all samples. Read counts in each consensus peak region were counted from BAM files using the featureCounts() function (Rsubread package) with options “isPairedEnd=TRUE, countMultiMappingReads=FALSE”
BAM files for sample replicates were merged using Picard MergeSamFiles before creation of BigWig files
Counts per million (CPM) normalized signal tracks were generated using deepTools8 (v3.3.0) bamCoverage command with parameters ““--binSize 20 --smoothLength 60 --normalizeUsing CPM --centerReads --extendReads” on the position-shifted BAM files
Assembly: GRCm38
Supplementary files format and content: matrix of raw read counts in txt format
Supplementary files format and content: Normalized signal tracks in BigWig format
Supplementary files format and content: peak files in BED format
Library strategy: CUT&RUN

source_name: Mouse Breast Cancer Cells

growth_protocol: Cells Grown in DMEM/F12 media supplemented with 5% ABS, 100 I.U./mL penicillin,100 (μg/mL), and 1X MEM Non-Essential Amino Acids in a humidified incubator with 5% CO2.

extract_protocol:
CUT&RUN was performed using  EpiCypher CUTANA™ CUT&RUN assays according to manufacturing protocol. Zeb1-DNA complexes were isolated using an anti-Zeb1 antibody.
NEB Ultra II with modifications from EpiCypher CUTANA Library Kit Manual v1.0
paired-end 76bp

treatment_protocol: Cells were treated with 300nM eribulin for 24, 48, and 72h.


title: Dermal-Fibro, Z00000423 reanalysis

description:
Dermal-Fibro, Z00000423
GSM5652204

source_name: Ad-dermal

value: Ad-dermal


title: sample_1293

description: medium: DMEM, atmosphere: CO2 5%, temperature: 37C, cAMP: 20 mM, time: 30 min, librarydate: 2019-10-23, biol rep: 4

value: 30 min


title: Heart-Fibro, Z0000041X reanalysis

description:
Heart-Fibro, Z0000041X
GSM5652203


title: Erubilin treatment 72hr replicate 1 (cutnrun-mouse)

description:
Tn5 fragmented genomic DNA
PB3-72.narrowPeak
PB3-72hr.merged.bw
PB3-72hr-1

value: Erubilin


title: Lin28bTg, Naïve, 2

value: T cells


title: Erubilin treatment 48hr replicate 2 (cutnrun-mouse)

description:
Tn5 fragmented genomic DNA
PB3-48.narrowPeak
PB3-48hr.merged.bw
PB3-48hr-2


title: sample_341

description: medium: DMEM, atmosphere: CO2 5%, temperature: 37C, cAMP: 20 mM, time: 90 min, librarydate: 2019-10-29, biol rep: 2

value: yeast cell


title: Heart-Fibro, Z0000041W reanalysis

description:
Heart-Fibro, Z0000041W
GSM5652202


title: Smooth-Musc, Z0000041U reanalysis

description:
Smooth-Musc, Z0000041U
GSM5652207

source_name: Aorta

value: Aorta


title: Erubilin treatment 48hr replicate 1 (cutnrun-mouse)

description:
Tn5 fragmented genomic DNA
PB3-48.narrowPeak
PB3-48hr.merged.bw
PB3-48hr-1


title: sample_335

description: medium: DMEM, atmosphere: CO2 5%, temperature: 37C, cAMP: 20 mM, time: 30 min, librarydate: 2019-10-29, biol rep: 2

value: WT


title: Heart-Fibro, Z0000041V reanalysis

description:
Heart-Fibro, Z0000041V
GSM5652201

value: Heart


title: Smooth-Musc, Z00000420 reanalysis

description:
Smooth-Musc, Z00000420
GSM5652208

source_name: Cornary artery

value: Cornary artery


title: Erubilin treatment 24hr replicate 2 (cutnrun-mouse)

description:
Tn5 fragmented genomic DNA
PB3-24.narrowPeak
PB3-24hr.merged.bw
PB3-24hr-2


title: Heart-Fibro, Z0000043R reanalysis

description:
Heart-Fibro, Z0000043R
GSM5652200


title: sample_245

description: medium: DMEM, atmosphere: CO2 5%, temperature: 37C, cAMP: 20 mM, time: 30 min, librarydate: 2019-11-04, biol rep: 1

value: cAMP 20 mM


title: sample_1305

description: medium: DMEM, atmosphere: CO2 5%, temperature: 37C, cAMP: 20 mM, time: 180 min, librarydate: 2019-10-23, biol rep: 4

value: 180 min


title: A pos dox 1

city: WUhan

first: Yuxi

last: Ma

address: Jiefang Avenue

country: China

institute: Huazhong University of Science and Technology

hyb_protocol: Washed and stained in the GeneChip Fluidics Station 450 (Afymetrix, USA)

scan_protocol: Arrays of different samples were scanned with a GeneChip Scanner 3000 7G (Afymetrix, USA) and signal strength was evaluated using the Expression Console Software (EC) v1.2 (ThermoFisher Scienti c).

data_processing: Acquired array data were analyzed using Multi Experiment Viewer (MeV v4.9.0; The Institute for Genomic Research) and miRNAs with an absolute value of fold change ≥ 0.5 were identi ed as potential miRNAs signi cantly changed upon DOX-induced XIST KD.

label: biotin

source_name: ALDH+ shXist-DOX SUM159 cells

label_protocol: miRNA-containing total RNA (300 ng) was biotin-labeled using the FlashTag Biotin RNA Labeling kit (Afymetrix, USA) and hybridized in the GeneChip Hybridization Oven 640 (Affymetrix, USA) at 48°C for overnight.

growth_protocol: SUM159 cells were cultured in Ham’s F-12 (ThermoFisher Scienti c) supplemented with 5% FBS (ThermoFisher Scienti c), 5 μg/mL insulin (Sigma-Aldrich, St. Louis, MO), 1μg/mL hydrocortisone (Sigma-Aldrich), and 1x antibiotic-antimycotic (ThermoFisher Scienti c, 100x).

extract_protocol: Total RNA and miRNA were extracted using RNeasy and miRNeasy Mini kit (Qiagen) respectively.

treatment_protocol: ALDH− and ALDH+ cells isolated from DOX-untreated SUM159-shXIST cells were treated with or without (CTL) DOX at 1μg/ml for 3 days, miRNAs from each sample were extracted using miRNeasy Mini kit (Qiagen) and analyzed by GeneChipTM miRNA 4.0 Array (ThermoFisher Scienti c) according to manufacturer’s instructions.

value: Breast cancer cell line-SUM159


title: Skeletal-Musc, Z00000427 reanalysis

description:
Skeletal-Musc, Z00000427
GSM5652205


title: A pos control 2

source_name: ALDH+ shXist SUM159 cells


title: Colon-Fibro, Z0000042C reanalysis

description:
Colon-Fibro, Z0000042C
GSM5652199

source_name: Colon

value: Colon


title: A pos control 1


title: Erubilin treatment 24hr replicate 1 (cutnrun-mouse)

description:
Tn5 fragmented genomic DNA
PB3-24.narrowPeak
PB3-24hr.merged.bw
PB3-24hr-1


title: A pos dox 2


title: Control replicate 2 (cutnrun-mouse)

description:
Tn5 fragmented genomic DNA
PB3.Cont.narrowPeak
PB3-Cont.merged.bw
PB3-Cont-2

value: Untreated


title: Colon-Fibro, Z0000042A reanalysis

description:
Colon-Fibro, Z0000042A
GSM5652198


title: A neg dox 2

source_name: ALDH- shXist-DOX SUM159 cells


title: Endothelium, Z0000042Y reanalysis

description:
Endothelium, Z0000042Y
GSM5652197

source_name: Pancreas

value: Pancreas


title: Control replicate 1 (cutnrun-mouse)

description:
Tn5 fragmented genomic DNA
PB3.Cont.narrowPeak
PB3-Cont.merged.bw
PB3-Cont-1


title: Endothelium, Z00000430 reanalysis

description:
Endothelium, Z00000430
GSM5652196


title: IgG control

description:
Tn5 fragmented genomic DNA
PB3-IgG.bw
PB3-IgG


title: 36

city: Bloomington

first: Patricia

last: Silveyra

email: psilveyr@iu.edu, ptrcslvr@gmail.com

state: Indiana

department: Environmental and Occupational Health

institute: Indiana University Bloomington

description: low-birth-weight infants with hemodynamically significant cardiac shunt (ICS) that develop bronchopulmonary dysplasia and pulmonary hypertension (ICS-BPD-PH)

data_processing:
Data were analyzed in excel using Ct values for each sample,  normalized to global means, and fold changes were calculated using the 2-ΔΔCT method.
Matrix normalized template shows miRNA Ct values normalized to global mean ΔCt = (Ct_miRNA − Ct_global mean)
For fold change calculations, ΔΔCt based fold-change values were obtained using an average of control sample Ct values (2^-ΔΔCt, where -ΔΔCt = -[ΔCtsample -ΔCtavgcontrol])). A fold change of 25 was considered as cutoff.
"Matrix non-normalized" are raw Ct values. "Matrix normalized" are normalized to the global mean. "Fold changes" are calculated with the livak method (2^-ΔΔCt, where -ΔΔCt = -[ΔCttest -ΔCtcontrol])

label: SYBR Green

source_name: ICS-BPD-PH

label_protocol: Small RNAs were retro-transcribed from 200 ng of total RNA using the miScript II RT kit (Qiagen). The expression of 1066 human miRNAs was assayed with the Human miRNome miScript® miRNA PCR Array (QIAGEN, MIHS-3216Z).

extract_protocol: MicroRNAs were purified from 0.5 mL of TAs with the Plasma/Serum RNA Purification Kit (Norgen Biotek Corp., Thorold, ON, Canada).

treatment_protocol: Tracheal aspirates were obtained from premature babies with sBPD and BPD-PH. Total RNA was purified from TAs and the expression of 1066 human miRNAs was detected with a PCR array.

value: tracheal aspirate

tag: ics-bpd

value: no

tag: ics-bpd-ph

value: yes


title: sample_257

description: medium: DMEM, atmosphere: CO2 5%, temperature: 37C, cAMP: 20 mM, time: 180 min, librarydate: 2019-11-04, biol rep: 1

value: DMEM


title: A neg control 2

source_name: ALDH- shXist SUM159 cells


title: 35

description: low-birth-weight infants with hemodynamically significant cardiac shunt (ICS) that develop bronchopulmonary dysplasia (ICS-BPD)

source_name: ICS-BPD


title: A neg control 1


title: Endothelium, Z0000042X reanalysis

description:
Endothelium, Z0000042X
GSM5652195


title: sample_962

description: medium: DMEM, atmosphere: CO2 5%, temperature: 37C, cAMP: 20 mM, time: 1440 min, librarydate: 2019-11-10, biol rep: 3


title: Endothelium, Z0000042D reanalysis

description:
Endothelium, Z0000042D
GSM5652194


title: 34


title: Vinorelbine replicate 2 (atacseq)

description:
Tn5 fragmented genomic DNA
VIN.idr0.01.bfilt.narrowPeak
VIN.bw
VIN_2

data_processing:
FASTQ files were generated using bcl2fastq v2.20.0.422 from Illumina Inc.
Raw reads were trimmed with Cutadapt (v1.9.1) and aligned to mm10 using Bowtie (v2.2.6) in “--local” mode with parameters “-X 2000 -k 2”
Duplicate reads were identified and removed using MarkDuplicates (Picard Tools) to create filtered BAMs, which were converted to tagAlign format and reads were shifted +4 bp and -5 bp on the + and – strands, respectively.
Peaks were called using MACS2 (v2.1.1) callpeak command with parameters “--shift -75 --extsize 150 --nomodel --keep-dup all --call-summits -p 1.0E-10” and filtered against the ENCODE mm10 blacklist
Irreproducible Discovery Rate (IDR) method was applied, retaining peaks with an IDR threshold of <0.01
IDR peak sets were merged across samples to create a consensus peak set. reads falling within the consensus peak set in each sample were counted using featureCounts.
BAM files for sample replicates were merged using Picard MergeSamFiles before create of BigWig files
Counts per million (CPM) normalized tn5 insertion signal tracks were generated using deepTools8 (v3.4.3) bamCoverage command with parameters “--binSize 5 --normalizeUsing CPM --effectiveGenomeSize 2913022398 --ignoreForNormalization chrX” on the position-shifted BAM files
Assembly: GRCm38
Supplementary files format and content: matrix of raw read counts in txt format
Supplementary files format and content: Normalized tn5 insertion signal tracks in BigWig format
Supplementary files format and content: peak files in BED format

source_name: Breast Cancer Cells

growth_protocol: Cells Grown in DMEM/F12 media supplemented with 5% ABS, 100 I.U./mL penicillin,100 (μg/mL), and 1X MEM Non-Essential Amino Acids in a humidified incubator with 5% Co2.

extract_protocol:
Nuclei extracted and tagmented per the Buenrostro ATAC-seq protocol, https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4374986/
Libraries constructed per the Buenrostro ATAC-seq protocol
paired-end 76bp

value: Vinorelbine

tag: cell line origin


title: sample_354

description: medium: DMEM, atmosphere: CO2 5%, temperature: 37C, cAMP: 20 mM, time: 1440 min, librarydate: 2019-10-29, biol rep: 2


title: Endothelium, Z0000045H reanalysis

description:
Endothelium, Z0000045H
GSM5652193

source_name: Lung alveolar

extract_protocol:
refer to GSE186458
refer to GSE186458

value: Lung alveolar


title: sample_956

description: medium: DMEM, atmosphere: CO2 5%, temperature: 37C, cAMP: 20 mM, time: 180 min, librarydate: 2019-11-10, biol rep: 3

value: yeast cell


title: sample_347

description: medium: DMEM, atmosphere: CO2 5%, temperature: 37C, cAMP: 20 mM, time: 180 min, librarydate: 2019-10-29, biol rep: 2


title: 33


title: Paclitaxel replicate 2 (atacseq)

description:
Tn5 fragmented genomic DNA
PAC.idr0.01.bfilt.narrowPeak
PAC.bw
PAC_2

value: Paclitaxel


title: Erubilin replicate 2 (atacseq)

description:
Tn5 fragmented genomic DNA
ERI.idr0.01.bfilt.narrowPeak
ERI.bw
ERI_2

value: Erubilin


title: sample_263

description: medium: DMEM, atmosphere: CO2 5%, temperature: 37C, cAMP: 20 mM, time: 1440 min, librarydate: 2019-11-04, biol rep: 1

value: WT


title: 32


title: Paclitaxel replicate 1 (atacseq)

description:
Tn5 fragmented genomic DNA
PAC.idr0.01.bfilt.narrowPeak
PAC.bw
PAC_1


title: A neg dox 1


title: 31


title: Endothelium, Z000000QK reanalysis

description:
Endothelium, Z000000QK
GSM5652192


title: sample_2705

description: medium: DMEM, atmosphere: CO2 5%, temperature: 30C, cAMP: none, time: 90 min, librarydate: 2021-01-26, biol rep: 5

value: cAMP none

value: 90 min


title: 30


title: Endothelium, Z000000RB reanalysis

description:
Endothelium, Z000000RB
GSM5652190

source_name: Liver

value: Liver


title: 29


title: Vinorelbine replicate 1 (atacseq)

description:
Tn5 fragmented genomic DNA
VIN.idr0.01.bfilt.narrowPeak
VIN.bw
VIN_1


title: sample_1311

description: medium: DMEM, atmosphere: CO2 5%, temperature: 37C, cAMP: 20 mM, time: 1440 min, librarydate: 2019-10-23, biol rep: 4

value: cAMP 20 mM


title: Erubilin replicate 1 (atacseq)

description:
Tn5 fragmented genomic DNA
ERI.idr0.01.bfilt.narrowPeak
ERI.bw
ERI_1


title: Endothelium, Z0000042R reanalysis

description:
Endothelium, Z0000042R
GSM5652189

source_name: Kidney tubular

value: Kidney tubular


title: Control replicate 2 (atacseq)

description:
Tn5 fragmented genomic DNA
Control.idr0.01.bfilt.narrowPeak
Control.bw
Control_rep2

value: Untreated


title: Control replicate 1 (atacseq)

description:
Tn5 fragmented genomic DNA
Control.idr0.01.bfilt.narrowPeak
Control.bw
Control_rep1


title: 28


title: sample_804

description: medium: DMEM, atmosphere: CO2 5%, temperature: 30C, cAMP: none, time: 90 min, librarydate: 2019-08-22, biol rep: 2


title: 27

description: low-birth-weight infants with hemodynamically significant cardiac shunt (ICS) that develop bronchopulmonary dysplasia and pulmonary hypertension (ICS-BPD-PH)


title: sample_944

description: medium: DMEM, atmosphere: CO2 5%, temperature: 37C, cAMP: 20 mM, time: 30 min, librarydate: 2019-11-10, biol rep: 3

value: 30 min


title: Endothelium, Z000000Q1 reanalysis

description:
Endothelium, Z000000Q1
GSM5652191


title: sample_3105

description: medium: DMEM, atmosphere: CO2 5%, temperature: 30C, cAMP: none, time: 90 min, librarydate: 2021-04-23, biol rep: 6


title: Endothelium, Z000000PX reanalysis

description:
Endothelium, Z000000PX
GSM5652187


title: ERI4, run3, Eribulin treated, 4 rounds, snRNA, multiome

city: Bengaluru

first: Mohamed Ashick

last: Mohamed Saleem

state: Karnataka

address: #1519/10, 8Th A Main, 'Akshaya', Sahakaranagar

country: India

institute: LifeBytes India Pvt Ltd

library_source: transcriptomic single cell

data_processing:
FASTQ and count matrix were generated using 10x Genomics cellranger-3.1.0, 10x Genomics cellranger-4.0.0 (Zheng et al., 2017) and 10x Genomics cellranger-arc-1.0.0 (Satpathy et al., 2019) for Run1, Run2 and Run3 respectively. Cellranger reference mm10 was used as reference for all runs.
Count matrices were analysed using Seurat v3.1.4 pipeline (Stuart et al., 2019). Briefly, low quality cells (number of genes expressed < 200, percentage of UMIs in mitochondrial and ribosomal genes individually > 50) are filtered out.
HTO multiplexed samples ERI1/ERI2/ERI3 and PAC1/PAC2/PAC3 will have a single paired-end FASTQ file respectively. These FASTQ files need to be processed in cellranger with additional HTO barcode in feature reference [lentiviral_barcodes_feature_reference_RNA_withHTObarcodes_forRun2.txt.gz] and then two barcode groups ['HTO' and 'Lentiviral'] need to be split into two assays. Using HTO assay, cells can be demultiplexed in Seurat pipeline using HTODemux or MULTIseqDemux modules.
Assembly: mm10
Supplementary files format and content: Raw data: <sample>_filtered_feature_bc_UMImatrix.tar.gz: contains the following files, 1) matrix.mtx: UMI count matrix in sparse format, 2) genes.tsv: features (row names) of UMI count matrix, 3) barcodes.tsv: cell barcodes (column names) of UMI count matrix
Supplementary files format and content: metadata_<sample>.txt: Each cells additional processed information (sample, treatment, run information, technique, pseudotime)
Supplementary files format and content: UMAP coordinates_<sample>.txt: UMAP coordinates each cells
Supplementary files format and content: lentiviral_barcodes_feature_reference_RNA.csv.gz: Lentiviral barcode feature reference

source_name: Mammary tumor

growth_protocol: Samples were grown in DMEM/F12 (1:1) media supplemented with L-glutamine, non-essential amino acids, and Penicillin/Streptomycin

extract_protocol:
Single cells were captured using 10x Genomics Chip G (3' v3 samples) or Chip J (Multiome samples)
Libraries were constructed following either the 10x Genomics 3' v3, or Multiome protocol
3' RNA/Multiome RNA: 28bp R1 (cell barcode + UMI), 98bp R2 (transcript); Multiome ATAC: 50bp R1 (insert), 50bp R2 (insert), 8bp I1 (index), 24bp I2 (cell barcode, includes 8bp dark cycles using custom recipe per 10x instructions). ERI1/ERI2/ERI3 and PAC1/PAC2/PAC3 samples from Run2 were multiplexed using Hashtag Oligos (HTO). HTO samplesheet is merged with feature reference file [lentiviral_barcodes_feature_reference_RNA_withHTObarcodes_forRun2.txt.gz]. Briefly, BC1 (GGAGAAGA), BC2 (CCACAATG) and BC3 (TGAGACCT) from 5P directional in Read2 represent ERI1, ERI2, and ERI3 respectively. Similarly, BC4 (GCACACGC), BC5 (AGAGAGAG) and BC6 (TCACAGCA) from 5P directional in Read2 represent PAC1, PAC2, and PAC3 respectively.
10x 3' RNA v3; 10x Mutliome RNA + ATAC

treatment_protocol: Treated with 500nM Eribulin for 72 hours, and allowed the cells to recover for 48 hours. This was repeated 3 more times for a total of 4 rounds of treatment

tag: disease state

value: Tumor

value: Eribulin

tag: source

value: Nuclei

value: Mammary tumor


title: sample_578

description: medium: DMEM, atmosphere: CO2 5%, temperature: 30C, cAMP: none, time: 90 min, librarydate: 2019-08-15, biol rep: 1

value: DMEM


title: Endothelium, Z0000045J reanalysis

description:
Endothelium, Z0000045J
GSM5652186

source_name: Kidney glomerular

tag: tissue

value: Kidney glomerular


title: 26

description: low-birth-weight infants with hemodynamically significant cardiac shunt (ICS) that develop bronchopulmonary dysplasia (ICS-BPD)

value: tracheal aspirate

value: yes

value: no


title: sample_3099

description: medium: DMEM, atmosphere: CO2 5%, temperature: 30C, cAMP: none, time: 30 min, librarydate: 2021-04-23, biol rep: 7

value: yeast cell

tag: genotype

value: WT


title: UNT, run1, Untreated, scRNA

description: UNT

treatment_protocol: No treatment

value: Cell


title: Endothelium, Z00000443 reanalysis

description:
Endothelium, Z00000443
GSM5652185


title: 25


title: 24


title: sample_1500

description: medium: DMEM, atmosphere: CO2 5%, temperature: 30C, cAMP: none, time: 90 min, librarydate: 2020-11-02, biol rep: 4

value: cAMP none

value: 90 min


title: Endothelium, Z000000Q5 reanalysis

description:
Endothelium, Z000000Q5
GSM5652184


title: sample_2699

description: medium: DMEM, atmosphere: CO2 5%, temperature: 30C, cAMP: none, time: 30 min, librarydate: 2021-01-26, biol rep: 6


title: PAC1_PAC2_PAC3, run2, Paclitaxel treated, 1-2-3 rounds, HTO multiplexed, scRNA

treatment_protocol: PAC1: Treated with 100nM Paclitaxel for 72 hours and allowed cells to recover.  PAC2: Treated with 100nM Paclitaxel for 72 hours and allowed cells to recover for 48 hours. Repeated treatment with 250nM Paclitaxel for a total of 2 rounds of treatment.  PAC3: Treated with 100nM Paclitaxel for 72 hours and allowed cells to recover for 48 hours. Repeated treatment with 250nM Paclitaxel and allowed cells to recover. This was repeated once more for a total of 3 rounds of treatment.

value: Paclitaxel


title: ERI1_ERI2_ERI3, run2, Eribulin treated, 1-2-3 rounds, HTO multiplexed, scRNA

treatment_protocol: ERI1: Treated with 500nM Eribulin for 72 hours, and allowed the cells to recover for 48 hours.  ERI2: Treated with 500nM Eribulin for 72 hours, and allowed the cells to recover for 48 hours. This was repeated once more for a total of 2 rounds of treatment.  ERI3: Treated with 500nM Eribulin for 72 hours, and allowed the cells to recover for 48 hours. This was repeated 2 more times for a total of 3 rounds of treatment.


title: 23


title: Endothelium, Z000000SB reanalysis

description:
Endothelium, Z000000SB
GSM5652183

source_name: Vascular saphenous

value: Vascular saphenous


title: sample_1238

description: medium: DMEM, atmosphere: CO2 5%, temperature: 30C, cAMP: none, time: 90 min, librarydate: 2019-08-19, biol rep: 3


title: UNT, run3, Untreated, snRNA, multiome

value: Untreated


title: sample_1488

description: medium: DMEM, atmosphere: CO2 5%, temperature: 30C, cAMP: none, time: 30 min, librarydate: 2020-11-02, biol rep: 4

value: 30 min


title: Endothelium, Z000000Q3 reanalysis

description:
Endothelium, Z000000Q3
GSM5652188

value: Kidney tubular


title: Endothelium, Z000000S7 reanalysis

description:
Endothelium, Z000000S7
GSM5652182


title: 21


title: ERI4_multiome

library_source: genomic single cell

data_processing:
FASTQ and count matrix were generated using 10x Genomics cellranger-3.1.0, 10x Genomics cellranger-4.0.0 (Zheng et al., 2017) and 10x Genomics cellranger-arc-1.0.0 (Satpathy et al., 2019) for Run1, Run2 and Run3 respectively. Cellranger reference mm10 was used as reference for all runs.
Peak count matrices were analysed using Signac v1.1.1 pipeline. Briefly, low quality cells (fragments in peak regions < 1000 and >75000, percentage of UMIs in peaks > 20, ratio of UMIs in blacklist regions to that of peak regions > 0.05, nucleosome signal > 10 and TSS enrichment < 2) are filtered out.
Assembly: mm10
Supplementary files format and content: Raw data: <sample>_filtered_feature_bc_UMImatrix.tar.gz: contains the following files, 1) matrix.mtx: UMI count matrix in sparse format, 2) genes.tsv: features (row names) of UMI count matrix, 3) barcodes.tsv: cell barcodes (column names) of UMI count matrix
Supplementary files format and content: metadata_<sample>.txt: Each cells additional processed information (sample, treatment, run information, technique, pseudotime)
Supplementary files format and content: UMAP coordinates_<sample>.txt: UMAP coordinates each cells
Supplementary files format and content: lentiviral_barcodes_feature_reference_ATAC.csv.gz: Lentiviral barcode feature reference

extract_protocol:
Single cells were captured using 10x Genomics Chip G (3' v3 samples) or Chip J (Multiome samples)
Libraries were constructed following either the 10x Genomics 3' v3, or Multiome protocol
3' RNA/Multiome RNA: 28bp R1 (cell barcode + UMI), 98bp R2 (transcript); Multiome ATAC: 50bp R1 (insert), 50bp R2 (insert), 8bp I1 (index), 24bp I2 (cell barcode, includes 8bp dark cycles using custom recipe per 10x instructions)
10x 3' RNA v3; 10x Mutliome RNA + ATAC

treatment_protocol:
Treated with 500nM Eribulin for 72 hours, and allowed the cells to recover for 48 hours. This was repeated 3 more times for a total of 4 rounds of treatment
See under SAMPLES above (Treatment protocol)

value: Tumor

value: Eribulin


title: sample_798

description: medium: DMEM, atmosphere: CO2 5%, temperature: 30C, cAMP: none, time: 30 min, librarydate: 2019-08-22, biol rep: 2

extract_protocol:
Frozen cell pellets were thawed on ice and 875m  TRIzol (Ambion 15-596-018) was added. Cells were then lysed with 750 ml 0.5mm silica-zirconia beads for 3 min in a Minibeadbeater (Biospec Products) and RNA isolated following the Trizol manufacturer’s protocol. Residual DNA was removed with the Turbo DNA-free Kit (Life Technologies AM1907) and polyA+ RNA isolated from ~1 mg of total RNA using the NEBNext Poly(A) mRNA Magnetic Isolation Module.
Libraries were constructed using the NEBNext Ultra Directional RNA Library Prep Kit from Illumina and samples were pooled at 10 nM. The pools were sequenced on a NextSeq 500 using the High75v2 kit as a 1x75 with 7bp Index1 and 6bp Index2 with 1% PhiX.  Fastq files were demultiplexed using the Illumina bcl2fastq2 allowing 1 bp mismatch.

value: DMEM


title: Endothelium, Z000000RM reanalysis

description:
Endothelium, Z000000RM
GSM5652181

data_processing:
BAM files were re-processed with the nf-core/methylseq pipeline using the biscuit aligner (https://github.com/ekushele/methylseq/blob/master/main_bams.nf ). The quality of fastQ files was assessed using FastQC (v0.11.9). TrimGalore (v0.6.4_dev) was used to trim adapters from all samples with the following parameters: ‘clip_r1 = 10 clip_r2 = 15 three_prime_clip_r1 = 10 three_prime_clip_r2 = 10’. We aligned the trimmed samples to the hg19 genome assembly, using the biscuit aligner (v0.3.15.20200318), with ‘-b 1’ for directional library. Duplicates were marked using samblaster (v0.1.24) with ‘--addMateTags’. Then, BAM files were sorted and indexed using Samtools (v1.9). The sorted and indexed BAMs were given as an input to ‘biscuit pileup’, to generate VCF files. We implemented a custom approach to filtering SNPs and generating Biscuit epiread files which contained a merged version of the two ends of each paired-end read. The code is available at https://github.com/ekushele/methylseq
Assembly: hg19
Supplementary files format and content: tab delimited file with the following columns: chromosome, start position, end position, read name, pair (1/2), strand,  CpG positions, methylation pattern, SNP positions, SNP patterns


title: 22


title: UNT

treatment_protocol:
No treatment
See under SAMPLES above (Treatment protocol)

value: Mammary tumor


title: ERI4, run1, Eribulin treated, 4 rounds, scRNA


title: 20

value: tracheal aspirate


title: Endothelium, Z0000043G reanalysis

description:
Endothelium, Z0000043G
GSM5652180

source_name: Aorta

value: Aorta


title: 19

value: no

value: yes


title: Endothelium, Z00000422 reanalysis

description:
Endothelium, Z00000422
GSM5652179


title: sample_572

description: medium: DMEM, atmosphere: CO2 5%, temperature: 30C, cAMP: none, time: 30 min, librarydate: 2019-08-15, biol rep: 1

value: yeast cell

value: WT


title: UNT_multiome


title: sample_3111

description: medium: DMEM, atmosphere: CO2 5%, temperature: 30C, cAMP: none, time: 180 min, librarydate: 2021-04-23, biol rep: 6

value: cAMP none

value: 180 min


title: Adipocytes, Z000000T5 reanalysis

description:
Adipocytes, Z000000T5
GSM5652178

source_name: Abdominal Subcut.

value: Abdominal Subcut.


title: 18


title: sample_1541

description: medium: DMEM, atmosphere: CO2 5%, temperature: 30C, cAMP: none, time: 30 min, librarydate: 2020-12-18, biol rep: 5


title: 17


title: ERI4


title: sample_1565

description: medium: DMEM, atmosphere: CO2 5%, temperature: 30C, cAMP: none, time: 180 min, librarydate: 2020-12-18, biol rep: 4


title: TBX5 KO M3 [RA10]

city: Chicago

first: Xinan

middle: Holly

last: Yang

state: IL

address: 900 East 57th Street, KCBD Room 5121

department: Pediatrics

institute: universty of Chicago

data_processing:
After evaluating the quality of these 51bp single-ended RNAseq reads by fastqc, for each sample we left trimmed 3 bp reads with the lowest quality scores using fastx_toolkit (version 0.0.13).
The 47 bp length RNA-seq reads were alimented to the Mouse genome mm10 using tophat (version 2.0.11).
Featurecount was performed using Rsubread (version 1.14.2).
Differential expression was analyzed using DEseq2 Bioconductor package with the by default parameters.
Assembly: Mm10
Supplementary files format and content: tab-delimited text file that was the output of DEseq2 that comparing TBX5 KO samples with CTRL samples

source_name: right atria

growth_protocol: Mice were raised according to university protocols (protocol # 71737).

extract_protocol:
Right atria were dissected from TBX5 removed and control 6‐8 week old mice. Tissues were mechanically homogenized in TRIzol Reagent (Invitrogen), chloroform was added, aqueous phase was isolated, ethanol was added, and then RNA was isolated using RNeasy Mini Columns. Overall, 12μg of total RNA for each sample was treated with the mouse GlobinClear kit (Ambion) to remove the majority of globin RNA. Libraries were prepared from this RNA starting with 1μg per sample and using the mRNA‐seq Sample Prep Kit (Illumina) as per recommended instructions. Cluster generation and sequencing were performed as per standard Illumina HiSeq2500 Rapid Run Mode protocols to generate single-end reads of 51bp. A single pool of libraries was sequenced in two individual lanes of the HiSeq2500 2‐lane flow cell.
Barcoded Libraries were prepared according to Illumina's instructions (2013) accompanying the TruSeq RNA Sample prep kit v2 (Part# RS‐122‐2001). Libraries were quantitated using the Agilent Bio‐analyzer (model 2100) and pooled in equimolar amounts. The pooled libraries were sequenced on the HiSeq2500 in Rapid Run Mode following the manufacturer's protocols (2013).
Total RNA-seq (Ribozero purification removed only ribosomal RNA, remaining total RNA was sequenced) of 50bp

treatment_protocol: A tamoxifen inducible cre recombinase driven by the ubiquitous R26 promoter was used to excise exon 3 of TBX5 as previously described (Arnolds et al JCI 2012). Excision of TBX5 was induced by IP tamoxifen for 3 days, 0.167mg tamoxifen/day. Mice were sacrificed at 1 week post tamoxifen and right and left atrial appendage were dissected.A tamoxifen inducible cre recombinase driven by the ubiquitous R26 promoter was used to excise exon 3 of TBX5 as previously described (Arnolds et al JCI 2012). Excision of TBX5 was induced by IP tamoxifen for 3 days, 0.167mg tamoxifen/day. Mice were sacrificed at 1 week post tamoxifen and right and left atrial appendage were dissected.

tag: strain

value: mix

value: right atria

value: R26Cre driven TBX5 removal

tag: age

value: 8-10 weeks

tag: Sex

value: M


title: 16


title: TBX5 KO M2 [RA9]


title: Adipocytes, Z000000T7 reanalysis

description:
Adipocytes, Z000000T7
GSM5652176


title: sample_1512

description: medium: DMEM, atmosphere: CO2 5%, temperature: 30C, cAMP: none, time: 180 min, librarydate: 2020-11-02, biol rep: 3

tag: cell type


title: sample_1232

description: medium: DMEM, atmosphere: CO2 5%, temperature: 30C, cAMP: none, time: 30 min, librarydate: 2019-08-19, biol rep: 3

tag: cell line

value: 30 min


title: TBX5 KO M1 [RA8]


title: sample_1244

description: medium: DMEM, atmosphere: CO2 5%, temperature: 30C, cAMP: none, time: 180 min, librarydate: 2019-08-19, biol rep: 2

tag: medium

value: DMEM


title: 14

description: low-birth-weight infants with hemodynamically significant cardiac shunt (ICS) that develop bronchopulmonary dysplasia and pulmonary hypertension (ICS-BPD-PH)


title: HepG2, sh_H3.3

city: Hefei

first: Pengfei

last: Zhang

address: 443 Huang-Shan Road

department: School of Life Sciences

institute: University of Science and Technology of China

data_processing:
Bcl2fastq(v1.8.4) was used for base-calling for output.
Raw data (raw reads) were processed using Trimmomatic. The reads containing ploy-N and the low quality reads were removed to obtain the clean reads.
The clean reads were mapped to reference genome (Human GRCh38/hg38) using Bismark (Bowtie2).
DNA methylation sites were identifited using MethylKit.
DMR and DMP analysis was performed using the MethylKit. Difference >=10%. Pvalue < 0.05 .
Assembly: hg38
Supplementary files format and content: Excel file includes CpG sites for each sample.
Supplementary files format and content: Excel file includes CpG DMR or DMP between two samples.

extract_protocol:
Whole genomic DNA was isolated by MasterPure™ DNA Purification Kit (Epicentre) according to the manufacturer’s instructions. Bisulfite treatment of 100 ng genomic DNA was performed using the Zymo EZ DNA Methylation Lightning Kit.
Library was prepared using TruSeq DNA Methylation Kit (illumina, EGMK91396).

value: hepatoma cell


title: TBX5 KO F3 [RA7]

value: F


title: 15

value: tracheal aspirate


title: HepG2, sh_ctrl

value: control


title: Spermatocytes, SP_NOA, 107, rep2

city: Shanghai

first: Wu

last: zhongqin

address: No.800 Dongchuan Road, Minhang District

institute: Shanghai Jiao Tong University

data_processing:
Trim_galore, Adapter and PolyA cut-off
STAR, align reads to hg38 genome
umi_homopolymer.py(UMI extraction)/umi_tools (Deduplication) provided by Foley, J.W., et al., Gene expression profiling of single cells from archival tissue with laser-capture microdissection and Smart-3SEQ. Genome research, 2019. 29(11): p. 1816-1825.
Extract UMI and deduplication reads
FeatureCounts, Align reads preferentially to 3'end and calculate the strand-specific reads counts
RSeQC, Show reads distribution on the gene bodies
Assembly: hg38
Supplementary files format and content: csv file includes count values for each sample

source_name: FFPE testicular biopsy tissue

extract_protocol:
RNA was released directly in PCR tube during lysis from spermatocytes, which were collected from FFPE testicular biopsy tissue using laser capture microdissection systembased on Smart-3SEQ method(Foley, J.W., et al., Gene expression profiling of single cells from archival tissue with laser-capture microdissection and Smart-3SEQ. Genome research, 2019. 29(11): p. 1816-1825.).
each library was constructed using Smart-3SEQ protocol (Foley, J.W., et al., Gene expression profiling of single cells from archival tissue with laser-capture microdissection and Smart-3SEQ. Genome research, 2019. 29(11): p. 1816-1825.)

value: FFPE testicular biopsy tissue

value: spermatocytes

tag: group

tag: patient id


title: TBX5 KO F1 [RA5]


title: Spermatocytes, SP_NOA, 107, rep1


title: sample_2711

description: medium: DMEM, atmosphere: CO2 5%, temperature: 30C, cAMP: none, time: 180 min, librarydate: 2021-01-26, biol rep: 5

data_processing:
Reads were aligned with Novoalign (version 4.03.02) and quantified with HTSeq (0.9.1) using the FungiDB KN99 alpha genome sequence. Quality control ensued in two phases. In Phase I, custom scripts were used to verify the Crypto C. neoformans strain in each sample by calculating CDS coverage over putatively deleted genes and the corresponding selectable deletion cassette, ensuring that the former were absent and the latter present. Strains that passed this step were labeled as ‘passing’ if they contained at least 1e6 reads aligned to protein coding regions and less than 7% of all reads failed to align.
In Phase 2, we evaluated replicate agreement using the Regularized Log Expression (RLE). First, we used DESeq2 (version 1.34.0) to estimate the effect of the library date (the known batch effect). We removed the batch effect using the DESeq coefficients for the library dates such that the data was standardized to a single date, resulting in adjusted expression levels on a log2 normalized scale. To compute the RLE value for a given gene, the median expression level of that gene, across all samples in a replicate set, was subtracted from the expression level of that the gene in each sample. For each sample, we then calculated the interquartile range of the distribution of these RLE values across genes. If the interquartile range of RLEs of a given sample was greater than 1, indicating that more than half of genes deviated from their respective medians by a factor of 2 in adjusted count, the sample was considered an outlier and failed for replicate agreement.
Assembly: ASM221672v1
Supplementary files format and content: Tab separated (tsv) raw counts and DESeq2 sizeFactor normalized counts

value: yeast cell

value: WT

tag: atmosphere

tag: temperature

tag: treatment


title: sample_584

description: medium: DMEM, atmosphere: CO2 5%, temperature: 30C, cAMP: none, time: 180 min, librarydate: 2019-08-15, biol rep: 1

value: cAMP none

tag: time

value: 180 min


title: 13

description: low-birth-weight infants with hemodynamically significant cardiac shunt (ICS) that develop bronchopulmonary dysplasia (ICS-BPD)

tag: ics-bpd

value: yes

tag: ics-bpd-ph

value: no


title: sample_3728

description: medium: DMEM, atmosphere: CO2 5%, temperature: 30C, cAMP: none, time: 1440 min, librarydate: 2021-09-15, biol rep: 4


title: Spermatocytes, SP_NOA, 100, rep2


title: TBX5 KO F2 [RA6]

value: mix

value: right atria

value: R26Cre driven TBX5 removal


title: 11