title: YS_p1_run1_NB68

description: Library name: YS_p1_run1_NB68_GL69_306_WN-S6-4_I10_YS_E10-5_HE_Runx1_S306


title: MCF7-COX2, DOX, 48hr, Rep2

status: Public on Sep 29 2025

type: SRA

city: Brandon

first: Mousumi

last: Majumder

state: Manitoba

address: 270 18th Street

department: Biology

country: Canada

institute: Brandon University

description: Library name: Sample 23

library_source: transcriptomic

data_processing:
In Linux, raw '.fastq' files were trimmed with Trimmomatic (v0.39). Trimmed files were aligned with STAR (v2.7.11b) (Human reference genome GRCh38.p14) sorted by coordinates. Alignments were counted with HTSeq (v2.0.8).
Assembly: GRCh38.p14
Supplementary files format and content: Tab-delimited text file containing raw counts for each sample (HTSeq)

molecule: polyA RNA

organism: Homo sapiens

source_name: Breast

growth_protocol: Cells were cultured in Roswell Park Memorial Institute (RPMI)-1640 media, supplemented with 10% fetal bovine serum and 1% Pen-Strep. Cells were incubated at 37˚C with 5% CO2. Transfected cells were maintained with 200ng/mL Geneticin (Cat. No: G418, Biobasic).

extract_protocol:
Samples were homogenized in Qiazol before shipment on dry ice to the third party sequencing service provider (Centre d'expertise et de services Génome Québec (CES) (McGill University, Montréal, Canada)). RNA extraction and QC checks were outsourced to a third party (Centre d'expertise et de services Génome Québec (CES) (McGill University, Montréal, Canada)). All samples passed QC with RNA Integrity Numbers (RINs) of 8.5 or higher.
PolyA-Enriched

treatment_protocol: Cells treated with either doxorubicn (0.8uM) or DMSO for 48 hours. Three biological replicates performed per cell line and condition.

tag: tissue

value: Breast

tag: cell line

tag: cell type

value: Adenocarcinoma

tag: genotype

tag: treatment

value: DOX, 48hr


title: 8C_F2_C

city: Gainesville

first: Zongliang

last: Jiang

state: FL

address: 2033 Mowry Rd

department: Animal Sciences

country: USA

institute: University of Florida

data_processing:
Multiplexed sequencing reads that passed filters were trimmed to remove low-quality reads and adaptors by TrimGalore (version 0.6.7) (-q 25 --length 20 --max_n 3 --stringency 3). The quality of reads after filtering was assessed by fastQC, followed by alignment to the mouse genome (GRCm39) by HISAT2 (version 2.2.1) with default parameters. The output SAM files were converted to BAM files and sorted using SAMtools6 (version 1.14). Read counts of all samples were quantified by using FeatureCount (Version 2.0.1) with mouse genome as a reference and were adjusted to provide CPM (Counts per million mapped reads). Principal component analysis (PCA) and cluster analysis were performed by using R (a free software environment for statistical computing and graphics). Differentially expressed genes (DEGs) was identified by using edgeR in R. The genes were considered differentially expressed if they provided a false discovery rate of <0.05 and fold change >2. ClusterProfiler was used to reveal the Gene Ontology (GO) and KEGG pathways in R.
Assembly: GRCm39
Supplementary files format and content: txt, normalized read counts

organism: Mus musculus

source_name: oocyte or embryo

extract_protocol:
Ten equal fractions were recovered and subjected to RNA isolation by Trizol reagent (Sigma).
The RNA-seq libraries were generated from individual fractions by using the Smart-seq2 v4 kit with minor modification from manufacturer’s instructions. Briefly, individual cells were lysed, and mRNA was captured and amplified with the Smart-seq2 v4 kit (Clontech). After AMPure XP beads purification, amplified RNAs were quality checked by using Agilent High Sensitivity D5000 kit (Agilent Technologies). High-quality amplified RNAs were subject to library preparation (Nextera XT DNA Library Preparation Kit; Illumina) and multiplexed by Nextera XT Indexes (Illumina). The concentration of sequencing libraries was determined by using Qubit dsDNA HS Assay Kit (Life Technologies) and KAPA Library Quantification Kits (KAPA Biosystems). The size of sequencing libraries was determined by means of High Sensitivity D5000 Assay in at Tapestation 4200 system (Agilent). Pooled indexed libraries were then sequenced on the Illumina HiSeq X platform with 150-bp paired-end reads.

treatment_protocol: Approximately 100 oocytes (GV or MII oocyte) or embryos at different developmental stages (zygote, 2-, 4-, 8-cell, morula, and blastocyst) were combined with lysis buffer containing 10 mM HEPES (pH 7.5), 5 mM KCL, 5 mM MgCL2, 2 mM DTT, 1% Triton X-100, 100 μg/ml cycloheximide, complete EDTA-free protease inhibitor (Roche), and 40 U/ml RNase inhibitor. Oocytes and embryos were disrupted by zirconium silica beads (Sigma) in the mixer mill apparatus MM301 (shake frequency 30, total time 45s, Retsch). Lysates were cleaned by centrifugation in 10,000 x g for 5 min at 4°C and the supernatants were loaded into 10-40 % linear sucrose gradients containing 10 mM HEPES (pH7.5), 100 mM KCL, 5 mM MgCl2, 2mM DTT, 100 μg/ml cycloheximide, complete EDTA-free protease inhibitor, and 5 U/ml RNase inhibitor. Ultracentrifugation was carried out with a SW55Ti rotor and Optima L-90 Ultracentrifuge (Beckman Coulter). Ribosome profiles were recorded by ISCO UV absorbance reader. The overall quality of particular ribosome fractionation experiment was monitored by analysis of a parallel Hek293 cells sample.

value: oocyte or embryo


title: 8C_F2_B


title: Parent_n=1

city: Camperdown

first: George

middle: Louis

last: Joun

state: NSW

address: John Hopkins Drive

department: School of Medical Sciences

country: Australia

institute: The University of Sydney

data_processing:
Dragen RNA pipeline
Assembly: Homo Sapiens HG38
Supplementary files format and content: Raw Counts

molecule: total RNA

growth_protocol: Stem Pro Neural Stem Cell Serum Free Media (ThermoFisher Scientific).

extract_protocol:
Qiagen RNeasy Minikit, manufacturer's protocol
Illumina mRNA stranded library preparation kit, manufacturer's protocol

value: Glioblastoma Stem Cell

value: WT

value: Untreated


title: YS_p1_run1_NB65

city: Manchester

first: Georges

last: Lacaud

state: England

address: Wilmslow Raod

department: Stem Cell Biology

country: United Kingdom

institute: Cancer Research UK Manchester Institute

description: Library name: YS_p1_run1_NB65_GL69_0800_WN-S6-3_A18_YS_E10-5_HE_Gfi1_S32

data_processing:
Nanopore sequencing data were basecalled using Dorado (v0.9.1) using the high-accuracy model (dna_r10.4.1_e8.2_400bps_hac@v5.0.0). Raw reads were trimmed for SMARTseq adapters using bbduk.sh (v39.08). Chimeric reads were filtered from the data using YACRD (v1.0.0) and porechop (v0.2.4). Cleaned reads were aligned to GENCODE transcripts (Release 37) using Minimap2 (v2.26), retaining a maximum of 10 alignments per read. Alignments were quantified using Nanocount (v1.0.0.post6). Abundance files were read into R (v4.3.0) filtered for low library size samples using findOutliers (scuttle v1.10.3; type = "lower", nmads = 1) and normalised using DESeq2 (v1.40.2). Estimated and normalised counts were subject to analysis using IsoformSwitchAnalyzeR and SplicingFactory as previously described.
Assembly: GENCODE transcripts (Release 37)
Supplementary files format and content: nanoCount_trans_Estcount.txt; nanoCount Estimated counts as TSV
Supplementary files format and content: nanoCount_trans_tpm.txt; nanoCount TPM as TSV

source_name: mouse embryo yolk sac

growth_protocol: fresh samples (AGM and Yolksac) were harvested from mouse embryos and directly processed for sequencing

extract_protocol:
Single cells were FACS sorted into wells of a 384-well plate containing lysis buffer and snap-frozen.
10ng full-length purified amplified cDNA from a miniaturised Smart-seq2 cDNA was purified using a 0.7x volume of AMPure XP reagent (Beckman Coulter). Purified amplification product was quantified by Qubit (ThermoFisher) and sized / quality checked by Fragment Analyzer (Agilent). 200fmol was used as input for the Ligation sequencing amplicons - Native Barcoding Kit 24 V14 (SQK-NBD114.24) protocol (revision H) (Oxford Nanopore). Sequencing was performed on a PromethION P2 Solo (Oxford Nanopore) using flow cell FLO-PRO114M

treatment_protocol: No treatments were performed. Cells were directly harvested from Embryos and FACS sorted into lyses buffer for sequence library preparation.

value: mouse embryo yolk sac

value: primary material

value: early YS hematopoietic progenitor (LMP skewed)


title: MCF7-COX2, DOX, 48hr, Rep1

description: Library name: Sample 22


title: AKTP MTO, RM-044, replicate 2

city: Barcelona

first: Adria-Jaume

last: Roura

address: Carrer de Baldiri Reixac, 10

country: Spain

institute: IRB Barcelona

description: Library name: Sample 4

library_source: genomic

data_processing:
bigwig
Assembly: GRCm39/mm39
Supplementary files format and content: bigwig

molecule: genomic DNA

source_name: Mouse Tumor Organoids (MTO)

extract_protocol:
Dissociation was done in 1.5 ml 1:10 TryplE medium for 30 min at 37 ºC with vigorously pipetted every 10 min, quenched in Advanced DMEM/F12 (Gibco, 12634028), supplemented with 10mM HEPES (Gibco, 11560496), Glutamax (Gibco, 11574466), and quickly centrifuged for 5 min at 500 g at 4 ºC. The pellet was washed in cold PBS and cells were lysed in 300 μl cold ATAC-seq resuspension buffer (RSB; 10 mM Tris-HCl pH 7.4, 10 mM NaCl, 3 mM MgCl2 in water) containing 0.1% IGEPAL CA-630 (Sigma, l8896) following centrifugation for 10 min at 500g at 4 ºC. 200 μl of supernatant was aspirated and centrifugation was repeated for 5 min. Counting was done in RSB with a Neubauer chamber and aliquots of 50.000 nuclei were prepared and resuspended in 50 μl transposition mix (25 μl 2x TD buffer (Illumina, 20034197), 2.5 μl transposase (Illumina, 20034197), 16.5 μl PBS, 0.5 μl 1% digitonin (Millipore, 300410), 0.5% 10% Tween-20 (Sigma-Aldrich, P9416) and 5 μl water) by pipetting up and down 10 times. Transposition reactions were incubated at 37 ºC for 30 min in a thermomixer and then cleaned up with Qiagen MinElute PCR Purification Kit (Qiagen, 28004).
Libraries were prepared as described in Buenrostro et al., 2015. Library concentration and profile were assessed with Qubit HS dsDNA (Invitrogen, Q33321) and Tapestation (Agilent, 5067-5589, 5067-5590), respectively, and sequencing was done with Illumina NextSeq 2000 2x100 bp PE sequencing for at least 200 M reads.

value: Mouse Tumor Organoids (MTO)

value: Epithelial malignant cells

value: AKTP mutant

value: RM-044 KRASi


title: MCF7-COX2, DMSO, 48hr, Rep3

description: Library name: Sample 21

value: DMSO, 48hr


title: YS_p1_run1_NB64

description: Library name: YS_p1_run1_NB64_GL69_705_WN-S6-4_J4_YS_E10-5_HE_Runx1_S705


title: MCF7-COX2, DMSO, 48hr, Rep2

description: Library name: Sample 20


title: AKTP MTO, RM-044, replicate 1

description: Library name: Sample 3


title: 8C_F2_A


title: YS_p1_run1_NB62

description: Library name: YS_p1_run1_NB62_GL69_398_WN-S6-4_H5_YS_E10-5_HE_Runx1_S398


title: 8C_F1_C


title: YS_p1_run1_NB41

description: Library name: YS_p1_run1_NB41_GL69_0910_WN-S6-4_I11_YS_E10-5_HE_Runx1_S142


title: MCF7-miR655, DOX, 48hr, Rep3

description: Library name: Sample 18


title: 8C_F1_A


title: P1_F, estradiol, replicate 2

city: San Diego

first: Yuejia

last: Liu

state: California

address: DNC 210, The Scripps Research Institute, 9060 Activity Road, Unit F

institute: The Scripps Research Institute

description: 10 x Genomics

library_source: genomic single cell

data_processing:
The “cellranger-atac count” command (v2.1.0) with default parameters was used to align reads from raw FASTQ files to the mm10 reference genome.
Assembly: mm10
Supplementary files format and content: Seurat object file of cell matrix of all conditions.

source_name: neocortex

extract_protocol:
Animals were anaesthetized on ice, 6 hours post-injection, followed by dissection of the entire neocortex on ice, excluding the amygdalar regions. Followed by a nuclei isolation protocol, GFP+ and 7-AAD+ nuclei were collected into cold PBS with 0.1% BSA by FACS.
The snATAC-seq libraries were constructed using the Chromium Next GEM Single Cell ATAC 40 Reagent Kits v2 (10x Genomics) following the manufacturer’s protocol.

treatment_protocol: Intraperitoneal injection of 5ug estradiol-benzoate or DMSO (vehicle) in sesame oil were administered in female pups at P1 (5-6 animals pooled per condition in each replicate).

value: neocortex

value: Estradiol-benzoate in sesame oil


title: AKTP MTO, vehicle control, replicate 2

description: Library name: Sample 2


title: MCF7-COX2, DMSO, 48hr, Rep1

description: Library name: Sample 19

value: Breast


title: MCF7-miR655, DOX, 48hr, Rep2

description: Library name: Sample 17

value: Adenocarcinoma


title: 4C_F10_C


title: YS_m2_run3_NB45

description: Library name: YS_m2_run3_NB45_GL69_151_WN-S6-3_H17_YS_E10-5_HE_Gfi1_S151

value: HE-YSA (late)


title: YS_p1_run1_NB53

description: Library name: YS_p1_run1_NB53_GL69_032_WN-S6-3_B18_YS_E10-5_HE_Runx1_S32


title: AKTP MTO, vehicle control, replicate 1

description: Library name: Sample 1


title: P1_F, vehicle, replicate 2

description: 10 x Genomics

value: DMSO in sesame oil


title: YS_m2_run3_NB64

description: Library name: YS_m2_run3_NB64_GL69_105_WN-S6-1_P6_YS_E10-5_HE_Gfi1_S105


title: 8C_F1_B

value: oocyte or embryo


title: MCF7-miR655, DOX, 48hr, Rep1

description: Library name: Sample 16

value: DOX, 48hr


title: ovis, AFB1_4

city: Changchun

first: qi

middle: Chuan

last: Wang

address: No. 5333 Xian Load

country: China

institute: Jilin university

description: Library name: T2_4

data_processing:
Reads obtained from the sequencing machines includes raw reads containing adapters or low quality bases which will affect the following assembly and analysis. Thus, to get high quality clean reads, reads were further filtered by Cutadapt (https://cutadapt.readthedocs.io/en/stable/,version:cutadapt-1.9). We aligned reads of all samples to the research species reference genome using HISAT2 (https://daehwankimlab.github.io/hisat2/,version:hisat2-2.2.1) package, which initially remove a portion of the reads based on quality information accompanying each read and then maps the reads to the reference genome.
The mapped reads of each sample were assembled using StringTie (http://ccb.jhu.edu/software/stringtie/,version:stringtie-2.1.6) with default parameters. Then, all transcriptomes from all samples were merged to reconstruct a comprehensive transcriptome using gffcompare software(http://ccb.jhu.edu/software/stringtie/gffcompare.shtml,version:gffcompare-0.9.8). After the final transcriptome was generated, StringTie and ballgown (http://www.bioconductor.org/packages/release/bioc/html/ballgown.html) were used to estimate the expression levels of all transcripts and perform expression abundance for mRNAs by calculating FPKM (fragment per kilobase of transcript per million mapped reads) value.
Genes differential expression analysis was performed by DESeq2 software between two different groups (and by edgeR between two samples). The genes with the parameter of false discovery rate (FDR) below 0.05 and absolute fold change ≥ 2 were considered differentially expressed genes. Differentially expressed genes were then subjected to enrichment analysis of GO functions and KEGG pathways.
Assembly: ARS-Ul Ramb v3.0
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

organism: Ovis aries

source_name: kidney

extract_protocol:
Total RNA was extracted using Trizol reagent (thermofisher, 15596018) following the manufacturer's procedure. The total RNA quantity and purity were analysis of Bioanalyzer 2100 and RNA 6000 Nano LabChip Kit (Agilent, CA, USA, 5067-1511) , high-quality RNA samples with RIN number > 7.0 were used to construct sequencing library.
mRNA was purified from total RNA (5ug) using Dynabeads Oligo (dT) (Thermo Fisher, CA, USA) with two rounds of purification. Following purification, the mRNA was fragmented into short fragments using divalent cations under elevated temperature (Magnesium RNA Fragmentation Module (NEB, cat.e6150, USA) under 94℃ 5-7min). Then the cleaved RNA fragments were reverse-transcribed to create the cDNA by SuperScript™ II Reverse Transcriptase (Invitrogen, cat. 1896649, USA), which were next used to synthesise U-labeled second-stranded DNAs with E. coli DNA polymerase I (NEB, cat.m0209, USA), RNase H (NEB, cat.m0297, USA) and dUTP Solution (Thermo Fisher, cat.R0133, USA). An A-base was then added to the blunt ends of each strand, preparing them for ligation to the indexed adapters. Each adapter contained a T-base overhang for ligating the adapter to the A-tailed fragmented DNA. Dual-index adapters were ligated to the fragments, and size selection was performed with AMPureXP beads. After the heat-labile UDG enzyme (NEB, cat.m0280, USA) treatment of the U-labeled second-stranded DNAs, the ligated products were amplified with PCR by the following conditions: initial denaturation at 95℃ for 3 min; 8 cycles of denaturation at 98℃ for 15 sec, annealing at 60℃ for 15 sec, and extension at 72℃ for 30 sec; and then final extension at 72℃ for 5 min. The average insert size for the final cDNA librarys were 300±50 bp. At last, we performed the 2×150bp paired-end sequencing (PE150) on an Illumina NovaseqTM 6000 following the vendor's recommended protocol.

treatment_protocol: CON, AFB1_CUR, AFB1

value: kidney

value: missing

tag: batch


title: 4C_F10_B


title: ovis, AFB1_5

description: Library name: T2_5


title: MCF7-miR655, DMSO, 48hr, Rep3

description: Library name: Sample 15


title: ovis, AFB1_2

description: Library name: T2_2


title: 4C_F9_A


title: 4C_F10_A


title: YS_m2_run3_NB35

description: Library name: YS_m2_run3_NB35_GL69_0884_WN-S6-3_H20_YS_E10-5_HE_Gfi1_S116

value: mouse embryo yolk sac

value: primary material


title: YS_m2_run3_NB37

description: Library name: YS_m2_run3_NB37_GL69_1415_WN-S6-3_P06_YS_E10-5_HE_Gfi1_S324


title: ovis, AFB1_3

description: Library name: T2_3


title: 4C_F9_C


title: ovis, AFB1_CUR5

description: Library name: T1_5


title: MCF7-miR655, DMSO, 48hr, Rep1

description: Library name: Sample 13


title: 4C_F8_C


title: YS_m2_run3_NB28

description: Library name: YS_m2_run3_NB28_GL69_236_WN-S6-4_E4_YS_E10-5_HE_Gfi1_S236


title: 4C_F8_B


title: YS_m2_run3_NB27

description: Library name: YS_m2_run3_NB27_GL69_259_WN-S6-4_C12_YS_E10-5_HE_Gfi1_S259


title: 4C_F9_B


title: MCF7-miR655, DMSO, 48hr, Rep2

description: Library name: Sample 14


title: MCF7-miR526b, DOX, 48hr, Rep1

description: Library name: Sample 10


title: ovis, AFB1_CUR4

description: Library name: T1_4


title: MCF7-miR526b, DMSO, 48hr, Rep3

description: Library name: Sample 9


title: ovis, AFB1_CUR3

description: Library name: T1_3


title: ovis, AFB1_1

description: Library name: T2_1


title: MCF7-miR526b, DOX, 48hr, Rep2

description: Library name: Sample 11


title: YS_m2_run3_NB03

description: Library name: YS_m2_run3_NB03_GL69_1157_WN-S7-1_J08_YS_E9-5_HE_Gfi1_S66


title: MCF7-miR526b, DMSO, 48hr, Rep2

description: Library name: Sample 8


title: 4C_F7_C


title: YS_m2_run3_NB16

description: Library name: YS_m2_run3_NB16_GL69_614_WN-S6-4_O2_YS_E10-5_HE_Gfi1_S614


title: MCF7-miR526b, DMSO, 48hr, Rep1

description: Library name: Sample 7


title: 4C_F8_A


title: ovis, AFB1_CUR2

description: Library name: T1_2


title: 4C_F7_B


title: YS_m2_run2_NB64

description: Library name: YS_m2_run2_NB64_GL69_681_WN-S6-4_N7_YS_E10-5_HE_Gfi1_S681


title: ovis, AFB1_CUR1

description: Library name: T1_1


title: 4C_F7_A


title: ovis, CON5

description: Library name: C5

value: CON


title: 4C_F6_C


title: YS_m2_run2_NB60

description: Library name: YS_m2_run2_NB60_GL69_329_WN-S6-1_P7_YS_E10-5_HE_Gfi1_S329


title: ovis, CON4

description: Library name: C4


title: MCF7, DOX, 48hr, Rep1

description: Library name: Sample 4


title: MCF7-miR526b, DOX, 48hr, Rep3

description: Library name: Sample 12


title: YS_m2_run3_NB14

description: Library name: YS_m2_run3_NB14_GL69_1417_WN-S6-4_H03_YS_E10-5_HE_Gfi1_S326


title: YS_m2_run3_NB13

description: Library name: YS_m2_run3_NB13_GL69_1053_WN-S6-3_K14_YS_E10-5_HE_Gfi1_S285


title: 4C_F6_B


title: YS_m2_run2_NB44

description: Library name: YS_m2_run2_NB44_GL69_1139_WN-S7-1_G05_YS_E9-5_HE_Gfi1_S48


title: MCF7, DOX, 48hr, Rep2

description: Library name: Sample 5


title: 4C_F6_A


title: ovis, CON3

description: Library name: C3


title: MCF7, DMSO, 48hr, Rep3

description: Library name: Sample 3


title: ovis, CON2

description: Library name: C2


title: YS_m2_run2_NB48

description: Library name: YS_m2_run2_NB48_GL69_1384_WN-S8-1_O07_YS_E9-0_HE_Gfi1_S293


title: MCF7, DMSO, 48hr, Rep2

description: Library name: Sample 2


title: YS_m2_run2_NB43

description: Library name: YS_m2_run2_NB43_GL69_175_WN-S6-4_D6_YS_E10-5_HE_Gfi1_S175


title: 4C_F5_C


title: ovis, CON1

description: Library name: C1


title: YS_m2_run2_NB39

description: Library name: YS_m2_run2_NB39_GL69_1099_WN-S7-1_B05_YS_E9-5_HE_Gfi1_S8


title: 4C_F5_B


title: YS_m2_run2_NB62

description: Library name: YS_m2_run2_NB62_GL69_1142_WN-S7-1_G08_YS_E9-5_HE_Gfi1_S51


title: MCF7, DOX, 48hr, Rep3

description: Library name: Sample 6


title: MCF7, DMSO, 48hr, Rep1

description: Library name: Sample 1


title: 4C_F5_A


title: YS_m2_run2_NB31

description: Library name: YS_m2_run2_NB31_GL69_1419_WN-S6-4_L06_YS_E10-5_HE_Gfi1_S328


title: ChIP-Seq, WT_SBP009_Li_Input

city: Montreal

first: Alain

last: Pacis

state: QC

address: 1010 Sherbrooke #1800

institute: Canadian Centre for Computational Genomics (C3G)

description: Library name: WT_SBP009_Li_Input

data_processing:
ChIP-seq reads were first trimmed for adapter sequences and low-quality score bases using Trimmomatic.
The resulting reads were mapped to the human reference genome (GRCh38) using BWA-MEM in paired-end mode at default parameters (-k 19 -w 100 -d 100).
Only reads that had a unique alignment (mapping quality > 20) were retained and PCR duplicates were marked using Picard tools.
Peaks were called using MACS2.
Assembly: GRCh38
Supplementary files format and content: Processed files contains MACS2 output, which includes 10 columns: "chromosome" "start" "end" "name" "score" "strand" "signalValue" "pValue" "qValue" "peak"

source_name: iPSCs were derived from human lymphocytes

growth_protocol: iPSCs were maintained on a Matrigel (Corning, Cat. #08-774-552) coated plate with mTeSR™1 medium (STEMCELL Technologies, Cat. #85870) along with Y-27632 (ROCK inhibitor, STEMCELL Technologies, Cat. # 72307) after each passage. During the course of induction of iPSC to NPCs (20 days), STEMdiff™ SMADi Neural Induction Kit (STEMCELL Technologies, Cat. #08581) was used. The method for induction of iPSC to NPCs was based on the STEMCELL™ neural induction EB-based method and was performed following the manufacturer’s protocol. On Day 0, a single-cell suspension of iPSC was generated using Gentle Cell Dissociation Reagent (STEMCELL Technologies, Cat. # 100-0485), and 10,000 cells per microwell were seeded in an ultralow attachment 96-well plate to generate Embryoid bodies (EBs), cultured in STEMdiff™ Neural Induction Medium + SMADi (STEMdiff™ SMADi Neural Induction Kit, Cat. # 08582) + 10 μM Y-27632. From Day 1 to Day 4, a daily partial (3/4) medium change was performed using STEMdiff™ Neural Induction Medium + SMADi. On Day 5, EBs were harvested using a wild-board 1ml serological pipettes and 40μm strainer and transferred to a single well of a 6-well plate coated with Poly-L-ornithine hydrobromide (PLO) and laminin. A daily full medium change was performed from Day 6 to Day 11. After the neural induction efficiency was determined higher than 75%, neural rosettes were manually selected using STEMdiff™ Neural Rosette Selection Reagent (STEMCELL Technologies, Cat. # 05832) on Day 12 and replated onto a single well of PLO/Laminin coated 6-well plate. With continuous daily full medium change, selected rosette-containing clusters attached, and NPC outgrowths formed a monolayer between the clusters. The NPCs were ready for passage 1 when cultures were approximately 80 - 90% confluent (typically on Day 19). NPCs were maintained and expanded (7-10 days) using DMEM/F12 with Glutamax (ThermoFisher, Cat. #10565042), N2 1x (ThermoFisher, Cat. # 17502001), B27 1x (ThermoFisher, Cat. #17504001), FGF2 20 ng/ml (PEPROTECH, Cat. #100-18B), and EGF 20 ng/ml (Gibco, Cat. # AF-100-15-1MG). For the final differentiation of NPCs into neurons, NPCs were detached using Accutase (STEMCELL Technologies, Cat. #7922) and then differentiated onto PLO/laminin-coated plates with final differentiation media of BrainPhys™ Neuronal Medium (STEMCELL Technologies, Cat. #05790) supplemented with Glutamax 1x (ThermoFisher, Cat. #35050061), N2 1x (ThermoFisher, Cat. #17502001), B27 1x (ThermoFisher, Cat. #17504001), 200nM ascorbic acid 200nM (STEMCELL Technologies, Cat. #72132), cyclic AMP 500 μg/ml (Sigma-Aldrich, Cat #A9501-1G), brain-derived neurotrophic factor 20 ng/ml (BDNF, GIBCO, Cat. #PHC7074), Wnt3a 10 ng/ml (R&D Systems, Cat. #5036-WN-500), and laminin 1 μg/ml (Gibco, Cat. #23017015) for 14 days (medium change of 3 times per week). Subsequently, the cells were maintained in STEMdiff™ Forebrain Neuron Maturation Kit for 11 days (STEMCELL Technologies, Cat. #08605) --final differentiation media was replaced by STEMdiff™ Forebrain Neuron Maturation Kit in the same dishware.

extract_protocol:
About 10 million neuronal cells per sample were grown and directly crosslinked on the plate with 1% formaldehyde (Sigma) for 10 minutes at room temperature and the reaction was stopped using 125nM Glycine for 5 minutes. Fixed cell preparations were washed with ice-cold PBS, scraped off the plate, pelleted, washed twice again in ice-cold PBS, and the flash-frozen pellets were stored at −80°C.
Library preparation was carried out using Kapa Hyper Prep library preparation reagents (Kapa Hyper Prep kit, Roche 07962363001) following the manufacturer’s protocol.

treatment_protocol: For AKAP11-KO clones only: To generate three isogenic knockout clones from the WT iPSC (SBP009), Ribonucleoprotein (RNP)-mediated CRISPR-Cas9 genome editing was performed using the Alt-R CRISPR-Cas9 system (IDT). Two synthetic crRNA guides were designed (TACTGGTATAAGGTACACCT PAM:TGG and CTGATGCAAGAATGTGTCCA PAM:AGG) to form a duplex with Alt-R® CRISPR-Cas9 tracrRNA, ATTO 550 (IDT, Cat. # 1075928) and coupled to the Alt-R© S.p. Cas9 Nuclease V3 (IDT). The Lipofectamine™ Stem Transfection (Invitrogen, Cat. #STEM00001) and PLUS™ Reagent (Invitrogen, Cat. #11514015) ratios were optimized with a lower volume than the manufacturer’s protocol. The transfected cells were incubated for 48 hours. Single ATTO550+ cells were then sorted into 96-well plates. A subset of the Het-AKAP11-KO dishes was treated with 1.5 mM lithium added to the STEMdiff™ Forebrain Neuron Maturation Kit media. They were maintained in the lithium-containing media for 11 days, to mimic chronic Li treatment, with media change every 4 days.

value: neuronal glial culture

value: WT-Li

tag: chip antibody


title: ChIP-Seq, Het_AKAP11-KO-Clone 21_Li_Input

description: Library name: Het_AKAP11-KO-Clone 21_Li_Input

value: iPSCs were derived from human lymphocytes


title: hCMEC/d3 cells, 4 hours T. pallidum exposure biorep 4

city: Burnaby

first: Travis

last: Blimkie

state: British Columbia

address: 8888 University Drive

department: MBB

institute: Simon Fraser University

data_processing:
Read quality was checked with FastQC 0.12.1
The fastq sequence reads were aligned to the Ensembl human reference genome using STAR v2.7.10b
Alignments output by STAR were counted using HTSeq’s “count” function 2.0.2
Sequence, alignment, and count quality metrics were assessed with MultiQC 1.13
Assembly: Ensembl GRCh38.98 (hg19) human reference genome
Supplementary files format and content: Process data files are tab-delmited counts

growth_protocol: hCMEC/d3 cells grown to near-confluence in complete EndoGRO MV culture media (millipore) at 5% CO2 37C

extract_protocol:
RNA was extracted using 1:1 RNAprotect cell and RNAprotect bacteria (Qiagen), then extracted using Qiagen RNeasy kit.
cDNA libraries were constructed from polyA-purified RNA using the Roche KAPA HyperPrep kit.

treatment_protocol: hCMEC/d3 cells exposed to in vivo grown T. pallidum, or a background media control lacking the pathogen. Incubations occurred at 34°C in a microaerophilic environment of 1.5% O2, 5% CO2, 93.5% N2 for 45 minutes, 4-, 12-, and 24-hours.

value: cerebral brain microvascular endothelial cell

value: WT

value: T. pallidum

tag: time

value: 4 hour exposure


title: YS_m2_run2_NB18

description: Library name: YS_m2_run2_NB18_GL69_360_WN-S6-4_E12_YS_E10-5_HE_Gfi1_S360


title: hCMEC/d3 cells, 4 hours T. pallidum exposure biorep 3


title: 4C_F4_C


title: YS_m2_run2_NB14

description: Library name: YS_m2_run2_NB14_GL69_715_WN-S6-4_I1_YS_E10-5_HE_Gfi1_S715


title: ChIP-Seq, Het_AKAP11-KO-Clone 20_Li_Input

description: Library name: Het_AKAP11-KO-Clone 20_Li_Input


title: hCMEC/d3 cells, 4 hours T. pallidum exposure biorep 2


title: 4C_F4_B


title: ChIP-Seq, Het_AKAP11-KO-Clone 16_Li_Input

description: Library name: Het_AKAP11-KO-Clone 16_Li_Input


title: YS_m2_run1_NB69

description: Library name: YS_m2_run1_NB69_GL69_1158_WN-S7-1_J09_YS_E9-5_HE_Gfi1_S67


title: 4C_F4_A


title: ChIP-Seq, WT_SBP009_Rep3_Li_ChIP

description: Library name: WT_SBP009_Rep3_Li_ChIP

value: rabbit polyclonal anti-H3K27ac Diagenode Cat. #C15410196, RRID:AB_2637079


title: hCMEC/d3 cells, 45 minutes T. pallidum exposure biorep 4

value: 45 minute exposure


title: YS_m2_run1_NB57

description: Library name: YS_m2_run1_NB57_GL69_739_WN-S6-4_I6_YS_E10-5_HE_Gfi1_S739

value: HE-YSA (late)


title: 4C_F3_B

value: oocyte or embryo


title: ChIP-Seq, WT_SBP009_Rep2_Li_ChIP

description: Library name: WT_SBP009_Rep2_Li_ChIP


title: YS_m2_run1_NB52

description: Library name: YS_m2_run1_NB52_GL69_161_WN-S6-4_E1_YS_E10-5_HE_Gfi1_S161


title: ChIP-Seq, WT_SBP009_Rep1_Li_ChIP

description: Library name: WT_SBP009_Rep1_Li_ChIP


title: hCMEC/d3 cells, 45 minutes T. pallidum exposure biorep 3


title: YS_m2_run1_NB48

description: Library name: YS_m2_run1_NB48_GL69_719_WN-S6-1_L10_YS_E10-5_HE_Gfi1_S719


title: hCMEC/d3 cells, 4 hours T. pallidum exposure biorep 5


title: 4C_F3_A


title: ChIP-Seq, Het_AKAP11-KO-Clone 21_Li_ChIP

description: Library name: Het_AKAP11-KO-Clone 21_Li_ChIP


title: YS_m2_run1_NB45

description: Library name: YS_m2_run1_NB45_GL69_1244_WN-S8-1_C13_AGM_E10-5_HE_Gfi1_S153


title: hCMEC/d3 cells, 45 minutes T. pallidum exposure biorep 2


title: YS_m2_run1_NB44

description: Library name: YS_m2_run1_NB44_GL69_0957_WN-S6-1_G13_YS_E10-5_HE_Gfi1_S189


title: ChIP-Seq, Het_AKAP11-KO-Clone 20_Li_ChIP

description: Library name: Het_AKAP11-KO-Clone 20_Li_ChIP


title: 4C_F2_B


title: hCMEC/d3 cells, 24 hours T. pallidum exposure biorep 5

value: 24 hour exposure


title: YS_m2_run1_NB31

description: Library name: YS_m2_run1_NB31_GL69_007_WN-S6-1_M5_YS_E10-5_HE_Gfi1_S7


title: ChIP-Seq, Het_AKAP11-KO-Clone 16_Li_ChIP

description: Library name: Het_AKAP11-KO-Clone 16_Li_ChIP


title: hCMEC/d3 cells, 4 hours T. pallidum exposure biorep 1


title: hCMEC/d3 cells, 24 hours T. pallidum exposure biorep 4


title: 4C_F2_A


title: ChIP-Seq, WT_SBP009_Input

description: Library name: WT_SBP009_UNT_Input

value: WT-Untreated


title: 4C_F1_C


title: 4C_F1_B


title: YS_m2_run1_NB21

description: Library name: YS_m2_run1_NB21_GL69_1148_WN-S7-1_H11_YS_E9-5_HE_Gfi1_S57


title: ChIP-Seq, Het_AKAP11-KO-Clone 21_Input

description: Library name: Het_AKAP11-KO-Clone 21_UNT_Input


title: 4C_F3_C


title: ChIP-Seq, Het_AKAP11-KO-Clone 20_Input

description: Library name: Het_AKAP11-KO-Clone 20_UNT_Input


title: 4C_F2_C


title: 4C_F1_A


title: hCMEC/d3 cells, 45 minutes T. pallidum exposure biorep 1


title: hCMEC/d3 cells, 24 hours T. pallidum exposure biorep 3


title: YS_m2_run1_NB01

description: Library name: YS_m2_run1_NB01_GL69_0925_WN-S6-4_J11_YS_E10-5_HE_Gfi1_S157


title: hCMEC/d3 cells, 12 hours T. pallidum exposure biorep 5

value: 12 hour exposure


title: YS_m1_run3_NB71

description: Library name: YS_m1_run3_NB71_GL69_347_WN-S6-4_O11_YS_E10-5_HE_Gfi1_S347

value: mouse embryo yolk sac

value: HE-YSA (early)


title: 2C_F10_C


title: ChIP-Seq, WT_SBP009_Rep3_ChIP

description: Library name: WT_SBP009_Rep3_UNT_ChIP


title: YS_m1_run3_NB61

description: Library name: YS_m1_run3_NB61_GL69_1104_WN-S7-1_C03_YS_E9-5_HE_Gfi1_S13

value: primary material


title: ChIP-Seq, WT_SBP009_Rep2_ChIP

description: Library name: WT_SBP009_Rep2_UNT_ChIP

value: neuronal glial culture


title: 2C_F10_B


title: hCMEC/d3 cells, 12 hours T. pallidum exposure biorep 4


title: YS_m1_run3_NB46

description: Library name: YS_m1_run3_NB46_GL69_473_WN-S6-4_M10_YS_E10-5_HE_Gfi1_S473


title: YS_m1_run3_NB43

description: Library name: YS_m1_run3_NB43_GL69_0908_WN-S6-3_K20_YS_E10-5_HE_Gfi1_S140


title: hCMEC/d3 cells, 12 hours T. pallidum exposure biorep 3


title: ChIP-Seq, WT_SBP009_Rep1_ChIP

description: Library name: WT_SBP009_Rep1_UNT_ChIP


title: 2C_F9_C


title: YS_m2_run1_NB07

description: Library name: YS_m2_run1_NB07_GL69_1108_WN-S7-1_C07_YS_E9-5_HE_Gfi1_S17


title: 2C_F10_A


title: hCMEC/d3 cells, 24 hours T. pallidum exposure biorep 2


title: YS_m1_run3_NB36

description: Library name: YS_m1_run3_NB36_GL69_154_WN-S6-4_J10_YS_E10-5_HE_Gfi1_S154


title: hCMEC/d3 cells, 24 hours T. pallidum exposure biorep 1


title: ChIP-Seq, Het_AKAP11-KO-Clone 21_ChIP

description: Library name: Het_AKAP11-KO-Clone 21_UNT_ChIP


title: YS_m1_run3_NB33

description: Library name: YS_m1_run3_NB33_GL69_427_WN-S6-4_C11_YS_E10-5_HE_Gfi1_S427


title: ChIP-Seq, Het_AKAP11-KO-Clone 16_Input

description: Library name: Het_AKAP11-KO-Clone 16_UNT_Input


title: 2C_F9_B


title: hCMEC/d3 cells, 12 hours T. pallidum exposure biorep 1


title: ChIP-Seq, Het_AKAP11-KO-Clone 16_ChIP

description: Library name: Het_AKAP11-KO-Clone 16_UNT_ChIP


title: WT_SBP009_Rep3_Li

description: Library name: WT_SBP009_Rep3_Li_RNAseq

data_processing:
Adaptor sequences and low-quality score bases (Phred score < 30) were first trimmed using Trimmomatic.
The resulting reads were aligned to the GRCh38 human reference genome assembly, using STAR.
Read counts were obtained using HTSeq with parameters-m intersection-nonempty-stranded=reverse.
For all downstream analyses, we excluded lowly expressed genes with an average read count lower than 20 across all samples, resulting in a total of 19,568  genes.
Assembly: GRCh38
Supplementary files format and content: tab-delimited text file contains the read counts matrix, with genes as rows and samples as columns

extract_protocol:
RNA was extracted from bulk neuronal culture 25 days post-differentiation using RNeasy Mini Kit and its protocol (Cat. #74104).
Library preparation from total RNA was performed using NEB rRNA-depleted (HMR) stranded library preparation kit according to the manufacturer’s instructions

value: Lithium


title: ChIP-Seq, Het_AKAP11-KO-Clone 20_ChIP

description: Library name: Het_AKAP11-KO-Clone 20_UNT_ChIP

value: iPSCs were derived from human lymphocytes


title: hCMEC/d3 cells, 4 hours control exposure biorep 5

value: cerebral brain microvascular endothelial cell

value: Control


title: 2C_F9_A


title: 2C_F8_C


title: YS_m1_run3_NB26

description: Library name: YS_m1_run3_NB26_GL69_0867_WN-S6-3_J16_YS_E10-5_HE_Gfi1_S99


title: 2C_F8_B


title: hCMEC/d3 cells, 4 hours control exposure biorep 2

value: WT


title: hCMEC/d3 cells, 12 hours T. pallidum exposure biorep 2

value: T. pallidum


title: hCMEC/d3 cells, 4 hours control exposure biorep 3

value: 4 hour exposure


title: 2C_F8_A


title: YS_m1_run3_NB18

description: Library name: YS_m1_run3_NB18_GL69_1137_WN-S7-1_G03_YS_E9-5_HE_Gfi1_S46


title: WT_SBP009_Rep2_Li

description: Library name: WT_SBP009_Rep2_Li_RNAseq


title: 2C_F7_C


title: YS_m1_run2_NB61

description: Library name: YS_m1_run2_NB61_GL69_650_WN-S6-1_O6_YS_E10-5_HE_Runx1_S650


title: WT_SBP009_Rep1_Li

description: Library name: WT_SBP009_Rep1_Li_RNAseq


title: hCMEC/d3 cells, 4 hours control exposure biorep 1


title: 2C_F7_B


title: Het_AKAP11-KO-Clone 20_Li

description: Library name: Het_AKAP11-KO-Clone 20_Li_RNAseq


title: Het_AKAP11-KO-Clone 21_Li

description: Library name: Het_AKAP11-KO-Clone 21_Li_RNAseq


title: hCMEC/d3 cells, 4 hours control exposure biorep 4


title: hCMEC/d3 cells, 45 minutes control exposure biorep 5

value: 45 minute exposure


title: Het_AKAP11-KO-Clone 16_Li

description: Library name: Het_AKAP11-KO-Clone 16_Li_RNAseq


title: YS_m1_run3_NB29

description: Library name: YS_m1_run3_NB29_GL69_728_WN-S6-1_K2_YS_E10-5_HE_Gfi1_S728


title: 2C_F6_C


title: WT_SBP009_Rep3_UNT

description: Library name: WT_SBP009_Rep3_UNT_RNAseq

value: Untreated


title: YS_m1_run2_NB57

description: Library name: YS_m1_run2_NB57_GL69_1198_WN-S7-1_P12_YS_E9-5_HE_Gfi1_S107


title: YS_m1_run2_NB55

description: Library name: YS_m1_run2_NB55_GL69_179_WN-S6-1_O1_YS_E10-5_HE_Gfi1_S179


title: hCMEC/d3 cells, 45 minutes control exposure biorep 3


title: 2C_F7_A

value: oocyte or embryo


title: hCMEC/d3 cells, 45 minutes control exposure biorep 4


title: YS_m1_run2_NB50

description: Library name: YS_m1_run2_NB50_GL69_465_WN-S6-3_C10_YS_E9-5_HE_Gfi1_S465


title: WT_SBP009_Rep2_UNT

description: Library name: WT_SBP009_Rep2_UNT_RNAseq


title: YS_m1_run2_NB42

description: Library name: YS_m1_run2_NB42_GL69_1106_WN-S7-1_C05_YS_E9-5_HE_Gfi1_S15


title: 2C_F6_B


title: YS_m1_run2_NB30

description: Library name: YS_m1_run2_NB30_GL69_387_WN-S6-2_G5_YS_E9-5_HE_Runx1_S387


title: 2C_F6_A


title: WT_SBP009_Rep1_UNT

description: Library name: WT_SBP009_Rep1_UNT_RNAseq


title: hCMEC/d3 cells, 45 minutes control exposure biorep 1


title: YS_m1_run2_NB12

description: Library name: YS_m1_run2_NB12_GL69_1105_WN-S7-1_C04_YS_E9-5_HE_Gfi1_S14


title: Het_AKAP11-KO-Clone 21_UNT

description: Library name: Het-AKAP11-KO-Clone 21_UNT_RNAseq


title: hCMEC/d3 cells, 45 minutes control exposure biorep 2


title: YS_m1_run2_NB32

description: Library name: YS_m1_run2_NB32_GL69_348_WN-S6-4_N9_YS_E10-5_HE_Gfi1_S348


title: Het_AKAP11-KO-Clone 20_UNT

description: Library name: Het-AKAP11-KO-Clone 20_UNT_RNAseq


title: hCMEC/d3 cells, 24 hours control exposure biorep 2

value: 24 hour exposure


title: hCMEC/d3 cells, 24 hours control exposure biorep 3


title: YS_m1_run1_NB67

description: Library name: YS_m1_run1_NB67_GL69_088_WN-S6-1_L9_YS_E10-5_HE_Gfi1_S88


title: T47D R5020 replicate 3 H3K27Ac ChIP

city: Aurora

first: Jessica

last: Finlay-Schultz

state: CO

department: Pathology

institute: University of Colorado Denver Anschutz Medical Campus

description: Library name: Sample 36

data_processing:
adpater trimming was done using cutadapt
alignment was doneusing Bowtie2 to human hg38
peak calling was done using macs2
Assembly: hg38
Supplementary files format and content: tab separated peaks

source_name: T47D cell line

growth_protocol: T47D cells were maintained in minimal Eagle’s medium, 5% FBS, 1X NEAA, 10^-9 M insulin, 0.1 mg/mL sodium pyruvate, and 2 mM L-glutamine.

extract_protocol:
Cells were fixed with 1% methanol-free formalin in PBS for 5 minutes. After quenching and cell harvest in Szak RIPA buffer, chromatin was fragmented using a Covaris ME220 sonicator
Libraries were prepared for sequencing using the New England Biolabs NEBNext Ultra II Directional DNA Library Prep Kit for Illumina and multiplex oligo set 1 according to manufacturer protocols.

treatment_protocol: Cells were treated with EtOH vehicle or R5020 for 1h

value: T47D cell line

value: ER+PR+ breast cancer


title: hCMEC/d3 cells, 24 hours control exposure biorep 4


title: YS_m1_run2_NB10

description: Library name: YS_m1_run2_NB10_GL69_160_WN-S6-4_C4_YS_E10-5_HE_Gfi1_S160

value: mouse embryo yolk sac


title: 2C_F5_A


title: 2C_F4_C


title: YS_m1_run1_NB73

description: Library name: YS_m1_run1_NB73_GL69_378_WN-S6-4_I4_YS_E10-5_HE_Gfi1_S378

value: HE-YSA (early)


title: hCMEC/d3 cells, 24 hours control exposure biorep 1


title: 2C_F4_A


title: hCMEC/d3 cells, 12 hours control exposure biorep 5

value: 12 hour exposure


title: YS_m1_run1_NB54

description: Library name: YS_m1_run1_NB54_GL69_143_WN-S6-3_C8_YS_E9-5_HE_Gfi1_S143

value: primary material


title: 2C_F5_C


title: hCMEC/d3 cells, 24 hours control exposure biorep 5


title: T47D R5020 replicate 3 Brf1 ChIP

description: Library name: Sample 35

value: BRF1 (Bethyl Laboratories A301-228A, lot #1)


title: T47D R5020 replicate 3 Maf1 ChIP

description: Library name: Sample 34

value: Maf1 (GeneTex GTX106776, lot #YJ4100879)


title: YS_m1_run1_NB34

description: Library name: YS_m1_run1_NB34_GL69_1196_WN-S7-1_O07_YS_E9-5_HE_Gfi1_S105


title: YS_m1_run1_NB39

description: Library name: YS_m1_run1_NB39_GL69_479_WN-S6-2_D11_YS_E9-0_HE_Runx1_S479


title: T47D R5020 replicate 3 POLR3A ChIP

description: Library name: Sample 33

value: POLR3A D5Y2D (Cell Signaling 12825, Lot #1)


title: T47D R5020 replicate 3 PR ChIP

description: Library name: Sample 32

value: PR F-4 (Santa Cruz sc-166169, lot #L1319)


title: hCMEC/d3 cells, 12 hours control exposure biorep 3

value: cerebral brain microvascular endothelial cell

value: WT

value: Control


title: Het_AKAP11-KO-Clone 16_UNT

description: Library name: Het-AKAP11-KO-Clone 16_UNT_RNAseq

value: iPSCs were derived from human lymphocytes

value: neuronal glial culture


title: 2C_F4_B

value: oocyte or embryo


title: 2C_F3_A


title: 2C_F5_B


title: hCMEC/d3 cells, 12 hours control exposure biorep 2


title: T47D R5020 replicate 3 input

description: Library name: Sample 31


title: 2C_F2_C


title: T47D R5020 replicate 2 H3K27Ac ChIP

description: Library name: Sample 30


title: 2C_F2_B


title: YS_m1_run1_NB29

description: Library name: YS_m1_run1_NB29_GL69_724_WN-S6-4_C5_YS_E10-5_HE_Gfi1_S724


title: MTX4

city: Daejeon

first: Bu-Yeo

last: Kim

address: 1672 Yuseongdae-ro, Yuseong-gu

department: Herbal Medicine Research Division

country: South Korea

institute: Korea Institute of Oriental Medicine

description: Library name: MTX4

data_processing:
Sequence reads from QuantSeq 3’ mRNA-Seq were aligned in Mus musculus mm10 reference genome indexes using Bowtie2 for assembling transcripts.
Abundance of transcript as read counts was estimated using coverage in Bedtools. Read count data were normalized using TMM+CPM method in EdgeR package.
Assembly: mm10
Supplementary files format and content: tab-delimited text files include read count values for each sample

source_name: skin

extract_protocol:
Total RNA was extracted from the skin of mice exposed to IMQ (and BJT) usingTRI-reagent based method according to the manufacturer’s instructions (Invitrogen, Carlsbad, CA, USA). RNA quality was assessed using the Agilent TapeStation 4000 system (Agilent Technologies, Amstelveen, Netherlands). RNA was quantified  using a NanoDrop-2000 Spectrophotometer (Thermo Fisher Scientific, Waltham, MA, USA). Only samples with RNA integrity > 7.0 were included in QuantSeq Analysis.
One 1μg of total RNA was processed for preparing mRNA sequencing library using MGIEasy RNA Directional Library Prep Kit (MGI) according to manufacturer’s instruction. The first step involves purifying the poly-A containing mRNA molecules using poly-T oligo attached magnetic beads. Following purification, the mRNA is fragmented into small pieces using divalent cations under elevated temperature. The cleaved RNA fragments are copied into first strand cDNA using reverse transcriptase and random primers.  Strand specificity is achieved in the RT directional buffer, followed by second strand cDNA synthesis. These cDNA fragments then have the addition of a single 'A' base and subsequent ligation of the adapter. The products are then purified and enriched with PCR to create the final cDNA library. The double stranded library is quantified using QauntiFluor ONE dsDNA System (Promega). The library is circularized at 37°C for 30min, and then digested at 37°C for 30min, followed by cleanup of circularization product. To make DNA nanoball (DNB), the library is incubated at 30°C for 25 min using DNB enzyme. Finally, Library was quantified by QauntiFluor ssDNA System (Promega). Sequencing of the prepared DNB was conducted on the MGIseq system (MGI) with 100 bp paired-end reads.

value: skin

value: female C57BL/6

value: Positive control MTX 1mg/kg/day treatment


title: YS_m1_run1_NB24

description: Library name: YS_m1_run1_NB24_GL69_1409_WN-S6-3_E17_YS_E10-5_HE_Gfi1_S318

value: mouse embryo yolk sac


title: MTX3

description: Library name: MTX3


title: T47D R5020 replicate 2 Maf1 ChIP

description: Library name: Sample 28

value: T47D cell line

value: ER+PR+ breast cancer


title: hCMEC/d3 cells, 12 hours control exposure biorep 4

value: 12 hour exposure


title: 2C_F2_A


title: YS_b3_run3_NB62

description: Library name: YS_b3_run3_NB62_GL69_187_WN-S6-3_N3_YS_E9-0_HE_Runx1_S187

value: primary material

value: HE-YSP (late)


title: 2C_F3_C


title: YS_m1_run1_NB20

description: Library name: YS_m1_run1_NB20_GL43_046_plate1_I02_Runx1_HE_S142

value: HE-YSA (early)


title: T47D R5020 replicate 2 Brf1 ChIP

description: Library name: Sample 29

value: BRF1 (Bethyl Laboratories A301-228A, lot #1)


title: T47D R5020 replicate 2 POLR3A ChIP

description: Library name: Sample 27

value: POLR3A D5Y2D (Cell Signaling 12825, Lot #1)


title: YS_m1_run1_NB32

description: Library name: YS_m1_run1_NB32_GL69_1315_WN-S8-1_H03_AGM_E10-5_ACE_pos_S224


title: 2C_F3_B


title: hCMEC/d3 cells, 12 hours control exposure biorep 1

value: cerebral brain microvascular endothelial cell

value: WT


title: MTX2

description: Library name: MTX2


title: 2C_F1_B


title: T47D R5020 replicate 2 PR ChIP

description: Library name: Sample 26

value: PR F-4 (Santa Cruz sc-166169, lot #L1319)


title: Zygote_F10_C


title: YS_b3_run3_NB32

description: Library name: YS_b3_run3_NB32_GL69_1176_WN-S7-1_L12_YS_E9-5_HE_Gfi1_S85


title: 2C_F1_A


title: YS_b3_run3_NB59

description: Library name: YS_b3_run3_NB59_GL69_676_WN-S6-3_I3_YS_E9-0_HE_Runx1_S676


title: YS_b3_run3_NB56

description: Library name: YS_b3_run3_NB56_GL69_065_WN-S6-2_A22_YS_E9-5_HE_Runx1_S65


title: T47D R5020 replicate 2 input

description: Library name: Sample 25


title: BJT1000_4

description: Library name: BJT1000_4

value: BJT 1000 mg/kg/day treatment


title: BJT1000_3

description: Library name: BJT1000_3


title: BJT1000_2

description: Library name: BJT1000_2


title: Zygote_F10_A

value: oocyte or embryo


title: T47D R5020 replicate 1 Brf1 ChIP

description: Library name: Sample 23


title: MTX1

description: Library name: MTX1

value: skin


title: YS_b3_run3_NB20

description: Library name: YS_b3_run3_NB20_GL69_144_WN-S6-4_L7_YS_E10-5_HE_Runx1_S144


title: T47D R5020 replicate 1 POLR3A ChIP

description: Library name: Sample 21


title: Zygote_F9_C


title: YS_b3_run3_NB31

description: Library name: YS_b3_run3_NB31_GL69_1064_WN-S6-3_K19_YS_E10-5_HE_Gfi1_S296


title: T47D R5020 replicate 1 H3K27Ac ChIP

description: Library name: Sample 24


title: Zygote_F9_B


title: 2C_F1_C


title: T47D R5020 replicate 1 Maf1 ChIP

description: Library name: Sample 22

value: Maf1 (GeneTex GTX106776, lot #YJ4100879)


title: YS_b3_run3_NB63

description: Library name: YS_b3_run3_NB63_GL69_1408_WN-S6-3_C20_YS_E10-5_HE_Runx1_S317


title: BJT500_3

description: Library name: BJT500_3

value: female C57BL/6

value: BJT 500 mg/kg/day treatment


title: BJT1000_1

description: Library name: BJT1000_1


title: T47D R5020 replicate 1 PR ChIP

description: Library name: Sample 20

value: T47D cell line


title: YS_b3_run3_NB19

description: Library name: YS_b3_run3_NB19_GL69_391_WN-S6-2_O2_YS_E9-5_HE_Runx1_S391

value: mouse embryo yolk sac


title: Zygote_F9_A


title: BJT500_2

description: Library name: BJT500_2


title: T47D R5020 replicate 1 input

description: Library name: Sample 19

value: ER+PR+ breast cancer


title: Zygote_F10_B


title: Zygote_F8_C


title: T47D OH replicate 3 H3K27Ac ChIP

description: Library name: Sample 18

value: EtOH 1h


title: YS_b3_run2_NB70

description: Library name: YS_b3_run2_NB70_GL69_454_WN-S6-2_M1_YS_E9-5_HE_Runx1_S454

value: primary material

value: HE-YSP (late)


title: YS_b3_run2_NB74

description: Library name: YS_b3_run2_NB74_GL69_1078_WN-S6-3_J10_YS_E9-0_HE_Runx1_S310


title: T47D OH replicate 3 Brf1 ChIP

description: Library name: Sample 17

value: BRF1 (Bethyl Laboratories A301-228A, lot #1)


title: BJT500_1

description: Library name: BJT500_1


title: BJT500_4

description: Library name: BJT500_4


title: Zygote_F8_A


title: Zygote_F8_B


title: BJT250_4

description: Library name: BJT250_4

value: BJT 250 mg/kg/day treatment


title: YS_b3_run2_NB69

description: Library name: YS_b3_run2_NB69_GL69_009_WN-S6-1_G11_YS_E10-5_HE_Gfi1_S9


title: Zygote_F7_C


title: T47D OH replicate 3 Maf1 ChIP

description: Library name: Sample 16


title: BJT250_3

description: Library name: BJT250_3


title: BJT250_2

description: Library name: BJT250_2


title: T47D OH replicate 3 POLR3A ChIP

description: Library name: Sample 15

value: POLR3A D5Y2D (Cell Signaling 12825, Lot #1)


title: Zygote_F7_B


title: YS_b3_run2_NB25

description: Library name: YS_b3_run2_NB25_GL69_487_WN-S6-4_I3_YS_E10-5_HE_Gfi1_S487


title: YS_b3_run3_NB08

description: Library name: YS_b3_run3_NB08_GL69_534_WN-S6-4_E3_YS_E10-5_HE_Runx1_S534


title: YS_b3_run2_NB37

description: Library name: YS_b3_run2_NB37_GL69_370_WN-S6-3_H3_YS_E9-0_HE_Runx1_S370


title: T47D OH replicate 3 PR ChIP

description: Library name: Sample 14


title: BJT250_1

description: Library name: BJT250_1


title: Zygote_F7_A


title: YS_b3_run2_NB11

description: Library name: YS_b3_run2_NB11_GL69_048_WN-S6-2_F17_YS_E9-0_HE_Runx1_S48


title: YS_b3_run2_NB09

description: Library name: YS_b3_run2_NB09_GL69_419_WN-S6-2_E6_YS_E9-5_HE_Gfi1_S419


title: IMQ4

description: Library name: IMQ4

value: Disease


title: IMQ3

description: Library name: IMQ3


title: Zygote_F6_C


title: T47D OH replicate 2 H3K27Ac ChIP

description: Library name: Sample 12


title: T47D OH replicate 3 input

description: Library name: Sample 13


title: YS_b3_run2_NB07

description: Library name: YS_b3_run2_NB07_GL69_1109_WN-S7-1_C08_YS_E9-5_HE_Gfi1_S18


title: Zygote_F6_B


title: YS_b3_run2_NB03

description: Library name: YS_b3_run2_NB03_GL69_038_WN-S6-2_G3_YS_E9-5_HE_Runx1_S38


title: Zygote_F6_A


title: IMQ2

description: Library name: IMQ2


title: T47D OH replicate 2 Brf1 ChIP

description: Library name: Sample 11


title: YS_b3_run1_NB71

description: Library name: YS_b3_run1_NB71_GL69_494_WN-S6-2_M3_YS_E9-5_HE_Runx1_S494


title: YS_b3_run1_NB60

description: Library name: YS_b3_run1_NB60_GL69_612_WN-S6-3_H11_YS_E9-0_HE_Gfi1_S612


title: Zygote_F5_C


title: IMQ1

description: Library name: IMQ1


title: T47D OH replicate 2 POLR3A ChIP

description: Library name: Sample 9


title: Zygote_F5_B


title: T47D OH replicate 2 PR ChIP

description: Library name: Sample 8

value: PR F-4 (Santa Cruz sc-166169, lot #L1319)


title: YS_b3_run1_NB55

description: Library name: YS_b3_run1_NB55_GL69_1071_WN-S6-4_J03_YS_E10-5_HE_Gfi1_S303


title: Zygote_F5_A


title: T47D OH replicate 2 Maf1 ChIP

description: Library name: Sample 10


title: Normal2

description: Library name: Normal2

value: Normal


title: T47D OH replicate 2 input

description: Library name: Sample 7


title: Normal4

description: Library name: Normal4


title: Normal3

description: Library name: Normal3


title: YS_b3_run1_NB33

description: Library name: YS_b3_run1_NB33_GL69_745_WN-S6-2_G10_YS_E9-5_HE_Gfi1_S745


title: Zygote_F4_C

value: oocyte or embryo


title: YS_b3_run1_NB30

description: Library name: YS_b3_run1_NB30_GL69_238_WN-S6-2_F23_YS_E9-0_HE_Gfi1_S238


title: Zygote_F4_B


title: T47D OH replicate 1 H3K27Ac ChIP

description: Library name: Sample 6


title: Normal1

description: Library name: Normal1

value: skin


title: YS_b3_run1_NB27

description: Library name: YS_b3_run1_NB27_GL69_422_WN-S6-2_H21_YS_E9-0_HE_Runx1_S422


title: Zygote_F4_A


title: T47D OH replicate 1 Brf1 ChIP

description: Library name: Sample 5


title: T47D OH replicate 1 Maf1 ChIP

description: Library name: Sample 4

value: Maf1 (GeneTex GTX106776, lot #YJ4100879)


title: AKTP MTO93 mouse tumor organoids, RM-044, JunB, replicate 1

description: Library name: Sample 11

data_processing:
CUT&RUN reads were processed using the nf-core/cutandrun pipeline v3.2.1 (Ewels et al., 2020) aligning to the Mus musculus reference genome (GRCm39/mm39, June 2020) and the Saccharomyces cerevisiae iGenome R-64-1-1 for the spike-in normalization. Spike-in reads were used to normalize signal across samples. The pipeline was executed with default parameters and peak calling was performed using MACS2, with narrow peaks.
Assembly: GRCm39/mm39
Supplementary files format and content: fastq.gz and bigwig
Library strategy: CUT&Run

extract_protocol:
Organoids were dissociated for 30 min with TryplE at 37ºC. Cells were washed twice in wash buffer for 3 min at 600 g, RT. Aliquots of 100,000 cells were prepared. Cells were then bound to Concavalin A-coated magnetic beads (BioMag®Plus, 86057-3) and permeabilised by resuspension in antibody buffer (wash buffer with 0.05% digitonin) and the appropriate dilution of antibody (H3K27ac, JunB, IgG). Samples were incubated overnight at 4ºC o/n a rocking platform. Next day, beads were resuspended in the digitonin-wash buffer containing pAG-MNase (Cell Signaling, 0366S). Samples were then incubated on a rocking platform for 1h at 4ºC. Beads were resuspended in digitonin-wash buffer and placed in an ice water bath (0 ºC) for 5 min. Chromatin digestion was performed by adding CaCl2 and incubating for 30 min at 4 ºC. After digestion, 2x STOP buffer was added and samples were incubated for 10 min at 37ºC. Tubes were centrifuged for 5 min at 16,000 g, 4 ºC, and placed on a magnetic rack. The supernatant containing the digested chromatin was purified using the Qiagen MinElute PCR Purification Kit (QIAGEN, 28006). DNA was eluted in 25 μl of Nuclease-Free Water, quantified with Qubit HS dsDNA (ThermoFisher, Q33231), and fragment size distribution was assessed using a D5000 ScreenTape (Agilent, 5067-5588) for the 4150 TapeStation system.
Libraries were prepared with the NEBNext Ultra II DNA Library Prep Kit (NEB, E7645L) without size selection before PCR amplification. Amplification was performed with Q5 Master Mix, Unique Dual Index Primer Pairs (NEB, E6440S), and 20 μl of library. The PCR program was the following: 45 sec at 98 ºC, 14 cycles consisting of 15 sec at 98 ºC and 10 sec at 60 ºC and a final extension of 1 min at 72 ºC. DNA purification was done in 1.1x volume AMPure XP beads (BECKMAN COULTER, 082A63881). Library concentration and size were assessed with Qubit HS dsDNA (ThermoFisher, Q33231) and D5000 ScreenTape (Agilent, 5067-5588) for the 4150 TapeStation system.

value: Mouse Tumor Organoids (MTO)

value: Epithelial malignant cells

value: AKTP mutant

value: RM-044 KRASi


title: AKTP MTO93 mouse tumor organoids, RM-044, JunB, replicate 2

description: Library name: Sample 12


title: Zygote_F3_C


title: T47D OH replicate 1 POLR3A ChIP

description: Library name: Sample 3

value: T47D cell line

value: ER+PR+ breast cancer


title: AKTP MTO93 mouse tumor organoids, RM-044, IgG, replicate 2

description: Library name: Sample 10


title: AKTP MTO93 mouse tumor organoids, RM-044, IgG, replicate 1

description: Library name: Sample 9


title: YS_b3_run1_NB08

description: Library name: YS_b3_run1_NB08_GL69_537_WN-S6-2_H4_YS_E9-5_HE_Runx1_S537

value: mouse embryo yolk sac

value: primary material


title: T47D OH replicate 1 PR ChIP

description: Library name: Sample 2

value: EtOH 1h


title: YS_b3_run1_NB02

description: Library name: YS_b3_run1_NB02_GL69_0928_WN-S6-3_M05_YS_E9-0_HE_Gfi1_S160

value: HE-YSP (late)


title: Zygote_F3_A


title: Zygote_F3_B


title: AKTP MTO93 mouse tumor organoids, RM-044, H3K27ac, replicate 2

description: Library name: Sample 8


title: YS_b2_run3_NB66

description: Library name: YS_b2_run3_NB66_GL69_0921_WN-S6-3_G10_YS_E9-0_HE_Runx1_S153

value: HE-YSP (early)


title: T47D OH replicate 1 input

description: Library name: Sample 1


title: Zygote_F2_C


title: Zygote_F2_B


title: AKTP MTO93 mouse tumor organoids, vehicle control, JunB, replicate 2

description: Library name: Sample 6


title: YS_b2_run3_NB57

description: Library name: YS_b2_run3_NB57_GL69_172_WN-S6-4_M9_YS_E10-5_HE_Runx1_S172


title: AKTP MTO93 mouse tumor organoids, RM-044, H3K27ac, replicate 1

description: Library name: Sample 7


title: lung carcinoma H1299 cell, ginseng-nanoparticle treated (control), replicate 2

city: Gyeonggido

first: gunwoo

last: park

address: 206, World cup-ro, Yeongtong-gu, Suwon-si,

institute: ajou univ

data_processing:
Each library was sequenced by using Illumina NovaSeq 6000. The raw sequences, which were obtained from bcl2fastq2 software (version 2.20) with the default parameters, were subjected to the adapter trimming by using Cutadapt (version 3.5). Each read was aligned onto the human reference genome (GRCh38.105) by using STAR (version 2.7.6a), and potential PCR duplicates were removed by using Picard MarkDuplicates (version 2.6). The numbers of deduplicated mapped reads aligned in individual gene regions were counted by htseq-count (version 2.0.2).
Assembly: GRCh38.105
Supplementary files format and content: tab-delimited text file includes raw counts for each sample

source_name: H1299 cell

growth_protocol: H1299 cells were purchased from Korea cell line bank (Seoul, Korea). The cells were cultured at 37°C under a 5% CO2 atmosphere using Dulbecco’s modified Eagle medium (HyClone, Logan, UT, USA) supplemented with 10% fetal bovine serum (GenDEPOT, katy, TX, F0600-050) and 1% penicillin-streptomycin (Welgene, Gyeongsan, Republic of Korea).

extract_protocol:
Total RNA was isolated using RNeasy Mini Kit columns (Qiagen, Hilden, Germany). RNA quality and quantity were assessed using a Bioanalyzer 2100 with an RNA 6000 Nano Chip (Agilent Technologies, Amstelveen, The Netherlands).
The library of each sample was constructed by using 300 ng of total RNA and Illumina TruSeq Stranded mRNA kit, according to the standard manufacturer's protocol.

treatment_protocol: H1299 cells were treated with or without the ginseng nanparticle.

value: H1299 cell

value: cell line

tag: disease

value: Lung carcinoma

value: Ginseng nanoparticle


title: lung carcinoma H1299 cell, ginseng-nanoparticle treated (control), replicate 1


title: Zygote_F2_A

value: oocyte or embryo


title: AKTP MTO93 mouse tumor organoids, vehicle control, JunB, replicate 1

description: Library name: Sample 5


title: lung carcinoma H1299 cell, PBS treated (control), replicate 2

value: PBS (control)


title: YS_b2_run3_NB24

description: Library name: YS_b2_run3_NB24_GL69_0881_WN-S6-4_G06_YS_E10-5_HE_Runx1_S113


title: YS_b3_run1_NB14

description: Library name: YS_b3_run1_NB14_GL69_169_WN-S6-2_C5_YS_E9-5_HE_Runx1_S169


title: Zygote_F1_C


title: lung carcinoma H1299 cell, PBS treated (control), replicate 1


title: YS_b2_run3_NB30

description: Library name: YS_b2_run3_NB30_GL69_565_WN-S6-2_M2_YS_E9-5_HE_Gfi1_S565


title: YS_b2_run3_NB23

description: Library name: YS_b2_run3_NB23_GL69_576_WN-S6-3_F3_YS_E9-0_HE_Runx1_S576


title: Zygote_F1_B


title: AKTP MTO93 mouse tumor organoids, vehicle control, IgG, replicate 1

description: Library name: Sample 3

value: Mouse Tumor Organoids (MTO)


title: AKTP MTO93 mouse tumor organoids, vehicle control, IgG, replicate 2

description: Library name: Sample 4

value: Epithelial malignant cells


title: OS833_Primary

city: San Francisco

first: Alex

middle: G

last: Lee

state: CA

address: 1550 4th Street

institute: UCSF

data_processing:
Raw FASTQ files were trimmed for adaptors and low-quality regions using Trimmomatic (v0.36). The processed reads were aligned to the human reference genome (hg38) with STAR aligner (v2.5.1b), using the ‘quantMode’ feature and gene annotations from GENCODE p5 for gene-level expression quantification. Aligned reads were normalized with the TMM method from the EdgeR package (v3.24.3) and transformed to log2(CPM + 1).
Assembly: hg38
Supplementary files format and content: tab delimited

source_name: From osteosarcoma PDX

growth_protocol: All cell lines were routinely tested for mycoplasma and STR tested to confirm identify.  Cells were cultured in standard DMEM media (Corning) supplemented with 10% bovine growth serum (Hyclone SH30541.03) and 1% penicillin–streptomycin–glutamine

extract_protocol:
RNA was harvested when the cells were ~80 confluent.RNA was extracted using the RNAeasy Mini Kit (Qiagen) and on-column DNA digestion with DNaseI according to the manufacturer protocol.
RNA-seq libraries were made using the TruSeq Stranded mRNA Kit (Illumina, RS-122-2101) in accordance with the manufacturer’s instructions. All manufacturer controls were used in preparation of the libraries. Libraries were quantified using the High Sensitivity D1000 ScreenTape (Agilent, 5067-5584) on the TapeStation 4200 (Agilent), the High Sensitivity DNA (Agilent, 5067-4626) on the Bioanalyzer 2100 (Agilent), or the High Sensitivity NGS (Agilent, DNF-474-22) on the Fragment Analyzer

value: From osteosarcoma PDX


title: YS_b2_run3_NB21

description: Library name: YS_b2_run3_NB21_GL69_1033_WN-S6-3_D22_YS_E10-5_HE_Runx1_S265


title: Zygote_F1_A


title: AKTP MTO93 mouse tumor organoids, vehicle control, H3K27ac, replicate 2

description: Library name: Sample 2

value: AKTP mutant


title: HuO9_Commercial


title: MII_F10_C


title: YS_b2_run3_NB12

description: Library name: YS_b2_run3_NB12_GL69_089_WN-S6-3_N8_YS_E9-0_HE_Runx1_S89


title: AKTP MTO93 mouse tumor organoids, vehicle control, H3K27ac, replicate 1

description: Library name: Sample 1


title: YS_b2_run3_NB09

description: Library name: YS_b2_run3_NB09_GL69_193_WN-S6-2_E14_YS_E9-0_HE_Runx1_S193


title: MII_F10_B


title: OS774_Primary


title: Reprogrammed adult SVZ/NSCs rep2

city: Valencia

first: Jordi

last: Planells

state: Valencia

address: Doctor Moliner, 50 street

department: Biologia celular, biologia funcional y antropologia fisica

institute: Universitat de València

description: Library name: iPSCs_rep2

data_processing:
Raw data quality was assessed with FastQC (0.12.1)
Adapters were trimmed with cutadapt -a [adapter] -q 20 -m 18
Adaptor trimmed reads were quantified at gene level with Salmon (1.10.1) in quasi-mapping mode, with automatic library detection (-l A) and sequence bias correction (--seqBias). Gencode release M23 was used as transcriptome reference.
Assembly: mm10, Gencode M23
Supplementary files format and content: Tabular file containing the raw count matrix (rows = genes, columns = samples) with gene name and gene id as identifiers.

source_name: Brain

growth_protocol: NSCs were grown as detailed in Belenguer et al. 2016 (https://doi.org/10.1016/j.diff.2016.01.005). For iPSCs growth 2i media supplemented with N2B27, LIF (1x, 1000x stock, homemade), iMEK inhibitor (1 µM, 10 mM stock, Millipore, Cat. No. 444968), and iGSK3β inhibitor (3 µM, 10 mM stock, Millipore, Cat. No. 361571) was used.

extract_protocol:
Trizol
Illumina TruSeq stranded mRNA Sample Preparation Kit v2

treatment_protocol: To generate iPSCs from adult NSCs exogenous Oct4 together with Klf4 (2F) were virally transfected for reprogramming as previously described (Kim et al., 2008; Kim et al., 2009). Parallely, in NSCs, a pMXs mCherry vector was used as a control transfection.

value: Brain

value: Reprogrammed adult NSCs

value: Oct4 + Klf4 transfection


title: YS_b2_run2_NB63

description: Library name: YS_b2_run2_NB63_GL69_220_WN-S6-1_H2_YS_E10-5_HE_Runx1_S220

value: mouse embryo yolk sac

value: primary material


title: OS742_Primary


title: OS766_Metastasis


title: MII_F10_A


title: MII_F9_C


title: Reprogrammed adult SVZ/NSCs rep1

description: Library name: iPSCs_rep1


title: OS384_Primary


title: MII_F9_B


title: U2OS_Commercial


title: Adult SVZ/NSCs rep3

description: Library name: NSCs_rep3

value: Adult NSCs

value: mCherry control transfection


title: SJSA_Commercial


title: YS_b2_run2_NB45

description: Library name: YS_b2_run2_NB45_GL69_669_WN-S6-4_I2_YS_E10-5_HE_Runx1_S669

value: HE-YSP (early)


title: MII_F8_C


title: YS_b2_run2_NB52

description: Library name: YS_b2_run2_NB52_GL69_212_WN-S6-3_H1_YS_E9-0_HE_Runx1_S212


title: MII_F9_A


title: SaOS2_Commercial


title: YS_b2_run2_NB33

description: Library name: YS_b2_run2_NB33_GL69_491_WN-S6-3_K2_YS_E9-0_HE_Runx1_S491


title: Adult SVZ/NSCs rep2

description: Library name: NSCs_rep2


title: YS_b2_run2_NB29

description: Library name: YS_b2_run2_NB29_GL69_0961_WN-S6-2_J12_YS_E9-0_HE_Gfi1_S193


title: E17.5 mdx 2, scRNAseq

city: Ottawa

first: Theodore

last: Perkins

state: ON

address: 501 Smyth Rd.

department: Cellular and Molecular Medicine

institute: Ottawa Hospital Research Institute

description: 10X Genomics

library_source: transcriptomic single cell

data_processing:
Fastq files were generated from raw sequencer output using the mkfastq command of cellranger 7.1.0
Cell-containing droplets were identified and quantified using the count command of cellranger 7.1.0
Transcripts were identified by alignment to the 10X Genomics mm10-2020A reference assembly
Assembly: GRCm38/mm10
Supplementary files format and content: HDF5 format files containing filtered feature-barcode matrices generated by 10X Cellranger (v7.1)

source_name: fetal limbs

extract_protocol:
Fetal muscle stem cells were FACS-isolated based on 7-AAD for viability and GFP.
Libraries were generated according to manufacturer's instructions (single cell 3' v3 protocol, 10X Genomics)

value: fetal limbs

value: fetal muscle stem cell


title: MG63.3_Commercial


title: MII_F8_B


title: YS_b2_run2_NB53

description: Library name: YS_b2_run2_NB53_GL69_0958_WN-S6-1_L01_YS_E10-5_HE_Runx1_S190


title: Thymic rosette APC

city: Fitzroy

first: Mark

last: Chong

state: Victoria

address: 9 Princes Street

institute: St Vincent's Institute of Medical Research

description:
Library name: Sample 1
10X Genomics

data_processing:
The Illumina sequencing data was demultiplexed and aligned to the Mus musculus genome (mm10) using the CellRanger pipeline (10X Genomics, v4.0.0) to generate the feature barcode matrix.
Assembly: Mouse mm10-2020-A
Supplementary files format and content: Tab-separated value files and matrix files

source_name: Thymus

extract_protocol:
Three thymi from 6-week old C57Bl/6 female mice were harvested and minced with scissors. The tissue pieces were washed in RPMI + 5mM EDTA with gentle rocking for 15 minutes to release free thymocytes. The fragments were then digested with 0.5mg/mL Collagenase D, 4μg/mL DNase I and 2% FCS in RPMI at room temperature with magnetic stirring three times for 15 min each to release rosettes. The resulting digest containing rosettes (and all subsequent washes) were centrifuged at 100xg for 7 minutes at 4°C and resuspended in RPMI. This suspension was overlaid on newborn calf serum and left to settle at room temperature. After 15-20 min of incubation, the cells within the RPMI layer were discarded. The serum layer, now enriched for rosettes were collected and washed with PBS, was resuspended in RPMI for subsequent sedimentations. A total 4 sedimentations were performed to enrich for rosettes. For flow cytometric sorting, rosettes were first dissociated into single cells using 0.25% v/v trypsin for one minute at 37°C.
3’ Gene Expression library was constructed using the standard Chromium Single Cell 3’ reagent kit (v3 chemistry) (10x Genomics). Briefly, Gel beads-in-emulsion (GEM) were generated, containing a single cell and a barcoded gel bead. Following GEM formation, the gel bead was dissolved to release primers, and the cell was lysed. The primers capture polyadenylated mRNA using a 30nt poly(dT) sequence, and they also contain a 16nt 10x barcode, a 12nt unique molecular identifier, and Illumina TruSeq Read 1 primer sequence. cDNA is then reverse transcribed from mRNA and amplified using PCR. P5 and P7 sequences were also attached to size-optimised cDNA. The library was then sequenced on an Illumina NextSeq 500.

value: Thymus

value: Antigen presenting cells

value: Wildtype


title: MG63_Commercial


title: E17.5 mdx 1, scRNAseq

description: 10X Genomics


title: MII_F8_A

data_processing:
Multiplexed sequencing reads that passed filters were trimmed to remove low-quality reads and adaptors by TrimGalore (version 0.6.7) (-q 25 --length 20 --max_n 3 --stringency 3). The quality of reads after filtering was assessed by fastQC, followed by alignment to the mouse genome (GRCm39) by HISAT2 (version 2.2.1) with default parameters. The output SAM files were converted to BAM files and sorted using SAMtools6 (version 1.14). Read counts of all samples were quantified by using FeatureCount (Version 2.0.1) with mouse genome as a reference and were adjusted to provide CPM (Counts per million mapped reads). Principal component analysis (PCA) and cluster analysis were performed by using R (a free software environment for statistical computing and graphics). Differentially expressed genes (DEGs) was identified by using edgeR in R. The genes were considered differentially expressed if they provided a false discovery rate of <0.05 and fold change >2. ClusterProfiler was used to reveal the Gene Ontology (GO) and KEGG pathways in R.
Assembly: GRCm39
Supplementary files format and content: txt, normalized read counts

extract_protocol:
Ten equal fractions were recovered and subjected to RNA isolation by Trizol reagent (Sigma).
The RNA-seq libraries were generated from individual fractions by using the Smart-seq2 v4 kit with minor modification from manufacturer’s instructions. Briefly, individual cells were lysed, and mRNA was captured and amplified with the Smart-seq2 v4 kit (Clontech). After AMPure XP beads purification, amplified RNAs were quality checked by using Agilent High Sensitivity D5000 kit (Agilent Technologies). High-quality amplified RNAs were subject to library preparation (Nextera XT DNA Library Preparation Kit; Illumina) and multiplexed by Nextera XT Indexes (Illumina). The concentration of sequencing libraries was determined by using Qubit dsDNA HS Assay Kit (Life Technologies) and KAPA Library Quantification Kits (KAPA Biosystems). The size of sequencing libraries was determined by means of High Sensitivity D5000 Assay in at Tapestation 4200 system (Agilent). Pooled indexed libraries were then sequenced on the Illumina HiSeq X platform with 150-bp paired-end reads.

value: oocyte or embryo


title: YS_b2_run2_NB26

description: Library name: YS_b2_run2_NB26_GL69_573_WN-S6-3_K4_YS_E9-0_HE_Runx1_S573


title: MII_F7_C


title: HOS_Commercial


title: MII_F7_B


title: YS_b2_run2_NB08

description: Library name: YS_b2_run2_NB08_GL69_222_WN-S6-3_G12_YS_E9-0_HE_Runx1_S222


title: E17.5 WT 1, scRNAseq

description: 10X Genomics


title: c143B_Commercial


title: YS_b2_run2_NB51

description: Library name: YS_b2_run2_NB51_GL69_753_WN-S6-4_O3_YS_E10-5_HE_Runx1_S753


title: YS_b2_run1_NB63

description: Library name: YS_b2_run1_NB63_GL69_415_WN-S6-3_D11_YS_E9-5_HE_Runx1_S415


title: RKI1_DTP_n=3

description: In the counts file, Parent = Untreated, DTP = 14 days CMPD1 25uM

data_processing:
FASTQ reads were aligned, genes were counted, using DESeq2
Assembly: hg38 Homo Sapiens
Supplementary files format and content: Contains the raw counts for each gene, within each samples

growth_protocol: RKI1 Glioblastoma stem cells were grown in Stem Pro Neural Stem Cell Serum Free Media (ThermoFisher Scientific) on matrigel coated flasks (0.15% Matrigel/PBS).

extract_protocol:
RNA extraction using Qiagen Rneasy Minikit
NEBNext® UltraTM RNALibrary Prep Kit for Illumina (NEB, USA) following manufacturers instructions

treatment_protocol: 24 hours after plating, cells were collected (Parent, untreated) or treated for 14 days with CMPD1 25uM). Media and drug was replaced twice per week. At the end of the treatment timecourse, samples were harvested, RNA collected, and subject to library preperation.

value: Glioblastoma Stem Cell

value: WT

value: CMPD1 25uM, 14 days


title: Adult SVZ/NSCs rep1

description: Library name: NSCs_rep1

value: Brain


title: MII_F6_C


title: RKI1_DTP_n=2


title: MII_F6_B


title: MII_F6_A


title: E17.5 WT 2, scRNAseq

description: 10X Genomics


title: YS_b2_run1_NB37

description: Library name: YS_b2_run1_NB37_GL69_051_WN-S6-1_N1_YS_E10-5_HE_Runx1_S51

data_processing:
Nanopore sequencing data were basecalled using Dorado (v0.9.1) using the high-accuracy model (dna_r10.4.1_e8.2_400bps_hac@v5.0.0). Raw reads were trimmed for SMARTseq adapters using bbduk.sh (v39.08). Chimeric reads were filtered from the data using YACRD (v1.0.0) and porechop (v0.2.4). Cleaned reads were aligned to GENCODE transcripts (Release 37) using Minimap2 (v2.26), retaining a maximum of 10 alignments per read. Alignments were quantified using Nanocount (v1.0.0.post6). Abundance files were read into R (v4.3.0) filtered for low library size samples using findOutliers (scuttle v1.10.3; type = "lower", nmads = 1) and normalised using DESeq2 (v1.40.2). Estimated and normalised counts were subject to analysis using IsoformSwitchAnalyzeR and SplicingFactory as previously described.
Assembly: GENCODE transcripts (Release 37)
Supplementary files format and content: nanoCount_trans_Estcount.txt; nanoCount Estimated counts as TSV
Supplementary files format and content: nanoCount_trans_tpm.txt; nanoCount TPM as TSV

extract_protocol:
Single cells were FACS sorted into wells of a 384-well plate containing lysis buffer and snap-frozen.
10ng full-length purified amplified cDNA from a miniaturised Smart-seq2 cDNA was purified using a 0.7x volume of AMPure XP reagent (Beckman Coulter). Purified amplification product was quantified by Qubit (ThermoFisher) and sized / quality checked by Fragment Analyzer (Agilent). 200fmol was used as input for the Ligation sequencing amplicons - Native Barcoding Kit 24 V14 (SQK-NBD114.24) protocol (revision H) (Oxford Nanopore). Sequencing was performed on a PromethION P2 Solo (Oxford Nanopore) using flow cell FLO-PRO114M


title: RKI1_Parent_n=3

value: Untreated


title: MII_F5_C


title: RKI1_Parent_n=2


title: YS_b2_run1_NB28

description: Library name: YS_b2_run1_NB28_GL69_410_WN-S6-4_F11_YS_E10-5_HE_Runx1_S410


title: YS_b2_run1_NB15

description: Library name: YS_b2_run1_NB15_GL69_602_WN-S6-3_F10_YS_E9-0_HE_Runx1_S602


title: MII_F5_B


title: YS_b2_run1_NB11

description: Library name: YS_b2_run1_NB11_GL69_1082_WN-S6-3_G14_YS_E10-5_HE_Runx1_S314


title: RKI1_Parent_n=1


title: MII_F5_A


title: MII_F7_A


title: YS_b2_run1_NB10

description: Library name: YS_b2_run1_NB10_GL69_450_WN-S6-4_B7_YS_E10-5_HE_Runx1_S450


title: Choroid_Plexus_Org_Rep2

city: Brisbane

first: Huiwen

last: Zheng

state: Queensland

address: The University of Queensland Brisbane

institute: The University of Queensland

data_processing:
The raw sequencing reads in fastq files were processed to generate the count matrix. BeeNet v1.1.X was used to align the fastq files against the human GRCh38 reference genome (https://download.honeycomb.bio/) using STAR alignment. The expected number of barcodes in each sample was set to 40% as suggested in the guide. In the end, an average of 84% reads mapped confidently to the transcriptome. The final unfiltered count matrix was kept as a gene*cell matrix that is available for further downstream analysis.
Assembly: GRCh38
Supplementary files format and content: Tab-separated value files contain the number of unique molecule counts for each transcriptome that is mapped to a specific gene in the reference genome.

growth_protocol: see Materials and Methods

extract_protocol:
Five 60-day old choroid plexus organoids were pooled, washed once with DPBS and dissociated using Papain Dissociation Kit (Worthington Biochemical Corporation, #LK003150) according to manufacturer’s instructions. Briefly collected organoids were dissociated by incubation on a temperature controlled shaker at 37°C at 190 rpm, and the enzymatic reaction was stopped by addition of stopping solution after 47 minutes. For quality control cell viability after dissociation was confirmed above 95% by Trypan Blue cell count and FACS analysis of DRAQ7 (Thermo Fisher, D15106) positive cells.
scRNAseq sample preparation was done using HIVE™ scRNAseq Solution kit (Perkin Elmer, #NOVA-HCB018) by loading 30.000 live cells into each HIVE sample collector. Sample preparation and library preparation were done according to manufacturer’s instructions. Sequencing was run using NovaSeq 6000 SP Reagent Kit v1.5 (Illumina, 20028401) on a NovaSeq 6000 System (Illumina), estimating 36.000 reads/cell.

value: WTC

tag: age

value: 2 months


title: YS_b2_run1_NB56

description: Library name: YS_b2_run1_NB56_GL69_1080_WN-S6-4_C02_YS_E10-5_HE_Runx1_S312

value: mouse embryo yolk sac

value: primary material


title: MII_F4_C


title: YS_b2_run1_NB46

description: Library name: YS_b2_run1_NB46_GL69_0869_WN-S6-4_F01_YS_E10-5_HE_Gfi1_S101


title: Choroid_Plexus_Org_Rep1


title: RKI1_DTP_n=1


title: YS_b2_run1_NB03

description: Library name: YS_b2_run1_NB03_GL69_659_WN-S6-2_I11_YS_E9-0_HE_Runx1_S659


title: 28120

type: RNA

city: Wocester

first: Rachel

middle: E

last: Twomey

state: MA

address: 100 Research Drive

department: Immunology

institute: AbbVie

hyb_protocol: none provided

scan_protocol: none provided

data_processing: RMA normalization

label: biotin

source_name: Salivary gland anti-CD40 15mpk IP/2x/week

label_protocol: none provided

extract_protocol: Left kidney was divided into thirds and one third from the end was placed into RNA later. Left whole salivary gland was placed into RNA later. Samples were stored at 4C overnight then transferred to -80C. Thereafter, tissues were homogenized and RNA extracted using the miRNeasy mini kit from Qiagen.

treatment_protocol: Mice were treated after the onset of disease with either vehicle control or 60 mg/kg of ABT-317 (JAK inhibitor), for the duration of the experiment. Young and baseline mice were not treated.

value: Salivary gland

value: disease onset

value: Kidney anti-CD40 15mpk IP/2x/week


title: AGM_5_run3_NB60

description: Library name: AGM_5_run3_NB60_GL34_276_GL_SC_3_plate1_F12_S276

source_name: mouse embryo

value: mouse embryo

value: HE-Hb


title: U-937, LAA+ATRA, rep2, RNA-seq

city: Miami

first: Luisa

last: Cimmino

state: Florida

address: 1501 NW 10th Ave, BRB 711

institute: University of Miami

data_processing:
Reads were adapter trimmed and and low-quality filtered using Novogene's in-house perl script
Salmon(v1.8.0) was used to quantify the fastq files against a decoy-aware transcriptome index based on Gencode V40 transcriptome and GRCh38 primary assembly genome. Quantification performed with automatic library type inference and default Salmon parameters
tximeta(v1.14.1) was used to generate transcript- and gene-level summaries from Salmon quantification
DESeq2(v1.36.0) was used to determine differential expression for each treatment group against the vehicle control
Assembly: hg38
Supplementary files format and content: Tab-delimited text file geneCount.txt contains count data for all samples
Supplementary files format and content: Tab-delimited text file "fpkm.txt" contains FPKM-normalized count data for all samples

growth_protocol: U-937 cells were cultured in vitro with RPMI 1640, 10% fetal bovine serum, and 10 units/mL penicillin and 10µg/mL streptomycin in a humidified incubator at 37˚C and 5% CO2.

extract_protocol:
Cells were collected and pelleted after treatment, and homogenized with a QIAshredder (Qiagen 79654). Total RNA was extracted using RNeasy Plus Mini kits (Qiagen 74136). Qiagen kits were used according to manufacturer's protcols.
Total RNA was sent to Novogene for library construction and sequencing. mRNA was enriched for by using poly-T magnetic beads, and library created using NEBNext Ultra II RNA Library Prep Kit for Illumina (NEB E7770).

treatment_protocol: Cells were treated for 72hr with 250µM L-ascorbic acid (LAA; Sigma A4544; dissolved in PBS), 1µM all-trans retinoic acid (ATRA; Sigma R2625; dissolved in DMSO), the combination thereof, or vehicle controls (PBS+DMSO).

value: pro-monocytic

value: LAA + ATRA


title: 28121


title: MII_F4_A

city: Gainesville

first: Zongliang

last: Jiang

address: 2033 Mowry Rd

institute: University of Florida

value: oocyte or embryo


title: U-937, LAA+ATRA, rep1, RNA-seq


title: AGM_5_run3_NB58

city: Manchester

first: Georges

last: Lacaud

institute: Cancer Research UK Manchester Institute

description: Library name: AGM_5_run3_NB58_GL34_262_GL_SC_3_plate1_D7_S262


title: 28117


title: AGM_5_run3_NB51

description: Library name: AGM_5_run3_NB51_GL34_259_GL_SC_3_plate1_F9_S259


title: MII_F3_C


title: MII_F3_B


title: 28118


title: 28114

source_name: Salivary gland ABT-317 60mpk PO/SID

value: Kidney ABT-317 60mpk PO/SID


title: 28113


title: U-937, ATRA, rep1, RNA-seq

value: All-trans retinoic acid (ATRA, 1uM)


title: AGM_5_run3_NB44

description: Library name: AGM_5_run3_NB44_GL34_275_GL_SC_3_plate1_G9_S275


title: 28115


title: 28119


title: U-937, ATRA, rep2, RNA-seq


title: 28116


title: U-937, LAA, rep2, RNA-seq

value: L-ascorbic acid (LAA, 250uM)


title: MII_F4_B


title: MII_F3_A


title: MII_F2_C


title: U-937, LAA, rep1, RNA-seq


title: AGM_5_run3_NB39

description: Library name: AGM_5_run3_NB39_GL34_263_GL_SC_3_plate1_G11_S263


title: AGM_5_run3_NB05

description: Library name: AGM_5_run3_NB05_GL34_222_GL_SC_3_plate1_P1_S222


title: U-937, vehicle, rep2, RNA-seq

value: Vehicle


title: MII_F2_B


title: U-937, vehicle, rep1, RNA-seq


title: AGM_5_run2_NB71

description: Library name: AGM_5_run2_NB71_GL34_251_GL_SC_3_plate1_C10_S251


title: AGM_5_run2_NB73

description: Library name: AGM_5_run2_NB73_GL34_272_GL_SC_3_plate1_H9_S272


title: MII_F1_C


title: MII_F1_B


title: AGM_5_run3_NB40

description: Library name: AGM_5_run3_NB40_GL34_266_GL_SC_3_plate1_C11_S266


title: U-937, LAA+ATRA, rep2, ATAC-seq

data_processing:
Reads were trimmed and filtered using cutadapt and Trim Galore
Reads were aligned to hg38 with Bowtie2(v2.3.5)
Duplicates discarded with Picard(v2.18.27)
MACS2(v2.1.0.20150731) was used to call peaks.
Assembly: hg38
Supplementary files format and content: .bigwig files containing indexed binary format alignment data for viewing on a genome browser
Supplementary files format and content: narrowPeak.gz files containing compressed peak data in bed format

extract_protocol:
Nuclei were extracted from 50,000 cells per sample, using the Diagenode ATAC-seq kit (C01080002).
Diagenode ATAC-seq kit (C01080002) also used for library construction along with unique dual-indexing primers for tagmented libraries (C01011034)


title: MII_F1_A


title: AGM_5_run2_NB54

description: Library name: AGM_5_run2_NB54_GL34_268_GL_SC_3_plate1_E9_S268


title: GV_F10_C


title: AGM_5_run2_NB49

description: Library name: AGM_5_run2_NB49_GL34_255_GL_SC_3_plate1_A7_S255


title: U-937, ATRA, rep2, ATAC-seq


title: U-937, LAA+ATRA, rep1, ATAC-seq


title: 28111

source_name: Salivary gland vehicle HPMC/Tween PO/SID

value: Kidney vehicle HPMC/Tween PO/SID


title: AGM_5_run2_NB41

description: Library name: AGM_5_run2_NB41_GL34_254_GL_SC_3_plate1_D12_S254


title: MII_F2_A

source_name: oocyte or embryo


title: 28110


title: U-937, ATRA, rep1, ATAC-seq


title: GV_F10_B


title: U-937, LAA, rep2, ATAC-seq


title: AGM_5_run2_NB24

description: Library name: AGM_5_run2_NB24_GL34_267_GL_SC_3_plate1_B9_S267


title: 28112


title: AGM_5_run2_NB02

description: Library name: AGM_5_run2_NB02_GL34_261_GL_SC_3_plate1_E12_S261


title: GV_F10_A


title: 28104

source_name: Salivary gland baseline


title: U-937, LAA, rep1, ATAC-seq


title: GV_F9_C


title: 28101

source_name: Salivary gland young

value: young


title: 28105


title: 28106


title: GV_F9_B


title: U-937, vehicle, rep1, ATAC-seq


title: GV_F9_A


title: 28108


title: 28102


title: AGM_5_run1_NB51

description: Library name: AGM_5_run1_NB51_GL34_214_GL_SC_3_plate1_E1_S214


title: 28100


title: 28109


title: 28107


title: 28099


title: AGM_5_run1_NB42

description: Library name: AGM_5_run1_NB42_GL34_218_GL_SC_3_plate1_P4_S218


title: A549 RNA-seq, H13N2, rep3

city: Jinan

first: Ran

last: Wei

state: Shandong

address: No. 23788, Gongye North Road, Licheng District, Jinan City, Shandong Province, China

institute: Poultry Institute, Shandong Academy of Agricultural Sciences, Ji’nan, China

description: Library name: Sample6

data_processing:
Sequencing data were aligned to the hg19 human genome using STAR with gene annotation gencode.v29lift37.
Assembly: hg19
Supplementary files format and content: Processed data files are provided in .xls format and include raw counts for each sample.

extract_protocol:
RNA extraction was performed according to the instructions of the SteadyPure RNA Extraction Kit (AG21024, AGbio, Changsha, China).
RNA samples were library-prepared and sequenced by  BGI (Beijing Genomics Institute).


title: A549 RNA-seq, H13N2, rep2

description: Library name: Sample5


title: GV_F8_B


title: 28098


title: 28097

source_name: Kidney anti-CD40 15mpk IP/2x/week

value: Kidney


title: GV_F8_C


title: AGM_5_run1_NB70

address: Wilmslow Raod

description: Library name: AGM_5_run1_NB70_GL34_227_GL_SC_3_plate1_M4_S227


title: 28103


title: AGM_5_run1_NB17

description: Library name: AGM_5_run1_NB17_GL34_239_GL_SC_3_plate1_C4_S239


title: U-937, vehicle, rep2, ATAC-seq


title: A549 RNA-seq, NC, rep3

description: Library name: Sample3


title: GV_F7_C


title: A549 RNA-seq, NC, rep2

description: Library name: Sample2


title: AGM_5_run1_NB09

description: Library name: AGM_5_run1_NB09_GL34_235_GL_SC_3_plate1_E6_S235


title: AGM_5_run1_NB13

description: Library name: AGM_5_run1_NB13_GL34_257_GL_SC_3_plate1_A12_S257


title: GV_F7_B


title: AGM_4_run3_NB72

description: Library name: AGM_4_run3_NB72_GL34_245_GL_SC_3_plate1_G1_S245

source_name: mouse embryo AGM-region

value: mouse embryo AGM-region

value: HE-AGM (late)


title: A549 RNA-seq, NC, rep1

description: Library name: Sample1


title: GV_F7_A


title: AGM_5_run1_NB25

description: Library name: AGM_5_run1_NB25_GL34_253_GL_SC_3_plate1_B11_S253

value: primary material


title: ESCC-CAF-shCDH11_2#3

city: fujian xiamen

first: yangfan

last: Zhou

address: 55 Zhenhai Road, Siming District, Xiamen, Fujian Province

institute: The First Affiliated Hospital of Xiamen University

description: Library name: R9

data_processing:
After filtering the FASTQ data, the reads were mapped to the reference genome (hg38) using HISAT2.2.2.1. The DEGs between groups were processed using the R package DESeq2. KEGG enrichment analysis was performed using the R packages, “clusterProfiler” and “org.Hs.eg.db.” The calculated p-values were FDR-corrected with FDR ≤ 0.05 as the threshold value.
Assembly: hg38
Supplementary files format and content: matirx txt

source_name: ESCC-CAF

extract_protocol:
To obtain surgically resected ESCC tissue, the tissue sample was placed in PBS buffer containing double antibiotic (penicillin and streptomycin), and ophthalmic scissors to cut the tissue into approximately 1–2-mm³ sections to facilitate subsequent digestion. The cut tissue pieces were transferred to a sterile centrifuge tube and an appropriate amount of trypsin-EDTA digestion solution was added (3–5 mL of digestion solution per gram of tissue). The centrifuge tube was placed in a shaker at 37°C and at 100–150 rpm for 30–60 min until the tissue mass was mostly disaggregated into single cells or small cell clusters. A serum-containing medium was added to terminate the digestion, The cells were gently blown to homogenize and then centrifuged at 1000–1500 rpm for 5–10 min, and the supernatant was discarded. The cell precipitate was discarded with the appropriate amount of DMEM complete medium and the cell concentration was adjusted to approximately 1×10⁶ to 5×10⁶ cells/mL. The cell suspension was inoculated into culture flasks and placed in the cell incubator at 37℃ with 5% CO₂. After 24–48 h of incubation, the supernatant was discarded the cells were gently rinsed with PBS buffer–two to three times to remove non-adherent cells and impurities, incubated, and passaged when the degree of cell fusion reached 70–80%. After two to three passages, pure human primary esophageal CAFs were obtained for subsequent experiments.
Total RNA was extracted using the TRIzol kit (Invitrogen, Carlsbad, CA, USA). Eukaryotic mRNA was enriched with oligo (dT) beads. Enriched mRNA was then fragmented into short fragments using fragmentation buffer and reverse-transcribed into cDNA using the NEBNext Ultra RNA Library Prep Kit for Illumina (NEB#7530, New England Biolabs, Ipswich, MA, USA) and PCR was conducted. The resulting cDNA library was sequenced using Illumina Novaseq X Plus (Repugene Technology, Hangzhou, China).

value: ESCC-CAF


title: AGM_4_run3_NB54

description: Library name: AGM_4_run3_NB54_GL34_236_GL_SC_3_plate1_L2_S236


title: 28094

value: disease onset

value: Kidney anti-CD40 15mpk IP/2x/week


title: GV_F6_C


title: ESCC-CAF-shCDH11_2#2

description: Library name: R8


title: A549 RNA-seq, H13N2, rep1

description: Library name: Sample4


title: 28095


title: 28096


title: 28093


title: GV_F8_A


title: 28092

source_name: Kidney ABT-317 60mpk PO/SID


title: AGM_4_run3_NB22

description: Library name: AGM_4_run3_NB22_GL34_226_GL_SC_3_plate1_I5_S226


title: ESCC-CAF-shCDH11_2#1

description: Library name: R7


title: AGM_4_run3_NB11

description: Library name: AGM_4_run3_NB11_GL34_246_GL_SC_3_plate1_P2_S246


title: ESCC-CAF-shCDH11_1#3

description: Library name: R6


title: AGM_4_run3_NB07

description: Library name: AGM_4_run3_NB07_GL34_219_GL_SC_3_plate1_M6_S219


title: 28089


title: GV_F5_B


title: 28090


title: GV_F5_C


title: ESCC-CAF-shCDH11_1#2

description: Library name: R5


title: 28091


title: 28088


title: GV_F5_A


title: GV_F6_B


title: AGM_4_run3_NB01

description: Library name: AGM_4_run3_NB01_GL34_221_GL_SC_3_plate1_O2_S221


title: AGM_4_run3_NB02

description: Library name: AGM_4_run3_NB02_GL34_224_GL_SC_3_plate1_M1_S224


title: ESCC-CAF-shcon3

description: Library name: R3


title: GV_F4_C


title: AGM_4_run2_NB40

description: Library name: AGM_4_run2_NB40_GL34_223_GL_SC_3_plate1_K5_S223


title: GV_F4_A


title: GV_F4_B


title: ESCC-CAF-shcon1

description: Library name: R1


title: AGM_4_run2_NB59

description: Library name: AGM_4_run2_NB59_GL34_256_GL_SC_3_plate1_A11_S256


title: AGM_4_run3_NB04

description: Library name: AGM_4_run3_NB04_GL34_211_GL_SC_3_plate1_M5_S211


title: ESCC-CAF-shCDH11_1#1

description: Library name: R4


title: ESCC-CAF-shcon2

description: Library name: R2


title: OS833_K27Ac_NONE_6

description: Library name: OS833_K27Ac_NONE_6

data_processing:
CUT&Run samples were processed using a custom pipeline scripted with CGPipe. FastQ files were paired, trimmed, and aligned to both human (hg38) and yeast (sac3) genomes using Bowtie2 with the ‘--dovetail’ setting. Reads were classified as human or yeast using the NGSUtilsJ bam-best function, and yeast-aligned reads were removed. Peak calling was performed with MACS3
Assembly: hg38
Supplementary files format and content: bedGraph pileups generated using MACS2
Library strategy: CUT&Run

extract_protocol:
Cells were harvested using trypsine and used as input for CUT&RUN libraries.
Briefly, cells were harvested, washed, and bound to activated Concanavalin A-coated magnetic beads (Cell Signaling Technology #93569S) and permeabilized. The bead-cell complex was incubated overnight with either an Acetyl-Histone H3 (Lys27) antibody (Cell Signaling Technology #8173, RRID:AB_10949503), Mono-Methyl-Histone H3 (Lys4) antibody (Cell Signaling Technology #5326, RRID:AB_10695148), Tri-Methyl-Histone H3 (Lys4) antibody (Cell Signaling Technology #9751, RRID:AB_2616028) or an IgG antibody control (Cell Signaling Technology #66362, RRID:AB_2924329) at 4°C. Cells were then washed with digitonin buffer (Cell Signaling Technology #16359S), resuspended in 50 μl of pAG/Mnase (Cell Signaling Technology #57813S) and incubated for 1hr at 4°C. Spike-In DNA (5ng, Cell Signaling Technology #36598S) was added to each reaction. DNA from enriched chromatin samples was purified using the DNA Purification Buffers and Spin Columns kit (Cell Signaling Technology #14209). DNA libraries were prepared using NEBNext® Ultra™ II DNA Library Prep Kit for Illumina® (NEB #E7645L) and NEBNext® Multiplex Oligos for Illumina® (NEB #E7600S). Fragment size and quality of the libraries were evaluated by Tapestation (4200 system, Agilent, RRID:SCR_018435). Libraries were sequenced in a NextSeq500 system (Illumina).

value: OS PDX-derived

tag: epitope


title: GV_F3_C


title: 28083

source_name: Kidney vehicle HPMC/Tween PO/SID


title: 28084


title: 28087


title: OS833_K27Ac_NONE_5

description: Library name: OS833_K27Ac_NONE_5


title: 28085


title: AGM_4_run2_NB28

description: Library name: AGM_4_run2_NB28_GL34_249_GL_SC_3_plate1_H4_S249


title: 28082

source_name: Kidney baseline


title: AGM_4_run2_NB20

description: Library name: AGM_4_run2_NB20_GL34_234_GL_SC_3_plate1_G3_S234


title: GV_F3_B


title: 28086


title: AGM_4_run2_NB17

description: Library name: AGM_4_run2_NB17_GL34_220_GL_SC_3_plate1_O5_S220


title: OS833_K27Ac_NONE_4

description: Library name: OS833_K27Ac_NONE_4


title: GV_F3_A


title: AGM_4_run2_NB06

description: Library name: AGM_4_run2_NB06_GL34_081_GL_SC_1_plate1_H10_S81


title: GV_F2_C


title: OS833_K27Ac_NONE_3

description: Library name: OS833_K27Ac_NONE_3


title: OS833_K27Ac_NONE_2

description: Library name: OS833_K27Ac_NONE_2


title: GV_F2_B


title: AGM_4_run2_NB05

description: Library name: AGM_4_run2_NB05_GL34_209_GL_SC_3_plate1_J1_S209


title: 28079


title: 28080


title: AGM_4_run1_NB74

description: Library name: AGM_4_run1_NB74_GL34_051_GL_SC_1_plate1_H19_S51


title: GV_F2_A


title: OS833_K27Ac_NONE_1

description: Library name: OS833_K27Ac_NONE_1


title: GV_F6_A


title: GV_F1_C


title: 28078


title: AGM_4_run1_NB59

description: Library name: AGM_4_run1_NB59_GL34_213_GL_SC_3_plate1_O3_S213


title: GV_F1_A


title: OS833_IgG_NONE_6

description: Library name: OS833_IgG_NONE_6

value: IgG


title: OS833_IgG_NONE_7

description: Library name: OS833_IgG_NONE_7


title: AGM_4_run1_NB50

description: Library name: AGM_4_run1_NB50_GL34_049_GL_SC_1_plate1_H21_S49


title: AGM_4_run1_NB66

description: Library name: AGM_4_run1_NB66_GL34_244_GL_SC_3_plate1_B5_S244


title: OS833_IgG_NONE_5

description: Library name: OS833_IgG_NONE_5


title: NAIVEJJ-10-114

city: Silver Spring

first: Aarti

last: Gautam

state: MD

address: 503 Robert Grant Avenue

department: Medical Readiness Systems Biology

institute: WRAIR

description: colon content rDNA was sequenced

library_source: other

data_processing:
Raw demultiplexed fastq files were imported into R and processed using the DADA2 package from Bioconductor
Reads were inspected for quality, filtered, truncated at 220 bp, the paired reads were merged, a sequence table of amplicon sequence variants (ASVs) was constructed, and chimeras were removed.
The taxonomic classification of the ASVs was generated by a q2-feature-classifiervia classify-sklearn plugin
The operational taxonomic unit (OTU) database was mapped on the Silva reference database v132 with 99% taxonomy reference to curate taxa4
Supplementary files format and content: 16s radiation data file contains the abundance of Taxonomic classifications of ASVs
Library strategy: 16S

molecule: other

source_name: Descending colon

extract_protocol:
PowerSoil DNA Isolation Kit
Illumina 16S Metagenomics Library Preparation

value: Descending colon

tag: radiation dose

value: 0 Gy

tag: timepoint

value: Day 1


title: Blastocyst_mRNA_D

value: oocyte or embryo


title: NAIVEJJ-10-113

description: colon content rDNA was sequenced


title: AGM_4_run1_NB23

description: Library name: AGM_4_run1_NB23_GL34_210_GL_SC_3_plate1_H3_S210


title: OS833_IgG_NONE_4

description: Library name: OS833_IgG_NONE_4


title: AGM_4_run1_NB18

description: Library name: AGM_4_run1_NB18_GL34_228_GL_SC_3_plate1_F3_S228


title: 28076

source_name: Kidney young


title: NAIVEJJ-10-112

description: colon content rDNA was sequenced


title: Morula_mRNA_D


title: OS833_IgG_NONE_8

description: Library name: OS833_IgG_NONE_8


title: 28075


title: 28074


title: AGM_4_run1_NB05

description: Library name: AGM_4_run1_NB05_GL34_283_GL_SC_3_plate1_E11_S283


title: 28081


title: OS833_IgG_NONE_3

description: Library name: OS833_IgG_NONE_3


title: NAIVEJJ-10-111

description: colon content rDNA was sequenced


title: AGM_3_run3_NB68

description: Library name: AGM_3_run3_NB68_GL34_215_GL_SC_3_plate1_F4_S215

value: HE-AGM (early)


title: OS833_IgG_NONE_2

description: Library name: OS833_IgG_NONE_2


title: 28077


title: GV_F1_B


title: 8C_mRNA_D


title: 4C_mRNA_D


title: AGM_3_run3_NB65

description: Library name: AGM_3_run3_NB65_GL43_278_plate2_D11_Gfi_HE_S86


title: JJ-13-393

description: colon content rDNA was sequenced

value: 9 Days


title: OS833_IgG_NONE_1

description: Library name: OS833_IgG_NONE_1


title: JJ-13-394

description: colon content rDNA was sequenced


title: AGM_3_run3_NB55

description: Library name: AGM_3_run3_NB55_GL34_289_GL_SC_3_plate1_B7_S289


title: 2C_mRNA_D


title: Zygote_mRNA_D


title: JJ-13-392

description: colon content rDNA was sequenced


title: OS774_K27Ac_NONE_1

description: Library name: OS774_K27Ac_NONE_1


title: JJ-13-391

description: colon content rDNA was sequenced


title: MII_mRNA_D


title: AGM_3_run3_NB53

description: Library name: AGM_3_run3_NB53_GL34_042_GL_SC_1_plate1_G9_S42


title: OS774_IgG_NONE_6

description: Library name: OS774_IgG_NONE_6


title: OS774_IgG_NONE_5

description: Library name: OS774_IgG_NONE_5


title: AGM_3_run3_NB49

description: Library name: AGM_3_run3_NB49_GL34_229_GL_SC_3_plate1_P3_S229


title: GV_mRNA_D


title: AGM_3_run3_NB47

description: Library name: AGM_3_run3_NB47_GL34_057_GL_SC_1_plate1_H13_S57


title: JJ-13-334

description: colon content rDNA was sequenced

value: 3 Days


title: AGM_3_run3_NB38

description: Library name: AGM_3_run3_NB38_GL43_089_plate2_D21_Gfi_HE_S185


title: Blastocyst_mRNA_C


title: OS774_K27Ac_NONE_2

description: Library name: OS774_K27Ac_NONE_2


title: JJ-13-333

description: colon content rDNA was sequenced


title: AGM_3_run3_NB42

description: Library name: AGM_3_run3_NB42_GL34_058_GL_SC_1_plate1_G2_S58


title: OS774_IgG_NONE_2

description: Library name: OS774_IgG_NONE_2


title: OS774_IgG_NONE_4

description: Library name: OS774_IgG_NONE_4


title: JJ-13-331

description: colon content rDNA was sequenced


title: OS774_IgG_NONE_3

description: Library name: OS774_IgG_NONE_3