title: MCF7, DRB Treatment, Rep2, H3K27ac, ChIP

value: Breast, mammary gland

value: epithelial cell

value: anti-H3K27ac (Abcam, ab4729)

value: DRB (2hr), 17beta-estradiol (1hr)


title: Deprived P5 barrel cortex 2

status: Public on Aug 07 2025

type: SRA

city: New York

first: Pinar

last: Ayata

state: New York

address: 1425 Madison Ave

department: Neuroscience

country: USA

institute: Icahn School of Medicine at Mt Sinai

description:
counttab_1.txt
Dori-AC16

library_source: transcriptomic

data_processing:
Sequencing reads were quality checked and trimmed using Trim Galore (v0.6.4; a wrapper program implementing Cutadapt v2.9 and FastQC v0.11.9)
Reads were then mapped to the GRCm38 (mm10) mouse genome using the HISAT2 package (v2.2.0).
Quantification of reads was then performed using featureCounts (v2.0.0) against the Ensembl v99 annotation.
Assembly: mm10
Supplementary files format and content: tab-delimited text file includes raw count for each sample

molecule: total RNA

organism: Mus musculus

source_name: Barrel cortex female

extract_protocol:
The brain tissue was thawed in an ice-cold  glass homogenizer containing 1 mL cell-lysis buffer. After manually homogenizing the samples with 3-5 gentle strokes, samples were  homogenized in a motor-driven overhead stirrer. A post-nuclear supernatant was prepared by centrifugation. Post-mitochondrial supernatant was prepared by centrifugation after NP40 and DHPC treatment. GFP-antibod-coated beads were added to each supernatant. After overnight incubation, the polysome-bound beads were washed with the high-salt buffer. RNA clean-up was performed using RNeasy Mini Kit (Qiagen) following the manufacturer’s instructions.
RNA integrity was assayed using an RNA Pico chip on a Bioanalyzer 2100 (Agilent, Santa Clara, CA), and only samples with RIN>9 were considered for subsequent analysis. Double-stranded cDNA was generated from 1-5 ng of RNA using the Nugen Ovation V2 kit (NuGEN, San Carlos, CA) following the manufacturer’s instructions. Libraries for sequencing were prepared using Nextera XT kit (Illumina, San Diego, CA, USA) following the manufacturer’s instructions. The quality of the libraries was assessed by 2200 TapeStation (Agilent).

treatment_protocol: To activate Tamoxifen-inducible Cre (CreErt2), Cx3cr1CreER/+ (Litt); Eef1a1LSL.eGFPL10a/+ mice were orally administered 50 µg tamoxifen (T5648, Sigma, St. Louis, MO) dissolved 10 mg/mL in corn oil (C8267, Sigma) once daily at ages P1, P2, and P3. Aldh1l1EGFP-L10a/+ mice were not injected with tamoxifen. Unilateral whisker lesioning was performed at P4. Mice were euthanized at P5 with CO2, and the barrel cortex region was dissected and flash-frozen for TRAP.

tag: tissue

value: Barrel cortex

tag: Sex

value: female

tag: cell type

value: whole tissue

tag: genotype

tag: treatment

value: Whiskers on the right side were cauterized at P4.


title: ND-ARM1

city: Changsha

first: Hu

last: Wanyu

address: 长沙市芙蓉区人民中路139号

country: China

institute: 中南大学湘雅二医院

description: ND gene_expression.xls

data_processing:
Total RNAs of ARMs and NARMs were isolated and followed by RNA-seq analysis in the company (The Beijing Genomics Institute, Shenzhen, China) using the Illumina high-throughput sequencing platforms. The differential expression of genes was selected by Log2FC > 0.6 or Log2FC < -0.6 and P < 0.05.
Assembly: mm10
Supplementary files format and content: FPKM, TPM, read count

source_name: ewat

extract_protocol:
Trizol was used to extract RNA from cells, 200 ng RNA was used for sequencing.
Total RNA of ARM/SM that were purified via FACS sorting was extracted by Trizol (Life Technologies, Cat#15596026) according to the manufacturer’s protocol.

value: ewat

value: WT

value: chow diet


title: MCF7, TRP Treatment, Rep1, ERalpha, ChIP

city: Bengaluru

first: Rajat

last: Mann

state: Karnataka

address: Rajiv Gandhi Nagar, Kodigehalli

country: India

institute: National Center for Biological Sciences

library_source: genomic

data_processing:
Raw fastq reads were aligned to the hg19 genome for human and dm3 reference genome for drosophila. Reads with quality score less than 30 were filtered out. The reads were first down sampled according to the sample with the lowest sequencing depth. Then, reads were further down sampled according to spike-in factor calculated as shown in (Egan et al., 2016).
Assembly: hg19 (for Human), dm3 (for Drosophila Spike-in)
Supplementary files format and content: bigwig files

molecule: genomic DNA

organism: Homo sapiens

source_name: Breast, mammary gland

growth_protocol: MCF-7 cells were maintained in DMEM with 10% FBS and 5% Penstrep. For experiments MCF-7 cells were grown in stripping media with 5% characol stripped FBS and 5% Penstrep for 72 hours.

extract_protocol:
Cells were fixed using 1% formaldehyde for 10 mins at room temperature on an orbital shaker. After 10mins, formaldehyde was quenched using 0.125M glycine for 5mins at room temperature on the orbital shaker. The cells were washed with cold 1XPBS and scraped. The cells were pelleted down at 3000rpm for 5mins at 4°C. The pellets were stored at -80°C. 10 million cells were resuspended in 1 ml of nuclear lysis buffer (NLB) (50mM Tris-HCl pH 7.4, 1% SDS, 10mM EDTA pH 8.0, and 1X PIC) and incubated in ice for 10mins. After nuclear lysis, cells were sonicated using Bioruptor pico for 28cycles with 30secs ON and 30secs OFF settings. The lysate was then spun at 12000rpm for 12mins at 4°C to clear off the cell debris. 100μg of chromatin was used for IP, further 3μg of sonicated S2 chromatin was added as spike-in for only H3K27ac ChIP. The IP was diluted 2.5 times with dilution buffer (20mM Tris-HCl pH 7.4, 100mM NaCl, 2mM EDTA pH 8.0, 0.5% Triton X-10, and 1X PIC). IP was set in a volume of 500μl. Additionally, 50μl was taken out and labelled as 10% input. For IP, main as well spike-in antibody was added in their respective amounts (ERα (sc-8002, Santa Cruz Biotech) 1μg, anti-PolII (Diagenode C15200004) 2μg, H3K27ac (ab4729, Abcam) 1μg and spike-in H2av 0.3ug (61686, Active Motif)). IP was incubated with antibodies overnight at 4°C at constant rotation of 12rpm. After incubation, 15μl of Protein G beads pre-blocked in BSA were added to the mix. It was incubated for 4 hours at 4°C on the rotor. After incubation, the beads were washed with wash buffers I, II, III and 1XTE sequentially (Li et al., 2013). The DNA-protein complexes were eluted from the beads by resuspending the beads in (100mM NaHCO3, 1%SDS, 2μg of RNaseA) at 37°C in a thermomixer with 1400rpm for 30mins. The crosslinked DNA-protein complexes were reverse-crosslinked over night at 65°C by the addition of NaCl. After that 2μl of Proteinase K (20mg/ml) was added to the mix and incubated for 2hours at 45°C. The ChIP DNA was then purified using PCI (Phenol:Chloroform:Isoamylalcohol) and ethanol precipitation. The pellet was resuspended in 10μl of NFW.
library preparation was done using NEBNext Ultra II DNA library Prep kit with Sample Purification Beads (E7103L).

treatment_protocol: After 72 hours cells were treated with β-estradiol (E2758, Sigma-Aldrich) at a concentration of 10nM for 1hour. In case of experiments involving transcription inhibitor treatment, cells were treated with DRB (D1916, Sigma) at 10uM and TRP (T3652, Sigma) at 1uM or DMSO for 1hour. After 1hour of inhibitor treatment, 10nM of E2 was added in the media and processed for ChIP-seq. For experiments involving knockdown, two rounds of transfection were done with the siRNAs. First transfection was done 24hours after cell seeding. Second round of transfection was done after 48 hours of keeping cells in stripping media. For FLAG-RRGG-ERα overexpression plasmids were transfected on the second day (48 hours in stripping media).

tag: cell line

tag: chip antibody

value: Estrogen Receptor alpha Antibody (F-10), sc-8002, scbt

value: TRP (2hr), 17beta-estradiol (1hr)


title: MCF7, DRB Treatment, Rep1, H3K27ac, ChIP


title: 5xFAD Cortex microglia rep 1

molecule: polyA RNA

source_name: Cortical microglia

extract_protocol:
Cortices were dissected from animals and frozen. Frozen cortices were lysed and microglial mRNAs were isolated using the TRAP protocol
cDNA was generated using Nugen Ovation V2 kit. Libraries were produced using TruSeq DNA Sample kit.
Multiplexed libraries were directly loaded on NextSeq 500 (Ilumina) with High Output single read sequencing for 75 cycles for RNA seq.

treatment_protocol: Mice were ravaged with Tamoxifen at 4-6 weeks of age

value: Cortical microglia

tag: strain

value: Black 6

value: Male

tag: age

value: 6 month old


title: ND-NARM1

address: 长沙市芙蓉区人民中路139号

description: ND gene_expression.xls


title: Deprived P5 barrel cortex 1

description:
counttab_1.txt
Dori-AC14

source_name: Barrel cortex male

value: male


title: Control P5 barrel cortex 2

description:
counttab_1.txt
Dori-AC15


title: Control Cortex microglia rep 3

value: Female


title: 5xFAD Cortex microglia rep 2


title: Control Cortex microglia rep 2


title: MCF7, DRB Treatment, Rep1, Flag, RRGG_mt, ChIP

value: Breast, mammary gland

value: epithelial cell

value: anti-FLAG (Sigma F7425)


title: ND-NARM2

address: 长沙市芙蓉区人民中路139号

description: ND gene_expression.xls


title: MCF7, DRB Treatment, Rep2, ERalpha, ChIP

value: DRB (2hr), 17beta-estradiol (1hr)


title: MCF7, DRB Treatment, Rep2, Flag, RRGG_mt, ChIP


title: Control Cortex microglia rep 1


title: MCF7, DRB Treatment, Pol II, ChIP

value: anti-PolII (Diagenode C15200004)


title: TA807NP_3

city: Hsinchu City

first: ShengLiang

last: Cheng

address: No. 101, Sec. 2, Guangfu Rd., East Dist.

department: Institute of Biomedical Engineering

country: Taiwan

institute: National Tsing Hua University

description:
Original_read_count -1.txt
DESeq2_normalized_read_counts -1.txt

data_processing:
Illumina Casava software used for basecalling.
FastQC and MultiQC were used to check fastq files for quality.The obtained raw paired-end reads were filtered by Trimmomatic (v0.38) to discard low-quality reads, trim adaptor sequences, and eliminate poor-quality bases with the following parameters: LEADING:3 TRAILING:3 SLIDINGWINDOW:4:20 MINLEN:36.
Read pairs from each sample were aligned to the reference genome by the HISAT2 software (v2.1.0).
FeatureCounts (v2.0.0) was used to count the reads numbers mapped to individual genes. For gene expression, the “Relative Log Expression” normalization (RLE) was performed DEGseq2 (v1.26.0).
Assembly: mm_GRChm38
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample
Supplementary files format and content: tab-delimited text files include TMM values for each Sample

source_name: tumor

growth_protocol: Murine HCC HCA-1 cells were orthotopically implanted in the liver of 6–8-week-old male C3H mice. 1 × 10^6 HCA-1 cells were injected in the subcapsular region through a 28-gauge needle.

extract_protocol:
The integrity of RNA extracted from the treatment and control groups using the RNeasy Kit (Qiagen) was evaluated with the RNA Nano6000 assay kit (Agilent Technologies, CA, USA)
RNA libraries were prepared for sequencing using KAPA mRNA HyperPrep Kit Illumina® Platforms protocol

treatment_protocol: The experimental design involved orthotopically implanting murine HCC (HCA-1) cells in C3H mice, followed by IV administration of nanoparticle loaded with CXCR4 inhibitor BPRCX807 on days 15, 16, and 17. Subsequent transcriptome analysis of the tumors was performed on day 17.

value: tumor

value: HCC

value: nanoparticle loaded with CXCR4 inhibitor BPRCX807.


title: ND-ARM2

address: 长沙市芙蓉区人民中路139号

description: ND gene_expression.xls

value: ewat

value: WT

value: chow diet


title: TA807NP_5


title: ATACseq_NGN2_ES24h_1855

city: Basel

first: Sevi

last: Durdu

address: Fabrikstrasse 24

department: Genome Regulation

country: Switzerland

institute: Friedrich Miescher Institute for Biomedical Research

data_processing:
Illumina RTA 2.4.11 and bcl2fastq2 v2.17 was used for basecalling and demultiplexing. ATAC-seq reads were trimmed using cutadapt version 1.18, (Martin, M. EMBnet.journal 17, 10 (2011)) with parameters -a CTGTCTCTTATACACA -A CTGTCTCTTATACACA -m 5 --overlap=1 and then mapped to mm10 using QuasR (Gaidatzis et al, Bioinformatics 2015) with default parameters.
Assembly: mm10
Supplementary files format and content: ExportWig function from the QuasR package was employed to generate the wig files with default parameters except scaling=1e6. pairedAsSingle is set to TRUE to quantify the 5'-read ends (Tn5 insertion sites) in the wig files.

source_name: embryonic stem cells

growth_protocol: Mouse ES cells were cultured as previously described (Mohn, F. et al. Mol. Cell, 2008). Briefly, cells were maintained in Dulbecco’s Modified Eagle Medium (DMEM, Invitrogen), supplemented with 15 % Fetal Calf Serum (Invitrogen), L-Glutamine (Gibco) and nonessential amino acids (Gibco), betamercaptoethanol (Sigma) and leukemia inhibitory factor (LIF; produced in-house). All experiments were performed with cells grown for several passages on plates coated with 0.2% gelatin (Sigma).

extract_protocol:
Tagmented DNA was purified using the MinElute PCR Purification Kit (Qiagen).
Tagmented DNA was amplified with 7 cycles.

treatment_protocol: mESCs were induced for differentiation by expressing NGN2 or MyoD1. 50000 cells per sample was collected for ATAC-seq protocol as described in Buenrostro et al, 2013.

value: embryonic stem cells

value: mESC

value: FCS/LIF+dox

tag: mouse strain

tag: experiment id


title: Control P5 barrel cortex 1

description:
counttab_1.txt
Dori-AC13

value: Barrel cortex

value: whole tissue

value: Whiskers on the right side were cauterized at P4.


title: TA807NP_1


title: Control P5 barrel cortex astrocytes 5

description:
counttab_1.txt
Dori-AC9

value: male

value: Astrocytes


title: MCF7, DMSO Control for TRP, Rep2, ERalpha, ChIP

value: Breast, mammary gland

value: epithelial cell

value: Estrogen Receptor alpha Antibody (F-10), sc-8002, scbt

value: DMSO (2hr), 17beta-estradiol (1hr)


title: MCF7, DMSO Control for DRB, Pol II, ChIP

value: anti-PolII (Diagenode C15200004)


title: ATACseq_NGN2mut_24h_1855

value: 24 hours N2B27(w/oVitA)+dox


title: MCF7, DMSO Control for TRP, Rep1, ERalpha, ChIP


title: Control_5

value: tumor

value: HCC

value: Untreated


title: Control P5 barrel cortex astrocytes 4

description:
counttab_1.txt
Dori-AC7

value: female


title: MCF7, DMSO Control for DRB, Rep1, H3K27ac, ChIP

value: anti-H3K27ac (Abcam, ab4729)


title: Deprived P5 barrel cortex astrocytes 3

description:
counttab_1.txt
Dori-AC6


title: MCF7, DMSO Control for DRB, Rep2, H3K27ac, ChIP


title: Control_4


title: Deprived P5 barrel cortex astrocytes 5

description:
counttab_1.txt
Dori-AC10


title: Control_1


title: Equinox day samples at Zeitgeber time 16 h replicate B

city: New Haven

first: Chun Chung

last: Leung

state: CT

address: YSB 424, 260 Whitney Avenue

department: MCDB

institute: Yale University

description: Library name: EquinoxDay_ZT16_Rep_B

data_processing:
Sequencing adapters, poly-A sequences and low quality reads were removed from the raw read file using cutadapt (v3.4) with the following parameters: -q 10,10. Sequences of known mature miRNAs (428 in total, but only 350 unique sequences) and tRFs (1,544,607 in total) were downloaded from miRBase (release 22.1) and the tREX database (2021 release). Bowtie2 (v2.5.1) was used to align reads with the following parameters: -a --end-to-end --score-min L,0,-0.6 --np 0 --rdg 9999,9999 --rfg 9999,9999. SAMTools were used to retrieve alignments where the reads covered the entirety of the sRNA annotations.
Assembly: miRBase (release 22.1) and the tREX database (2021 release)
Supplementary files format and content: Bowtie2-quantified read counts in comma-separated values

organism: Arabidopsis thaliana

source_name: Whole seedlings

growth_protocol: Seeds were sterilized before being sown onto 1/2 Murashige and Skoog medium plates lined with autoclaved filter papers. For germination, seeds were stratified in the dark for 48 hours before being transferred to a growth chamber under a 12L:12D photoperiod . After germination, seedlings were kept in the same condition for 10 days. On day 11, the seedlings were transferred to 16L:8D, 12L:12D, or 8L:16D photoperiod. On day 13, whole seedlings including shoots and roots were harvested and snap-frozen in liquid nitrogen.

extract_protocol:
Total RNA was extracted from approximately 200 mg of pulverized whole Arabidopsis seedlings (shoot, hypocotyl, and root) using TRIzol reagent (ThermoFisher) according to manufacturer’s protocol. RNA samples were treated with RNase-free DNase (QIAGEN, 79254) to remove DNA contaminants. Protein contaminants were removed by extraction with phenol-chloroform mixture (phenol:chloroform:isoamyl-alchohol 25:24:1; Thermo Fisher, AM9730) followed by precipitation using 3 M sodium acetate solution.
All sequencing libraries were prepared at Yale Center for Genome Analysis (YCGA). All samples passed a quality check with ≥7.0 in RNA integration number (Agilent Bio-analyzer). For sRNA-sequencing, small RNAs (expected size ≤40 nucleotides) were size-selected from total RNA samples through gel electrophoresis at YCGA. The NEBNext Small RNA Library Prep Set for Illumina kit was used.

value: Whole seedlings

value: Columbia 0

value: Equinox day

tag: time


title: DAP_myod-tcf12_d2_rep2_3037

data_processing:
Illumina RTA 1.18.64 and bcl2fastq2 v2.17 was used for basecalling and demultiplexing for single-read experiments. Illumina RTA 2.4.11 and bcl2fastq2 v2.17 was used for basecalling and demultiplexing for paired-read experiments. ChIP-seq samples were aligned to the mm10 assembly of the mouse genome using QuasR (Gaidatzis et al, Bioinformatics 2015), which internally uses Bowtie 2 (Langmead, Genome Biology 2009). Bowtie was run with QuasR default parameters.
Assembly: mm10
Supplementary files format and content: ExportWig function from the QuasR package was employed to generate the wig files with default parameters except scaling=1e6 and only for single-end experiments setting shift to 120.
Library strategy: DAP-seq

growth_protocol: Rosetta(DE3)pLysS Competent Cells (Millipore) were induced to express GST-tagged protein encoded in pGEX-6P-1 plasmids for DAPseq (NGN2, MyoD1, bHLH domains of TCF3-E12,TCF3-E47,TCF4,TCF12). 2ml fresh culture were added into 50ml LB and grow to an OD600 of 0.5 and induced with IPTG for 3 hours at 37DEgC for NGN2 and MyoD1 and 16DegC for TCFs. Cells were lysed and soluble fractions were mixed in combinations. GST tagged proteins were isolated using Promega MagneGST beads.

extract_protocol:
DNA was purified by AMPure beads with a ratio of 2:1 beads to sample volume.
Isolated DNA was subjected to library preparation (NEBNext Ultra II DNA Library Prep Kit, Illumina). In the library preparation protocol, samples were amplified using 12 PCR cycles.

treatment_protocol: Protocol was performed for Small-scale DAP-seq using E. coli-expressed recombinant protein as previously described (Bartlett et al, Nature Protocols, 2017) with modifications. Brielfy, freshly isolated GST-bHLH proteins bound to magnetic beads were incubated with 10ug of gemonic DNA sonicated to an average size range of 150-200bp for 1 hour in PBS. Beads were washed 4x with 200ul of PBS + 0.05%NP40, then washed 2x with 200ul PBS. Finally, beads were resuspended in 30ul 10 mM Tris-Cl, pH 8.5 + 2ul 10mg/ml Proteinase K and incubated at 50DegC for 3 hours.

value: embryonic stem cells

value: mESC

value: DNMT1-/-; DNMT3a-/-; DNMT3b-/-

tag: treatment (proteins)


title: ATACseq_mESC_r2_1855

value: FCS/LIF


title: ATACseq_NGN2_24h_1855


title: ATACseq_mESC_r1_1855


title: Deprived P5 barrel cortex astrocytes 2

description:
counttab_1.txt
Dori-AC4

value: Barrel cortex

value: Astrocytes

value: Whiskers on the right side were cauterized at P4.


title: MCF7, DMSO Control for DRB, Rep2, Flag, RRGG_mt, ChIP

value: Breast, mammary gland

value: epithelial cell

value: anti-FLAG (Sigma F7425)

value: DMSO (2hr), 17beta-estradiol (1hr)


title: SAM, int-c.5, LP/SP, rep2

city: Wageningen

first: Wilma

last: Van Esse

address: Droevendaalsesteeg 1

country: Netherlands

institute: Wageningen University & Research

data_processing:
Raw paired RNA-seq reads were cleaned using Trimmomatic 0.39 (Bolger et al., 2014) using the command: ILLUMINACLIP:adapters.fa:2:30:10 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:36, adapters.fa is a file containing nucleotide sequences of the used Illumina adapters. From the trimmed reads, transcripts were quantified taking the MorexV3 transcriptome as reference (Mascher et al., 2021) using salmon (Patro et al., 2017) with the softclip parameter.
Assembly: MorexV3
Supplementary files format and content: text file of transcripts per million (TPM) and number of reads per gene in the genome annotation as per output using salmon quant

organism: Hordeum vulgare

source_name: developing inflorescence

growth_protocol: Seeds of cv. Bowman and int-c.5 were sown in 84-well trays. To improve equal germination, a stratification treatment was provided by exposing the seeds at 4°C in the dark for three days. After that, germination of seeds and growth of plants took place in a growth chamber under long day (LD) conditions (16h light/ 8h dark) at 20°C. Developmental stages of the meristems were scored using the Waddington scale (WADDINGTON et al., 1983) by dissecting three plants of each genotype on the day of sampling. Shoot apical meristems were sampled over time at four different stages: W0, vegetative apex (VA); W1, transition apex (TA); W2.25, triple mound (TM); and W3-3.5, lemma and stamen primordia (LP/SP). Samples were taken in the afternoon (6 hours before the end of the LD period). Leaves surrounding the apex were removed manually, before cutting the apex.

extract_protocol:
Frozen tissue was disrupted using the Tissuelyser LT (Qiagen). RNA extraction was performed on disrupted tissues using columns from the GeneJET plasmid miniprep kit (Thermo Fischer Scientific), as described previously (Yaffe et al., 2012) (doi:10.1186/1756-0500-5-45). Extracted RNA was treated with DNase I (Qiagen) and RiboLock (Fermentas). Extracted RNA samples that were used for RNA-Seq were send to Novogene, where mRNA was purified from total RNA using poly-T oligo-attached magnetic beads. After fragmentation, the first strand cDNA was synthesized using random hexamer primers, followed by the second strand cDNA synthesis.
Illumina Truseq (performed by Novogene)

value: developing inflorescence

value: Lemma + Stamen primordia (LP/SP)


title: ATACseq_MYOD1_24h_r2_2276

value: 24 hours N2B27(w/oVitA)+dox


title: ATACseq_GFP_24h_1855


title: Control P5 barrel cortex astrocytes 2

description:
counttab_1.txt
Dori-AC3

value: female


title: SAM, int-c.5, LP/SP, rep1


title: MCF7, DMSO Control for DRB, Rep2, ERalpha, ChIP

value: Estrogen Receptor alpha Antibody (F-10), sc-8002, scbt


title: SAM, int-c.5, LP/SP, rep3


title: ATACseq_MYOD1_24h_r1_2276


title: Deprived P5 barrel cortex astrocytes 4

description:
counttab_1.txt
Dori-AC8


title: Deprived P5 barrel cortex astrocytes 1

description:
counttab_1.txt
Dori-AC2

value: male


title: MCF7, TRP Treatment, Rep2, ERalpha, ChIP

value: TRP (2hr), 17beta-estradiol (1hr)


title: Endoderm differentiation, 5 histone marks and IgG control, 1 round, scMTR-seq, sublibrary8, RNA

city: Cambridge

first: Laura

last: Biggins

address: Babraham Research Campus

department: Bioinformatics

country: United Kingdom

institute: The Babraham Institute

description:
polyA RNA
read1 file contains transcript; read2 files contains cell barcodes, Ab id, UMI and transcript
DNA sublibrary8 and RNA sublibrary8 are from same sample

data_processing:
After sequencing, cell barcodes and UMI information were extracted with modified Reachtools (https://doi.org/10.1038/s41592-021-01060-3). Sequences from fixed positions of Read2 were extracted: 1st-8th for BC3, 39th-46th for BC2, 77th-84th for BC1, 115th-119th for RT-ID in RNA data or for antibody-ID in DNA data, 120th-127th for UMI. Barcode combinations (BC1:BC2:BC3:RT-ID/antibody-ID) were mapped to all possible barcode combinations with Bowtie (version: 1.3.1, doi:10.1186/gb-2009-10-3-r25, version, --norc -m 1 -v 0). Mapped cell IDs and UMI were stored in read names of genome sequences. Trim-galore (version:0.6.10) was used to trim adapter sequences with default settings. Trimmed reads were mapped mapped to GRCh38 for human samples and mm10 for mouse samples using Bowtie2 (version: 2.5.3, DOI: 10.1038/nmeth.1923) for DNA data and STAR (version: 2.7.11b, DOI: 10.1093/bioinformatics/bts635) for RNA data with default settings. Only unique mapped reads were kept by samtools filtering (version: 1.19.2, MAPQ>50 for RNA data and MAPQ>10 for DNA data). For the paired-end mapping data, only proper mapped reads with correct orientation were kept. Duplicated reads were identified by the mapping positions and UMIs for each cellid of RNA data. Duplicated reads were identified by mapping positions only for each cellid of DNA data. RNA deduplicated data were feature counted by custom script with splitpoolquantitation (https://github.com/laurabiggins/nf_yang_wang/tree/main/splitpoolquantitation) and converted to sparse matrix. DNA deduplicated data were converted to fragment files for downstream analyses.
Assembly: mm10 for mouse sample, GRCh38 for human sample
Supplementary files format and content: Tab-separated values files and matrix files
Supplementary files format and content: single cell RNA data: barcodes.tsv.gz; features.tsv.gz; matrix.mtx.gz
Library strategy: scMTR-seq

growth_protocol: H9 cells were grown in 5% CO2, 5% O2 at 37°C and maintained in Essential8 medium (ThermoFisher Scientific) on 0.5% Geltrex (ThermoFisher Scientific). Embryos at approximately E3.5 were collected by flushing the uterus with M2 medium (Sigma-Aldrich) 94– to 98-hours after human chorionic gonadotropin injection. Embryos were cultured in KSOM medium (Millipore, MR-121-D) for 24 hours at 37°C in a 5% CO2 incubator under light mineral oil (Millipore, ES-005-C).

extract_protocol:
H9 cells and samples collected from different time points during endoderm differentiation were dissociated into single cells with TrypLE Express (ThermoFisher Scientific). Zona pellucidae was removed from E4.5 embryos using Acidic Tyrode’s solution (Sigma) and washed through three drops of M2 media. Embryos were washed in PBSI (PBS without calcium or magnesium supplemented with 1x Protease Inhibitor Cocktail [PIC], 0.05 U/μL SuperaseIn RNase Inhibitor, 0.1 U/μL Protector RNAse Inhibitor and 0.2% BSA) and dissociated into single cells with TrypLE Express.
Nuclei were prepared with Nuclei Extraction buffer and fixed with 0.2% formaldehyde at room temperature for 5 min. Concanavalin A beads were added to the samples to bind nuclei. Preincubated antibody and proteinA-Tn5-MEBdU were added to the nuclei and incubated at RT for 1 hour or overnight at 4°C. Nuclei were washed three times and tagmented at 37°C for 1 hour in the presence of MgCl2. Reaction was stopped with EDTA. Tagmentation was repeated for sequential tagmentation. Followed, reverse transcription was crried out to capture polyA-mRNA transcripts. Three rounds of split-pool barcoding was performed to add combinatory barcodes for each single cells. Nuclei was counted and aliquoted into sublibraries. Reverse crosslinking was performed at 55°C for 1 hour in reverse crosslinking buffer with proteinase K and RNase inhibtors. PMSF was used to inactivate proteinase K. DNA and cDNA were separated by C1 Streptavidin beads. For DNA library, tagmented genomic DNA fragments were purified with Ampure XP beads. Eluted DNA was performed adapter switching and amplified. For RNA library, templated switch was performed and preammplified. MEA adapters were added to the RNA library by Tn5-MEA mediated tagmentation. The concentration of libraries was measured with a Qubit. Samples were run on a Bioanalyzer to check the size distribution of library fragments before submited for seuqencing.

treatment_protocol: Endoderm differentiation: H9 cells were seeded on Geltrex in Essential8 medium. The next day, cells were washed with 0.1% BSA in DMEM, and then cultured in endoderm induction medium comprised of 50% IMDM (ThermoFisher Scientific), 50% F-12 Nutrient Mix (ThermoFisher Scientific), 1% Chemically Defined Lipids (ThermoFisher Scientific), 0.1% BSA Fraction V (ThermoFisher Scientific), 15μg/mL Transferrin (Merck), 450μM Monothioglycerol (Merck), 0.7μg/mL Insulin (Merck), 100ng/mL Activin-A (Cambridge Stem Cell Institute), 100nM PI-103 (Tocris Bio-Techne), 3μM CHIR99021 (Cambridge Stem Cell Institute),  10ng/mL FGF2 (Cambridge Stem Cell Institute), 3ng/mL BMP4 (R&D Systems) and 10μg/mL Heparin (Merck). After 24 hours, cells were cultured in modified endoderm induction medium whereby CHIR99021 and BMP4 were removed, the concentration of FGF2 was increased to 20ng/mL, and LDN193189 (Axon Medchem) was added to 250nM.

value: Human primed stem cells

tag: antibody

value: Human definitive endoderm differentiation

tag: library type

value: mRNA


title: ATACseq_NGN_24h_r2_2276

value: embryonic stem cells

value: mESC


title: Control P5 barrel cortex astrocytes 1

description:
counttab_1.txt
Dori-AC1

value: Barrel cortex

value: Astrocytes

value: Whiskers on the right side were cauterized at P4.


title: Mouse cerebellum, ATM-KO_11M

city: Hong Kong

first: Hei-Man Kim

last: Chow

address: Room 604, Mong Man Wai Building, CUHK

department: School of Life Sciences

country: Hong Kong

institute: The Chinese University of Hong Kong

data_processing:
The FASTQ files were first assessed using FastQC (V. 0.11.9) provided by Babraham Bioinformatics, which serves as a quality control tool for high throughput sequence data.
Once the data is evaluated and the quality is ensured, the genome indexes were generated using the STAR software.
The indexes were generated using the mouse annotation and mouse genome assembly provided by Gencode, Release 28 (GRCm39), which was released in May 2021.
The subsequent clean data was then aligned using the STAR alignment software using the genome indexes.
featureCounts was then used to quantify the sequencing data. Data extraction, matrix construction and differential gene expression analysis was then performed using DESeq2.
Assembly: mm39
Supplementary files format and content: tab-delimited text files include raw values from featureCounts for each sample.

source_name: Mouse cerebellum

extract_protocol:
RNA was using TriZOL method and the total crude RNA was sent to Novogene for purification and the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared by the service purchased from the Novogene

value: Mouse cerebellum

value: ATM -/-


title: Mouse cerebellum, ATM-KO_12M


title: SAM, Bowman, LP/SP, rep3

value: developing inflorescence

value: Bowman


title: Endoderm differentiation, 5 histone marks and IgG control, 1 round, scMTR-seq, sublibrary7, RNA

description:
polyA RNA
read1 file contains transcript; read2 files contains cell barcodes, Ab id, UMI and transcript
DNA sublibrary7 and RNA sublibrary7 are from same sample


title: Control P5 barrel cortex astrocytes 3

description:
counttab_1.txt
Dori-AC5


title: SAM, Bowman, LP/SP, rep1

value: Lemma + Stamen primordia (LP/SP)


title: MCF7, DMSO Control for DRB, Rep1, Flag, RRGG_mt, ChIP

value: Breast, mammary gland

value: epithelial cell

value: anti-FLAG (Sigma F7425)

value: DMSO (2hr), 17beta-estradiol (1hr)


title: Endoderm differentiation, 5 histone marks and IgG control, 1 round, scMTR-seq, sublibrary4, RNA

description:
polyA RNA
read1 file contains transcript; read2 files contains cell barcodes, Ab id, UMI and transcript
DNA sublibrary4 and RNA sublibrary4 are from same sample

value: Human primed stem cells


title: ATACseq_GFP_24h_r2_2276

value: 24 hours N2B27(w/oVitA)+dox


title: Mouse cerebellum, ATM-KO_7F


title: Endoderm differentiation, 5 histone marks and IgG control, 1 round, scMTR-seq, sublibrary6, RNA

description:
polyA RNA
read1 file contains transcript; read2 files contains cell barcodes, Ab id, UMI and transcript
DNA sublibrary6 and RNA sublibrary6 are from same sample

value: Human definitive endoderm differentiation

value: mRNA


title: SAM, Bowman, LP/SP, rep2


title: Mouse cerebellum, ATM-KO_1M


title: ATACseq_NGN_24h_r1_2276

value: embryonic stem cells

value: mESC


title: ATACseq_GFP_6h_r2_2028

value: 6 hours N2B27(w/oVitA)+dox


title: ATACseq_GFP_24h_r1_2276


title: SAM, int-c.5, TM, rep1

value: Triple mound (TM)


title: ATACseq_GFP_6h_r1_2028


title: SAM, int-c.5, TM, rep3


title: ATACseq_MYOD1_6h_r2_2028


title: Endoderm differentiation, 5 histone marks and IgG control, 1 round, scMTR-seq, sublibrary3, RNA

description:
polyA RNA
read1 file contains transcript; read2 files contains cell barcodes, Ab id, UMI and transcript
DNA sublibrary3 and RNA sublibrary3 are from same sample


title: SAM, Bowman, TM, rep3


title: Mouse cerebellum, Control_32M

value: Mouse cerebellum

value: ATM +/+


title: Endoderm differentiation, 5 histone marks and IgG control, 1 round, scMTR-seq, sublibrary2, RNA

description:
polyA RNA
read1 file contains transcript; read2 files contains cell barcodes, Ab id, UMI and transcript
DNA sublibrary2 and RNA sublibrary 2 are from same sample


title: SAM, int-c.5, TM, rep2

value: developing inflorescence


title: SAM, Bowman, TM, rep2

value: Bowman


title: Mouse cerebellum, Control_7M


title: SAM, Bowman, TM, rep1


title: Endoderm differentiation, 5 histone marks and IgG control, 1 round, scMTR-seq, sublibrary8, DNA

description:
Tn5 taggmented DNA
read1 file contains genomic fragment; read2 files contains cell barcodes, Ab id, UMI and genomic fragments
DNA sublibrary8 and RNA sublibrary8 are from same sample

value: H3K27me3 (CST, #9733S); H3K27ac (Abcam, #ab4729); H3K36me3 (Abcam, #ab9050); H3K4me1 (Abcam, #ab8895); H3K4me3 (Abcam, #ab8580); Normal rabbit IgG (R&D, #AB-105-C)

value: gDNA


title: ATACseq_NGN2mut_6h_r2_1854


title: Endoderm differentiation, 5 histone marks and IgG control, 1 round,scMTR-seq, sublibrary1, RNA

description:
polyA RNA
read1 file contains transcript; read2 files contains cell barcodes, Ab id, UMI and transcript
DNA sublibrary1 and RNA sublibrary 1 are from same sample


title: Endoderm differentiation, 5 histone marks and IgG control, 1 round, scMTR-seq, sublibrary5, RNA

description:
polyA RNA
read1 file contains transcript; read2 files contains cell barcodes, Ab id, UMI and transcript
DNA sublibrary5 and RNA sublibrary5 are from same sample


title: THP1,Compound49,24h,ATACseq,biol rep3

first: Salih

last: Topal

address: 500 Technology Square Suite 700

institute: Foghorn Therapeutics

description: Library name: THP1_Compound_24h_ATACseq_Rep3

data_processing:
Reads were trimmed for adapter sequences using  cutdapt3 and aligned to version hg38 of the human genome using bowtie2 (parameters -k 4, -X2000, --local ,--mm). Multimapping alignments were removed and only the the alignment with the highest score for each read pair was kept.
Duplicate reads were removed using Picard Tookit and alignments mapping to mitochondrial genome were excluded. Alignments were filtered for size smaller than 120 bp and read ends shifted +4 or -5 nucleotides depending on the direction of the read.
Peak calling was performed using MACS2.0 with a shift parameter of -75 and an extension size of 150 without modelling. Signal tracks were created using the fold enrichment option. Consistent peaks among replicates were obtained using IDR using a soft idr threshold of 0.1. Differential genome accessibility calculation was performed using limma package.
Motif enrichment was performed using Meme suite tools (MEME-chip)7 and CISBP transcription motif data from MEME motif database version 12.19. Ridge regression analysis was performed using glmnet R package with coefficients calculated using the minimum estimated lambda.
Genomic context annotation was performed using the annotatePeaks function of HOMER package using hg38 version of the human genome
Assembly: hg38
Supplementary files format and content: bigWig, narrowPeak

extract_protocol:
DNA extraction was performed as described in Buenrostro et al., 2013
ATAC-seq library was generated as described in Buenrostro et al., 2013. Following library generation, left- and right- size selection was performed with SPRIselect beads (Beckman Coulter) according to the manufacturer’s recommendations.

value: AML

value: WT

value: dual SMARCA4/SMARCA2 inhibition


title: ATACseq_NGN2mut_6h_r1_1854


title: Endoderm differentiation, 5 histone marks and IgG control, 1 round, scMTR-seq, sublibrary7, DNA

description:
Tn5 taggmented DNA
read1 file contains genomic fragment; read2 files contains cell barcodes, Ab id, UMI and genomic fragments
DNA sublibrary7 and RNA sublibrary7 are from same sample

value: Human primed stem cells


title: THP1,Compound49,24h,ATACseq,biol rep2

description: Library name: THP1_Compound49_24h_ATACseq_Rep2


title: SAM, int-c.5, TA, rep2

value: Transition apex (TA)


title: Mouse cerebellum, Control_2M


title: Endoderm differentiation, 5 histone marks and IgG control, 1 round, scMTR-seq, sublibrary5, DNA

description:
Tn5 taggmented DNA
read1 file contains genomic fragment; read2 files contains cell barcodes, Ab id, UMI and genomic fragments
DNA sublibrary5 and RNA sublibrary5 are from same sample

value: Human definitive endoderm differentiation


title: ATACseq_NGN2_6h_r1_1854


title: SAM, Bowman, TA, rep3


title: Mouse cerebellum, Control_13M


title: THP1,Compound49,24h,ATACseq,biol rep1

description: Library name: THP1_Compound49_24h_ATACseq_Rep1


title: ATACseq_NGN2_6h_r2_1854


title: Endoderm differentiation, 5 histone marks and IgG control, 1 round, scMTR-seq, sublibrary6, DNA

description:
Tn5 taggmented DNA
read1 file contains genomic fragment; read2 files contains cell barcodes, Ab id, UMI and genomic fragments
DNA sublibrary6 and RNA sublibrary6 are from same sample


title: Endoderm differentiation,  5 histone marks and IgG control, 1 round, scMTR-seq, sublibrary4, DNA

description:
Tn5 taggmented DNA
read1 file contains genomic fragment; read2 files contains cell barcodes, Ab id, UMI and genomic fragments
DNA sublibrary4 and RNA sublibrary4 are from same sample


title: SAM, Bowman, TA, rep1


title: THP1,DMSO,24h,ATACseq,biol rep2

description: Library name: THP1_DMSO_24h_ATACseq_Rep2

value: negative control


title: THP1,DMSO,24h,ATACseq,biol rep3

description: Library name: THP1_DMSO_24h_ATACseq_Rep3


title: Endoderm differentiation, 5 histone marks and IgG control, 1 round, scMTR-seq, sublibrary3, DNA

description:
Tn5 taggmented DNA
read1 file contains genomic fragment; read2 files contains cell barcodes, Ab id, UMI and genomic fragments
DNA sublibrary3 and RNA sublibrary3 are from same sample


title: ATACseq_GFP_6h_r1_1854

value: embryonic stem cells


title: ATACseq_MYOD1_6h_r1_2028

value: mESC


title: Endoderm differentiation, 5 histone marks and IgG control, 1 round, scMTR-seq, sublibrary2, DNA

description:
Tn5 taggmented DNA
read1 file contains genomic fragment; read2 files contains cell barcodes, Ab id, UMI and genomic fragments
DNA sublibrary2 and RNA sublibrary 2 are from same sample


title: SAM, int-c.5, VA, rep3

value: Vegetative apex (VA)


title: ChIPseq_IGG_mESC_2330

data_processing:
Illumina RTA 1.18.64 and bcl2fastq2 v2.17 was used for basecalling and demultiplexing for single-read experiments. Illumina RTA 2.4.11 and bcl2fastq2 v2.17 was used for basecalling and demultiplexing for paired-read experiments. ChIP-seq samples were aligned to the mm10 assembly of the mouse genome using QuasR (Gaidatzis et al, Bioinformatics 2015), which internally uses Bowtie (Langmead, Genome Biology 2009). Bowtie was run with QuasR default parameters.
Assembly: mm10
Supplementary files format and content: ExportWig function from the QuasR package was employed to generate the wig files with default parameters except scaling=1e6 and setting shift to 80 as the average of all samples after quantifying the estimated fragment length (half).

growth_protocol: Mouse ES cells were cultured as previously described (Mohn, F. et al. Mol. Cell, 2008). Briefly, cells were grown for several passages at 37℃ 7% CO2 seeded on plates coated with 0.2% gelatin (Sigma) and maintained in serum/LIF (Dulbecco’s modified Eagle medium (DMEM, Invitrogen), supplemented with 15% fetal calf serum (Invitrogen),L-glutamine (Gibco), nonessential amino acids (Gibco), 0.001% 2-Mercaptoethanol (Sigma) and leukemia inhibitory factor (produced in-house).

extract_protocol:
DNA was purified with AmpureXP beads
Immunoprecipitated DNA was subjected to library preparation (NEBNext Ultra II DNA Library Prep Kit, Illumina).

treatment_protocol: To induce expression with TETON system, cells were washed with PBS and treated with 1 μg/ml doxycycline (Sigma, no. D989) in induction media, also referred as N2B27w/oVitA, (DMEM/F12/Glutamax (LifeTech, no. 31331-028), 1× B27 without vitamin A (LifeTech, no. 12587-010), 1× N2 supplement (LifeTech, no. 17502-048), ) or in serum/LIF media as indicated.

value: Serum/LIF

value: IGG control


title: THP1,DMSO,24h,ATACseq,biol rep1

description: Library name: THP1_DMSO_24h_ATACseq_Rep1


title: SAM, int-c.5, VA, rep2


title: H9, H3K4me3, ST, -AS

description:
Tn5 taggmented DNA
read1 file contains genomic fragment; read2 files contains genomic fragment

data_processing:
After sequencing, cell barcodes and UMI information were extracted with modified Reachtools (https://doi.org/10.1038/s41592-021-01060-3). Sequences from fixed positions of Read2 were extracted: 1st-8th for BC3, 39th-46th for BC2, 77th-84th for BC1, 115th-119th for RT-ID in RNA data or for antibody-ID in DNA data, 120th-127th for UMI. Barcode combinations (BC1:BC2:BC3:RT-ID/antibody-ID) were mapped to all possible barcode combinations with Bowtie (version: 1.3.1, doi:10.1186/gb-2009-10-3-r25, version, --norc -m 1 -v 0). Mapped cell IDs and UMI were stored in read names of genome sequences. Trim-galore (version:0.6.10) was used to trim adapter sequences with default settings. Trimmed reads were mapped mapped to GRCh38 using Bowtie2 (version: 2.5.3, DOI: 10.1038/nmeth.1923) for DNA data and STAR (version: 2.7.11b, DOI: 10.1093/bioinformatics/bts635) for RNA data with default settings. Only unique mapped reads were kept by samtools filtering (version: 1.19.2, MAPQ>50 for RNA data and MAPQ>10 for DNA data). For the paired-end mapping data, only proper mapped reads with correct orientation were kept. Duplicated reads were identified by the mapping positions and UMIs for each cellid of RNA data. Duplicated reads were identified by mapping positions only for each cellid of DNA data. RNA deduplicated data were feature counted by custom script with splitpoolquantitation (https://github.com/laurabiggins/nf_yang_wang/tree/main/splitpoolquantitation) and converted to sparse matrix. DNA deduplicated data were converted to fragment files for downstream analyses.
Assembly: GRCh38 for human sample
Supplementary files format and content: Tab-separated fragment files
Library strategy: scMTR-seq

growth_protocol: H9 cells were grown in 5% CO2, 5% O2 at 37°C and maintained in Essential8 medium (ThermoFisher Scientific) on 0.5% Geltrex (ThermoFisher Scientific).

extract_protocol:
H9 cells were dissociated into single cells with TrypLE Express (ThermoFisher Scientific).
Nuclei were prepared with Nuclei Extraction buffer and fixed with 0.2% formaldehyde at room temperature for 5 min. Concanavalin A beads were added to the samples to bind nuclei. Preincubated antibody and proteinA-Tn5-MEBdU were added to the nuclei and incubated at RT for 1 hour or overnight at 4°C. Nuclei were washed three times and tagmented at 37°C for 1 hour in the presence of MgCl2. Reaction was stopped with EDTA. Tagmentation was repeated for sequential tagmentation. Followed, reverse transcription was crried out to capture polyA-mRNA transcripts. Three rounds of split-pool barcoding was performed to add combinatory barcodes for each single cells. Nuclei was counted and aliquoted into sublibraries. Reverse crosslinking was performed at 55°C for 1 hour in reverse crosslinking buffer with proteinase K and RNase inhibtors. PMSF was used to inactivate proteinase K. DNA and cDNA were separated by C1 Streptavidin beads. For DNA library, tagmented genomic DNA fragments were purified with Ampure XP beads. Eluted DNA was performed adapter switching and amplified. For RNA library, templated switch was performed and preammplified. MEA adapters were added to the RNA library by Tn5-MEA mediated tagmentation. The concentration of libraries was measured with a Qubit. Samples were run on a Bioanalyzer to check the size distribution of library fragments before submited for seuqencing.

value: H3K4me3 (Abcam, #ab8580)


title: SAM, Bowman, VA, rep3

value: developing inflorescence


title: Vaccine boosted splenic CAR-T cells rep 4 [S4.4.d186057]

first: Charles

middle: Arthur

last: Whittaker

state: MA

institute: Koch Institute

data_processing:
Illumina NextSeq 500 using v3 chemistry. NextSeq Software: Control v4.0.0.19, RTA 2.11.3. BCL files were converted to fastq using bcl2qseq. Indexes were split using custom scripts allowing 1 mismatch.
Paired-end RNA-seq data was used to quantify transcripts from the mm10 mouse assembly with the Ensembl version 100 annotation using Salmon version 1.2.1 (Patro et al. 2017). Gene level summaries for were prepared using tximport version 1.16.0 (Soneson, Love, and Robinson 2015) running under R version 4.0.0 (R Core Team 2021).
Assembly: mm10 with ensembl version 100
Supplementary files format and content: 200317Irv_intCt.txt.gz is a tab delimited text file of integer count data
Supplementary files format and content: 200317Irv_l2tpm.txt.gz is a tab delimited text file of tpm data transformed to log2 space with a +1 offset

source_name: Spleen

growth_protocol: T cells were isolated from spleen, activated and transduced with retroviruses-expressing an EGFRvIII targeting CAR. T cells were cultured in condition medium for 4 days and then transferred into lymphdepleted mice intravenously.

extract_protocol:
Qiagen RNeasy Plus Mini Kit
RNA was cleaned using RNAclean XP beads (Beckman Coulter) and quantified using an Agilent FemtoPulse. ~200pg of RNA was converted to cDNA using SMARTseq2 using 16 cycles of amplification (Picelli et al., 2014) and prepared into Illumina libraries using NexteraXT at a 1:12 reaction reduction on a SPT Mosquito HV (Mildrum et al., 2020). Libraries were characterized on an Agilent Fragment Analyzer and quantified by qPCR on a Roche LC480 prior to sequencing on an Illumina NextSeq500 using paired end 40nt reads.

treatment_protocol: Each dose of vaccine was prepared by mixing 10ug peptide equivalent amph-ligand vaccine and 25 of cyclic-do-GMP in PBS. Vaccines were given to mice subcutaneously at the tail base weekly after CAR T transfer

value: Spleen

value: splenic CAR_T cell

value: amph-ligand vaccine


title: SAM, int-c.5, TA, rep1


title: ChIPseq_TCF3_V5_mESC_3229

value: anti-V5 antibody (Invitrogen, MA5-32053)


title: SAM, int-c.5, VA, rep1


title: Vaccine boosted splenic CAR-T cells rep 3 [S4.3.d186056]


title: SAM, int-c.5, TA, rep3


title: H9, H3K4me1, ST, -AS

value: H3K4me1 (Abcam, #ab8895)

value: gDNA


title: Vaccine boosted splenic CAR-T cells rep 5 [S4.5.d186058]


title: SAM, Bowman, VA, rep2

value: Bowman


title: Endoderm differentiation, 5 histone marks and IgG control, 1 round, scMTR-seq, sublibrary1, DNA

description:
Tn5 taggmented DNA
read1 file contains genomic fragment; read2 files contains cell barcodes, Ab id, UMI and genomic fragments
DNA sublibrary1 and RNA sublibrary 1 are from same sample

value: Human primed stem cells

value: H3K27me3 (CST, #9733S); H3K27ac (Abcam, #ab4729); H3K36me3 (Abcam, #ab9050); H3K4me1 (Abcam, #ab8895); H3K4me3 (Abcam, #ab8580); Normal rabbit IgG (R&D, #AB-105-C)


title: ATACseq_GFP_6h_r2_1854

value: 6 hours N2B27(w/oVitA)+dox


title: vtRNA1-2 KO 3

city: Bern

first: Daniel

last: Sanchez-Taltavull

address: Murtenstrasse 35

department: Department of BioMedical Research

institute: University of Bern

data_processing:
Read alignment (STAR)
Counting Features (featureCounts)
Assembly: GRCh38 (Ensembl release 104)
Supplementary files format and content: data.csv (read count matrix)

growth_protocol: Huh7 cells were grown to 80% confluency in DMEM F12 supplemented with 10% HI FBS and antibiotics (pen/strep) in humidified atmosphere at 37C and 5% CO2

extract_protocol:
according to manufacturer's instructions: Quick-RNA™ Miniprep Kit (Zymo)
according to manufacturer's instructions: TruSeq stranded mRNA kit (Illumina)

value: tumorigenic cell

value: vtRNA1-2 KO


title: H9, 5 histone marks and IgG control, 1 round, MT

description:
Tn5 taggmented DNA
read1 file contains genomic fragment; read2 files contains Ab id, UMI and genomic fragments


title: SAM, Bowman, TA, rep2

value: Transition apex (TA)


title: vtRNA1-2 KO 2


title: Vaccine boosted splenic CAR-T cells rep 1 [S4.1.d186054]


title: Vaccine boosted splenic CAR-T cells rep 2 [S4.2.d186055]


title: Control splenic CAR-T cells rep 5 [S1.5.d186039]

value: PBS


title: vtRNA1-1 KO 3

value: vtRNA1-1 KO


title: vtRNA1-1 KO 2


title: Control splenic CAR-T cells rep 4 [S1.4.d186038]


title: SAM, Bowman, VA, rep1

value: Vegetative apex (VA)


title: vtRNA1-2 KO 1


title: Control splenic CAR-T cells rep 3 [S1.3.d186037]


title: Exp2 BCDE+L36F, biol rep 2

city: San Antonio

first: Venus

middle: Shawn

last: Stanton

state: Texas

address: One UTSA Circle

department: Molecular Microbiology and Immunology (MMI)

institute: University of Texas, San Antonio

description: Library name: 2579_2_S101

data_processing:
After RNA-seq libraries were subjected to quantification process, pooled for subsequent 100bp paired end sequencing run with Illumina NovaSeq platform S4 flow cell. After the sequencing run, demultiplexing was employed to generate the fastq file, with the average of ~8-10M reads per sample.
Assembly: NCBI V. cholerae 345073
Supplementary files format and content: Processed_MetadataKloseBCDE2024.xlsx contains all raw read counts for each strain.

organism: Vibrio cholerae O395

source_name: Bacterial RNA

growth_protocol: V. cholerae cells were grown in LB + streptomycin (200 ug/ml) overnight at 37 °C, then subcultured 1:100 in 5 mls of fresh media plus antibiotic and grown to mid-log (OD600 ~0.6) prior to lysis and RNA extraction.

extract_protocol:
RNA was isolated using Trizol RNA extraction, then treated with Dnase to remove contaminating genomic DNA. RNA concentration and purity was verified by A260/A280 absorbance readings using a NanoDrop spectrophotometer.
Approximately 500ng Total RNA was used for stranded mRNA-seq library preparation by following the NEB Directional RNA library preparation guide with NEBNext rRNA depletion kit v2 (human/mouse/rat) (New England Biolabs, Ipswich, MA). The first step in the workflow involved the depletion of rRNA by hybridization of complementary DNA oligonucleotides, followed by treatment with RNase H and DNase to remove rRNA duplexed to DNA and original DNA oligonucleotides, respectively. Following rRNA removal, the left RNA was fragmented into small pieces using divalent cautions under elevated temperature and magnesium. The cleaved RNA fragments were copied into first strand cDNA using reverse transcriptase and random primers. This was followed by second strand cDNA synthesis using DNA Polymerase I and RNase H. Strand specificity was achieved by replacing dTTP with dUTP in the Second Strand Marking Mix (SMM). The incorporation of dUTP in second strand synthesis effectively quenches the second strand during amplification, since the polymerase used in the assay will not incorporate past this nucleotide. These cDNA fragments then went through an end repair process, the addition of a single ‘A’ base, and then ligation of the adapters. The products were then purified and enriched with PCR to create the final RNA-Seq library. After RNA-seq libraries were subjected to quantification process, pooled for subsequent 100bp paired end sequencing run with Illumina NovaSeq platform S4 flow cell. After the sequencing run, demultiplexing was employed to generate the fastq file, with the average of ~8-10M reads per sample.

value: Bacterial RNA

value: Bacteria

tag: batch


title: Exp2 BCDE+L36F, biol rep 3

description: Library name: 2579_3_S102


title: Exp2 BCDE, biol rep 3

description: Library name: 2530_3_S99


title: Exp2 BCDE+L36F, biol rep 1

description: Library name: 2579_1_S100


title: vtRNA1-1 KO 1


title: WT 3

value: WT


title: Exp2 BCDE, biol rep 2

description: Library name: 2530_2_S98


title: Control splenic CAR-T cells rep 2 [S1.2.d186036]

value: Spleen

value: splenic CAR_T cell


title: Control splenic CAR-T cells rep 1 [S1.1.d186035]


title: WT 2


title: Exp2 BCDE, biol rep 1

description: Library name: 2530_1_S97


title: Vaccine boosted intratumor CAR-T cells rep 5 [T4.5.d186024]

source_name: EGFRv3+,CT2A flank tumor

value: EGFRv3+,CT2A flank tumor

value: intratumor CAR-T cell

value: amph-ligand vaccine


title: Exp2 WT, biol rep 2

description: Library name: 598_2_S95


title: Exp2 WT, biol rep 1

description: Library name: 598_1_S94


title: HY_CAC_miRNA_2021_C04

type: RNA

city: Guri

first: Jae Gon

last: Lee

address: 153 Gyeongchun-ro

country: South Korea

institute: Hanyang University Guri Hospital

description: AOM/DSS group sample

hyb_protocol: Labeled RNA was denatured at 99°C for 5 minutes, incubated at 45°C for 5 minutes, and hybridized to the GeneChip™ miRNA 4.0 Array for 16 hours at 48°C using the Affymetrix 450 Fluidics Station.

scan_protocol: Arrays were washed and stained using the GeneChip Fluidics Station 450 and scanned using the Affymetrix GCS 3000 scanner (Affymetrix, Santa Clara, CA, USA).

data_processing: Fluorescent images were digitized, and raw intensity data were extracted and normalized using the Affymetrix GeneChip Command Console (AGCC) software. Differential expression analysis was performed using a symmetric fold-change approach.

label: biotin

source_name: Mouse colon

label_protocol: Total RNA was labeled using the FlashTag™ Biotin RNA Labeling Kit (Genisphere, Hatfield, PA, USA).

growth_protocol: Mice were maintained under SPF conditions with standard chow and water ad libitum.

extract_protocol: Total RNA was extracted from mouse colon tissues using the miRNeasy Mini Kit (Qiagen) according to the manufacturer’s protocol. RNA quality and quantity were assessed prior to labeling.

treatment_protocol: Control mice received no treatment. Chronic colitis was induced by dextran sulfate sodium (DSS), and colorectal tumors were induced by azoxymethane (AOM) followed by DSS administration.

tag: group

value: AOM/DSS group sample


title: Exp2 WT, biol rep 3

description: Library name: 598_3_S96

tag: tissue


title: ATAC-seq_H-fib-control_1-1

city: nanjing

first: xiaoyun

last: chen

state: nanjing

address: nanjing

institute: xiangya

description: ATAC-seq on human fibroblasts: control treated cells

data_processing:
Raw sequencing data were quality-checked using FastQC; Trimmomatic was used to remove low-quality reads and adapter sequences.Cleaned reads were aligned to the human reference genome (GRCh38).Heatmaps and clustering plots were generated using deepTools for data visualization.
Assembly: Human reference genome GRCh38
Supplementary files format and content: Processed data files include peak call files in BED format

source_name: dermis

extract_protocol:
Genomic DNA was extracted from cell samples using the Novoprotein Kit according to the manufacturer’s instructions.
Libraries were constructed using the Illumina NovaSeq 6000. DNA fragments were sonicated to a size of 200-300 bp, followed by end repair, A-tailing, and adapter ligation.

treatment_protocol: Fibroblasts were treated with control or IL-1β (10 ng/mL) for 24 hours in 6-well plates.

tag: organ

value: skin

value: dermis

value: Primary Fibroblast

value: Fibroblast

value: control


title: HY_CAC_miRNA_2021_C07

description: AOM/DSS group sample


title: ATAC-seq_H-fib-IL1B_2-1

description: ATAC-seq on human fibroblasts: IL-1B treated cells

tag: cell type


title: Vaccine boosted intratumor CAR-T cells rep 4 [T4.4.d186023]


title: Vaccine boosted intratumor CAR-T cells rep 3 [T4.3.d186022]


title: WT 1

value: tumorigenic cell

tag: genotype


title: HY_CAC_miRNA_2021_B04

description: DSS group sample

value: DSS group sample


title: Vaccine boosted intratumor CAR-T cells rep 2 [T4.2.d186021]

tag: treatment


title: Exp1 BCDE, biol rep 3

description: Library name: 3328_3_S12


title: HY_CAC_miRNA_2021_C01

description: AOM/DSS group sample


title: ATAC-seq_H-fib-IL1B_1-1

tag: cell line


title: Exp1 BCDE, biol rep 2

description: Library name: 3328_2_S11


title: HY_CAC_miRNA_2021_C06

description: AOM/DSS group sample


title: M4-MKH10-4

city: Copenhagen

first: Danillo

middle: Oliveira

last: Alvarenga

address: Universitetsparken 15

country: Denmark

institute: University of Copenhagen

data_processing:
Trimming and adapter removal with Trimmomatic 0.36
De novo assembly with Trinity 2.14.0
Annotation and mapping with Comparative Metatranscriptomics Workflow 1.0.0
Mapping with BWA 0.7.17-r1188
Sequence selection for Cyanobacteria and Bryopsida with Kraken 2.1.2
Assembly: Trinity 2.14.0

organism: Hylocomium splendens

source_name: feather moss shoots incubated alone

extract_protocol:
RNeasy PowerPlant Kit
NEBNext rRNA Depletion Kit, QIAseq FastSelect –rRNA Plant, NEBNext Ultra II RNA Library Prep Kit

value: moss


title: HY_CAC_miRNA_2021_C05

description: AOM/DSS group sample


title: Control intratumor CAR-T cells rep 8 [rT1.4.d186009]

value: PBS


title: Exp1 H135N, biol rep 3

description: Library name: 3415_3_S18

value: Bacterial RNA

value: Bacteria


title: HY_CAC_miRNA_2021_B07

description: DSS group sample


title: Control intratumor CAR-T cells rep 6 [rT1.2.d186007]


title: M3-MKH10-3


title: Control intratumor CAR-T cells rep 7 [rT1.3.d186008]


title: Exp1 H135N, biol rep 2

description: Library name: 3415_2_S17


title: Exp1 BCDE, biol rep 1

description: Library name: 3328_1_S10


title: M2-MKH10-2


title: Control intratumor CAR-T cells rep 5 [rT1.1.d186006]


title: HY_CAC_miRNA_2021_A05

description: Control group sample

value: Control group sample


title: HY_CAC_miRNA_2021_B02

description: DSS group sample


title: HY_CAC_miRNA_2021_B06

description: DSS group sample


title: Exp1 H135N, biol rep 1

description: Library name: 3415_1_S16


title: HY_CAC_miRNA_2021_B03

description: DSS group sample


title: M1-MKH10-1


title: HY_CAC_miRNA_2021_B05

description: DSS group sample


title: Lamprey endostyle T30, replicate three

city: Pasadena

first: Jan

last: Stundl

address: 1200E California Blvd

department: BBE

institute: California Institute of Technology

description: Library name: T30_endostyle_3

data_processing:
Reads were mapped to the lamprey genome assembly (kPetMar1.0) in the Stowers Institute SIMRBASE using Bowtie2. Transcript counts were calculated using featureCounts. The differential gene expression analysis was performed using DESeq2 in R, and statistically significant differentially expressed genes were identified globally based on an adjusted p-value threshold of ≤ 0.05. A subset of genes previously identified as being part of the neural crest and thyroid/endostyle formation gene regulatory network was then isolated from the count matrix and plotted as a heatmap using ComplexHeatmap package in Rstudio.
Assembly: kPetMar1.0
Supplementary files format and content: tab-delimited text files that includes featurecounts values for each sample
Supplementary files format and content: tab-delimited csv files that includes z-scores used for cross species comparison

organism: Petromyzon marinus

source_name: endostyle

extract_protocol:
RNAqueous kit (Ambion), prepared according to the manufacturer's instructions.
The libraries were built according to Illumina Standard Protocols.

value: endostyle

value: WT


title: HY_CAC_miRNA_2021_C03

description: AOM/DSS group sample


title: Lamprey endostyle T30, replicate two

description: Library name: T30_endostyle_2


title: Exp1 L36F, biol rep 3

description: Library name: 3296_3_S15


title: HY_CAC_miRNA_2021_C02

description: AOM/DSS group sample


title: Exp1 L36F, biol rep 2

description: Library name: 3296_2_S14


title: Control intratumor CAR-T cells rep 2 [T1.2.d186002]

value: EGFRv3+,CT2A flank tumor

value: intratumor CAR-T cell


title: cortex,P3_WT,rep2

city: Shanghai

first: TongYe

last: Fu

address: 138 Yi Xue Yuan Road

institute: Fudan University

description:
Library name: Sample2
10x Genomics

library_source: transcriptomic single cell

data_processing:
High-quality sequences (clean reads) were processed using Cell Ranger to obtain quantitative gene expression data
Assembly: ASM1176430v1.1
Supplementary files format and content: Tab-separated values files and matrix files (In barcodes.tsv: barcode_3 = rep1, barcode_4 = rep2)

organism: Mustela putorius furo

source_name: cortex

extract_protocol:
P3 ferret pups were deeply anesthetized, and their brains were immediately harvested and immersed in ice-cold Hanks' Balanced Salt Solution (Gibco 14175-095). The dorsal cortices were dissected into small pieces and dissociated into a single-cell suspension using the Papain Cell Dissociation Kit, following the manufacturer’s instructions (Miltenyi Biotec, catalog no. 130-092-628).
Single-cell RNA sequencing (scRNA-Seq) libraries were prepared using the Chromium droplet-based sequencing platform (10X Genomics), in accordance with the manufacturer’s guidelines (manual document part number: CG00052 Rev C). The cDNA libraries were purified, quantified using an Agilent 2100 Bioanalyzer, and sequenced on an Illumina HiSeq 4000.

value: cortex


title: HY_CAC_miRNA_2021_A04

description: Control group sample


title: HY_CAC_miRNA_2021_A02

description: Control group sample


title: cortex,P3_WT,rep1

description:
Library name: Sample1
10x Genomics


title: HY_CAC_miRNA_2021_A06

description: Control group sample


title: HY_CAC_miRNA_2021_B01

description: DSS group sample


title: HY_CAC_miRNA_2021_A01

description: Control group sample


title: HY_CAC_miRNA_2021_A03

description: Control group sample


title: Lamprey endostyle T30, replicate one

description: Library name: T30_endostyle_1


title: H9, 6 histone marks and IgG control, 6 rounds, MT

value: Human primed stem cells

value: gDNA


title: Control intratumor CAR-T cells rep 4 [T1.5.d186005]


title: Exp1 WT, biol rep 3

description: Library name: 598_3_S9


title: Lamprey endostyle T29, replicate three

description: Library name: T29_endostyle_3


title: H9, 6 histone marks and IgG control, 3 rounds, MT


title: Control intratumor CAR-T cells rep 1 [T1.1.d186001]


title: Lamprey endostyle T29, replicate two

description: Library name: T29_endostyle_2


title: Exp1 WT, biol rep 2

description: Library name: 598_2_S8


title: Control intratumor CAR-T cells rep 3 [T1.3.d186003]


title: HUVEC(TERT)_wildtype_1

city: Grand Forks

first: Bryon

middle: Dennis

last: Grove

state: ND

address: 1301 N Columbia Rd

department: Biomedical Sciences

institute: University of North Dakota School of Medicine and Health Sciences

description:
Library name: HUVEC-TERT_WT1
Wild_Type_a

data_processing:
The libraries were sequenced in a HiSeqX instrument, and 40 million, 150 bp paired-end reads were generated. Preliminary quality control analysis of fastq files was performed with FastQC v0.11.8.
Adapters were trimmed using Trimmomatic v0.39
Reads were aligned to a human genome (hg19) with STAR v2.7.1a software
Gene expression was quantified using CuffNorm v2.2.1 (Trapnell et al., 2010).
Read counts were summarized using featureCounts v1.4.6 (Liao et al., 2014).
Differential expression analysis of AKAP12v1 KO vs. WT samples was performed using the R/Bioconductor package DESeq2 v1.24.0  (Love et al., 2014).
Genes were considered differentially expressed if they had an FDR of 0.05 or less. Gene Ontology (GO) and Signaling Pathway Impact Analysis (SPIA) enrichment analyses were performed using the R/Bioconductor package clusterProfiler v3.12.0 (Yu et al., 2012).
Assembly: Reads were aligned to a human genome (hg19) with STAR v2.7.1a software
Supplementary files format and content: tab-delimited text files including fpkm normalized count values for each sample in the matrix.

source_name: Immortalized (Tert) Human Umbilical Vein Endothelial cells

growth_protocol: HUVECs were cultured in VascuLife basal media (Fredrick, MD; Cat. No LL-0003) supplemented with FBS (2%), basic FGF, VEGF, EGF each at 5 ng/mL, IGF (15 ng/mL), L-glutamine (10 mM), hydrocortisone hemisuccinate (1 mg/mL), ascorbic acid (50 µg/mL) and heparin sulfate (0.75 U/mL). The cells were passaged 1:5 at sub-confluent cell densities and maintained at 37o C in a humidified atmosphere of 5% CO2 - 95% air.

extract_protocol:
RNA was extracted using the RSC Maxwell system using a SimplyRNA kit and the quality of the RNA was analyzed using a Bioanalyzer system (Agilent Technologies). RNA with an RIN (RNA Integrity Number) greater than seven was used for RNA-Seq library preparation.
RNA-Seq libraries with Ribo-depletion were prepared using an NEBNext Ultra™ II RNA Library Prep Kit for Illumina (NEB, #E7770).

value: Endothelial cells

value: Wild Type


title: Lamprey endostyle T29, replicate one

description: Library name: T29_endostyle_1


title: Exp1 WT, biol rep 1

description: Library name: 598_1_S7


title: H9, H3K9me3, ST, +AS, +10mM SB

value: H3K9me3 (Abcam, #ab8898)

value: with 10 mM sodium butyrate


title: H9, H3K4me1, ST, +AS, +10mM SB

value: H3K4me1 (Abcam, #ab8895)


title: HUVEC(TERT)_AKAP12KO_Clone3_2

description:
Library name: HUVEC-TERT_AKAP12KO_C3-2
Grav2_14_b

value: Immortalized (Tert) Human Umbilical Vein Endothelial cells

value: AKAP12 v1 negative


title: Exp1 L36F, biol rep 1

description: Library name: 3296_1_S13

value: Bacterial RNA


title: Naïve-2, Day14, rep2

city: Columbia

first: Rajiv

middle: R

last: Mohan

state: Missouri

address: 1520 East Rollins University of Missouri

department: Department of Veterinary Medicine and Surgery

institute: University of Missouri

description:
Library name: Naïve-2
10x Genomics

data_processing:
Processed using Cell Ranger v7.0.0 (by 10x Genomics) Demultiplexing of sequencing reads Barcode processing UMI counting Alignment to reference genome
Assembly: Rabbit genome GCF_009806435.1_UM_NZW_1.0
Supplementary files format and content: The expression matrices are provided in Matrix Market (.mtx) format, including both raw UMI counts (expression_matrix_raw.mtx) and log-normalized values (expression_matrix_logNorm.mtx). Associated metadata such as cell barcodes (All_Samples_barcode.csv) and per-cell annotations (cell_metadata.csv) are included as comma-separated values (CSV) files. The Seurat object (All_Samples_Clusters.rds) contains normalized expression data, dimensional reductions (e.g., PCA, UMAP), and cluster assignments. Differentially expressed genes are supplied in CSV format for both clusters (DEGs_Markers.csv) and ECM remodeling subclusters (DEGs_subcluster.csv).

organism: Oryctolagus cuniculus

source_name: Cornea

extract_protocol:
Rabbit corneas were harvested 14 days post-alkali injury (n=3) along with naïve controls (n=3) and processed into single-cell suspensions using an optimized enzymatic digestion protocol designed to preserve cellular integrity. Each eye was sectioned into eighths, and four pieces (half a cornea) were placed in Falcon™ Round-Bottom Polystyrene Tubes (Fisher Scientific, 14-959-5) containing 300 µL of digestion buffer at 4°C. The buffer comprised 2.5 mg Liberase TL (Thermo Fisher, 17101015), 2 mg DNase I (Fisher Scientific, AAJ62229MB), and 1 mL incomplete RPMI 1640 medium with L-glutamine (Thermo Fisher, 11875119). Tissues were finely chopped in the buffer and incubated at 37°C with shaking (400 rpm) for 30 minutes. Tissue clumps were disrupted using a 200 µL pipette tip and agitated every 5 minutes until full dissociation. To terminate enzymatic activity and stabilize cells, 300 µL of heat-inactivated fetal bovine serum (Thermo Fisher, 10082147) was added and mixed thoroughly. The suspension was pipetted repeatedly, filtered through a 70 µm Falcon™ Cell Strainer (Fisher Scientific, 08-771-2), and transferred to 15 mL tubes. Cells were washed three times with 3 mL of FACS buffer (PBS + 2% FBS), centrifuged at 200×g (1000 rpm) for 5 minutes with brake set to 1, and the supernatant was gently removed by pipetting. The final cell pellet was resuspended in 300 µL FACS buffer or adjusted based on concentration requirements.
scRNA sequencing was conducted via the 10x Genomics Chromium platform following standard protocols for single-cell library preparation. The 10x Genomics single-cell 3’ library preparation was performed by the Genomics Technology Core at the Bond Life Sciences Center. Sequencing was conducted on an Illumina NovaSeq X Plus instrument, generating 100 base-pair (bp), paired-end reads. The expected sequencing depth was ~50,000 read pairs per cell per library, optimized for 3' RNA sequencing, with a target of 10,000 single-cell transcriptomes per sample to ensure high coverage and resolution. The scRNA-Seq libraries were constructed via 10x Genomics Chromium Chip technology, with precise library preparation to ensure optimal cell recovery, minimal background noise, and accurate unique molecular identifier (UMI) processing.

treatment_protocol: All animal experiments were approved by the Institutional Animal Care and Use Committee at the University of Missouri and the Harry S. Truman Memorial Veterans’ Hospital, and were conducted in accordance with the ARVO Statement for the Use of Animals in Ophthalmic and Vision Research. Six male New Zealand White rabbits (2–3 kg) were used, with corneal alkali wounds induced in the right eye of three rabbits while the other three served as unwounded controls. Anesthesia was administered intramuscularly using ketamine and xylazine, followed by topical proparacaine before procedures. Corneal injury was induced by applying 1 M sodium hydroxide using an 8 mm filter paper to the central cornea for 30 seconds, followed by thorough rinsing with balanced salt solution. Wound healing and fibrotic changes were monitored over 14 days using slit-lamp and stereo biomicroscopy, intraocular pressure measurements, and digital imaging.

value: Cornea

tag: Sex

value: Male

value: Day 14

value: 8-10 weeks


title: HUVEC(TERT)_AKAP12KO_Clone2_2

description:
Library name: HUVEC-TERT_AKAP12KO_C2-2
Grav2_11_b


title: Lamprey endostyle T28, replicate one

description: Library name: T28_endostyle_1

value: endostyle

value: WT


title: Lamprey endostyle T28, replicate two

description: Library name: T28_endostyle_2


title: Naïve-3, Day14, rep3

description:
Library name: Naïve-3
10x Genomics


title: Naïve-1, Day14, rep1

description:
Library name: Naïve-1
10x Genomics


title: HUVEC(TERT)_wildtype_2

description:
Library name: HUVEC-TERT_WT2
Wild_Type_b


title: Lamprey endostyle T27, replicate three

description: Library name: T27_endostyle_3


title: HUVEC(TERT)_AKAP12KO_Clone2_1

description:
Library name: HUVEC-TERT_AKAP12KO_C2-1
Grav2_11_a


title: Alkali burn-3, Day 14, rep3

description:
Library name: Alkali burn-3
10x Genomics

value: Topical,1M NaOH, 30s


title: H9, H3K36me3, ST, +AS, +10mM SB

value: Human primed stem cells


title: H9, H3K27me3, ST, +AS, +10mM SB

value: H3K27ac (Abcam, #ab4729)

value: gDNA


title: Alkali burn-2, Day 14, rep2

description:
Library name: Alkali burn-2
10x Genomics


title: Lamprey endostyle T27, replicate two

description: Library name: T27_endostyle_2


title: HUVEC(TERT)_AKAP12KO_Clone1_2

description:
Library name: HUVEC-TERT_AKAP12KO_C1-2
Grav2_1_b

value: Endothelial cells


title: H9, H3K27ac, ST, +AS, +10mM SB


title: HUVEC(TERT)_AKAP12KO_Clone1_1

description:
Library name: HUVEC-TERT_AKAP12KO_C1-1
Grav2_1_a


title: Lamprey endostyle T27, replicate one

description: Library name: T27_endostyle_1


title: Alkali burn-1, Day 14, rep1

description:
Library name: Alkali burn-1
10x Genomics


title: HUVEC(TERT)_AKAP12KO_Clone3_1

description:
Library name: HUVEC-TERT_AKAP12KO_C3-1
Grav2_14_a


title: H9, H3K4me3, ST, +AS, +10mM SB

value: H3K4me3 (Abcam, #ab8580)


title: Lamprey endostyle T28, replicate three

description: Library name: T28_endostyle_3


title: MAF-928 cells, hypoxia, biol rep 3

status: Public on Aug 06 2025

type: genomic

city: Aurora

first: Andrew

middle: M

last: Donson

state: CO

department: Pediatrics

institute: CU Anschutz Medical Campus

description: Cell line: childhood brain tumor PFA ependymoma

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

scan_protocol: Standard Illumina iScan scanner settings for Methylation EPIC Beadchips

data_processing:
unprocessed .idat files were directly uploaded to the molecularneuropathology.org portal to obtain medulloblastoma subgroup classification and CNV predictions.
IDAT files were batch normalized and background corrected using default settings of the R package ChAMP.

label: Cy5 and Cy3

extract_protocol: DNA was extracted from snap frozen surgical samples using Qiagen Allprep (as per kit protocol)

tag: characteristic

tag: replicate

value: :biol rep 3


title: MAF-811 cells, hypoxia, biol rep 3

label_protocol: bisulphite converted DNA was amplified, fragmented and hybridized to Illumina Infinium Human MethylationEPIC Beadchip using standard Illumina protocol


title: MAF-928 cells, normoxia, biol rep 2

value: :biol rep 2


title: MAF-811 cells, hypoxia, biol rep 1

value: :biol rep 1


title: MAF-811 cells, hypoxia, biol rep 2


title: MAF-928 cells, hypoxia, biol rep 2


title: MAF-928 cells, normoxia, biol rep 1


title: MAF-928 cells, normoxia, biol rep 3


title: MAF-928 cells, hypoxia, biol rep 1


title: H9, 6 histone marks and IgG control, 1 round, MT


title: MAF-811 cells, normoxia, biol rep 3


title: MAF-811 cells, normoxia, biol rep 1


title: Kasumi-1 sgSETD8 #2 H4K20me1

city: changchun

first: yongwei

last: su

address: 2699 qianjin street

institute: Jilin university

description: Library name: Sample 4

data_processing:
Libraries were sequenced on the Illumina NovaSeq 6000 platform using 150 × 150 paired-end sequencing. Adapter trimming and sequence filtering were performed using Cutadapt.
Assembly: high-quality reads were aligned to the human genome build hg38 using Bowtie 2.
Supplementary files format and content: csv
Library strategy: CUT&Tag

growth_protocol: Kasumi-1 were cultured in Roswell Park Memorial Institute 1640 medium with 10% fetal bovine serum, supplemented with streptomycin (100 μg/mL) and penicillin (50 U/mL).

extract_protocol:
1 × 10^5 cells were used for library construction using the Epi™ CUT&Tag Library Fast Kit (D202203, Epibiotek) according to the manufacturer’s instructions. Epi™ DNA Clean Beads (R1809, Epibiotek) were used to purify the DNA product.
Quantification and quality control of the libraries were performed using the Bioptic Qsep100 Analyzer.

treatment_protocol: SETD8 knockout with CRISPR/Cas9

value: acute myeloid leukemia cell lins

value: SETD8 knockout

tag: cut&tag antibody


title: Kasumi-1 sgSETD8 H3K27ac

description: Library name: Sample 4


title: Kasumi-1 sgNT H3K27ac

description: Library name: Sample 3


title: Kasumi-1 sgNT#2

description: Library name: Sample 3

data_processing:
Unique mapping paired reads were extracted and sorted using SAMtools. Peak calling was performed using MACS2 (v2.1.2). Viewable bigwig files were generated using DeepTools software. Genomic annotation was conducted using the ChIPseeker R package.
Assembly: Adapters were removed using Cutadapt, and high-quality reads were aligned to the human genome build hg38 using Bowtie 2.
Supplementary files format and content: csv

extract_protocol:
5 × 104 cells were used for library construction using the Epi™ One-Step ATAC-seq Kit (D231102, Epibiotek) according to the manufacturer’s instructions. Epi™ DNA Clean Beads (R1809, Epibiotek) were employed for DNA product purification.
Quantification and quality control of the libraries were performed using the Bioptic Qsep100 Analyzer (Bioptic Inc.). Libraries were sequenced on the Illumina NovaSeq 6000 platform using 150 × 150 paired-end sequencing.


title: Kasumi-1 sgNT#2 H4K20me1

description: Library name: Sample 3


title: Liver aspiration samples from  CHB_3

city: Huzhou

first: Yunliang

last: Yao

state: Zhejiang

address: 759 East Second Ring Road

department: Medical School

institute: Huzhou University

description:
Library name: D192100033
Column name in gene_expression.cvs: D192100033

data_processing:
Agilent 4200 bioanalyzer was employed to evaluate the concentration and size distribution of cDNA library before sequencing with an Illumina novaseq6000
The protocol of high-throughput sequencing was fully according to the manufacturer's instructions (Illumina)
The raw reads were filtered by Seqtk before mapping to genome using Hisat2 (version:2.0.4)
The fragments of genes were counted using stringtie(v1.3.3b) followed by TMM (trimmed mean of M values) normalization
Assembly: GRCh38
Supplementary files format and content: csv files include FPKM and counts values for  each sample

source_name: Liver

extract_protocol:
Total RNA was extracted from liver aspiration samples using TRIzol reagent.
Total RNA was extracted fromliver aspiration samples followed by library preparation according to Illumina standard instruction (VAHTS Universal V6 RNA-seq Library Prep Kit for Illumina® )

value: Liver


title: Liver aspiration samples from  CHB_1

description:
Library name: D192100026
Column name in gene_expression.cvs: D192100026


title: Liver aspiration samples from  PBC_3

description:
Library name: D192100024
Column name in gene_expression.cvs: D192100024


title: Liver aspiration samples from  AIH_3

description:
Library name: D192100025
Column name in gene_expression.cvs: D192100025


title: Liver aspiration samples from  PBC_2

description:
Library name: D192100020
Column name in gene_expression.cvs: D192100020


title: Liver aspiration samples from  AIH_1

description:
Library name: D192100008
Column name in gene_expression.cvs: D192100008


title: Liver aspiration samples from  AIH_2

description:
Library name: D192100018
Column name in gene_expression.cvs: D192100018


title: Liver aspiration samples from  PBC&AIH_1

description:
Library name: D192100003
Column name in gene_expression.cvs: D192100003


title: Liver aspiration samples from  CHB_2

description:
Library name: D192100027
Column name in gene_expression.cvs: D192100027


title: MAF-811 cells, normoxia, biol rep 2


title: Liver aspiration samples from  PBC&AIH_2

description:
Library name: D192100017
Column name in gene_expression.cvs: D192100017


title: 7232-JF-1

city: Ann Arbor

first: Poulami

last: Dey

address: 1301 Catherine St

institute: Michigan Medicine

description: Library name: 7232-JF-1

data_processing:
“BCL Convert Software (Illumina) was used to generate de-multiplexed Fastq files and the CellRanger Pipeline (10X Genomics) was used to align reads and generate count matrices.”
Assembly: GRCh38
Supplementary files format and content: cellranger output format

source_name: skin

extract_protocol:
Skin samples are incubated with dispase overnight, followed by tissue dissociation using collagenase and trypsin-EDTA. The epidermis and dermis are minced, incubated with enzymes, and then processed through mesh filtration and centrifugation. After cell counting, the epidermal and dermal cells are recombined in a desired ratio for library preparation.
https://cdn.10xgenomics.com/image/upload/v1722286172/support-documents/CG000331_Chromium_Next_GEM_Single_Cell_5_v2_UserGuide_RevF.pdf

value: skin

tag: disease state

value: PPP

value: PPP-3 lesional


title: 7232-JF-2

description: Library name: 7232-JF-2

value: PPP-3 nonlesional


title: 7351-JF-2

description: Library name: 7351-JF-2

value: PPP-4 nonlesional


title: 6929-JF-3

description: Library name: 6929-JF-3

value: Healthy


title: 6974-JF-1

description: Library name: 6974-JF-1


title: 6911-JF-3

description: Library name: 6911-JF-3


title: 7351-JF-1

description: Library name: 7351-JF-1

value: PPP-4 lesional


title: 6085-AB-2

description: Library name: 6085-AB-2

value: PPP-1 nonlesional


title: Kasumi-1 sgSETD8#2

description: Library name: Sample 4


title: Caco-2_hFABP1as_Rep1

city: La Plata

first: Natalia

last: Scaglia

country: Argentina

institute: INIBIOLP (National University of La Plata/National Research Council of Argentina)

description: Library name: Sample_4

data_processing:
Base calling through the integrated primary analysis software RTA (Real Time Analysis). The BCL (base calls) binary was converted into FASTQ utilizing illumina package bcl2fastq. Quality check on raw sequences was performed by FasQC v0.11.7, trimming and alignment were done with Trimmomatic 0.38 and HISAT version 2.1.0, Bowtie2 2.3.4.1 and transcript assembly and quantification were done with StringTie version 1.3.4d.
Assembly: GRCh37
Supplementary files format and content: csv file include read counts, FPKMs and TPMs for each sample

growth_protocol: Cells were maintained in Dulbecco’s modified Eagle’s medium supplemented with 10% heat inactivated fetal bovine serum (FBS), 100 U/ml penicillin and 100 µg/ml streptomycin (P/S), 1% MEM vitamin solution and 1% non-essential amino acids, at 37 °C, 5% CO2 and 100% humidity.

extract_protocol:
RNA was isolated using TRIzol Reagent (Thermo Fisher, USA). The RNA integrity was assessed with a 2100 Bioanalyzer (Agilent) and samples with RNA Integrity Number (RIN)> 9 were used
TruSeq Stranded mRNA Sample Preparation Guide, Part #15031047 Rev. E

value: colorectal tumor cell line


title: Caco-2_hFABP1as_Rep2

description: Library name: Sample_5


title: Caco-2_hFABP1as_Rep3

description: Library name: Sample_6


title: Caco-2_pcDNA3_Control_Rep2

description: Library name: Sample_2

value: WT


title: Screen_12_CCCP_high biol rep 2

city: Bethesda

first: Derek

last: Narendra

state: MD

address: 35 CONVENT DR RM 2A-215

department: National Institute of Neurological Disorders and Stroke

institute: National Institutes of Health

description:
Library name: Sample 24
HEK_rra_low_CCCP_vs_high_CCCP.gene_summary.txt
HEK_rra_low_CCCP_vs_high_CCCP.sgrna_summary.txt

data_processing:
First step (R1 and R3) – assign the guide sequence to the gene using Weissman library list (library_1_2_unbalanced.csv) and check for recombinance (hits = both guides for same gene) using parsr swarm file
Assembly: GRCh38 (Weissman library)
Supplementary files format and content: Correctly matched dual guide hit file from r1 were analyzed using MAGeCK-Vispr robust ranked algorithm pipeline (RRA). txt files for gene summary and sgrna summary (counts) provided
Library strategy: CRISPR Screen

extract_protocol:
genomic DNA was extracted via the NucleoSpin Blood L, midi kit for DNA from blood from Macherey-Nagel accoding to manufacturor's instructions
gemonic DNA was PCR amplified using custom primers and NEB Next Ultra II Q5 according to manufacturer's instruction

value: CCCP


title: Screen_12_CCCP_low_biol_rep_2

description:
Library name: Sample 23
HEK_rra_low_CCCP_vs_high_CCCP.gene_summary.txt
HEK_rra_low_CCCP_vs_high_CCCP.sgrna_summary.txt


title: Screen_12_NT_high_biol_rep_2

description:
Library name: Sample 22
HEK_rra_low_NT_vs_high_NT.gene_summary.txt
HEK_rra_low_NT_vs_high_NT.sgrna_summary.txt

value: Non-treated


title: Caco-2_pcDNA3_Control_Rep1

description: Library name: Sample_1


title: Screen_12_NT_low_biol_rep_2

description:
Library name: Sample 21
HEK_rra_low_NT_vs_high_NT.gene_summary.txt
HEK_rra_low_NT_vs_high_NT.sgrna_summary.txt


title: Liver aspiration samples from  PBC_1

description:
Library name: D192100002
Column name in gene_expression.cvs: D192100002


title: Screen_11_NT_high_biol_rep_1

description:
Library name: Sample 18
HEK_rra_low_NT_vs_high_NT.gene_summary.txt
HEK_rra_low_NT_vs_high_NT.sgrna_summary.txt


title: Screen_11_CCCP_low_biol_rep_1

description:
Library name: Sample 19
HEK_rra_low_CCCP_vs_high_CCCP.gene_summary.txt
HEK_rra_low_CCCP_vs_high_CCCP.sgrna_summary.txt


title: 6967-JF-5

description: Library name: 6967-JF-5


title: Screen_11_CCCP_high_biol_rep_1

description:
Library name: Sample 20
HEK_rra_low_CCCP_vs_high_CCCP.gene_summary.txt
HEK_rra_low_CCCP_vs_high_CCCP.sgrna_summary.txt


title: 7027-JF-3

description: Library name: 7027-JF-3


title: Screen_11_NT_low_biol_rep_1

description:
Library name: Sample 17
HEK_rra_low_NT_vs_high_NT.gene_summary.txt
HEK_rra_low_NT_vs_high_NT.sgrna_summary.txt


title: Screen_8_AO_high_biol_rep_2

description:
Library name: Sample 16
HeLa_no_Parkin_rra_low_AO_vs_high_AO.gene_summary.txt
HeLa_no_Parkin_rra_low_AO_vs_high_AO.sgrna_summary.txt

source_name: HeLa

value: HeLa

value: AO


title: Screen_8_AO_low_biol_rep_2

description:
Library name: Sample 15
HeLa_no_Parkin_rra_low_AO_vs_high_AO.gene_summary.txt
HeLa_no_Parkin_rra_low_AO_vs_high_AO.sgrna_summary.txt


title: Screen_7_AO_high_biol_rep_1

description:
Library name: Sample 12
HeLa_no_Parkin_rra_low_AO_vs_high_AO.gene_summary.txt
HeLa_no_Parkin_rra_low_AO_vs_high_AO.sgrna_summary.txt


title: Screen_7_NT_high_biol_rep_1

description:
Library name: Sample 10
HeLa_no_Parkin_rra_low_NT_vs_high_NT.gene_summary.txt
HeLa_no_Parkin_rra_low_NT_vs_high_NT.sgrna_summary.txt


title: Screen_7_AO_low_biol_rep_1

description:
Library name: Sample 11
HeLa_no_Parkin_rra_low_AO_vs_high_AO.gene_summary.txt
HeLa_no_Parkin_rra_low_AO_vs_high_AO.sgrna_summary.txt


title: Screen_7_NT_low_biol_rep_1

description:
Library name: Sample 9
HeLa_no_Parkin_rra_low_NT_vs_high_NT.gene_summary.txt
HeLa_no_Parkin_rra_low_NT_vs_high_NT.sgrna_summary.txt


title: Screen_8_NT_low_biol_rep_2

description:
Library name: Sample 13
HeLa_no_Parkin_rra_low_NT_vs_high_NT.gene_summary.txt
HeLa_no_Parkin_rra_low_NT_vs_high_NT.sgrna_summary.txt


title: Screen_6_AO_low_biol_rep_2

description:
Library name: Sample 7
HeLa_with_Parkin_rra_screen5_low_AO_vs_high_AO.gene_summary.txt
HeLa_with_Parkin_rra_screen5_low_AO_vs_high_AO.sgrna_summary.txt

source_name: HeLa with Parkin

value: HeLa with Parkin


title: Screen_6_AO_high_biol_rep_2

description:
Library name: Sample 8
HeLa_with_Parkin_rra_screen5_low_AO_vs_high_AO.gene_summary.txt
HeLa_with_Parkin_rra_screen5_low_AO_vs_high_AO.sgrna_summary.txt


title: Screen_6_NT_high_biol_rep_2

description:
Library name: Sample 6
HeLa_with_Parkin_rra_low_NT_vs_high_NT.gene_summary.txt
HeLa_with_Parkin_rra_low_NT_vs_high_NT.sgrna_summary.txt


title: Caco-2_pcDNA3_Control_Rep3

description: Library name: Sample_3


title: Screen_5_AO_high_biol_rep_1

description:
Library name: Sample 4
HeLa_with_Parkin_rra_screen5_low_AO_vs_high_AO.gene_summary.txt
HeLa_with_Parkin_rra_screen5_low_AO_vs_high_AO.sgrna_summary.txt


title: Screen_5_AO_low_biol_rep_1

description:
Library name: Sample 3
HeLa_with_Parkin_rra_screen5_low_AO_vs_high_AO.gene_summary.txt
HeLa_with_Parkin_rra_screen5_low_AO_vs_high_AO.sgrna_summary.txt


title: Screen_6_NT_low_biol_rep_2

description:
Library name: Sample 5
HeLa_with_Parkin_rra_low_NT_vs_high_NT.gene_summary.txt
HeLa_with_Parkin_rra_low_NT_vs_high_NT.sgrna_summary.txt


title: THP1 UBA6 shRNA rep 2

city: Cincinnati

first: Kwangmin

last: Choi

state: Ohio

address: 333 Burnet Avenue

department: Experimental Hematology & Cancer Biology

institute: Cincinnati Children's Hospital Medical Center

description:
Library name: THP1 UBA6 shRNA rep 2
shRNA lentivirally transduced

data_processing:
FastQC (v0.11.2) was used to test read quality.
Paired-end reads were aligned against mm10 genome using HISAT (v2.0.5). Stranded (RF)
Gene counts were summarized using featureCounts (v1.5.2)
Assembly: hg38
Supplementary files format and content: rawCounts.tsv
Supplementary files format and content: Tab-delimted raw gene counts

growth_protocol: THP1 were cultured in RPMI-1640 media with 10% of FBS and 1% penicillin/streptomycin

extract_protocol:
The cells were collected, and RNA was extracted using ZYMO RESEARCH Quick-RNA Miniprep Kit (#R1055)
After the confirmation of the RNA quality using Agilent 2100 Bioanalyzer, the libraries were prepared with polyA selection using the Truseq RNA Library Prep Kit, and the libraries were sequenced at an average depth of 30M paired-end 100bp nucleotide reads. After the quality of reads was examined using FastQC (v0.11.7, https://www.bioinformatics.babraham.ac.uk/projects/fastqc), paired-end reads were aligned against human (GRCh38) genome (iGenome,https://support.illumina.com/sequencing/sequencing_software/igenome.html) using HISAT2 (v2.0.5,http://daehwankimlab.github.io/hisat2). The raw gene counts were calculated using featureCounts (v1.5.2, http://subread.sourceforge.net/) and normalized using edgeR (v3.16.5, https://bioconductor.org/packages/release/bioc/html/edgeR.html) in iGEAK (https://pubmed.ncbi.nlm.nih.gov/30841853/). Differentially expressed genes were predicted using limma/voom (v3.30.6, https://bioconductor.org/packages/release/bioc/html/limma.html).

treatment_protocol: THP1 cells were infected with lentivirus for shRNA studies.

value: UBA1 WT

value: UBA6 shRNA


title: THP1 UBA6 shRNA rep 1

description:
Library name: THP1 UBA6 shRNA rep 1
shRNA lentivirally transduced


title: THP1 UBA6 shRNA rep 3

description:
Library name: THP1 UBA6 shRNA rep 3
shRNA lentivirally transduced


title: THP1 UBA1 shRNA rep 3

description:
Library name: THP1 UBA1 shRNA rep 3
shRNA lentivirally transduced

value: UBA1 shRNA


title: THP1 UBA1 shRNA rep 2

description:
Library name: THP1 UBA1 shRNA rep 2
shRNA lentivirally transduced


title: THP1 UBA1 shRNA rep 1

description:
Library name: THP1 UBA1 shRNA rep 1
shRNA lentivirally transduced


title: THP1 Scramble control rep 3

description:
Library name: THP1 Scramble control rep 3
shRNA lentivirally transduced

value: Scramble shRNA


title: THP1 UBA1 MUT M41V rep 2

description:
Library name: THP1 UBA1 MUT M41V rep 2
isogenic mutant UBA1 cell line

value: UBA1 M41V


title: THP1 Scramble control rep 1

description:
Library name: THP1 Scramble control rep 1
shRNA lentivirally transduced


title: THP1 UBA1 MUT M41V rep 1

description:
Library name: THP1 UBA1 MUT M41V rep 1
isogenic mutant UBA1 cell line


title: THP1 Scramble control rep 2

description:
Library name: THP1 Scramble control rep 2
shRNA lentivirally transduced


title: Screen_8_NT_high_biol_rep_2

description:
Library name: Sample 14
HeLa_no_Parkin_rra_low_NT_vs_high_NT.gene_summary.txt
HeLa_no_Parkin_rra_low_NT_vs_high_NT.sgrna_summary.txt


title: THP1 UBA1 MUT M41V rep 3

description:
Library name: THP1 UBA1 MUT M41V rep 3
isogenic mutant UBA1 cell line


title: THP1 UBA1 WT-control rep 3

description:
Library name: THP1 UBA1 WT-control rep 3
Isogenic control cell line


title: THP1 UBA1 WT-control rep 2

description:
Library name: THP1 UBA1 WT-control rep 2
Isogenic control cell line


title: Vaccine boosted intratumor CAR-T cells rep 1 [T4.1.d186020]

city: Cambridge

first: Charles

last: Whittaker

institute: Koch Institute

data_processing:
Illumina NextSeq 500 using v3 chemistry. NextSeq Software: Control v4.0.0.19, RTA 2.11.3. BCL files were converted to fastq using bcl2qseq. Indexes were split using custom scripts allowing 1 mismatch.
Paired-end RNA-seq data was used to quantify transcripts from the mm10 mouse assembly with the Ensembl version 100 annotation using Salmon version 1.2.1 (Patro et al. 2017). Gene level summaries for were prepared using tximport version 1.16.0 (Soneson, Love, and Robinson 2015) running under R version 4.0.0 (R Core Team 2021).
Assembly: mm10 with ensembl version 100
Supplementary files format and content: 200317Irv_intCt.txt.gz is a tab delimited text file of integer count data
Supplementary files format and content: 200317Irv_l2tpm.txt.gz is a tab delimited text file of tpm data transformed to log2 space with a +1 offset

extract_protocol:
Qiagen RNeasy Plus Mini Kit
RNA was cleaned using RNAclean XP beads (Beckman Coulter) and quantified using an Agilent FemtoPulse. ~200pg of RNA was converted to cDNA using SMARTseq2 using 16 cycles of amplification (Picelli et al., 2014) and prepared into Illumina libraries using NexteraXT at a 1:12 reaction reduction on a SPT Mosquito HV (Mildrum et al., 2020). Libraries were characterized on an Agilent Fragment Analyzer and quantified by qPCR on a Roche LC480 prior to sequencing on an Illumina NextSeq500 using paired end 40nt reads.

value: EGFRv3+,CT2A flank tumor

value: intratumor CAR-T cell

value: amph-ligand vaccine


title: THP1 UBA1 WT-control rep 1

description:
Library name: THP1 UBA1 WT-control rep 1
Isogenic control cell line


title: ATAC-seq_H-fib-control_2-1

description: ATAC-seq on human fibroblasts: control treated cells

value: skin

value: dermis

value: Primary Fibroblast

value: Fibroblast

value: control


title: RNA-Con-rep3

city: Nanchang

first: Junyao

last: Jiang

address: 1 Minde Road, Nanchang City, Jiangxi Province

department: Department of Clinical Laboratory

institute: The Second Affiliated Hospital, Jiangxi Medical College, Nanchang University

description:
Library name: RNA_Con3
Supplementary_files_format_and_content: The txt file of Ribo-seq include the FPKM values for every gene.

data_processing:
For ribo-seq, Low quality reads were filtered by fastp. Raw reads without inserted fragment or containing over 10% of N bases were removed. Adapter sequences were trimmed. Reads with length between 25-36bp were retained for subsequent analysis. Short reads alignment tool Bowtie (v1.3.1) was used for mapping reads to ribosome RNA (rRNA) database. The reads mapped to rRNAs were removed. Raw reads were were aligned to the genome by STAR(v2.7.10b). After that, quantitative analysis of gene expression was performed. Then RFPs were assigned to different genomic features (exon, intron, intergenic) based on the position of the 5’ end of the alignment. Reads uniquely mapped to a gene were remained for downstream analysis, Quantitative analysis of gene expression was performed by featureCounts. RPKM values were generated to represent the gene expression level of each specific gene. For RNA-seq, Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts. In this step, clean data (clean reads) were obtained by trimming reads containing adapter, ploy-N or with low quality from raw data. At the same time,Q20, Q30 and GC content of the clean data were calculated. All the downstream analyses were performed based on the clean data with high quality. Quantitative analysis of gene expression was performed by featureCounts. RPKM values were generated to represent the gene expression level of each specific gene.
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

source_name: Multiple myeloma

extract_protocol:
For ribo-seq，Sample was treated with specific lysis buffer with cycloheximide to acquire the lysate, cell lysate was treated with unspecific endoribonuclease RNase I. Monosomes were purified from the lysateby fractionation on a linear sucrose gradient. For RNA-seq, total RNA was extracted from cells using RNA isolater Total RNA Extraction Reagent.
For Ribo-seq, following PAGE purification, the both ends of RPF were phosphorylated and ligated with 5’ and 3’ adapters respectively. The RNA samples were then treated with rRNA depletion kit (Qiagen, Germany) to deplete as much rRNA contamination as possible before PAGE purification of the relatively short (25~36nt) RPFs. Then the fragments were reversely transcribed to the cDNAs and amplified by PCR. Concentration of the cDNA was measured by Qubit® 2.0 Fluorometer. After library construction（Multiplex Small RNA Library Prep Set for ILLumina (Set1)，NEB）, the concentration of library was measured by Qubit® 2.0 Fluorometer. Agilent 2100 Bioanalyzer was deployed to examine the insert size of the acquired library. The cDNA library products were generated using VAHTS Small RNA Library Prep Kit.; RNA libraries for RNA-seq were prepared using ployA enrichment method following manufacturer's protocol

value: Multiple myeloma

value: Multiple myeloma cells

value: WT

value: No treatment


title: RNA-Con-rep2

description:
Library name: RNA_Con2
Supplementary_files_format_and_content: The txt file of Ribo-seq include the FPKM values for every gene.


title: RNA-Con-rep1

description:
Library name: RNA_Con1
Supplementary_files_format_and_content: The txt file of Ribo-seq include the FPKM values for every gene.


title: Ribo-Tre-rep3

description:
Library name: Ribo_Tre3
Supplementary_files_format_and_content: The txt file of Ribo-seq include the FPKM values for every gene.

data_processing:
For ribo-seq, Low quality reads were filtered by fastp. Raw reads without inserted fragment or containing over 10% of N bases were removed. Adapter sequences were trimmed. Reads with length between 25-36bp were retained for subsequent analysis. Short reads alignment tool Bowtie (v1.3.1) was used for mapping reads to ribosome RNA (rRNA) database. The reads mapped to rRNAs were removed. Raw reads were were aligned to the genome by STAR(v2.7.10b). After that, quantitative analysis of gene expression was performed. Then RFPs were assigned to different genomic features (exon, intron, intergenic) based on the position of the 5’ end of the alignment. Reads uniquely mapped to a gene were remained for downstream analysis, Quantitative analysis of gene expression was performed by featureCounts. RPKM values were generated to represent the gene expression level of each specific gene. For RNA-seq, Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts. In this step, clean data (clean reads) were obtained by trimming reads containing adapter, ploy-N or with low quality from raw data. At the same time,Q20, Q30 and GC content of the clean data were calculated. All the downstream analyses were performed based on the clean data with high quality. Quantitative analysis of gene expression was performed by featureCounts. RPKM values were generated to represent the gene expression level of each specific gene.
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample
Library strategy: Ribo-seq

value: METTL5 shRNA infection in RPMI-8226 cells

value: METTL5 shRNA infection


title: RNA-Tre-rep2

description:
Library name: RNA_Tre2
Supplementary_files_format_and_content: The txt file of Ribo-seq include the FPKM values for every gene.