title: OE_SMN1_3

city: Wuhan

first: Jun

last: Zhou

address: No.9 Zhangzhidong Road

institute: Renmin Hospital of Wuhan University

data_processing:
Raw sequencing reads containing more than 2-N bases were first discarded. Subsequently, the raw reads were trimmed of adaptors and low-quality bases using a FASTX-Toolkit (v.0.0.13; http://hannonlab.cshl.edu/fastx toolkit/).
In addition, short reads of less than 16 nt were dropped to retain clean reads, which were subsequently aligned to the GRch38 genome by HISAT2 . Uniquely mapped reads were ultimately used to calculate read number and paired-end fragments per kilobase of exon per million fragments mapped (FPKM) for each gene.
The software DEseq2, which is specifically used to analyze the differential expression of genes, was applied to screen the RNA-seq data for DEGs. The results were analyzed based on the fold change (FC≥2 or ≤0.5) and false discovery rate (FDR<0.05) to determine whether a gene was differentially expressed.
The alternative splicing events (SMN1-AS) and regulated alternative splicing events (SMN1-RAS) between ***-OE and control samples were defined and quantified using the SUVA pipeline described previously . The frequency and proportion of reads of SUVA AS events (pSAR) were calculated.
Assembly: GRCh38
Supplementary files format and content: tab-delimited text files include reads counts for each Sample
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

source_name: SHSY5Y cells

extract_protocol:
Total RNAs were extracted from SHSY5Y cells using TRIzol Reagent (Invitrogen, Cat. No. 15596026) following the methods proposed by Chomczynski et al.DNA digestion was carried out after RNA extraction using DNase I. RNA quality was determined by examining A260/A280 with a NanoDrop One spectrophotometer (   RNA integrity was confirmed using 1.5% agarose gel electrophoresis. Qualified RNAs were finally quantified using Qubit3.0 with a Qubit RNA broad-range assay kit (Life Technologies, Q10210).
2 μg total RNAs were used for stranded RNA sequencing library preparation using a KCTM Stranded mRNA Library Prep Kit for Illumina (Catalog No. DR08402, Wuhan SeqHealth Co., Ltd., China) following the manufacturer’s protocol. PCR products corresponding to 200–500 bps were enriched, quantified, and finally sequenced on a Novaseq 6000 sequencer (Illumina) with a PE150 model.

value: SHSY5Y cells

value: SMN1 overexpressed  in SHSY5Y cell


title: ZCCHC8_FKBP12^F36V, Z12H clone, Ctrl, 180min, rep2

status: Public on Jun 19 2025

type: SRA

city: Oxford

first: Guifeng

last: Wei

address: South Parks Road

department: Department of Biochemistry

country: United Kingdom

institute: University of Oxford

library_source: transcriptomic

data_processing:
Estimation of RNA half-life was performed using GRAND-SLAM. Briefly, the paired-end sequencing reads were first aligned to rRNA, and then the unmapped reads were mapped to mouse genome mm10 by STAR (v2.5.2b) with the key parameters (--twopassMode Basic --outSAMstrandField intronMotif --outSAMattributes All --outFilterMultimapNmax 1 --outFilterMismatchNoverReadLmax 0.06 --alignEndsType EndToEnd). Given that T to C conversion is the signature of SLAMseq, the T to C conversion rate was calculated as 4sU incorporation and the average of all the rest of the conversions was calculated as background due to errors from sequencing or library preparation. The T to C conversion rate and background rate were calculated accordingly for each sample. The RNA decay was assumed to follow an exponential model, so the corresponding background corrected T2C rates were fitted to the exponential model to estimate the Xist RNA’s half-life. Regarding X-linked gene silencing and Xist expression level, same procedure of allelic analysis was performed as ChrRNA-seq data.
Assembly: mm10
Supplementary files format and content: tsv file

molecule: total RNA

organism: Mus musculus

source_name: Endogenous Xist promoter was replaced with TetOn Promoter (129S allele)

growth_protocol: ES cells were grown in DMEM media supplemented with 10% fetal calf serum (Seralab), 2 mM L-glutamine, 1X non-essential amino acids, 50 µM β-mercaptoethanol, 1X penicillin / streptomycin (all from Life Technologies) and 1000 U/mL LIF (made in-house). Mitomycin-inactivated mouse fibroblasts were used as feeders. All ES cells were grown in feeder-dependent conditions on gelatinised plates at 37°C with 5% CO2.

extract_protocol:
When reaching 60 to 70% confluency, cells were either untreated or dTAG-13 treated for 2 hours, followed by additional 1 μg/ml doxycycline induction for 20 hours. Then, transcribed RNA was labelled with 4sU by incubation with medium containing 500 μM 4sU (Lexogen) and 1 μg/ml doxycycline for another 4 hours. Next, 4sU was withdrawn for all samples by medium washout. Different samples were washed with medium containing 1 μg/ml doxycycline and 50 mM uridine (in excess, Lexogen) for 1.5 and 3 hours. Cells are quickly washed with PBS once and directly lysed with Trizol/chloroform for total RNA isolation.
Equal amount of RNA samples (5 μg) was treated with Iodoacetamide to modify the 4-thiol group of S4U-containing nucleotides via the addition of a carboxyamidomethyl group by the SLAMseq Kinetics Kit. The RNA was recovered using RNAClean XP beads (Beckman Coulter), followed by resuspension in nuclease free water. Approximately 500 ng RNA of each sample was taken forward for library preparation using the Illumina TruSeq stranded total RNA kit. Quantification of the libraries was conducted by qPCR using KAPA Library Quantification DNA standards. Finally, the libraries were pooled and paired-end sequencing was performed using Illumina NextSeq500.

treatment_protocol: Inducible Xist expression was driven by a TetOn promoter induced by addition of 1.0 µg/mL of doxycycline for 24 hours. Degron for protein of interest, i.e. METTL3, YTHDC1, ZCCHC8 in this study, are induced by dTAG-13 for two hours, which is sufficient to acute deplete the FKBP12^F36V fused protein.

tag: strain background

value: Cast x 129S

tag: cell type

value: mouse embryonic stem cell

tag: xist type

value: Endogenous Xist + Bgl

tag: cell line

tag: treatment

value: Dox


title: OCT4-lin-mini ChIP OSKM48h

city: Edinburgh

first: Abdenour

last: Soufi

address: 5 Little France Drive

department: School of Biological Sciences

institute: University of Edinburgh

description: Library name: OCT4-lin-mini ChIP OSKM48h

library_source: genomic

data_processing:
The ChIP-seq pair-end reads were mapped to the human genome assembly GRCh37 (hg9) using Bowtie (version 2.3.4.1) and very sensitive parameters.
Duplicated reads were then removed using MarkDuplicates from the Picard toolkit.
Reads mapping to the backlisted regions as determined by Encyclopaedia of DNA Elements (ENCODE) were discarded.
The sequencing coverage and the insert size distribution were measured from the resulting bam files using Qualimap (version 2.2.1).
The peaks of OCT4 wild-type and mutants showing significant enrichment over input DNA were called using MACS2 (version 2.1.1.20160309), and a fragment size of 200 bp and were controlled to a q-value (minimum FDR) cut-off of 0.01. The peaks that overlapped with the ENCODE blacklist were removed.
Assembly: GRCh37 (hg19)
Supplementary files format and content: The aligned ChIP-seq reads were normalised for sequencing coverage to 1x genome depth (reads per genome coverage, RPGC) using the bamCoverage tool from DeepTools and a bin size of 10 bp and extendReads parameters. Replicates were merged before normalized for coverage to produce the final BigWig (.bw) file.

molecule: genomic DNA

organism: Homo sapiens

source_name: human fibroblasts

growth_protocol: human fibroblasts (HF176) were cultured in GMEM supplemented with 10% FCS, 1X 13 non-essential amino acids, 1 mM Sodium Pyruvate, 1 mM glutamine and 0.1 mM 2-mercaptoethanol at 37C and 5% CO2. Human Embryonic Stem Cells (hESCs) Master Sheffield 7 (MS7) and human induced pluripotent stem cells (hiPSCs) were cultured in Essential 8 Medium (#A2858501, Gibco) in plates coated with 4g/mL of Human Recombinant Laminin 521/DPBS Ca++, Mg++ (#800110, BioLamina; #14040133, Gibco) at 37C and 5% CO2.

extract_protocol:
Cells were washed 3X with PBS at RT on 15 cm dishes. After final wash, 15mL of PBS/MgCl2 was added to each plate and 120ul of fresh DSG (0.25M stock prepared by adding 613L DMSO to 50mg of DSG) were added to each plate to get a final concentration of 2mM. Plates were incubated at RT for 45min in a horizontal shaker with constant moving followed by 3X washes of PBS. After the last wash, 20 mL of PBS were added to each plate followed by adding 3mL of Formaldehyde crosslinking buffer (50mM HEPES-KOH, pH7.5, 100mM NaCl, 1mM EDTA, 0.5mM EGTA, 11% formaldehyde). Crosslinking was blocked by adding 1.65 mL of 2.5M Glycine and incubating for 5 minutes at room temperature. Cells were harvested using a silicon scraper and centrifuged for 5 minutes at 1,350 rcf at 4C. Cell pellets were then re-suspended in 10ml Lysis Buffer 1 (50mM HEPES-KOH pH7.5, 140mM NaCl, 1mM EDTA, 10% Glycerol, 0.5% NP-40 Substitute, 0.25% Triton X100 and cOmplete Ultra Protease Inhibitor rotated for 10 minutes at 4C. Cells were disrupted using a tight 7mL dounce homogeniser with 80 strokes on ice. Nuclei were collected by centrifugation at 1350rcf for 5 minutes at 4C. The nuclei were washed in 10ml Lysis Buffer 2 (10mM Tris-HCl pH 8, 200mM NaCl, 1mM EDTA, 0.5mM EGTA and cOmplete Ultra Protease Inhibitor) for 10 minutes a rotator at room temperature. The nuclei were collected by centrifugation and resuspended in Lysis Buffer 3 (10mM Tris-HCl pH8, 100mM NaCl, 1mM EDTA, 0.5mM EGTA 0.1% Na-deoxycholate, 0.5% N-lauroylsarcosine and cOmplete Ultra Protease Inhibitor). Samples were sonicated for 140 min in 10 minutes intervals using a Covaris M220 sonicator. To solubilise chromatin following sonication, 100ul of 10% Triton X-100 was added per 1ml of sonicated chromatin. Before ChIP, 50ul of sonicated chromatin were collected to confirm optimum DNA fragmentation (~ 200 bp) was achieved by agarose gel electrophoresis. Three ChIPs were performed for each ChIP-seq sample (OCT4 WT and mutants). Dyna G Magnetic Beads were transferred to a Prechilled LoBind tube and washed 3X with 1ml of Blocking buffer (0.5 BSA in PBS). Beads were resuspended in 800 ul of Blocking buffer and incubated with 10ug of OCT4 antibody per ChIP and incubated for 6 hr (minimum) on a rotating platform at 4C. Beads were washed 3X in 1ml of blocking solution and resuspended in 100ul Lysis buffer 3. Sonicated chromatin (40 ug) were added to each ChIP and volume was top up to 900 ul with Lysis buffer 3 buffer containing protease inhibitors. ChIPs were incubated overnight in a rotating platform at 4C. To reduce background the ChIP reactions were transferred to fresh pre-chill LoBind tube. Beads were washed 4X with cold RIPA-wash buffer (50 mM Hepes-KOH pH 7.6, 500 mM LiCl, 1 mM EDTA, 1% NP-40, 0.7% Na-Deoxycholate) using magnetic rack. Beads were washed once with TE+NaCl (10mM Tris-HCl pH 8, 1mM EDTA pH 8 and 50mM NaCl), followed by a spin at 300 x g for 3 minutes at 4C and to remove any residual TE buffer. Bound chromatin fragments were eluted by addin 210 ul elution buffer to the beads and incubated at 65C for 30 minutes shaking at 1200rpm. Tubes were centrifuged at 16,000 x g for 1 minute at room temperature and 200ul of supernatant was transferred to a new tube. In parallel, 50ul of sonicated chromatin from the INPUT after sonication was thawed before adding 150ul of ChIP elution buffer. ChIPs and input were reverse cross-linked by incubating at 65C overnight (shake 700rpm). An equal volume (200ul) of TE (10mM Tris-HCl pH8, 1mM EDTA) was added and incubated with 0.2mg/mL RNAse A for 2 hours at 37C. Proteins were then digested by incubating with 0.2mg/mL Proteinase K for 2 hours at 55C. To extract DNA, 400ul Phenol:chloroform:isoamyl alcohol were added to the samples to separate phases by spinning the sample at top speed for 5 min. The aqueous layer was transferred to a new tube containing 16ul of 5M NaCl (200 mM final concentration) and 1.5ul of 20 g/L glycogen (30 g total). DNA precipitation was performed by adding 0.8ml of cold 100% EtOH and incubated for 180 min at least at -20C. Tubes were centrifuged 20,000 x g for 10 minutes at 4C to pellet DNA. Supernatants were carefully decanted without disturbing the DNA pellet, which was further washed with 500ul of 80% EtOH and spining at 20,000 x g for 10 minutes at 4C. Supernatants were removed by pipetting and pellets were allowed to dry for 5 min. Each pellet was resuspended in 20ul MiniPrep Elution buffer (10mM Tris-HCl pH8.5, Qiagen) using a P20 pipette. DNA was quantified by Qubit 2.0 using the HS dsDNA quantification kit.
ChIP-seq DNA libraries were prepared using 20-50ng ChIP-DNA prepared by pooling equal volumes of 3X ChIP replicates for each OCT4 (WT and mutant) using the NEBNext Ultra II Library Preparation Kit with Dual Index Primers. Size selection for DNA fragments of approximately 200bp was carried out using SpeedBeads, which comprise magnetic carboxylate modified particles. PCR amplification during library preparation was limited such that samples underwent 10 cycles of PCR amplification. Libraries were quantified using a Qubit 2.0 device with a high sensitivity dsDNA kit and fragment size was determined using an Agilent 2200 Tapestation with D1000 HS reagents. The DNA libraries were then pooled by mixing an equal concentration of each ChIP DNA library. The concentration of the ChIP DNA library pool was determined by an Agilent 2200 Tapestation with D1000 HS reagents.

treatment_protocol: human fibroblasts were transduced with concentrated lentiviruses encoding for OCT4 (WT or mutants), SOX2, c-MYC, KLF4 at M.O.I of 5, and rtTA2M2 lentivirus at M.O.I of 3. After 16 hours of infection, the culture medium was replaced, and cells were cultured for 48 hours. OSKM protein expression was then induced by adding fresh medium containing 1g/mL of doxycycline. Cells were cultured for 48 hours at 37C and 5% CO2 before collection.

value: human fibroblasts

tag: genotype

value: wildtype

value: human fibroblasts overexpressing OSKM for 48 hours


title: OE_SMN1_2

country: China


title: 38_5C-0min_S1

city: Durham

first: Steven

middle: B

last: Haase

state: North Carolina

department: Biology

country: USA

institute: Duke University

description: scer_38_5C_timeseries - 0

data_processing:
Sequenced reads mapped to the respective yeast genome using STAR.
Transcripts were quantified in Transcripts Per Million (TPM) using RSEM.
These resulting TPM were combined into a single .tsv file containing all transcripts at all timepoints
This final .tsv file was z-score normalized and quantile normalized to produce the cleaned .tsv file
Assembly: Saccharomyces cerevisiae S288C Ensembl R64-1-1 downloaded from Illumina iGenomes.
Supplementary files format and content: Each dataset has a final raw .tsv file. Consisting of either FPKM/TPM transcript levels (see above) for each each for each timepoint
Supplementary files format and content: Each dataset has a final cleaned .tsv file. Consisting of the Z-score normalized and then quantile normalized  (z-score quantile normalized) data for each gene for each timepoint.

organism: Saccharomyces cerevisiae

source_name: BF264-15D MATa bar1

growth_protocol: Cells were grown in YEPDextrose at 38.5c.

extract_protocol:
Cells were removed at each time point and flash frozen on dry ice. RNA was harvested using standard yeast methods using  an acid phenol/chloroform protocol.
Illumina Stranded mRNA Prep, NovaSeq 6000 S-Prime.

treatment_protocol: Synchronous G1 populations collected by alpha-factor mating pheromone (40 ng/ml, 150 minutes) arrest-release.

tag: time

value: 0 minutes

tag: experimental conditions

value: YEPDextrose 38.5C


title: Brn3b WT, rep3, HA-IP

city: Evanston

first: Yue

last: Yang

state: IL

address: 2200 Campus Dr

department: Neurobiology

institute: Northwestern University

description:
Brn3bWT3_IP
raw_counts2.xlsx

data_processing:
Reads were aligned to the mm10 reference genome using the Smart-seq3 github pipeline (https://github.com/sandberg-lab/Smart-seq3)
Assembly: mm10
Supplementary files format and content: .xlsx files contain raw counts for each RNA-seq library

source_name: retina

extract_protocol:
Retinas from the same animal were combined and homogenized in lysis buffer (50 mM Tris-HCl pH 7.4, 100 mM KCl, 12 mM MgCl2, 1% NP-40, 0.4 unit/ml RNase inhibitor, 1 mM DTT, 100 μg/ml cycloheximide) with a dounce homogenizer. Lysates were incubated with 1 µg/µl heparin for 2 minutes on ice prior to centrifugation. The lysates were spun down at 10,000g for 10 minutes at 4C and the supernatant was used for immunoprecipitation using an antibody against HA-tag with Dynabeads protein G for overnight at 4C. 1.5% of lysate was saved as an input. After extensive washes with cold washing buffer (50 mM Tris-HCl pH 7.4, 300 mM KCl, 12 mM MgCl2, 1% NP-40, 0.5 mM DTT, 100 μg/ml cycloheximide), immunoprecipitated RNA and input RNA were purified with a RNeasy Micro Kit (Qiagen) following the manufacturer’s instructions and eluted in 10 µl of water.
2 µl of purified RNA were used for sequencing library preparation using the Smart-seq3 protocol with modifications. After reverse transcription followed by PCR amplification, 25 ng of cDNA was used for the Tn5 tagmentation reaction. Tagmentated cDNA was amplified with 8 cycles of PCR using primers containing indexes and Illumina adaptors.

tag: tissue

value: retina

value: ipRGCs

value: Opn4-Cre; Rpl22-HA

tag: Sex

value: female


title: ZCCHC8_FKBP12^F36V, Z12H clone, Ctrl, 90min, rep2

value: Endogenous Xist promoter was replaced with TetOn Promoter (129S allele)


title: OE_SMN1_1


title: Brn3b WT, rep2, HA-IP

description:
Brn3bWT2_IP
raw_counts2.xlsx

value: male


title: ZCCHC8_FKBP12^F36V, Z12H clone, Ctrl, 0min, rep2


title: Brn3b WT, rep1, HA-IP

description:
Brn3bWT1_IP
raw_counts2.xlsx


title: NC_3

value: SHSY5Y cells

value: SHSY5Y cell(control plasmid)


title: Evf12 GAPDH TSTS CHIRPseq

city: Chicago

first: Jhumku

last: Kohtz

state: Illinois

address: 303 E Chicago

department: Neurology

description:
Evf2_expression_data.mtx
Evf2_cell_data.csv
Evf2_gene_data.csv

data_processing:
After mapping the reads, the peak callingwas performed using theMACS2 program (Zhang et al., 2008). An FDR cutoff of 0.05 was used to call the final set of peaks. The UCSC browser was used to visualize peaks, and perform alignments. Evf1/2 regulated peaks were defined are overlapping odd and even bound peaks in Evf1/2++ samples, absent from Evf1/2TSTS and GAPDH peaks.
Assembly: mm9
Supplementary files format and content: Tab separated values files and matrices
Library strategy: CHIRP

source_name: Ventral forebrain

extract_protocol:
The method described in (Chu et al., 2011) was followed, and modified for embryonic day 13.5 ganglionic eminences (13.5GEs). For each sample ~16 E13.5GEs were dissected for each genotype (Evf1/2+/+, Evf1/2TS/TS) in ice cold L15, pipetted to produce a single cell suspension, pelleted for 4min, X 800 RCF, resuspended in PBS, pelleted for 4min, X 800 RCF, and resuspended in 5mL of 1% glutaraldehyde. Cells were cross-linked for 10 minutes, quenched with 500 µL of 1.25 M glycine for 5 minutes, pelleted for 5 min X 2000 RCF, 4°C, washed with PBS, pelleted for 5 min X 2000 RCF for 5min, 4°C, resuspended 1mL 4°C PBS per 8 embryos, pelleted X 2000 RCF for 3 minutes at 4°C, supernatant aspirated, and cell pellets flash frozen in liquid nitrogen and stored at -80°C.
Libraries were created with NEBNext Multiplex Oligos for Illumina (Dual Index Primers Set 1), and 10M reads from PE100 sequenced on NOVAseq. Raw sequencing reads for ChIRPdatasets were aligned using bowtie2 (Langmead and Salzberg, 2012) mapper with the following settings '--local --very-sensitive-local --no-mixed --no-discordant --phred33 -I 10 -X 700’.The datasets weremappedagainst the mm9 version of the mouse genome.

value: Ventral forebrain

tag: age

tag: region

value: Ganglionic Eminence

value: Evf12 TSTS


title: Brn3b cKO, rep2, HA-IP

description:
Brn3bcKO2_IP
raw_counts2.xlsx

value: Opn4-Cre; Rpl22-HA; Brn3bcKO-AP


title: Evf2TSTS Smarcc2 rep2 CutandRun

data_processing:
Paired-end CUT&RUN reads of different transcription factors and their respective Ig controls from Evf2+/+ and Evf2TS/TS samples were first mapped on mm9 genome using Bowtie2 v2.1.0 (Langmead and Salzberg, 2012) with options ‘–local –very-sensitive-local –no-unal –nomixed –no-discordant –phred33 -I 10 -X 700’. We used the Picard toolkit command ‘MarkDuplicates’ to mark PCR duplicates and remove them from the final mm9 genome mapped bam files. Next, we separated the sequence fragments into ≤120 and ≥150 bp classes that provided the mapping of the local vicinity of a DNA-binding protein. The base-pair sizes can vary depending on the steric access to the DNAby the tethered MNase (Skene et al., 2018). Fragments mapping to repeat elements were removed, and replicates were joined before peak calling. The peak calling was performed using MACS2 (Zhang et al., 2008) callpeak options ‘-t -c –f BED-gmm–keep-dup all –bdg –nomodel –slocal 500 –llocal 5000 –-extsize 120/150’. An FDR
cutoff of 0.05 was used to call the final set of peaks (Janssens et al., 2018). Differential CUT&RUN analysis of transcription factor-binding peaks between Evf2+/+ and Evf2TS/TS was performed using MACS2 program by treating one of the samples as the ‘control’ for the other.
Assembly: mm9
Supplementary files format and content: Tab separated values files and matrices
Library strategy: Cut&Run

extract_protocol:
The protocol is described in detail (Cajigas et al. 2021, modified from Skene et al 2018). For Cut&Run, E13.5 ganglionic eminences were dissected from Evf2+/+ and Evf2TS/TS embryos in L15 medium (six embryos per genotype). Tissues were pooled for each genotype, triturated by pipetting and filtered through a cell-strainer capped 5 ml polystyrene roundbottomed tube (BD Falcon) to generate single-cell suspensions. Cells were counted using the Luna Automated Cell Counter (Logos Biosystems). The appropriate volume of cells to obtain 250,000 cells per sample was centrifuged at 600 g for 3 min at 4°C. The supernatant was removed and the cell pellet was gently resuspended in ice-cold wash buffer [20 mM HEPES (pH 7.5), 150 mM NaCl, 0.5 mM spermidine and EDTA-free protease inhibitor cocktail]. The cells were centrifuged at 600 g for 3 min at 4°C. The supernatant was removed and cells were gently resuspended in 1 ml of wash buffer.
Anti-Smarcc2 (Bethyl, Cat# A301-038A; RRID:AB_817992) and anti-Nono (Bethyl, Cat#A300-587A; RRID:AB_495510) were used for Cutand Run. CUT&RUN libraries were prepared using the KAPA Hyper Prep Kit protocol, with some modifications. The total volume of CUT&RUN DNA was used for library construction. For adapter ligation, 5 μl of 3 μM adapter stock from the KAPA Dual-Indexed Adapter Kit was used. The ligation was incubated at 20°C for 15 min. The library was amplified using the following cycling conditions: 14 cycles of 98°C for 45 s, 98°C for 15 s and 60°C for 10 s; 72°C for 1 min. After library amplification, the libraries were purified using 50 μl of KAPA Pure Beads and eluted in 20 μl of water. CUT&RUN sample quality was analyzed by TapeStation prior to sequencing on a NovaSeq 6000 (SP 100 cycles).


title: Rpl22-HA mice, rep2, HA input

description:
Rpl22HA-2_input
raw_counts.xlsx

value: retinal cells

value: pooled male and female


title: ZCCHC8_FKBP12^F36V, Z12H clone, dTAG, 90min, rep2

value: Cast x 129S

value: mouse embryonic stem cell

value: Endogenous Xist + Bgl

value: dTAG-13, Dox


title: NC_2


title: Evf2TSTS Smarcc2 rep1 CutandRun


title: YTHDC1_FKBP12^F36V, Y12H clone, dTAG, 90min, rep2


title: Rpl22-HA mice, rep2, HA IP

description:
Rpl22HA-2_IP
raw_counts.xlsx

value: retina

value: ipRGCs


title: NC_1


title: Evf12 even ++ rep1 CHIRPseq

value: Wildtype


title: YTHDC1_FKBP12^F36V, Y12H clone, dTAG, 0min, rep2

value: Endogenous Xist promoter was replaced with TetOn Promoter (129S allele)


title: Evf12 even ++ rep2 CHIRPseq


title: Evf2++ Smarcc2 rep2 CutandRun


title: ctrl mice, rep2, input

description:
noHA-2_input
raw_counts.xlsx


title: Evf12 even TSTS CHIRPseq


title: YTHDC1_FKBP12^F36V, Y12H clone, Ctrl, 180min, rep2

value: Dox


title: ctrl mice, rep2, HA IP

description:
noHA-2_IP
raw_counts.xlsx


title: Evf2++ Smarcc2 rep1 CutandRun


title: 120DIV_11A3_GEO2

city: San antonio

first: Karina

middle: Kaisha

last: Meyer-Acosta

state: TX

address: One UTSA circle

department: Neuroscience, developmental, and regenerative biology

institute: University of Texas at San Antonio

description:
Library name: UKBiO11A3_GEO_4
Column name in Master_Countdata.csv: UKBiO11A3_GEO_4

data_processing:
Analysis performed and plots created using Pluto (https://pluto.bio). paired_end FASTQ files were processed using the nf-core-rnaseq pipeline (v3.12.0)(auto strandedness)(Ewels et al., 2020). Adapter sequences were removed with Trim Galore. Reads were aligned with STAR (Dobin et al., 2012) to GRCh38 (NCBI, p.14, release 110) and quantified to gene counts using RSEM (Li and Dewey, 2011).
Assembly: GRCh38
Supplementary files format and content: Master_Countdata.csv contains the reads for each gene (rows) and each sample (columns)

extract_protocol:
Genomic DNA was extracted from iPSCs using DNeasy® Blood & Tissue Kit (QIAprep #69504) following the manufacturer’s instructions Organoids (3 pooled) were harvested and RNA extracted using the Qiagen miRNeasy Mini Kit (Cat. No. 217004) according to manufacturer instructions for all gene expression experiments. The concentration and purity of the RNA samples were measured by using Nano-drop (Thermo Fisher Scientific). The extracted RNA (500 ng) was reverse transcribed according to the protocol supplied with SuperScript III First-Strand Synthesis System for RT (Invitrogen, Cat. No. 18080-051). RIN values were assessed to ensure cDNA library purity and quality.
75 paired-end RNAseq (2x75bp flowcell) was performed by the UTSA genomics core on all 32 samples at the same time with Element Biosciences AVITI DNA Sequencer, using the Freestyle Cloudbreak chemistry at a depth of 25-30 million reads per sample.

value: male

tag: organoid type

value: GEO

tag: time point_(div)

value: 120 DIV

tag: batch


title: ZN-GBM1

first: Xuan

last: Liu

address: Donghu Road, No. 115, Wuchang District, Wuhan, Hubei Province, P.R. China

institute: Wuhan university

data_processing:
raw sequencing data were first processed using the CellRangerV4.0.0 pipeline.
we used DoubletFinder to remove doublet.
we used seurat to generate the sparse count matrix and downstream analysis.
we used infercnv(V1.2.0) to calculate copy number variant. And params were cutoff=0.1,HMM=TRUE, others are defult.
Assembly: UCSC mm10
Supplementary files format and content: Matrix table with gene counts for every gene and every cell
Supplementary files format and content: tsv files include cell barcode files and gene files

source_name: GBM cells

extract_protocol:
Tumor tissues were dissected and enzymatically digested into single cells, then they were suspended in cold PBS.
Libraries were constructed using the Single Cell 3′ Library Kit V2 (10× Genomics) .

value: GBM


title: 120DIV_11A3_GEO1

description:
Library name: UKBiO11A3_GEO_3
Column name in Master_Countdata.csv: UKBiO11A3_GEO_3


title: YTHDC1_FKBP12^F36V, Y12H clone, Ctrl, 90min, rep2


title: Evf2TSTS Nono rep2 CutandRun

value: Ventral forebrain

value: Ganglionic Eminence


title: YTHDC1_FKBP12^F36V, Y12H clone, dTAG, 180min, rep2


title: Rpl22-HA mice, rep1, HA input

description:
Rpl22HA-1_input
raw_counts.xlsx

value: retinal cells

value: Opn4-Cre; Rpl22-HA


title: Evf2TSTS Nono rep1 CutandRun


title: 30DIV_11A3_GEO2

description:
Library name: UKBiO11A3_GEO_2
Column name in Master_Countdata.csv: UKBiO11A3_GEO_2

value: 30 DIV


title: YTHDC1_FKBP12^F36V, Y12H clone, Ctrl, 0min, rep2

value: Cast x 129S

value: mouse embryonic stem cell


title: Rpl22-HA mice, rep1, HA IP

description:
Rpl22HA-1_IP
raw_counts.xlsx

value: pooled male and female


title: METTL3_FKBP12^F36V, 12D clone, dTAG, 180min, rep2

value: Endogenous Xist + Bgl

value: dTAG-13, Dox


title: 30DIV_11A3_GEO1

description:
Library name: UKBiO11A3_GEO_1
Column name in Master_Countdata.csv: UKBiO11A3_GEO_1


title: Evf2++ Nono rep2 CutandRun

value: Wildtype


title: Evf2++ Nono rep1 CutandRun


title: ctrl mice, rep1, input

description:
noHA-1_input
raw_counts.xlsx

value: retina


title: METTL3_FKBP12^F36V, 12D clone, dTAG, 90min, rep2

value: Endogenous Xist promoter was replaced with TetOn Promoter (129S allele)


title: 120DIV_11A3_CO2

description:
Library name: UKBiO11A3_CO_4
Column name in Master_Countdata.csv: UKBiO11A3_CO_4

value: male

value: CO


title: METTL3_FKBP12^F36V, 12D clone, dTAG, 0min, rep2


title: ctrl mice, rep1, HA IP

description:
noHA-1_IP
raw_counts.xlsx


title: 120DIV_11A3_CO1

description:
Library name: UKBiO11A3_CO_3
Column name in Master_Countdata.csv: UKBiO11A3_CO_3

value: 120 DIV


title: METTL3_FKBP12^F36V, 12D clone, Ctrl, 180min, rep2

value: Dox


title: Evf2TSTS scRNA-seq

library_source: transcriptomic single cell

data_processing:
A custom mm9 transcriptome, in which the Evf1 and Evf2 transcripts were annotated as separate genes, was built using the Cellranger (version 3.1.0) mkref function. Sequencing reads were aligned to the custom transcriptome using Cellranger (version 6.1.1). A genes by cell matrix was generated from Cellranger output files within Monocle (monocle_2.24.1)(Trapnell et al., 2014) (Qiu et al., 2017a; Qiu et al., 2017b) dimension reduction was performed on the 2763 most highly variable genes determined from the transcripts/10,000 transcripts normalized matrix. Dimension reduction was performed on the top 12 principal components after regressing the effect of read depth on gene expression variance (total number of RNAs and the number of genes expressed) using uniform manifold approximation and projection (UMAP) method from the uwot package (McInnes, 2020; Melville, 2023), cells were clustered using standard approaches, with clusters assigned cell type annotations based on marker gene enrichment as performed previously (Brodie-Kommit et al., 2021; Clark et al., 2019; Lu et al., 2020).
Differential expression was determined using the differentialGeneTest function within monocle, using fullModelFormulaStr = “~genotype” and a reducedModelForulaStr = “~genotype + Total_mRNAs” to reduce the impact of read-depth on differential expression testing. Significant differential expression was determined when q-values < 1e-5.
Assembly: mm9
Supplementary files format and content: Tab separated values files and matrices

molecule: polyA RNA

extract_protocol:
For scRNAseq, E13.5GE dissections from Evf2+/+ and Evf2TS/TS embryos were collected into ice cold Leibovitz’s L-15 medium and 1% fetal bovine serum. For the single cell dissociation, papain dissociation kit, protocol II (Worthington Biochemical, LK003150). In the last step, the supernatant was removed and pelleted cells were resuspended in 1ml pre-chilled L15 medium + 1% fetal bovine serum.  Cells were counted using a Luna cell counter, and viability determined to be ~90%.
The 10X Genomics microfluidics system and the 10X Genomics Chromium Single Cell 3’ Reagent Kit v3 were used for single cell separation and library preparation, following all protocol recommendations, including PCR cycles (12 cycles for cDNA amplification of 5000 cells and 14 cycles for index PCR.

value: Ventral forebrain


title: Xenium SAT, Lean, Rep3, Slide3

type: RNA

city: London

first: William

middle: Robert

last: Scott

address: Hammersmith Hospital, Du Cane Road

department: Institute of Clinical Sciences

institute: Imperial College London

hyb_protocol: 5µm FFPE tissue sections on Xenium slides were deparaffinised and permeabilised to make the mRNA accessible. Gene panel probes were hybridised for 20hrs overnight followed by washing, ligation of probe ends to targeted RNAs generating circular DNA probes with high specificity. Rolling Circle Amplification was used to generate hundreds of copies of gene-specific barcodes for each RNA-binding event,

scan_protocol: Tissues sections were stained with DAPI nuclear stain and Xenium slides were loaded onto the Xenium instrument for imaging, and decoding of image data to transcripts

data_processing: FFPE tissues were analysed on the 10X Xenium Analyser instrument following 10X Genomics Xenium in situ Gene Expression protocols CG000580, CG000582 and CG000584

label: Human Multi-Tissue + 100 Custom Genes

source_name: Periumbilical Adipose Tissue, Lean

extract_protocol: Slide preparation: FFPE blocks were stored at 4C. Xenium slides stored at -20C were equilibrated to room temperature for 30min prior to sectioning. FFPE blocks were rehydrated in an ice bath with distilled water for 10-30min, and sectioned at 5µm thickness. Sections were floated in a 42C water bath and slides containing tissue sections were incubated at 42C for 3hrs, and then dried overnight at room temperature in a desiccator. Slides were kept at 4C in a desiccator until use. All histology was performed in RNase free conditions using sterilised equipment.

value: Female


title: Xenium SAT, Lean, Rep4, Slide4


title: Evf2++ rep2 scRNA-seq

value: Ganglionic Eminence

value: Wildtype Control


title: METTL3_FKBP12^F36V, 12D clone, Ctrl, 0min, rep2


title: 30DIV_11A3_CO2

description:
Library name: UKBiO11A3_CO_2
Column name in Master_Countdata.csv: UKBiO11A3_CO_2

value: 30 DIV


title: Evf2++ rep1 scRNA-seq


title: Xenium SAT, Lean, Rep1, Slide1


title: T2-3

city: Hangzhou

first: Fei

last: Li

address: 866 Yuhangtang Road

department: Department of Medicine

institute: Zhejiang University

data_processing:
Reads were further filtered by fastp (version 0.18.0).
Short reads alignment tool Bowtie2 (version 2.2.8) was used for mapping reads to ribosome RNA (rRNA) database. The rRNA mapped reads then will be removed. The remaining clean reads were further used in assembly and gene abundance calculation.
An index of the reference genome was built, and paired-end clean reads were mapped to the reference genome using HISAT2. 2.4 and other parameters set as a default.
The mapped reads of each sample were assembled by using StringTie v1.3.1.For each transcription region, a FPKM (fragment per kilobase of transcript per million mapped reads) value was calculated to quantify its expression abundance and variations, using RSEM software.
Assembly: mm10
Supplementary files format and content: TXT files includes raw counts and FPKM and matrix files for each sample

source_name: cell

growth_protocol: Bone marrow cells were harvested from femurs and tibias of WT mice. After removing RBCs and adhesion culture for 2 hours, unattached cell was resuspended to a density of 2 × 106/mL in Iscove’s Modified Dulbecco’s Medium (Gibco) supplemented with 20% FBS (Vistech), 2 mM L-glutamine (GlutaMAX™, Gibco), 5 × 105 M β-ME (Sigma-Aldrich), MEM Non-Essential Amino Acids (11140050, Gibco), 1 mM sodium pyruvate (11360070, Gibco), and 100 U/mL penicillin/streptomycin. The cytokines murine SCF (100 ng/mL) and murine FLT3-Ligand (100 ng/mL) were supplemented to the culture for 4 days. On day 4, cells were washed and treated in the presence of IL-5 (10 ng/mL, R&D systems) for the duration of the culture. FAC, DFO was treatment on days 4. RNAseq were analysis on Day 7.

extract_protocol:
Total RNA was extracted using Trizol reagent kit (Invitrogen, Carlsbad, CA,USA) according to the manufacturer’s protocol. RNA quality was assessed on an Agilent 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA, USA) and checked using RNase free agarose gel electrophoresis.
After total RNA was extracted, eukaryotic mRNA was enriched by Oligo(dT) beads, Then the enriched mRNA was fragmented into short fragments using fragmentation buffer and reversly transcribed into cDNA by using NEBNext Ultra RNA Library Prep Kit for Illumina(NEB #7530,New England Biolabs, Ipswich, MA, USA).The purified double-stranded cDNA fragments were end repaired, A base added, and ligated to Illumina sequencing adapters.The ligation reaction was purified with the AMPure XP Beads(1.0X).Ligated fragments were subjected to size selection by agarose gel electrophoresis and polymerase chain reaction (PCR) amplified.

treatment_protocol: DFO:5 μM, FAC；10 μM

value: cell

value: Eosinophils

value: eosinophils

value: WT

value: IL-4, IL35,GM-CSF


title: METTL3_FKBP12^F36V, 12D clone, Ctrl, 90min, rep2

value: Cast x 129S

value: mouse embryonic stem cell

value: Endogenous Xist + Bgl


title: T2-2

value: IL-4, IL34,GM-CSF


title: Xenium SAT, Weight Loss, Pair4, Slide4

source_name: Periumbilical Adipose Tissue, Weight Loss


title: ZCCHC8_FKBP12^F36V, Z12H clone, dTAG, 180min, rep1

value: Endogenous Xist promoter was replaced with TetOn Promoter (129S allele)

value: dTAG-13, Dox


title: 120DIV_11A4_GEO1

description:
Library name: UKBiO11A_GEO_3
Column name in Master_Countdata.csv: UKBiO11A_GEO_3

value: male

value: GEO

value: 120 DIV


title: 30DIV_11A3_CO1

description:
Library name: UKBiO11A3_CO_1
Column name in Master_Countdata.csv: UKBiO11A3_CO_1

value: CO


title: T2-1

value: IL-4, IL33,GM-CSF


title: ZCCHC8_FKBP12^F36V, Z12H clone, dTAG, 90min, rep1


title: Xenium SAT, Weight Loss, Pair3, Slide3

value: Female


title: con3

value: cell

value: untreated


title: ZCCHC8_FKBP12^F36V, Z12H clone, Ctrl, 180min, rep1

value: Dox


title: con2

value: Eosinophils

value: eosinophils

value: WT


title: 30DIV_11A4_GEO2

description:
Library name: UKBiO11A_GEO_2
Column name in Master_Countdata.csv: UKBiO11A_GEO_2

value: 30 DIV


title: 30DIV_11A4_GEO1

description:
Library name: UKBiO11A_GEO_1
Column name in Master_Countdata.csv: UKBiO11A_GEO_1


title: 120DIV_11A4_CO2

description:
Library name: UKBiO11A_CO_4
Column name in Master_Countdata.csv: UKBiO11A_CO_4


title: ZCCHC8_FKBP12^F36V, Z12H clone, Ctrl, 90min, rep1

value: Cast x 129S

value: mouse embryonic stem cell

value: Endogenous Xist + Bgl


title: ZCCHC8_FKBP12^F36V, Z12H clone, dTAG, 0min, rep1

value: Endogenous Xist promoter was replaced with TetOn Promoter (129S allele)

value: dTAG-13, Dox


title: Xenium SAT, Weight Loss, Pair2, Slide2


title: 120DIV_11A4_GEO2

description:
Library name: UKBiO11A_GEO_4
Column name in Master_Countdata.csv: UKBiO11A_GEO_4

value: male

value: GEO


title: Xenium SAT, Obese, Pair4, Slide4

source_name: Periumbilical Adipose Tissue, Obese


title: 120DIV_11A4_CO1

description:
Library name: UKBiO11A_CO_3
Column name in Master_Countdata.csv: UKBiO11A_CO_3

value: CO

value: 120 DIV


title: ZCCHC8_FKBP12^F36V, Z12H clone, Ctrl, 0min, rep1


title: Xenium SAT, Weight Loss, Pair1, Slide1

value: Female


title: con1

value: cell


title: Xenium SAT, Lean, Rep2, Slide2


title: 30DIV_11A4_CO2

description:
Library name: UKBiO11A_CO_2
Column name in Master_Countdata.csv: UKBiO11A_CO_2


title: Xenium SAT, Obese, Pair3, Slide3


title: IMM, Untrained, rep4

city: Thuwal

first: Vincenzo

last: Lagani

address: 4700 King Abdullah University of Science and Technology

country: Saudi Arabia

description: Library name: 10X_21_011

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software version 7.1.0 (https://www.10xgenomics.com/support/software/cell-ranger/latest)
Assembly: Chicken GRCg7b
Supplementary files format and content: R serialized file, containing Seurat object

molecule: nuclear RNA

organism: Gallus gallus

source_name: Intermediate medial mesopallium

extract_protocol:
Frozen IMM from the left hemisphere was homogenized in a Nuclei PURE Lysis Buffer, (NUC-201, Sigma, formulated for solid tissues) supplemented with DTT, Triton X-100, protease inhibitors and 0.5% RNasin Plus RNase inhibitor (Promega).  The procedure was carried out in a 1 ml Dounce homogenizer (Wheaton) using 10 strokes of the loose Dounce pestle followed by 10 strokes of the tight pestle to liberate nuclei. Homogenate was strained through a 30 μm cell strainer (Miltenyi Biotech) and centrifuged at 900 x g for 10 minutes to pellet nuclei. The supernatant was carefully removed. The pellet was resuspended in homogenisation buffer and strained through a 20 μm cell strainer. The filtered suspension was centrifuged at 900 x g for 10 minutes to pellet nuclei. Further separation of nuclei from myelin debris was carried our as described by Zhou et al, (2020). Nuclei pellets were resuspended in 500 uL Nuclei Wash buffer (1% BSA in PBS with 0.2 U/uL RNasin (Promega) and 900 uL 1.8 M Sucrose. This combined 1400 uL mixture was carefully layered on 500 uL 1.8 M sucrose and centrifuged at 13,000 x g for 45 min at 4 oC. The nuclear pellet obtained was strained through a 30 μm cell strainer, resuspended in Foetal bovine serum + DMSO (90% +10%) and stored for further experiments at -70 0C.
Frozen nuclei suspensions were thawed, washed in a small volume of PBS/BSA/RNase inhibitor at 500 g centrifugation and strained again. Libraries were prepared with a Chromium Controller and the Chromium Single Cell 3p RNA library v3 chemistry (10X Genomics, USA), according to the manufacturer's instructions.

value: Intermediate medial mesopallium

value: Brain cells

value: Untrained

value: M


title: IMM, GoodLearner, rep3

institute: King Abdullah University of Science and Technology

description: Library name: 10X_21_010

value: WT

value: GoodLearner

value: F


title: 30DIV_11A4_CO1

description:
Library name: UKBiO11A_CO_1
Column name in Master_Countdata.csv: UKBiO11A_CO_1

value: 30 DIV


title: YTHDC1_FKBP12^F36V, Y12H clone, dTAG, 90min, rep1

value: Cast x 129S

value: mouse embryonic stem cell

value: Endogenous Xist + Bgl


title: 30DIV_37A4_GEO2

description:
Library name: Bi0Ni037A4_GEO_5
Column name in Master_Countdata.csv: Bi0Ni037A4_GEO_5

value: female


title: YTHDC1_FKBP12^F36V, Y12H clone, dTAG, 180min, rep1

value: Endogenous Xist promoter was replaced with TetOn Promoter (129S allele)

value: dTAG-13, Dox


title: Xenium SAT, Obese, Pair2, Slide2


title: YTHDC1_FKBP12^F36V, Y12H clone, dTAG, 0min, rep1


title: Xenium SAT, Obese, Pair1, Slide1


title: IMM, GoodLearner, rep2

description: Library name: 10X_21_006


title: IMM, Untrained, rep3

description: Library name: 10X_21_007


title: 30DIV_37A4_GEO1

description:
Library name: Bi0Ni037A4_GEO_4
Column name in Master_Countdata.csv: Bi0Ni037A4_GEO_4

value: GEO


title: IMM, Untrained, rep2

description: Library name: 10X_21_005


title: YTHDC1_FKBP12^F36V, Y12H clone, Ctrl, 180min, rep1

value: Dox


title: 120DIV_37A4_GEO2

description:
Library name: Bi0Ni037A4_GEO_2
Column name in Master_Countdata.csv: Bi0Ni037A4_GEO_2

value: 120 DIV


title: YTHDC1_FKBP12^F36V, Y12H clone, Ctrl, 90min, rep1


title: dRNA_293T_nopromoter

city: Worcester

first: Athma

last: Pai

state: MA

address: 55 Lake Avenue North

department: RTI

institute: UMass Chan Medical School

description:
Library name: dRNA_293T_nopromoter
Direct RNA- long read sequencing with Oxford Nanopore on polyclonal 293T cells containing synthetic contructs that differ in promoter identity. CAG promoter

data_processing:
Basecalling was performed on-device using the ‘super-accurate basecalling’ model in dorado version 7.4.12.
Fastq files were aligned using minimap2 version 2.26 (flags: -ax splice -uf -k14) to custom human reference genomes combining GRCh38 v108 with the plasmid sequence for each construct
Assembly: hg38, concatenated with plasmid construct sequence
Supplementary files format and content: bams containing mapped reads

source_name: Kidney

growth_protocol: HEK293T cells (ATCC, CRL-3216) were cultured using DMEM (Genesee Scientific, 25-501) plus 10% FBS (Genesee Scientific, 25-514H) and incubated at 37°C with 5% CO2. Cells were passaged at 80-90% confluence, in which spent media was aspirated, and cells were washed with PBS (Sigma-Aldrich, P4417-100TAB) then subsequently dissociated with 0.25% Trypsin-EDTA (Genesee Scientific, 25-510) diluted in PBS. After four minutes, cells were spun down at 400 rcf for 5 minutes, resuspended in media, then transferred to a new flask. Media was replaced with fresh DMEM + 10% FBS every 2-3 days.

extract_protocol:
RNA from polyclonal PiggyBac-integrated cell lines was isolated using the Monarch Total RNA Miniprep Kit with an additional Dnase I treatment step. RNA samples were eluted into 50 μL of nuclease-free water.
Direct RNA sequencing was performed on an Oxford Nanopore GridION device using the Direct Sequencing Kit (SQK-RNA004, date accessed 15 May 2024), MinION RNA flow cell (FLO-MIN00RA), and data pre-processing was performed with MinKNOW (v24.06.10). Libraries were constructed individually with the following modifications to optimize fragment yield and quantity: (1) approximately 1.2 μg of total RNA was used in 8 μL total volumes; and (2) All binding and elution steps were doubled, with a minimum bead binding time of 5 minutes.

value: Kidney


title: IMM, Untrained, rep1

description: Library name: 10X_21_003

value: Intermediate medial mesopallium

value: Brain cells


title: dRNA_293T_hPGK

description:
Library name: dRNA_293T_hPGK
Direct RNA- long read sequencing with Oxford Nanopore on polyclonal 293T cells containing synthetic contructs that differ in promoter identity. hPGK promoter

data_processing:
Basecalling was performed on-device using the ‘super-accurate basecalling’ model in dorado version 7.4.12.
Fastq files were aligned using minimap2 version 2.26 (flags: -ax splice -uf -k14) to custom human reference genomes combining GRCh38 v108 with the plasmid sequence for each construct
Assembly: hg38, concatenated with plasmid construct sequence
Supplementary files format and content: bamb_all_reads_cpm.tsv

value: HEK293T cells containing hPGK promoter


title: 120DIV_37A4_GEO1

description:
Library name: Bi0Ni037A4_GEO_1
Column name in Master_Countdata.csv: Bi0Ni037A4_GEO_1


title: YTHDC1_FKBP12^F36V, Y12H clone, Ctrl, 0min, rep1


title: IMM, GoodLearner, rep1

description: Library name: 10X_20_071

value: WT


title: dRNA_293T_EFS

description:
Library name: dRNA_293T_EFS
Direct RNA- long read sequencing with Oxford Nanopore on polyclonal 293T cells containing synthetic contructs that differ in promoter identity. EFS promoter

value: HEK293T cells containing EFS promoter


title: XX, XO, XY, Del1, Del2, Del3 [scRNA-seq]

city: Rotterdam

first: Beatrice

last: Tan

address: Dr. Molewaterplein 40

department: Developmental Biology

country: Netherlands

institute: Erasmus MC

description:
Library name: XX_XO_XY_del1_2_3
Female (XY: male)
Single cell RNA-seq library of mESCs (Deletion 1, deletion 2, deletion 3, XY) and iPSCs (XO, XX) with either a 129/Cast (deletion 1, deletion 2, deletion 3, XO, XX) or Bl6/Cast (XY) genotype.

data_processing:
Single-cell RNA-seq data was obtained as fastq files from BGI Genomics. The zUMIs (Parekh et al. 2018) pipeline was used to map reads using STAR (Dobin et al. 2013) (v2.7.1a) with the options ‘--clip3pAdapterSeq CTGTCTCTTATACACATCT’. Reads containing barcodes which corresponded to XX, XO, Deletion 1, Deletion 2, or Deletion 3 cells were mapped to an GRC38.p6 mouse reference genome N-masked for SNPs between the 129/SvJ and Cast strains and SNPs between Bl6 and 129. Reads containing barcodes which corresponded to XY cells were mapped to an GRC38.p6 mouse reference genome N-masked for SNPs between the Bl6 and Cast strains. Reads were filtered such that reads containing at least 3 bases with Phred quality score less than 20 were omitted. Allele-resolution counts were generated using a publicly available script ‘get_variant_overlap_CAST.R’ (https://github.com/sandberg-lab/Smart-seq3/) (Hagemann-Jensen et al. 2020) and a custom list of SNPs between 129/SvJ and Cast, with overlapping SNPs between 129/SvJ and Bl6, as well as overlapping SNPs between Cast and Bl6 omitted. Allelic exon UMI counts were used to generate Seurat  (Hao et al. 2021) (v4.2.1) objects, which were then filtered such that cells with less than 10,000 UMIs for either allele were omitted. Read counts were normalized to TPM (transcripts per million).
Assembly: GRCm38
Supplementary files format and content: zUMIs output and allelic post-processing output
Supplementary files format and content: Tab-separated files, loom files, rds files, and text files

source_name: Pluripotent mouse stem cells

growth_protocol: Cells with heterozygous deletions located between Tfe3 and Zic3, Zic3 and Dusp9, as well as between Dusp9 and Nr0b1 were generated and validated previously (Song et al. 2019). XO mouse induced pluripotent stem cells used in single-cell experiments were generated by passaging mouse induced pluripotent stem cells to passage 14 before sorting for single-cell RNA-sequencing. Mouse embryonic fibroblasts (MEFs) were cultured in MEF medium [DMEM (Gibco, 10829-018) supplemented with 10% (v/v) fetal bovine serum (FBS, Gibco, 10500-064), 1% (v/v) penicillin/streptomycin (P/S, Gibco, 15140122), 1% (v/v) Glutamax (Gibco, 35050038), 1% (v/v) non-essential amino acids (NEAA, Gibco, 11140035), and 0.008% (v/v) beta-mercaptoethanol (Gibco, 31350010)]. Mouse embryonic stem cells and mouse induced pluripotent stem cells were cultured in mESC medium [KnockOut DMEM (Gibco, 10829-018) supplemented with 15% FBS (Gibco, 10500-064), 1% (v/v) penicillin/streptomycin (P/S, Gibco, 15140122), 1% (v/v) Glutamax (Gibco, 35050038), 1% (v/v) non-essential amino acids (NEAA, Gibco, 11140035), 0.008% (v/v) beta-mercaptoethanol (Gibco, 31350010), and mouse LIF (1000U/mL, home-made).

extract_protocol:
Cells were dissociated using trypsin digestion and subsequently washed in incubation buffer (1x PBS, 0.5% BSA,  2mM EDTA) and filtered through a Falcon 40um Cell Strainer (Corning, 352340). Cell death exclusion was performed by adding DAPI (Sigma-Aldrich, D9542). Sorting was performed on a BD FACSAria Fusion (BD Biosciences) and performed by expert operators at the VIB FACS core. Cells were sorted into a 384 well plate.
Single-cell RNA-seq libraries were prepared by following a previously published protocol (Hagemann-Jensen et al. 2022), with minor modifications. Library quality was checked using an Agilent Tapestation as well as an Agilent 2100 Bioanalyzer. Library concentration was checked with a Qubit fluorometer (Qubit dsDNA HS Assay).
Single-cell RNA-seq libraries were sequenced in paired-end mode (150bp) by BGI Genomics (Shenzhen, China) on a DNBSEQ-G400 sequencer (MGI Tech).

value: Pluripotent mouse stem cells

value: XX, XO:iPSCs; XY, Del1/2/3:mESCs

tag: strain

value: 129/Cast (XY:Bl6/Cast)

value: XX, XO, XY, Deletion 1 +/-, Deletion 2 +/-, Deletion 3 +/-


title: 30DIV_37A4_CO2

description:
Library name: Bi0Ni037A4_CO_5
Column name in Master_Countdata.csv: Bi0Ni037A4_CO_5

value: CO

value: 30 DIV


title: METTL3_FKBP12^F36V, 12D clone, dTAG, 180min, rep1

value: Cast x 129S

value: mouse embryonic stem cell

value: Endogenous Xist + Bgl

value: Endogenous Xist promoter was replaced with TetOn Promoter (129S allele)


title: 30DIV_37A4_CO1

description:
Library name: Bi0Ni037A4_CO_4
Column name in Master_Countdata.csv: Bi0Ni037A4_CO_4

value: female


title: dRNA_293T_UbC

description:
Library name: dRNA_293T_UbC
Direct RNA- long read sequencing with Oxford Nanopore on polyclonal 293T cells containing synthetic contructs that differ in promoter identity. UbC promoter

value: Kidney

value: HEK293T cells containing UbC promoter


title: dRNA_293T_CMV

description:
Library name: dRNA_293T_CMV
Direct RNA- long read sequencing on polyclonal 293T cells containing synthetic contructs that differ in promoter identity.  CMV promoter

value: HEK293T cells containing CMV promoter


title: METTL3_FKBP12^F36V, 12D clone, dTAG, 90min, rep1

value: dTAG-13, Dox


title: METTL3_FKBP12^F36V, 12D clone, dTAG, 0min, rep1


title: 120DIV_37A4_CO2

description:
Library name: Bi0Ni037A4_CO_2
Column name in Master_Countdata.csv: Bi0Ni037A4_CO_2

value: 120 DIV


title: METTL3_FKBP12^F36V, 12D clone, Ctrl, 180min, rep1

value: Dox


title: dRNA_293T_EF1a

description:
Library name: dRNA_293T_EF1a
Direct RNA- long read sequencing with Oxford Nanopore on polyclonal 293T cells containing synthetic contructs that differ in promoter identity.  EF1a promoter

value: HEK293T cells containing EF1a promoter


title: dRNA_293T_CAG

description:
Library name: dRNA_293T_CAG
Direct RNA- long read sequencing with Oxford Nanopore on polyclonal 293T cells containing synthetic contructs that differ in promoter identity. CAG promoter

value: HEK293T cells containing CAG promoter


title: 30DIV_37A3_GEO2

description:
Library name: Bi0Ni037A_GEO_5
Column name in Master_Countdata.csv: Bi0Ni037A_GEO_5

value: GEO


title: 120DIV_37A4_CO1

description:
Library name: Bi0Ni037A4_CO_1
Column name in Master_Countdata.csv: Bi0Ni037A4_CO_1


title: RNA Nsp2 WT rep2

city: Seoul

first: Sunghan

last: Lee

state: South Korea

address: Building 203 Room 526, 1, Gwanak-ro, Gwanak-gu

country: South Korea

institute: Seoul National University

description: RNA-seq

data_processing:
Sequencing reads were first mapped to the combined human-SARS-CoV-2 genome using STAR with options accommodating non-canonical viral junctions. Only uniquely mapped reads were used for gene-level quantification with featureCounts. Normalized gene counts were calculated using the R/Bioconductor package DESeq2.
Assembly: STAR index were built using concatenated genome of human genome (GRCh38.primary_assembly) and SARS-CoV-2 genome (NC_045512.2).
Supplementary files format and content: Comma-delimited csv files include the DESeq2-normalized counts of RNA-seq samples.

extract_protocol:
RNAs were isolated using Direct-zol RNA miniprep kit (Zymo Research).
The library was constructed following the manufacturer’s instructions using the MGIEasy RNA Directional Library Prep Set (MGI tech).

value: human lung cancer cell line

value: wildtype


title: 30DIV_37A3_GEO1

description:
Library name: Bi0Ni037A_GEO_4
Column name in Master_Countdata.csv: Bi0Ni037A_GEO_4

value: 30 DIV


title: RNA Nsp2 WT rep1

description: RNA-seq


title: METTL3_FKBP12^F36V, 12D clone, Ctrl, 0min, rep1

value: Cast x 129S


title: 120DIV_37A3_GEO2

description:
Library name: Bi0Ni037A_GEO_2
Column name in Master_Countdata.csv: Bi0Ni037A_GEO_2


title: METTL3_FKBP12^F36V, H5 clone, dTAG 26h, Rep2

data_processing:
Total RNA-seq data analysis procedure is similar to ChrRNA-seq regarding the raw fastq reads mapping. PCR duplicates were removed by Picard command line, MarkDuplicates. Differentially expressed genes and transposable elements were called by TEtranscripts. Up and down regulated genes called were further cross compared with m6A annotations from previous studies.
Assembly: mm10
Supplementary files format and content: text file

growth_protocol: ES cells were grown in DMEM media supplemented with 10% fetal calf serum (Merck), 2 mM L-glutamine, 1X non-essential amino acids, 50 µM β-mercaptoethanol, 1X penicillin / streptomycin (all from Life Technologies) and 1000 U/mL LIF (made in-house). Mitomycin-inactivated mouse fibroblasts were used as feeders. All ES cells were grown in feeder-dependent conditions on gelatinised plates at 37°C with 5% CO2.

extract_protocol:
Chromatin RNA was extracted from one confluent T25 plates of mESCs. Briefly, cells were trypsinised and washed in PBS. Cells were lysed on ice in RLB (10 mM Tris pH 7.5, 10 mM KCl, 1.5 mM MgCl2, and 0.1% NP40), and nuclei were purified by centrifugation through a sucrose cushion (24% sucrose in RLB). The nuclei pellet was resuspended in NUN1 (20 mM Tris pH 7.5, 75 mM NaCl, 0.5 mM EDTA, 50% glycerol), then lysed with NUN2 (20 mM Hepes pH 7.9, 300 mM, 7.5 mM MgCl2, 0.2 mM EDTA, 1 M Urea). Samples were incubated for 15 minutes on ice then centrifuged at 2800 g to isolate the insoluble chromatin fraction. The chromatin pellet was resuspended in TRIzol by passing multiple times through a 23 gauge needle. Finally chromatin-associated RNA was purified through standard TRIzol/chloroform extraction followed by isopropanol precipitation. Samples were then treated with Turbo DNAse.
Approximal 200 - 500 ng of RNA was used for library preparation using the Illumina TruSeq stranded total RNA kit. Libraries were quantified by qPCR with KAPA Library Quantification DNA standards (KAPA Biosystems). The libraries were pooled and 2X 81 paired end sequencing was performed using Illumina NextSeq 500/550.

treatment_protocol: either treated with dTAG-13 for 26 hours or not

value: mouse embryonic stem cell

value: Endogenous Xist

value: dTAG-13, NoDox


title: RNA Nsp2 del rep2

description: RNA-seq

value: Nsp2 del


title: 120DIV_37A3_GEO1

description:
Library name: Bi0Ni037A_GEO_1
Column name in Master_Countdata.csv: Bi0Ni037A_GEO_1

value: female


title: METTL3_FKBP12^F36V, H5 clone, Rep2

value: Endogenous Xist promoter was replaced with TetOn Promoter (129S allele)

value: NodTAG, NoDox


title: IMSN + PA + ADSCmedia

city: Kanazawa

first: Alessandro

last: Nasti

state: Ishikawa

address: 13-1 Takaramachi, Medical Building B, b34

department: Graduate School of Medical Sciences

country: Japan

institute: Kanazawa University

description: Gene expression

hyb_protocol: Complementary RNA was hybridized to the Whole Mouse Genome 4×44K Array (Agilent Technologies).

scan_protocol: The Agilent G2505B Microarray Scanner used for the reading. Scanned images were analyzed with the Feature Extraction 12.1.1.1  Software (Agilent Technologies) using default parameters (protocol: GE1_105_Dec08.

data_processing:
BRB-ArrayTools v. 4.6.2 - Beta_1 (February 2021) (http://linus.nci.nih.gov/BRBArrayTools.html), and R v. 3.5.1 (2018-07-02) were used to analyze gene expression.
final quantitative data files: Upreg in IMSN+PA down in IMSN:  Gene list of upregulated genes in IMS/N plus PA condition (downregulated in IMS/N condition) is obtained, and used for MetaCore Enrichment Pathway analysis, respectively, files: Upreg in IMSN+PA down in IMSN_gene list.txt, and, Upreg in IMSN+PA down in IMSN_pathways.xls.
final quantitative data files: UpIMSN+PA down IMSN+PA+ADSCmedia: Gene list of upregulated genes in IMS/N plus PA condition (downregulated in IMS/N plus PA plus ADSCs' media condition) is obtained, and used for MetaCore Enrichment Pathway analysis, respectively, files: UpIMSN+PA down IMSN+PA+ADSCmedia_genelist.txt, and, UpIMSN+PA down IMSN+PA+ADSCmedia_pathways.xls.

source_name: IMSN + PA + ADSCmedia

label_protocol: Total RNAs were purified, amplified and labeled with Cy3 with the Quick Amp Labeling Kit (Agilent Technologies, Santa Clara, CA, USA).

extract_protocol: According to the manufacturer's protocol, total RNA was extracted from the IMS/N using ISOSPIN Cell & Tissue RNA (Nippon Gene, Tokyo, Japan).

treatment_protocol: IMS/N cells were cultured  with or without PA, and with or without media derived from the cell culture of ADSCs. Then total RNA was isolated from IMS/N cells.

tag: adsc

value: Mus musculus strain C57BL/6J

tag: imsn

value: Immortalized mouse stellate cells from normal mouse (IMS/N) were obtained (FEBS Letters 479 (2000) 146-148) as described:Hepatic stellate cells were isolated from the livers of normal 129/Sv mice, and immortalized by infection of SV40 virus.

value: Subcutaneous adipose tissue was harvested from the inguinal region of C57BL/6J mice (8-10 weeks old, male), followed by homogenization and digestion with 0.1% Liberase (Roche) to obtain adipose tissue-derived stem cells (ADSC), and cultured (Hepatology 58.3 (2013):1133-1142).


title: 30DIV_37A3_CO2

description:
Library name: Bi0Ni037A_CO_5
Column name in Master_Countdata.csv: Bi0Ni037A_CO_5

value: CO


title: METTL3_FKBP12^F36V, C3 clone, dTAG 26h, Rep2

tag: strain background

tag: cell type


title: METTL3_FKBP12^F36V, C3 clone, Rep2

tag: xist type

tag: cell line


title: 30DIV_37A3_CO1

description:
Library name: Bi0Ni037A_CO_4
Column name in Master_Countdata.csv: Bi0Ni037A_CO_4

tag: genotype


title: METTL3_FKBP12^F36V, 12D clone, Ctrl, 90min, rep1

data_processing:
Estimation of RNA half-life was performed using GRAND-SLAM. Briefly, the paired-end sequencing reads were first aligned to rRNA, and then the unmapped reads were mapped to mouse genome mm10 by STAR (v2.5.2b) with the key parameters (--twopassMode Basic --outSAMstrandField intronMotif --outSAMattributes All --outFilterMultimapNmax 1 --outFilterMismatchNoverReadLmax 0.06 --alignEndsType EndToEnd). Given that T to C conversion is the signature of SLAMseq, the T to C conversion rate was calculated as 4sU incorporation and the average of all the rest of the conversions was calculated as background due to errors from sequencing or library preparation. The T to C conversion rate and background rate were calculated accordingly for each sample. The RNA decay was assumed to follow an exponential model, so the corresponding background corrected T2C rates were fitted to the exponential model to estimate the Xist RNA’s half-life. Regarding X-linked gene silencing and Xist expression level, same procedure of allelic analysis was performed as ChrRNA-seq data.
Assembly: mm10
Supplementary files format and content: tsv file

extract_protocol:
When reaching 60 to 70% confluency, cells were either untreated or dTAG-13 treated for 2 hours, followed by additional 1 μg/ml doxycycline induction for 20 hours. Then, transcribed RNA was labelled with 4sU by incubation with medium containing 500 μM 4sU (Lexogen) and 1 μg/ml doxycycline for another 4 hours. Next, 4sU was withdrawn for all samples by medium washout. Different samples were washed with medium containing 1 μg/ml doxycycline and 50 mM uridine (in excess, Lexogen) for 1.5 and 3 hours. Cells are quickly washed with PBS once and directly lysed with Trizol/chloroform for total RNA isolation.
Equal amount of RNA samples (5 μg) was treated with Iodoacetamide to modify the 4-thiol group of S4U-containing nucleotides via the addition of a carboxyamidomethyl group by the SLAMseq Kinetics Kit. The RNA was recovered using RNAClean XP beads (Beckman Coulter), followed by resuspension in nuclease free water. Approximately 500 ng RNA of each sample was taken forward for library preparation using the Illumina TruSeq stranded total RNA kit. Quantification of the libraries was conducted by qPCR using KAPA Library Quantification DNA standards. Finally, the libraries were pooled and paired-end sequencing was performed using Illumina NextSeq500.

value: Endogenous Xist + Bgl

tag: treatment

value: Dox


title: embryo E8.0 rep2

city: nanjing

first: yi

last: yang

address: sipailou 2

institute: southeast university

description: Library name: Sample 6

data_processing:
Sequencing reads were processed with the SAW workflow (https://github.com/BGIResearch/SAW), which encompasses several critical steps: mRNA spatial location restoration, data filtering, mRNA genome alignment, gene region annotation, MID correction, expression matrix generation, and tissue region extraction. These Clean Reads were mapped to the NCBI-referenced genome using STAR (v2.5.3).
Assembly: GRCm38
Supplementary files format and content: h5ad; gene expression matrix where the rows are genes and columns are single cells

source_name: Whole embryo

extract_protocol:
Stereo-seq
Briefly, following cryosection, tissue sections are mounted on Stereo-seq chips, incubated at 37°C, and fixed with 20°C methanol. The chips underwent ssDNA staining and imaging with a Nikon Ti-7 Eclipse microscope. Tissue permeabilization was performed with 0.1% pepsin in HCl buffer, followed by washing with SSC buffer containing RNAase Inhibitor. Captured mRNA was reverse transcribed at 42°C. Post in situ reverse transcription, the chips were treated with tissue removal buffer and then washed. cDNA was released from the chips using a cDNA Release Mix at 55°C, followed by fragmentation, amplification, and purification to produce a DNBs library.

value: Whole embryo

value: WT


title: embryo E8.0 rep1

description: Library name: Sample 5


title: IMS/N + IL17A

description: Gene expression

data_processing:
BRB-ArrayTools v. 4.6.2 - Beta_1 (February 2021) (http://linus.nci.nih.gov/BRBArrayTools.html), and R v. 3.5.1 (2018-07-02) were used to analyze gene expression.
UpregIMSN+IL17A_downIMSN: Gene list of upregulated genes in IMS/N plus IL17A condition (downregulated in IMS/N condition) is obtained, and used for MetaCore Enrichment Pathway analysis, respectively, files: UpregIMSN+IL17A_downIMSN_gene list.txt, and UpregIMSN+IL17A_downIMSN_pathways.xls.
UpregIMSN+IL17A_downIMSN+IL17A+ADSCmedia: Gene list of upregulated genes in IMS/N plus IL17A condition (downregulated in IMS/N plus IL17A plus ADSCs' media condition) is obtained, and used for MetaCore Enrichment Pathway analysis, respectively, files: UpregIMSN+IL17A_downIMSN+IL17A+ADSCmedia_gene list.txt, and UpregIMSN+IL17A_downIMSN+IL17A+ADSCmedia_pathways.xls.

source_name: IMS/N + IL17A

treatment_protocol: IMS/N cells were cultured  with or without IL17A, and with or without media derived from the cell culture of ADSCs. Then total RNA was isolated from IMS/N cells.

value: strain 129/Sv

value: recombinant murine

value: Recombinant Murine IL-17A; Peprotech, Catalog# 210-17.


title: METTL3_FKBP12^F36V, H5 clone, dTAG 26h, Rep1

value: Cast x 129S

value: mouse embryonic stem cell

value: Endogenous Xist


title: IMSN + PA

description: Gene expression

source_name: IMSN + PA


title: IMSN

description: Gene expression

source_name: IMSN


title: embryo E7.75 rep2

description: Library name: Sample 4


title: 120DIV_37A3_CO1

description:
Library name: Bi0Ni037A_CO_1
Column name in Master_Countdata.csv: Bi0Ni037A_CO_1

value: female

value: 120 DIV


title: METTL3_FKBP12^F36V, H5 clone, Rep1

source_name: Endogenous Xist promoter was replaced with TetOn Promoter (129S allele)

value: NodTAG, NoDox


title: IMSN + ADSCmedia

description: Gene expression

source_name: IMSN + ADSCmedia

value: Mus musculus strain C57BL/6J


title: embryo E7.75 rep1

description: Library name: Sample 3


title: RNA Nsp2 del rep1

description: RNA-seq

value: human lung cancer cell line

value: Nsp2 del


title: IMS/N + IL17A + ADSCmedia

description: Gene expression

source_name: IMS/N + IL17A + ADSCmedia

value: Immortalized mouse stellate cells from normal mouse (IMS/N) were obtained (FEBS Letters 479 (2000) 146-148) as described:Hepatic stellate cells were isolated from the livers of normal 129/Sv mice, and immortalized by infection of SV40 virus.

value: Subcutaneous adipose tissue was harvested from the inguinal region of C57BL/6J mice (8-10 weeks old, male), followed by homogenization and digestion with 0.1% Liberase (Roche) to obtain adipose tissue-derived stem cells (ADSC), and cultured (Hepatology 58.3 (2013):1133-1142).


title: METTL3_FKBP12^F36V, C3 clone, dTAG 26h, Rep1

value: Endogenous Xist promoter was replaced with TetOn Promoter (129S allele)

value: dTAG-13, NoDox


title: Small RNAs in PjELNs rep1

city: Yayoi, Bunkyo-ku

first: Tomoatsu

last: Hayashi

state: Tokyo

institute: The University of Tokyo

data_processing:
Adapter sequence and poly-A in the raw reads were trimmed with Trim Galore! (v. 0.6.7), retaining only reads of at least 20 bp.
Pre-processed reads were aligned to existing miRNA sequences (Release 22, 271 organisms, 38,589 sequences) from miRbase (https://www.mirbase.org/) using bowtie with the -n 2 option.
miRNA count data were generated from the alignment results using SAMtools.
Assembly: miRbase (Relaease 22)
Supplementary files format and content: tab-delimited text files include raw read counts per miRNA

organism: Peucedanum japonicum

source_name: Leaf

growth_protocol: Peucedanum japonicum were purchased from a local grocery store. After washing with water, they were crushed using a household juicer. The crushed material was then subjected to centrifugation at 3,000 x g for 20 minutes once, followed by two rounds of centrifugation at 10,000 x g for 40 minutes to remove solid debris. Subsequently, the fraction containing EVs was pelleted by ultracentrifugation at 150,000 x g for 90 minutes. The obtained pellet was resuspended in PBS and layered onto a sucrose density gradient consisting of 60%, 45%, 30%, and 8% sucrose solutions. The samples were then ultracentrifuged at 150,000 x g for 90 minutes, and fractions were collected. The fraction at the 30-45% sucrose density boundary was labeled as Band2, while the fraction at the 8-30% boundary was labeled as Band1. Each fraction was pelleted again by ultracentrifugation at 150,000 x g for 90 minutes, resuspended in PBS, and particle size and concentration were measured using Nanoparticle Tracking Analysis (NTA). The obtained EVs were stored at 4°C or -80°C.

extract_protocol:
Small RNAs in PjELNs were extracted using RNA Clean & Concentrator (ZYMO RESEARCH) and the quality and yield of small RNAs were measured with an Agilent 2200 TapeStation.
Library construction and sequencing were performed using the NEBNext Multiplex Small RNA Library Prep Set for Illumina® (Set 1) and the Illumina Novaseq 6000, respectively.

value: Leaf

value: Exosome-like nanovesicles


title: embryo E7.5 rep2

description: Library name: Sample 2

value: Whole embryo

value: WT


title: IMS/N

description: Gene expression

source_name: IMS/N

value: strain 129/Sv


title: METTL3_FKBP12^F36V, C3 clone, Rep1

value: Cast x 129S

value: mouse embryonic stem cell


title: 120DIV_37A3_CO2

description:
Library name: Bi0Ni037A_CO_2
Column name in Master_Countdata.csv: Bi0Ni037A_CO_2

value: female

value: CO


title: embryo E7.5 rep1

description: Library name: Sample 1


title: 1d_MI_spleen_LYVE1low_rep3

status: Public on Jun 18 2025

city: Birmingham

first: Min

last: Gao

state: AL

address: 1900 University Blvd, THT Building Suite #130G

institute: University of Alabama at Birmingham

data_processing:
Standard Illumina adaptors were used to trim reads with TrimGalore (version 0.4.5). The ENCODE options for standard long RNA-seq were utilized for mapping using STAR (version 2.5.3)
Read counts were counted using htseq-count of HTSeq package (version 0.7.2)
Assembly: mm10
Supplementary files format and content: read counts for each sample
Supplementary files format and content: tab-delimited text files include normalized read counts for all samples

source_name: Spleen

growth_protocol: Naive and 1 d post myocardial infarcted tissue.

extract_protocol:
250 cells were collected in lysis buffer at room temperature, pelleted and processed for cDNA library preparation according to the kit protocol.
RNA libraries for RNA-seq were prepared using SMART-Seq v4 Ultra Low Input RNA Kit (Takara Bio USA Inc.) following manufacturer's protocols.

treatment_protocol: Live mononuclear cells (blood, heart and spleen) isolated from naïve and 1 d post MI heart were stained with SYTOX (live/dead staining), and CD45, CD64, Tim4, CD169 and LYVE1 antibodies.

value: Spleen

value: 1 d MI


title: 1d_MI_spleen_LYVE1low_rep2


title: 1d_MI_spleen_LYVE1high_rep3


title: 1d_MI_spleen_LYVE1low_rep1


title: 1d_MI_spleen_LYVE1high_rep1


title: 1d_MI_spleen_LYVE1high_rep2


title: Naive_spleen_LYVE1low_rep3

value: Naive


title: Small RNAs in PjELNs rep2


title: Naive_spleen_LYVE1high_rep3


title: Naive_spleen_LYVE1high_rep2


title: Naive_spleen_LYVE1high_rep1


title: 1d_MI_heart_LYVE1low_rep3

source_name: Heart

value: Heart


title: 1d_MI_heart_LYVE1low_rep2


title: Naive_spleen_LYVE1low_rep2


title: 1d_MI_heart_LYVE1low_rep1


title: 1d_MI_heart_LYVE1high_rep1


title: Naive_heart_LYVE1low_rep2


title: Naive_heart_LYVE1low_rep1


title: Naive_heart_LYVE1high_rep3


title: Naive_heart_LYVE1high_rep2


title: Naive_heart_LYVE1high_rep1


title: plasmid DNA sequencing, UTRome, plate C

city: Ithaca

first: Andrew

middle: William

last: Grimson

state: NY

address: 526 Campus Rd

department: Molecular Biology and Genetics

institute: Cornell University

library_source: other

data_processing:
Adapters were trimmed from raw reads with cutadapt -q 20 -j 25 -a CTGTCTCTTATACACATCTCCGAGCCCACGAGAC -A CTGTCTCTTATACACATCTGACGCTGCCGACGA.
Reads were mapped to a custom genome consisting of the expected 3′UTR sequences with 250 nt flanking plasmid sequence using bowtie2 (with parameters -X 1000).
A custom python script was used to identify and count reads containing the barcode region
The barcode 3′UTR linkages were further filtered in R (e.g. to remove lowly detected barcode sequences likely due to PCR or sequencing errors).
Assembly: Custom plasmid genome
Supplementary files format and content: A file containing the final filtered barcode-3′UTR linkages is provided (barcode_3UTR_linkages.tsv).
Library strategy: plasmid-seq

molecule: other

organism: Escherichia coli

source_name: plasmids grown in E. coli

growth_protocol: Plasmids were amplified in E. coli grown in luria broth at 37°C.

extract_protocol:
Plasmid DNA was extracted from E. coli with the Promega PureYield Plasmid Midiprep Kit.
To determine the appropriate ratio of DNA to Tn5 transposase, 50 ng of each plasmid pool was combined with various dilutions of in house purified Tn5 transposase in a 25 µl reaction (reaction conditions 10 mM Tris pH 7.5, 5mM MgCl2, 10% DMF) and incubated at 55°C for 8 minutes. The tagmentation reactions were stopped with 2.5 µl 1% SDS. The optimization reactions were PCR amplified and ran on a 6% PAGE gel. The reaction that yielded the most library in the size range 400 to 1000 bp was selected for full scale amplification. Five µl of the tagmentation reaction was PCR amplified in a 50 µl reaction with Phusion polymerase for 7 cycles, ethanol precipitated and size selected (400 to 1000 bp) on a 6% native PAGE gel.

value: plasmids grown in E. coli


title: plasmid DNA sequencing, UTRome, plate B


title: 207687890022_R02C01

type: genomic

city: Tampa

first: Jan

last: Dahrendorff

state: Florida

address: 3720 Spectrum Blvd

department: Department of Global, Environmental, and Genomic Health Science

institute: University of South Florida

description: DNA methylation profiling of peripheral blood collected prior to transcranial magnetic stimulation treatment for major depressive disorder, assayed using the Illumina Infinium MethylationEPIC BeadChip (850K).

hyb_protocol: Bisulphite converted DNA was amplified, fragmented and hybridizied to human Infinium MethylationEPIC BeadChip (Illumina) using standard Illumina protocol

scan_protocol: Arrays were imaged using Illumina iScan System and standard Illumina scanner settings

data_processing:
Raw DNAm data were preprocessed and quality controlled in in R version 4.0.5 (https://cran.r-project.org/) using standardized consortium-developed pipelines
Beta values (proportion methylated) for individual samples

label: biotin

source_name: Periphereral Blood

label_protocol: Standard Illumina Protocol

extract_protocol: DNA was extracted from ten 3mm blood punches derived from the filter paper, per sample, using the QIAamp DNA Micro Kit

treatment_protocol: TMS treatments at both participant recruitment sites were delivered with the NeuroStar® TMS system (Malvern, PA, USA) operated by site personnel. Briefly, the treatment is administered by placing the participants in a recliner, and ear plugs are inserted to minimize possible hearing impairment from the repetitive machine noise. The TMS treatment parameters are captured automatically including information on the session date, treatment location, motor thresholds (MT), number of administered pulses per treatment, pulse duration, intertrain interval, and number of treatment sessions. Resting MT threshold is determined at the first treatment session via single pulses stimulation of the participant’s motor cortex area corresponding to the abductor pollicis brevis. The Beam F3 method and 5 cm rule was used for coil placement over the dorsolateral prefrontal cortex (DLPFC) target. Patients treated with high frequency left DLPFC receive 10 Hz stimulation at 120% of the estimated motor threshold as 4 seconds of stimulation with 11 second intertrain interval for a total of 3000 pulses (N = 12; 26.1%) and patients treated with low frequency right DLPFC stimulation (N = 5; 10.9 %)  receive 1 Hz stimulation at 110% of the estimated motor threshold as 1 second of stimulation with no interval for a total of 3000 pulses. Patients receiving both high frequency left, and low frequency right were characterized as sequential bilateral (N = 12; 26.1%). The remaining participants received a “combination” of protocols i.e. switching from left or right DLPFC to sequential bilateral (N = 17; 37.0%). Standard of care treatment consists of 36 sessions of left DLPFC rTMS at 10 Hz. Protocols were characterized accordingly when 80% or more treatment sessions met the criteria for a specific protocol.

value: Periphereral Blood

value: Transcranial Magnetic Stimulation (TMS)

value: F

tag: white

tag: african american

tag: hispanic or latino

tag: more than one race

value: Left


title: 206530730146_R08C01

tag: tissue

tag: Sex

tag: age

value: Right


title: 206530730146_R07C01

value: M


title: 207262930074_R05C01


title: Naive_spleen_LYVE1low_rep1

value: WT


title: 1d_MI_heart_LYVE1high_rep3


title: 207687890006_R06C01


title: 1d_MI_heart_LYVE1high_rep2


title: 206530730130_R07C01

value: Sequential Bilateral


title: 206530730130_R06C01

value: Combination


title: 206530730130_R08C01


title: Naive_heart_LYVE1low_rep3


title: 206530730146_R01C01


title: 206530730130_R01C01


title: plasmid DNA sequencing, UTRome, plate A


title: IMS/N + ADSCmedia

description: Gene expression

source_name: IMS/N + ADSCmedia

value: strain 129/Sv

value: Mus musculus strain C57BL/6J

value: Immortalized mouse stellate cells from normal mouse (IMS/N) were obtained (FEBS Letters 479 (2000) 146-148) as described:Hepatic stellate cells were isolated from the livers of normal 129/Sv mice, and immortalized by infection of SV40 virus.

value: Subcutaneous adipose tissue was harvested from the inguinal region of C57BL/6J mice (8-10 weeks old, male), followed by homogenization and digestion with 0.1% Liberase (Roche) to obtain adipose tissue-derived stem cells (ADSC), and cultured (Hepatology 58.3 (2013):1133-1142).


title: 206530730117_R06C01


title: 206530730117_R02C01


title: Hepatocytes of mice fed with atherogenic high-fat diet (AT-HFD) for 12w, 3

description: Gene expression

scan_protocol: The Agilent G2505B Microarray Scanner used for the reading. Scanned images were analyzed with the Feature Extraction 10.5.1.1 Software (Agilent Technologies) using default parameters (protocol: GE1_105_Dec08.

data_processing:
BRB-ArrayTools v. 4.6.0 – Stable (October 2018) (http://linus.nci.nih.gov/BRBArrayTools.html), and R v. 3.5.1 (2018-07-02) were used to analyze gene expression.
Normalized Log-Transformed Gene Expressions for Genes related to Perk mediated UPR response (reference gene set GO:0036499; GO_PERK_MEDIATED_UNFOLDED_PROTEIN_RESPONSE; file: ExpressionTable Perk mediated UPR response.xlsx), to Atf6 mediated UPR response (reference gene set GO:0036500; GO_ATF6_MEDIATED_UNFOLDED_PROTEIN_RESPONSE; file: ExpressionTable Atf6 mediated UPR response.xlsx), and to Ire1 mediated UPR response (reference gene set GO:0036498; GO_IRE1_MEDIATED_UNFOLDED_PROTEIN_RESPONSE; file: ExpressionTable Ire1 mediated UPR response.xlsx) were obtained.

source_name: MASH mice were established by feeding an atherogenic high-fat diet for 12 weeks, then hepatocytes isolated from liver tissues were obtained for the analysis, 3

extract_protocol: According to the manufacturer's protocol, total RNA was extracted from the hepatocytes using ISOSPIN Cell & Tissue RNA (Nippon Gene, Tokyo, Japan).

treatment_protocol: Liver tissue were collected from mice after the specific feeding, then hepatocytes isolated.

value: Hepatocytes

tag: gender

value: Female


title: Hepatocytes of mice fed with high-fat diet (HFD-60) for 12w, 1

description: Gene expression

source_name: Simple steatosis mice were established by feeding an HFD-60 for 12 weeks, then hepatocytes isolated from liver tissues were obtained for the analysis, 1


title: 206530730117_R01C01

value: Sequential bilateral


title: 206530730072_R08C01


title: 206530730072_R06C01


title: 206530730072_R05C01


title: Hepatocytes of mice fed with atherogenic high-fat diet (AT-HFD) for 12w, 1

description: Gene expression

source_name: MASH mice were established by feeding an atherogenic high-fat diet for 12 weeks, then hepatocytes isolated from liver tissues were obtained for the analysis, 1


title: Hepatocytes of mice fed with high-fat diet (HFD-60) for 12w, 3

description: Gene expression

source_name: Simple steatosis mice were established by feeding an HFD-60 for 12 weeks, then hepatocytes isolated from liver tissues were obtained for the analysis, 3


title: 206530730072_R04C01


title: 206530730130_R05C01


title: 206530730072_R03C01


title: 206530730060_R08C01


title: Hepatocytes of mice fed with atherogenic high-fat diet (AT-HFD) for 12w, 2

description: Gene expression

source_name: MASH mice were established by feeding an atherogenic high-fat diet for 12 weeks, then hepatocytes isolated from liver tissues were obtained for the analysis, 2


title: 206530730072_R01C01


title: 206530730060_R06C01


title: 206530730060_R07C01


title: 206530730130_R04C01


title: 206530730060_R03C01


title: 206530730060_R04C01


title: 206530730059_R08C01


title: 206530730117_R04C01


title: 206530730059_R07C01


title: 206530730060_R01C01


title: 206530730059_R04C01


title: 206530730072_R02C01


title: 206530730059_R03C01


title: 206530730059_R01C01


title: Hepatocytes of mice fed with high-fat diet (HFD-60) for 12w, 2

description: Gene expression

source_name: Simple steatosis mice were established by feeding an HFD-60 for 12 weeks, then hepatocytes isolated from liver tissues were obtained for the analysis, 2


title: 206530730060_R05C01


title: 205549610170_R06C01


title: 205549610170_R01C01


title: 205549610170_R05C01


title: 205549610135_R08C01


title: 205549610170_R04C01


title: 205549610135_R07C01


title: 205549610135_R03C01


title: 205549610133_R06C01


title: 205549610133_R05C01


title: 205549610133_R04C01


title: CN_124

city: Berlin

first: Leonille

last: Schweizer

address: Charitépl. 1

country: Germany

institute: Charité - Universitätsmedizin

hyb_protocol: Methylation analysis was performed with the Illumina Infinium Methylation EPIC BeadChip (n = 129 tumor samples), Illumina Infinium Methylation EPICv2 BeadChip (n = 1) or the Illumina Infinium Human Methylation 450k array (n = 14)

scan_protocol: not applicable

data_processing:
Data was analyzed using the R minfi package v1.30.0 and NOOB preprocessing [Fortin, J.P., T.J. Triche, Jr., and K.D. Hansen, Preprocessing, normalization and integration of the Illumina HumanMethylationEPIC array with minfi. Bioinformatics, 2017. 33(4): p. 558-560]. Probes with p-values ≥ 0.01 in 90% of the samples, probes located on sex chromosomes, and cross-reactive probes [Chen, Y.A., et al., Discovery of cross-reactive probes and polymorphic CpGs in the Illumina Infinium HumanMethylation450 microarray. Epigenetics, 2013. 8(2): p. 203-9.] were removed before beta-value calculation. Furthermore, probes with poor correlation between both array types and absolute differences ≥ 0.1 in beta-values [Fernandez-Jimenez, N., et al., Comparison of Illumina 450K and EPIC arrays in placental DNA methylation. Epigenetics, 2019. 14(12): p. 1177-1182.] were discarded. The filtering resulted in 339,381 sites for the n = 111 primary tumors and 339,394 sites for the n = 133 primary and recurrent tumors.
Processed value definition:  beta values for the n = 133 primary and recurrent central neurocytoma samples.

label: Cy3, Cy5

source_name: central neurocytoma (FFPE)

label_protocol: not applicable

growth_protocol: not applicable

extract_protocol: DNA was isolated from FFPE material using the Maxwell® RSC FFPE Plus DNA Kit (Promega).

treatment_protocol: not applicable

value: central neurocytoma (FFPE)

tag: diagnosis

tag: case


title: CN_125


title: CN_121


title: CN_122


title: CN_116


title: CN_119


title: 206530730058_R01C01

value: Periphereral Blood


title: CN_114


title: CN_93


title: CN_94


title: CN_120


title: CN_112_recurrence


title: CN_118


title: CN_92_recurrence


title: CN_92


title: CN_95


title: CN_90


title: CN_96


title: CN_91


title: CN_88


title: CN_111


title: CN_87


title: CN_86


title: CN_89


title: CN_123


title: CN_84


title: CN_117


title: CN_82


title: CN_83


title: CN_81


title: CN_80


title: CN_79


title: CN_77


title: CN_76


title: CN_76_recurrence


title: CN_113


title: CN_72


title: CN_74


title: CN_75


title: CN_71


title: CN_67


title: CN_69


title: CN_70_recurrence


title: CN_68


title: CN_64_recurrence


title: CN_63


title: CN_66


title: CN_60


title: CN_62


title: CN_61


title: CN_85


title: CN_59


title: CN_57_recurrence_1


title: CN_56


title: CN_78


title: CN_55


title: CN_54


title: CN_53


title: CN_73_recurrence


title: CN_51


title: CN_65


title: CN_52


title: CN_50_recurrence


title: CN_46


title: CN_48_recurrence


title: CN_47


title: CN_43_recurrence


title: CN_40


title: CN_44_recurrence


title: CN_58


title: CN_42


title: CN_41


title: CN_38


title: CN_35_recurrence


title: CN_36


title: CN_34_recurrence_2


title: CN_39_recurrence


title: CN_54_recurrence


title: CN_34_recurrence_1


title: CN_32


title: CN_33


title: CN_30_recurrence_2


title: CN_34


title: CN_31


title: CN_30_recurrence_1


title: CN_30


title: CN_49_recurrence


title: CN_45


title: CN_29


title: CN_27


title: CN_28


title: CN_26


title: CN_24


title: CN_37


title: CN_25_recurrence


title: CN_23


title: CN_22


title: CN_19


title: CN_21


title: CN_20


title: CN_17


title: CN_18


title: CN_11


title: CN_16


title: CN_13


title: CN_10


title: CN_14


title: CN_7


title: CN_9


title: CN_8


title: CN_6


title: CN_5


title: CN_4


title: CN_6_recurrence


title: CN_3


title: CN_1


title: CN_2


title: AN_194

type: other

first: Saya

last: Dennis

address: 680 N. Lake Shore Dr.

department: Preventive Medicine

hyb_protocol: Standard Illumina Protocol

scan_protocol: Standard Illumina Protocol

data_processing: SeSAMe R software (version 1.20.0)

source_name: AN tissue from cancer patient CUB-194 with grade III ER+ PgR+ HER2- ---------

extract_protocol: Tissue was homogenized and extracted using QIAGEN’s AllPrep DNA/RNA Kit. DNA quality was assessed using a NanoDrop 1000 Spectrophotometer.

value: AN


title: AN_157

source_name: AN tissue from cancer patient CUB-157 with grade II ER- PgR- HER2- IDC


title: AN_058

source_name: AN tissue from cancer patient CUB-058 with grade II ER+ PgR+ HER2- IDC


title: AN_034

source_name: AN tissue from cancer patient CUB-034 with grade II ER+ PgR+ HER2- IDC


title: CN_12


title: AN_037

source_name: AN tissue from cancer patient CUB-037 with grade nan ER+ PgR+ HER2- ILC


title: AN_192

source_name: AN tissue from cancer patient CUB-192 with grade II ER+ PgR+ HER2- IDC


title: CN_15


title: AN_316

source_name: AN tissue from cancer patient CUB-316 with grade III ER- PgR- HER2- IDC


title: AN_043

source_name: AN tissue from cancer patient CUB-043 with grade III ER- PgR- HER2- IDC


title: AN_213

source_name: AN tissue from cancer patient CUB-213 with grade III ER+ PgR- HER2- IDC


title: AN_181

source_name: AN tissue from cancer patient CUB-181 with grade III ER- PgR- HER2+ IDC


title: AN_014

source_name: AN tissue from cancer patient CUB-014 with grade III ER- PgR- HER2- IDC


title: AN_080

source_name: AN tissue from cancer patient CUB-080 with grade III ER- PgR- HER2- IDC


title: AN_291

source_name: AN tissue from cancer patient CUB-291 with grade II ER+ PgR+ HER2- IDC


title: AN_167

source_name: AN tissue from cancer patient CUB-167 with grade III ER+ PgR+ HER2- IDC


title: AN_215

source_name: AN tissue from cancer patient CUB-215 with grade III ER+ PgR+ HER2- IDC


title: AN_134

source_name: AN tissue from cancer patient CUB-134 with grade nan ER+ PgR+ HER2- ILC


title: AN_303

source_name: AN tissue from cancer patient CUB-303 with grade III ER- PgR- HER2- IDC


title: AN_182

source_name: AN tissue from cancer patient CUB-182 with grade nan ER+ PgR+ HER2- ILC


title: AN_019

source_name: AN tissue from cancer patient CUB-019 with grade I ER- PgR- HER2+ IDC


title: AN_186

source_name: AN tissue from cancer patient CUB-186 with grade nan ER+ PgR+ HER2- ILC


title: AN_084

source_name: AN tissue from cancer patient CUB-084 with grade nan ER+ PgR+ HER2nan DCIS


title: AN_141

source_name: AN tissue from cancer patient CUB-141 with grade II ER- PgR- HER2- IDC


title: AN_204

source_name: AN tissue from cancer patient CUB-204 with grade nan ER+ PgR+ HER2- ILC


title: AN_290

source_name: AN tissue from cancer patient CUB-290 with grade III ER- PgR- HER2+ IDC


title: AN_130

source_name: AN tissue from cancer patient CUB-130 with grade II ER+ PgR+ HER2- IDC


title: AN_176

source_name: AN tissue from cancer patient CUB-176 with grade III ER- PgR- HER2- --------


title: AN_051

source_name: AN tissue from cancer patient CUB-051 with grade III ER- PgR- HER2- IDC


title: AN_039

source_name: AN tissue from cancer patient CUB-039 with grade III ER- PgR- HER2- IDC


title: AN_068

source_name: AN tissue from cancer patient CUB-068 with grade I ER+ PgR+ HER2- IDC


title: AN_289

source_name: AN tissue from cancer patient CUB-289 with grade III ER- PgR- HER2- IDC


title: AN_318

source_name: AN tissue from cancer patient CUB-318 with grade III ER+ PgR+ HER2- IDC


title: AN_304

source_name: AN tissue from cancer patient CUB-304 with grade III ER- PgR- HER2+ IDC


title: AN_086

source_name: AN tissue from cancer patient CUB-086 with grade III ER+ PgR+ HER2- IDC


title: AN_053

source_name: AN tissue from cancer patient CUB-053 with grade III ER+ PgR+ HER2+ IDC


title: AN_322

source_name: AN tissue from cancer patient CUB-322 with grade III ER- PgR- HER2- IDC


title: AN_056

source_name: AN tissue from cancer patient CUB-056 with grade nan ER- PgR- HER2nan DCIS


title: AN_107

source_name: AN tissue from cancer patient CUB-107 with grade nan ER+ PgR+ HER2- ILC


title: AN_308

source_name: AN tissue from cancer patient CUB-308 with grade II ER- PgR- HER2+ IDC


title: AN_135

source_name: AN tissue from cancer patient CUB-135 with grade III ER- PgR- HER2- IDC


title: AN_315

source_name: AN tissue from cancer patient CUB-315 with grade nan ER- PgR- HER2+ DCIS


title: AN_283

source_name: AN tissue from cancer patient CUB-283 with grade II ER+ PgR+ HER2- IDC


title: AN_189

source_name: AN tissue from cancer patient CUB-189 with grade nan ER+ PgR+ HER2- ILC


title: AN_142

source_name: AN tissue from cancer patient CUB-142 with grade II ER+ PgR+ HER2- IDC


title: AN_023

source_name: AN tissue from cancer patient CUB-023 with grade nan ER+ PgR+ HER2- ILC


title: AN_035

source_name: AN tissue from cancer patient CUB-035 with grade III ER- PgR- HER2- IDC


title: AN_226

source_name: AN tissue from cancer patient CUB-226 with grade I ER+ PgR¬± HER2- IDC


title: AN_314

source_name: AN tissue from cancer patient CUB-314 with grade II ER+ PgR- HER2- IDC


title: AN_138

source_name: AN tissue from cancer patient CUB-138 with grade II ER+ PgR¬± HER2- IDC


title: AN_183

source_name: AN tissue from cancer patient CUB-183 with grade nan ER+ PgR+ HER2- ILC


title: AN_128

source_name: AN tissue from cancer patient CUB-128 with grade nan ER+ PgR+ HER2- ILC


title: AN_298

source_name: AN tissue from cancer patient CUB-298 with grade III ER- PgR- HER2+ IDC


title: AN_085

source_name: AN tissue from cancer patient CUB-085 with grade III ER- PgR- HER2- IDC


title: AN_195

source_name: AN tissue from cancer patient CUB-195 with grade III ER- PgR- HER2- IDC


title: AN_158

source_name: AN tissue from cancer patient CUB-158 with grade III ER- PgR- HER2- IDC


title: AN_265

source_name: AN tissue from cancer patient CUB-265 with grade I ER+ PgR+ HER2- IDC


title: AN_114

source_name: AN tissue from cancer patient CUB-114 with grade nan ER+ PgR+ HER2nan DCIS


title: AN_321

source_name: AN tissue from cancer patient CUB-321 with grade II ER- PgR- HER2+ IDC


title: AN_059

source_name: AN tissue from cancer patient CUB-059 with grade nan ER+ PgR+ HER2+ ILC


title: AN_154

source_name: AN tissue from cancer patient CUB-154 with grade II ER+ PgR+ HER2- IDC


title: AN_312

source_name: AN tissue from cancer patient CUB-312 with grade nan ER- PgR- HER2- ILC


title: TU_316

source_name: TU tissue from cancer patient CUB-316 with grade III ER- PgR- HER2- IDC

value: TU


title: CUB_058

source_name: CUB tissue from cancer patient CUB-058 with grade II ER+ PgR+ HER2- IDC

value: CUB


title: CUB_167

source_name: CUB tissue from cancer patient CUB-167 with grade III ER+ PgR+ HER2- IDC


title: TU_058

source_name: TU tissue from cancer patient CUB-058 with grade II ER+ PgR+ HER2- IDC


title: CUB_085

source_name: CUB tissue from cancer patient CUB-085 with grade III ER- PgR- HER2- IDC


title: CUB_316

source_name: CUB tissue from cancer patient CUB-316 with grade III ER- PgR- HER2- IDC


title: OQ_085

source_name: OQ tissue from cancer patient CUB-085 with grade III ER- PgR- HER2- IDC

value: OQ


title: TU_157

source_name: TU tissue from cancer patient CUB-157 with grade II ER- PgR- HER2- IDC


title: OQ_157

source_name: OQ tissue from cancer patient CUB-157 with grade II ER- PgR- HER2- IDC


title: TU_298

source_name: TU tissue from cancer patient CUB-298 with grade III ER- PgR- HER2+ IDC


title: TU_158

source_name: TU tissue from cancer patient CUB-158 with grade III ER- PgR- HER2- IDC


title: TU_181

source_name: TU tissue from cancer patient CUB-181 with grade III ER- PgR- HER2+ IDC


title: TU_053

source_name: TU tissue from cancer patient CUB-053 with grade III ER+ PgR+ HER2+ IDC


title: CUB_084

source_name: CUB tissue from cancer patient CUB-084 with grade nan ER+ PgR+ HER2nan DCIS


title: CUB_318

source_name: CUB tissue from cancer patient CUB-318 with grade III ER+ PgR+ HER2- IDC


title: OQ_068

source_name: OQ tissue from cancer patient CUB-068 with grade I ER+ PgR+ HER2- IDC


title: OQ_011

source_name: OQ tissue from cancer patient CUB-011 with grade II ER- PgR- HER2+ IDC


title: CUB_053

source_name: CUB tissue from cancer patient CUB-053 with grade III ER+ PgR+ HER2+ IDC


title: OQ_181

source_name: OQ tissue from cancer patient CUB-181 with grade III ER- PgR- HER2+ IDC


title: TU_318

source_name: TU tissue from cancer patient CUB-318 with grade III ER+ PgR+ HER2- IDC


title: OQ_312

source_name: OQ tissue from cancer patient CUB-312 with grade nan ER- PgR- HER2- ILC


title: CUB_011

source_name: CUB tissue from cancer patient CUB-011 with grade II ER- PgR- HER2+ IDC


title: OQ_189

source_name: OQ tissue from cancer patient CUB-189 with grade nan ER+ PgR+ HER2- ILC


title: CUB_068

source_name: CUB tissue from cancer patient CUB-068 with grade I ER+ PgR+ HER2- IDC


title: CUB_312

source_name: CUB tissue from cancer patient CUB-312 with grade nan ER- PgR- HER2- ILC


title: OQ_318

source_name: OQ tissue from cancer patient CUB-318 with grade III ER+ PgR+ HER2- IDC


title: OQ_186

source_name: OQ tissue from cancer patient CUB-186 with grade nan ER+ PgR+ HER2- ILC


title: TU_186

source_name: TU tissue from cancer patient CUB-186 with grade nan ER+ PgR+ HER2- ILC


title: CUB_130

source_name: CUB tissue from cancer patient CUB-130 with grade II ER+ PgR+ HER2- IDC


title: TU_130

source_name: TU tissue from cancer patient CUB-130 with grade II ER+ PgR+ HER2- IDC


title: OQ_130

source_name: OQ tissue from cancer patient CUB-130 with grade II ER+ PgR+ HER2- IDC


title: TU_312

source_name: TU tissue from cancer patient CUB-312 with grade nan ER- PgR- HER2- ILC


title: TU_084

source_name: TU tissue from cancer patient CUB-084 with grade nan ER+ PgR+ HER2nan DCIS


title: OQ_315

source_name: OQ tissue from cancer patient CUB-315 with grade nan ER- PgR- HER2+ DCIS


title: TU_315

source_name: TU tissue from cancer patient CUB-315 with grade nan ER- PgR- HER2+ DCIS


title: OQ_308

source_name: OQ tissue from cancer patient CUB-308 with grade II ER- PgR- HER2+ IDC


title: CUB_260

source_name: CUB tissue from cancer patient CUB-260 with grade III ER- PgR- HER2- IDC


title: TU_226

source_name: TU tissue from cancer patient CUB-226 with grade I ER+ PgR¬± HER2- IDC


title: CUB_154

source_name: CUB tissue from cancer patient CUB-154 with grade II ER+ PgR+ HER2- IDC


title: OQ_154

source_name: OQ tissue from cancer patient CUB-154 with grade II ER+ PgR+ HER2- IDC


title: OQ_260

source_name: OQ tissue from cancer patient CUB-260 with grade III ER- PgR- HER2- IDC


title: TU_189

source_name: TU tissue from cancer patient CUB-189 with grade nan ER+ PgR+ HER2- ILC


title: CUB_135

source_name: CUB tissue from cancer patient CUB-135 with grade III ER- PgR- HER2- IDC


title: OQ_226

source_name: OQ tissue from cancer patient CUB-226 with grade I ER+ PgR¬± HER2- IDC


title: OQ_135

source_name: OQ tissue from cancer patient CUB-135 with grade III ER- PgR- HER2- IDC


title: CUB_019

source_name: CUB tissue from cancer patient CUB-019 with grade I ER- PgR- HER2+ IDC


title: OQ_019

source_name: OQ tissue from cancer patient CUB-019 with grade I ER- PgR- HER2+ IDC


title: OQ_084

source_name: OQ tissue from cancer patient CUB-084 with grade nan ER+ PgR+ HER2nan DCIS


title: TU_183

source_name: TU tissue from cancer patient CUB-183 with grade nan ER+ PgR+ HER2- ILC


title: TU_090

source_name: TU tissue from cancer patient CUB-090 with grade III ER- PgR- HER2- IDC


title: OQ_183

source_name: OQ tissue from cancer patient CUB-183 with grade nan ER+ PgR+ HER2- ILC


title: CUB_226

source_name: CUB tissue from cancer patient CUB-226 with grade I ER+ PgR¬± HER2- IDC


title: OQ_090

source_name: OQ tissue from cancer patient CUB-090 with grade III ER- PgR- HER2- IDC


title: CUB_308

source_name: CUB tissue from cancer patient CUB-308 with grade II ER- PgR- HER2+ IDC


title: CUB_090

source_name: CUB tissue from cancer patient CUB-090 with grade III ER- PgR- HER2- IDC


title: OQ_053

source_name: OQ tissue from cancer patient CUB-053 with grade III ER+ PgR+ HER2+ IDC


title: CUB_315

source_name: CUB tissue from cancer patient CUB-315 with grade nan ER- PgR- HER2+ DCIS


title: TU_308

source_name: TU tissue from cancer patient CUB-308 with grade II ER- PgR- HER2+ IDC


title: CUB_158

source_name: CUB tissue from cancer patient CUB-158 with grade III ER- PgR- HER2- IDC


title: OQ_298

source_name: OQ tissue from cancer patient CUB-298 with grade III ER- PgR- HER2+ IDC


title: CUB_183

source_name: CUB tissue from cancer patient CUB-183 with grade nan ER+ PgR+ HER2- ILC


title: TU_321

source_name: TU tissue from cancer patient CUB-321 with grade II ER- PgR- HER2+ IDC


title: OQ_158

source_name: OQ tissue from cancer patient CUB-158 with grade III ER- PgR- HER2- IDC


title: OQ_321

source_name: OQ tissue from cancer patient CUB-321 with grade II ER- PgR- HER2+ IDC