title: WT-RESP-2

description: Library name: Sample17


title: POLII ChIPseq, siC (siTOP2B), VEH, 45 min

status: Public on Dec 31 2025

type: SRA

city: Madrid

first: Felipe

last: Cortés Ledesma

state: Madrid

address: Melchor Fernández Almagro 3

department: Molecular Oncology

country: Spain

institute: CNIO

library_source: genomic

data_processing:
Tags were aligned to human genome (hg19) using Bowtie (version 1.2.0).
Peaks were called using MACS2 and broad peak mode. Peaks from differente biological repeats were merged.
For genome tracks, we used bamCoverage (deepTools) to convert aligned reads to signal tracks (bigwig) using RPGC normalization (bin size of 50 bps and 300 bps read extension). Spike-in normalization was applied to all ChIPseq experiments to correct technical biases and global differences. Spike-in normalization was performed using mouse chromatin in our human experiments, basically as described by Minchell et al. 2020.
Assembly: hg19
Supplementary files format and content: bigWig (Coverage files)
Supplementary files format and content: bed (called peaks)

molecule: genomic DNA

organism: Homo sapiens

growth_protocol: MEM with Earle´s salts supplemented with 50 U/ml Penicillin, 50 µg/ml Streptomycin, 2 mM L-Glutamine, 10% FBS and non-essential amino acids. Cells maintained in HEPA class 100 incubators at 37ºC and 5% CO2.

extract_protocol:
MCF-7 cells were fixed by adding formaldehyde to a final concentration of 1% and incubated at 37ºC for 10 min before quenching with 125 mM glycine. Subsequently, culture plates were washed twice with cold PBS and collected in protease inhibitor cocktail, centrifuged and lysed in two steps: 10 min incubation in 1 ml Lysis Buffer A (5 mM Pipes pH 8, 85 mM KCl, 0,5% NP40, 1 mM PMSF, 1x Complete Protease inhibitor cocktail) for nuclei isolation and then, adding 300 µl Lysis Buffer B (50 mM Tris HCl pH 8.1, 1% SDS, 10 mM EDTA, 1 mM PMSF, 1x Complete Protease inhibitor cocktail) to pelleted nuclei (4000 rpm, 5 min) for nuclear lysis. Sonication was performed using Bioruptor (Diagenode, UCD-200) at high intensity for 25 min (30” sonication, 30” pause). Chromatin was clarified by centrifugation (17,000 × g, 10 min, 4 °C).
Libraries were prepared by ChIPmentation as described by Schmidl et al. 2015 using NEBNext HF Polymerase and sequenced using Illumina NextSeq 500.

treatment_protocol: MEM with Earle's salts without phenol-red and supplemented with 50 U/ml Penicillin, 50 µg/ml Streptomycin, 2 mM L-Glutamine, 5% Charcoal-stripped FBS and non-essential amino acids. Cells maintained in HEPA class 100 incubators at 37ºC and 5% CO2 for 48 hours prior treatments.

tag: cell line

tag: cell type

value: ER positive breast cancer cell line

tag: treatment

value: siC 60h + 45min EtOH


title: dsir2_a_factor_rep1

city: Chuncheon-si, Gangwon-do

first: soojin

last: yeom

address: 1 Kangwondaehak-gil

country: South Korea

institute: Kangwon National University

description: Library name: dsir2-a-1

library_source: transcriptomic

data_processing:
Sequencing was performed on an Illumina Hi-seq 2500 instrument to generate 101 bp paired-end reads for each sample.
Trimmomatic v.0.36 performed the sequencing adapter removal and quality-based trimming on raw data with TruSeq adapter sequence
Cleaned reads were mapped to the S. cerevisiae reference genome (SacCer3) using TopHat2 v.2.0.11 with the default parameter
featureCounts was used for counting to measure the expression level of each gene, and data were normalized by DESeq2
Assembly: sacCer3
Supplementary files format and content: bw

molecule: total RNA

organism: Saccharomyces cerevisiae BY4741

source_name: α-factor induced

growth_protocol: S. cerevisiae strains were grown in YPD media (1% yeast extracts, 2% peptone, 2% glucose) at 30˚C. Overnigh cultured cells were diluted to OD600 of 0.1 into fresh 10ml YPD and grown at 30˚C until OD600 of 1.0.

extract_protocol:
Total RNA was extracted using NucleoSpin® RNA (MN, MN740955) according to the protocol of the manufacturer
mRNA was captured using NEBNext® Poly(A) mRNA Magnetic Isolation Module (NEB, E7490). The library for sequencing was prepared following the manufacturer's instructions of NEBNext Ultra II Directional RNA Library Prep Kit for Illumina (NEB, Cat. No: E7760).

treatment_protocol: α-Factor (9.6 μg/mL) was added to the culture and incubated for 1.5 hours at 30°C with shaking, followed by a second treatment under the same conditions

value: S. cerevisiae BY4741 (haploid)

tag: genotype

value: SIR2 Knockout

value: α-factor


title: dcdc73_a_factor_rep2

description: Library name: dcdc73-a-2

value: CDC73 Knocoout


title: dsir2_rep2

description: Library name: dsir2-2

source_name: Normal condition

value: X


title: POLII ChIPseq, ICRF-187, E2, 45 min

value: ICRF-187 100uM 60min + 45 min 10 nM E2


title: Bexa-4 (scRNA)

city: Pittsburgh

first: Iliya

last: Lefterov

state: PA

address: 130 De Soto St

department: Environmental and Occupational Health

country: USA

institute: University of Pittsburgh

description: Library name: A2913

library_source: transcriptomic single cell

data_processing:
Cell Ranger pipeline v6.1
Seurat package (v 4.1.0)
Assembly: mm10
Supplementary files format and content: Filtered feature matrix from 10x cell ranger output in H5 format.

organism: Mus musculus

source_name: brain

extract_protocol:
Mice were perfused with cold PBS, and half of each brain tissue, excluding olfactory and cerebellum, were immediately dissected and dissociated using Adult Brain Dissociation Kit (Miltenyi).
Libraries were prepared using the Chromium Next GEM Single Cell 3’ Kit v3.1 and Chip G Single Cell Kit (10x Genomics, USA) according to manufacturer’s protocol.

treatment_protocol: The treatment group got 10-day oral administration of Bexarotene (100mg/kg/day), and the control group were treated with vehicle solution (corn oil with 1% DMSO).

tag: tissue

value: brain

value: APP/PS+

value: Bexarotene


title: C57, SHAM4, Day7

city: Shanghai

first: hui

last: chen

address: 639 Zhizaoju Road, Shanghai 200011, People’s Republic of China

country: China

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

description: Library name: A-4

data_processing:
Illumina Casava1.7 software used for basecalling.
Raw reads of fastq format were firstly processed using fastp and the low quality reads were removed to obtain the clean reads.
The clean reads were mapped to the reference genome using HISAT2. FPKM of each gene was calculated and the read counts of each gene were obtained by HTSeq-count
Assembly: GRCm39
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample.

source_name: Heart

growth_protocol: All adult male C57BL/6 mice (approximately 20 g;) were housed under controlled temperature conditions (20±2°C), with a 12-hour light-dark cycle, and provided with adequate food and water.

extract_protocol:
Total RNA was extracted using the Total RNA Extraction Kit 2.0 Plus according to the manufacturer’s protocol.
The libraries were constructed using VAHTS Universal V6 RNA-seq Library Prep Kit according to the manufacturer’s instructions.

treatment_protocol: in this study, C57BL/6 mice were used to investigate the protective effects of Decursin on myocardial ischemia-reperfusion injury. A total of 18 mice were randomly divided into three groups, with 6 mice in each group:SHAM Group, IR (Ischemia-Reperfusion) Group,  IR + Decursin Group. All mice were sacrificed at 7 days post-surgery, and heart tissues were collected for RNA sequencing (RNA-seq) analysis. This design aims to elucidate the molecular mechanisms by which Decursin may confer cardioprotective effects in the context of ischemia-reperfusion injury, with a focus on gene expression changes associated with the treatment.

value: Heart

value: WT

value: SHAM

tag: batch


title: WT-RESP-1

city: Cincinnati

first: Konrad

last: Thorner

state: OH

address: 3333 Burnet Ave

institute: Cincinnati Children's Hospital Medical Center

description: Library name: Sample16

data_processing:
Processed with the nf-core-rnaseq pipeline, version 3.13.2, with STAR/Salmon selected for the alignment/quantification.
Assembly: GRCh38
Supplementary files format and content: Length-corrected raw counts

source_name: Respiratory mesenchyme

extract_protocol:
RNA was extracted from tissue samples using the Macherey-Nagel Nucleospin RNA Kit.
For library preparation, 150 to 300ng of total RNA determined by InvitrogenTM QubitTM high-sensitivity spectrofluorometric measurement was poly-A selected and reverse transcribed using Illumina’s TruSeq stranded mRNA library preparation kit.

value: Respiratory mesenchyme

value: Mesenchyme differentiation


title: D mixed sample of D-D_TAG_11, D_TAG_14, D_TAG_16, scRNA seq

city: Beijing

first: Yuqi

last: Xing

state: Beijing

address: Peking University

institute: Peking University

description:
Library name: D mixed sample
GEXSCOPER

data_processing:
Raw reads from scRNA-seq were used to generate gene expression matrices. In short, Raw readings were first used with fastQC (Andrews et al., 2010) v0.11.4 (https://www.bioinformatics.babraham.ac.uk/projects/fastqc/) and fastp (Chen et al., 2018) deal with removing low quality Reads, cutadapt (Martin 2011) was used to trim the poly-A tail and adaptor sequences. After extracting cell barcodes and UMI, we mapped Resds to the reference genome mm10 using STAR (Daehwan et al., 2013) v2.5.3a. The UMI number and gene expression of each cell were obtained using FeatureCounts(Liao et al., 2014) v1.6.2 software and used to generate expression matrix files for subsequent analysis.
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Mouse breast cancer

extract_protocol:
Samples were washed three times with Hanks balanced salt solution (HBSS) and cut into 1-2 mm pieces. Cells were passed through a 40-micron sterile filter (Falco) and centrifuged (eppendor) at 300g for 5 min. The supernatant was then removed and the precipitate was resuspended in 1ml of PBS (Hyclone).Cells were centrifuged at 500 × g in a microcentrifuge for 5 min at 15 to 25°C and resuspended in PBS (Hyclone). Samples from cell mixtures were stained with trypan blue and counted by microscopy to a concentration of 1×105 cells /mL, and subsequent sample processing was allowed once cell viability exceeded 80%.
Single cell suspensions were prepared at a concentration of 1×105 cells /mL in PBS. The single-cell suspension is then loaded onto the microfluidic device, scRNA-seq libraries were constructed using the GEXSCOPE Single-Cell RNA Library Kit (Singleron Biotechnologies) according to the Singleron GEXSCOPE protocol. Cell lysis, mRNA capture, labeling of cells (barcodes) and mRNA (UMI), reverse transcription of mRNA into cDNA and amplification, and finally fragmentation of cDNA were performed. Individual libraries were diluted to 4 nM and pooled for sequencing. Sequencing was performed on an Illumina HiSeq X using 150 bp paired end reads.

value: Mouse breast cancer

tag: sample group

value: D mixed sample


title: dsir2_rep1

description: Library name: dsir2-1


title: P mixed sample of D-D_TAG_8, D_TAG_9, D_TAG_10, scRNA seq

description:
Library name: P mixed sample
GEXSCOPER

value: P mixed sample


title: Veh-4 (scRNA)

description: Library name: A2914

value: Vehicle


title: WT-ESOPH-3

description: Library name: Sample15

source_name: Esophageal mesenchyme

value: Esophageal mesenchyme


title: WT-ESOPH-2

description: Library name: Sample14


title: POLII ChIPseq, ICRF-187, VEH, 45 min

value: ER positive breast cancer cell line

value: ICRF-187 100uM 60min + 45min EtOH


title: POLII ChIPseq, siTOP2B, VEH, 45 min

value: siTOP2B 60h + 45min EtOH


title: POLII ChIPseq, DMSO (ICRF-187), E2, 45 min

value: DMSO 60 min + 45 min 10 nM E2


title: WT_a_factor_rep2

description: Library name: FM391-a-2

value: S. cerevisiae BY4741 (haploid)

value: α-factor


title: Bexa-3 (scRNA)

description: Library name: A2909

value: brain

value: APP/PS+

value: Bexarotene


title: WT_a_factor_rep1

description: Library name: FM391-a-1

value: WT


title: WT_rep2

description: Library name: FM391-2

value: X


title: WT-ESOPH-1

description: Library name: Sample13

value: Mesenchyme differentiation


title: Veh-3 (scRNA)

description: Library name: A2910


title: 83-12-SPM-3

description: Library name: Sample12

source_name: Splanchinc mesoderm

value: Splanchinc mesoderm


title: POLII ChIPseq, MERB, E2, 45 min

value: Merb 100uM 60min + 45 min 10 nM E2


title: POLII ChIPseq, DMSO (ICRF-187), VEH, 45 min

value: DMSO 60min + 45min EtOH


title: 83-12-SPM-2

description: Library name: Sample11


title: DSP-1001660013460-E-A01

city: Novato

first: Fei

last: Wu

state: CA

address: 8001 Redwood Blvd

institute: Buck Institute for Research on Aging

description: FFPE GeoMx DSP profiling

data_processing:
Geomx sequencing data was analyzed with the standR (version 1.5.3), edge R (version 3.40.2), and limma (version 3.54.2) packages.
Assembly: mm10
Supplementary files format and content: .dcc files
Library strategy: GEOMx Spatial Transcriptomics

organism: synthetic construct

extract_protocol:
Formalin-fixed paraffin embedded (FFPE) spleen tissue from two cohorts of WT mice was used to construct a tissue-micro array (TMA)
Library preparation was performed according to the NanoString GeoMx-NGS Readout Library Prep user guide (MAN-10153-01).

value: DSP-Quality control


title: POLII ChIPseq, MERB, VEH, 45 min

value: Merb 100uM 60min + 45min EtOH


title: WT_rep1

description: Library name: FM391-1


title: POLII ChIPseq, DMSO (Merb), E2, 45 min

value: ER positive breast cancer cell line


title: 83-12-SPM-1

description: Library name: Sample10


title: Bexa-2 (scRNA)

description: Library name: A2898


title: POLII ChIPseq, DMSO (Merb), VEH, 45 min


title: 83-12-SC-3

description: Library name: Sample9

source_name: Stem cell for mesenchyme differentiation


title: Bexa-1 (scRNA)

description: Library name: A2902


title: Veh-1 (scRNA)

description: Library name: A2905

value: Vehicle


title: 83-12-SC-2

description: Library name: Sample8

value: Stem cell for mesenchyme differentiation


title: 83-12-SC-1

description: Library name: Sample7


title: ZATT ChIPseq, VEH, 45 min, rep2

value: 45 min EtOH


title: TOP2A ChIPseq, E2, 45 min, rep2

value: 45 min 10 nM E2


title: 83-12-RESP-4

description: Library name: Sample6

value: Respiratory mesenchyme


title: THP-1 cells,scrambled-3

city: Taiyuan

first: Jiangxia

last: cui

address: xinjian road

institute: Shanxi Natural Science Foundation of China

description: Library name: sample3

data_processing:
Use the fastp software to perform quality control on the raw sequencing data for each sample, including overrepresentation analysis, front-end trimming, and sliding window quality filtering (parameters: --overrepresentation_analysis --trim_front1 2 --trim_front2 2 --cut_front --cut_tail --cut_window_size 3 --cut_mean_quality 30), to obtain clean data for downstream analysis.
Utilize the HISAT2 software to align the quality-controlled clean data reads to the GRCh38.p14 reference genome (parameter: --dta), generating .sam or .bam files containing alignment records for subsequent assembly preparation.
Apply the StringTie software to perform transcript assembly on the alignment results for each sample (default parameters), obtaining individual sample annotation files (e.g., sample1.gtf); then merge all sample annotations using the stringtie --merge command to generate a unified all_sample.gtf file.
Use the gffcompare software to compare all_sample.gtf with the reference genome annotation (reference.gtf) (default parameters), extract unannotated transcripts (class_code==u), and filter those with length greater than or equal to 100 and at least 2 exons as predicted novel transcripts (novel.gtf).
Assembly: GRCh38
Supplementary files format and content: detailed_gene_fpkm.txt files include fpkm values for each sample

growth_protocol: THP-1 cells were cultured in Rosewell Park Memorial Institute (RPMI) 1640 medium supplemented with 10% fetal bovine serum (FBS)

extract_protocol:
Method for RNA Extraction Using Trizol，>1ug of total RNA was used for the construction of sequencing libraries
Using 1 µg RNA as input for each sample, sequencing libraries were prepared with the NEBNext® UltraTM RNA Library Prep Kit for Illumina®, including mRNA purification using poly-T magnetic beads, fragmentation, cDNA synthesis, blunt-end processing, 3' end adenylation, adaptor ligation, size selection (250~300 bp, using AMPure XP system), USER enzyme treatment, PCR amplification, purification, and quality assessment on the Agilent Bioanalyzer 2100 system.

value: Human monocytic leukemia cell line

value: no


title: TCN2 cKO-2

city: Xi'an

first: Xiaofan

last: Xiong

address: 157 West Fifth Road

institute: Xi'an Jiaotong University

description: Library name: Sample 4

data_processing:
CLC Genomics Workbench v 11.0.1
Seqences reads were trimmed for adaptor sequence using CLC GENOMIC BENCHWORK (parameter-Qualitylimit：0.05).
Trimmed sequence reads were mapped using CLC genomic benchwork.
Assembly: mm10
Supplementary files format and content: txt files include FPKM values for each sample

source_name: bone

growth_protocol: Cells were cultured in complete DMEM (10mM HEPES, 2 mM L-Glutamine, 1% MEM Non-Essential Amino Acids Solution) with 10% FBS

extract_protocol:
Total RNA from cells were harvested using extraction reagent. 1.5 ug of tatal RNA was used for the construction of sequencing libraies.
RNA libraies for RNA-seq were prepared using SMARTER mRNA-seq Library Prep Kit following manufacturer's protocols.

value: bone

value: bone marrow-derived macrophages

value: primary culture cell

value: TCN2 cKO

value: M-CSF

tag: time

value: Day 8


title: THP-1 cells,shPAMM-1

description: Library name: sample4

value: PAMM Knockdown


title: THP-1 cells,shPAMM-2

description: Library name: sample5


title: THP-1 cells,scrambled-2

description: Library name: sample2

value: WT


title: TOP2A ChIPseq, VEH, 45 min, rep2


title: WT-2

description: Library name: Sample 2


title: THP-1 cells,scrambled-1

description: Library name: sample1


title: 83-12-RESP-2

description: Library name: Sample4

value: Mesenchyme differentiation


title: TOP2A ChIPseq, E2, 45 min, rep1

value: ER positive breast cancer cell line


title: 83-12-RESP-3

description: Library name: Sample5


title: WT-1

description: Library name: Sample 1


title: shZBTB20_2_2

city: Guangzhou

first: jieru

last: huang

address: 195 Dongfeng West Road, Yuexiu District, Guangzhou

institute: Guangzhou Medical University

description:
Library name: Sample 6
Colum name in raw counts All Samples.text:shZBTB20

data_processing:
CLC Genomics Workbench v11.0.1
Sequence reads were trimmed for adaptor sequence/ low-quality sequence using CLCgenomic benchwork(parameter-Quality limit:0.05)
Trimmed sequence reads were mapped to GRCh38.p14 using CLC genomic benchwork(parameters-mismath cost:2 insertion cost:3 deletion cost:3 length fraction:0.8similarity fraction:0.8)
Read count extraction and normalization were performed using CLC genomic benchwork
Assembly: GRCh38.p14
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample
Supplementary files format and content: csv files include FPKM values for each Sample

source_name: colon

growth_protocol: SW620 mesenchymal cells were maintained in L15 supplemented with 10% fetalbovine serum(FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
Total RNA was extracted using TRIzol reagent (Invitrogen). cDNA was synthesized using the High-Capacity cDNA Reverse Transcription Kit (Applied Biosystems).
RNA libraries for RNA-seq were prepared using SMARTER mRNA-Seq Library Prep Kitfollowing manufacturer's protocols.

treatment_protocol: For stable cell lines, lentiviral particles were produced in HEK293T cells using psPAX2 and pMD2.G packaging plasmids and transduced into SW620 cells, followed by puromycin selection.

value: colon

value: Mesenchymal stem cell

value: ZBTB20 knockdown

value: adipogenic differentiation


title: TCN2 cKO-1

description: Library name: Sample 3


title: THP-1 cells,shPAMM-3

description: Library name: sample6


title: 83-12-ESOPH-3

description: Library name: Sample3

value: Esophageal mesenchyme


title: TOP2A ChIPseq, VEH, 45 min, rep1

value: 45 min EtOH


title: shZBTB20_2_1

description:
Library name: Sample 5
Colum name in raw counts All Samples.text:shZBTB20


title: Replicate4, SVFcells with DoxSa treatment

first: Xiaoxue

last: Wang

address: 319, Yueyang Rd, Xuhui District, Shanghai

institute: SIII, CAS

description:
Library name: Sample8
Dox4 column in FPKM_anno

data_processing:
Fastp
HISAT2
FPKM calculation:Htseq_count
Assembly: NCBI_GRCm39
Supplementary files format and content: xls format include FPKM values for each sample

source_name: Gonadal tissue

extract_protocol:
Total RNA was extracted using the TRIzol reagent (Invitrogen, CA, USA) according to the manufacturer’s protocol.
The libraries were constructed using  VAHTS Universal V6 RNA-seq Library Prep Kit according to the manufacturer’s instructions.

value: Gonadal tissue

value: Stromal Vascular Fraction

value: Mature adipocyte

value: DoxSa


title: ZATT ChIPseq, E2, 45 min, rep2

value: 45 min 10 nM E2


title: Replicate3, SVFcells with DoxSa treatment

description:
Library name: Sample7
Dox3 column in FPKM_anno


title: TOP2B ChIPseq, E2, 45 min


title: Veh-2 (scRNA)

description: Library name: A2899

value: brain

value: APP/PS+

value: Vehicle


title: shZBTB20_1_2

description:
Library name: Sample 4
Colum name in raw counts All Samples.text:shZBTB20


title: Replicate2, SVFcells with DoxSa treatment

description:
Library name: Sample6
Dox2 column in FPKM_anno

value: WT


title: 83-12-ESOPH-2

description: Library name: Sample2

value: Mesenchyme differentiation


title: TOP2B ChIPseq, VEH, 45 min

value: ER positive breast cancer cell line


title: Replicate1, SVFcells with DoxSa treatment

description:
Library name: Sample5
Dox1 column in FPKM_anno


title: shZBTB20_1_1

description:
Library name: Sample 3
Colum name in raw counts All Samples.text:shZBTB20

value: colon


title: TOP2B ChIPseq


title: scramble_2

description:
Library name: Sample 2
Colum name in raw counts All Samples.text:shControl

value: Mesenchymal stem cell


title: 83-12-ESOPH-1

description: Library name: Sample1


title: Replicate4, SVFcells with DMSO treatment

description:
Library name: Sample4
DMSO4 column in FPKM_anno

value: DMSO


title: scramble_1

description:
Library name: Sample 1
Colum name in raw counts All Samples.text:shControl

value: adipogenic differentiation


title: 6C-P_rep3 ATAC-seq

first: Jie

last: Hao

state: 北京

address: Beijing

institute: Tsinghua University

description: Library name: sample9

data_processing:
ATAC-seq adapter sequence were identified and trimmed with cutadapt tool.
ATAC-seq reads were aligned to human hg19 reference genome using BWA-MEM with default parameters. Fragments were identified as read pairs with mapping quality >10 and non-mitochondrial reads.
PCR duplicates were removed with sambamba (v0.8.0). The start and end of the fragments were adjusted (+4 for +strand and −5 for −strand) to account for the Tn5 transposase enzyme occupied region.
ATAC peak calling was performed using MACS with a p-value threshold of 0.01, and with other settings as --nomodel --shift -75 --extsize 150 --SPMR.
ATAC bigWig files were generated using the bamCoverage tools. Score represents the normalized coverage of DNA fragments at a given genomic coordinate.
Assembly: hg19
Supplementary files format and content: bigWig
Supplementary files format and content: bed

source_name: H9 hESC

extract_protocol:
Samples were digested with Accutase, and collected in HCM medium. Frozen PHH purchased from Celsis IVT (Lot: ONO) were defrosted according to manufacturer’s instructions  and collected in HCM medium.
ATAC library was prepared using Omni-ATAC protocol as previously described. Briefly, 50,000 cells were washed with cold PBS once and resuspend with 50μl cold ATAC-Resuspension Buffer (RSB) (10 mM Tris-HCl, 10 mM NaCl, 3 mM MgCl, pH 7.4) containing 0.1% NP40 and 0.1% Tween-20 for lysis. After incubation on ice for 3 minutes, 1 ml of cold ATAC-RSB containing 0.1% Tween-20 (without NP40) was added to cell lysis and the tubes were inverted for 3 times to mix. The nuclei were collected by centrifuging for 10 minutes at 500g at 4°C 10min. For the transposition reaction, nuclei were incubated with Tn5 Transposition mix (10 μl 5×TTBL buffer, 3 μl TTE Mix V50 transposase, 16.5μl PBS, 0.5μl 10% Tween-20, 20μl H2O) at 37 °C for 30  minutes (TruePrep® DNA Library Prep Kit V2 for Illumina, Vazyme, China). After tagmentation, the stop buffer was directly added to the reaction to end the tagmentation. PCR was performed to amplify the library for 12 cycles. After the PCR reaction, the libraries were purified with 1.2×AMPure beads (Beckman, Germany).

value: H9 hESC

value: Pluripotent stem cells derived hepatocytes

value: 6C-P sample were generated by culturing fHep with 5C(6C medium minus PD0325901) medium for 15days, and medium was changed every other day.


title: Replicate3, SVFcells with DMSO treatment

description:
Library name: Sample3
DMSO3 column in FPKM_anno

value: Gonadal tissue

value: Stromal Vascular Fraction


title: 6C-P_rep2 ATAC-seq

description: Library name: sample8


title: ERA ChIPseq, E2, 45 min


title: Replicate2, SVFcells with DMSO treatment

description:
Library name: Sample2
DMSO2 column in FPKM_anno

value: Mature adipocyte


title: HCT116, Ab: P-SF3B1 (T235), experiment2

city: München

first: Caroline

last: Friedel

address: Amalienstr. 17

department: Institut für Informatik

country: Germany

institute: Ludwig-Maximilians-Universität München

description: Library name: HCT116_P-SF3B1_(T235)_exp2

data_processing:
Raw sequencing reads were aligned to the human genome (GRCh38) using BWA and resulting sam output was converted to bam using samtools.
Sequence reads with an alignment score <20 reads were discarded.
Duplicates were removed with samtools rmdup
Resulting bam files were converted into bedgraph format using the genomecov command of bedtools.
Assembly: GRCh38
Supplementary files format and content: bedGraph, read coverage per genome position

extract_protocol:
ChIP was performed using the following antibodies for each biological technical replicate: 30 ul of P-SF3B1 (T211 or T235) in two technical replicates that were pooled together to obtain one biological replicate. In brief, 20 µl of Dynabeads protein G (Thermo Fisher Scientific, 10009D) per immunoprecipitation were pre-blocked with 0.2 mg/ml BSA (Thermo Fisher Scientific, AM2616) for 4 hours, washed 3× with RIPA buffer, followed by incubation with the specific antibody at 4 °C for at least 4 hours. HCT116 cells (70 % confluency) were treated with 50 nM SY-351 for 2 h. Cells were cross-linked with 1 % formaldehyde for 10 min, and the reaction was quenched with glycine (final concentration 125 mM) for 5 min. Cells were washed 2× with ice-cold PBS, scraped and split to several tubes so that there was about 20 µl packed cell pellet per tube. Each 20 µl packed cell pellet was lysed in 650 µl of RIPA buffer and sonicated 20× 7 s (amplitude 0.85) using a 5/64 probe (QSonica Q55A). Supernatant (13000 g/4 °C/10 min) was pooled and pre-cleared by incubating with Dynabeads protein G (Thermo Fisher Scientific, 10009D) at 4 °C for 2‒4 hours. Pre-cleared extracts were split into two technical replicates (900 µl each) and incubated overnight with antibody (P-CDK11, SF3B1)-bound Dynabeads protein G. Beads were sequentially washed once with low-salt buffer (20 mM Tris-Cl, (pH 8), 150 mM NaCl, 2 mM EDTA, 1% Triton X 100, 0.1% SDS), once with high-salt buffer (20 mM Tris-Cl, (pH 8), 500 mM NaCl, 2 mM EDTA, 1% Triton X 100, 0.1% SDS), once with LiCl buffer (20 mM Tris-Cl, (pH 8), 250 mM LiCl, 2 mM EDTA, 1% NP 40, 1% sodium deoxycholate) and 2× with TE buffer (10 mM Tris Cl, (pH 8), 1 mM EDTA). Immunoprecipitated complexes were eluted 2× 15 min with 250 µl of elution buffer (1% SDS, 0.1 M NaHCO3). NaCl was added to final concentration of 0.2 M and samples were incubated at 65 °C for at least 4 hours to reverse cross-linking. Tris, pH 7.8, proteinase K (Sigma-Aldrich, P5568) and GlycoBlue (Thermo Fisher Scientific, AM9516) were added to final concentration of 30 mM, 0.04 mg/ml and 0.06 mg/ml, respectively, and incubated at 42 °C for 2 hours. After phenol–chloroform extraction (Sigma-Aldrich, P3803), immunoprecipitated DNA was dissolved in 17 µl of water and technical replicates were pooled.
ChIP–seq libraries were generated using KAPA Biosystems Hyper Prep Kit (Roche, KK8502) and NEBNext Multiplex Oligos for Illumina (New England Biolabs, E7335S, E7500S).

treatment_protocol: Indicated samples were treated with DMSO or 50nM SY-351 for 2 hours.


title: RAD21 ChIPseq, siTOP2B, E2, 45 min

value: siTOP2B 60h + 45 min 10 nM E2


title: 6C_rep3 ATAC-seq

description: Library name: sample6

value: 6C-Heps were differentiated by culturing fHep with 6C medium for 15days, and 6C medium was changed every other day.


title: HCT116, Ab: P-SF3B1 (T211), experiment2

description: Library name: HCT116_P-SF3B1_(T211)_exp2


title: 6C_rep2 ATAC-seq

description: Library name: sample5


title: RAD21 ChIPseq, siTOP2B, VEH, 45 min

value: siTOP2B 60h + 45min EtOH


title: Cc10-Cre;Rhoafl/fl+CRE3

city: Baltimore

first: Peisong

last: Gao

state: MARYLAND

address: 5501 Hopkins Bayview Circle

institute: Johns Hopkins Asthma & Allergy Center

description:
Library name: D3
KO+CRE3

data_processing:
Quality control  Raw data (raw reads) of FASTQ format were firstly processed through fastp. In this step, clean data (clean reads) were obtained by removing reads containing adapter and poly-N  sequences and reads with low quality from raw data. At the same time, Q20, Q30 and GC content of the clean data were calculated. All the downstream analyses were based on the  clean data with high quality.  Mapping to reference genome  Reference genome and gene model annotation files were downloaded from genome website browser (NCBI/UCSC/Ensembl) directly. Paired-end clean reads were aligned to the  reference genome using the Spliced Transcripts Alignment to a Reference (STAR) software, which is based on a previously undescribed RNA-seq alignment algorithm that uses  sequential maximum mappable seed search in uncompressed suffix arrays followed by seed clustering and stitching procedure. STAR exhibits better alignment precision and sensitivity  than other RNA-seq aligners for both experimental and simulated data
Assembly: mm10
Supplementary files format and content: txt, rawcounts

source_name: Lung

extract_protocol:
total RNA was extracted using RNeasy Mini Kit (QIAGEN). mRNA was enriched using oligo dT beads and then fragmented chemically by incubating at 94℃ for 8 min.
A total amount of 1 μg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext? UltraTM RNA  Library Prep Kit for Illumina? (NEB, USA) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample. Briefly, mRNA was  purified from total RNA using poly-T oligo-attached magnetic beads. Fragmentation was carried out using divalent cations under elevated temperature in NEBNext First Strand  Synthesis Reaction Buffer (5X). First strand cDNA was synthesized using random hexamer primer and M-MuLV Reverse Transcriptase (RNase H-). Second strand cDNA synthesis  was subsequently performed using DNA Polymerase I and RNase H. Remaining overhangs were converted into blunt ends via exonuclease/polymerase activities. After adenylation of  3’ ends of DNA fragments, NEBNext Adaptor with hairpin loop structure were ligated to prepare for hybridization. In order to select cDNA fragments of preferentially 150~200 bp in  length, the library fragments were purified with AMPure XP system (Beckman Coulter, Beverly, USA). Then 3 μl USER Enzyme (NEB, USA) was used with size-selected, adaptor ligated cDNA at 37 °C for 15 min followed by 5 min at 95 °C before PCR. Then PCR was performed with Phusion High-Fidelity DNA polymerase, Universal PCR primers and  Index (X) Primer. At last, PCR products were purified (AMPure XP system) and library quality was assessed on the Agilent Bioanalyzer 2100 system.

value: Lung

value: RhoACKO

value: CRE


title: RAD21 ChIPseq, siC, E2, 45 min

value: ER positive breast cancer cell line

value: siC 60h + 45 min 10 nM E2


title: APPLondon_5

city: New York

first: Andrew

middle: A

last: Sproul

state: NY

address: 650 West 168th Street

institute: Columbia Univeristy

description: Library name: Sample 51

data_processing:
Illumina bcl2fastq 2.17 software
Possible adapter sequences and mucleotides rewmoed by using Trimmomatic v.0.36
Trimmed reads were mapped to Homo sapiens reference genome with STAR aligner v.2.5.2b
Hit counts were calculated by using featureCounts from the Subread package v.1.5.2
Assembly: Homo_sapiens.GRCh38
Supplementary files format and content: tab-delimited files contain raw counts for each sample

extract_protocol:
RNAs were harvested using QIAGEN mini RNA easy kit. 2 ul RNA was used for construction of RNA sequence
RNA libraries built woth NEBNext Ultra II RNA Library Prep Kit.


title: APPLondon_4

description: Library name: Sample 50


title: 6C_rep1 ATAC-seq

description: Library name: sample4


title: RAD21 ChIPseq, siC, VEH, 45 min

value: siC 60h + 45min EtOH


title: Cc10-Cre;Rhoafl/fl+CRE2

description:
Library name: D2
KO+CRE2


title: pure_aHep_223 ATAC-seq

description: Library name: sample3

value: human pluripotent stem cells (hPSCs) were maintained in matrigel-coated plates with mTeSR (Stem Cells). For mesendoderm differentiation, hPSCs were cultured in RPMI1640 (Gibco) supplemented with 100 ng/ml Activin A (R&D), 3μM CHIR-99021 (Selleck), 1% GlutamaxTM (Gibco) and 1% penicillin/streptomycin (Gibco) for one day. For endoderm differentiation, mesendoderm cells were cultured in RPMI 1640 supplemented with 0.2% FBS (Gibco), 100ng/ml Activin A, 1% GlutamaxTM and 1% penicillin/ streptomycin for 1 day, and then cultured in RPMI1640 supplemented with 2% FBS (Gibco), 100ng/ml Activin A, 1% GlutamaxTM and 1% penicillin/ streptomycin for another day. For hepatoblast differentiation, endoderm cells were induced in DMEM (Gibco) supplemented with 20ng/ml bFGF (Invitrogen), 20ng/ml human BMP4 (R&D), 0.5μM A83-01 (Tocris Bioscience), 0.1μM Dex (Invitrogen), 0.05% BSA (Invitrogen), 2% B27 (Gibco) and 1%P/S for 4 days, and the medium was changed every other day. For fHep differentiation, hepatoblasts were further cultured in hepatocyte differentiated medium (HDM) for 10 days. HDM medium was prepared with HCM (without EGF, Lonza) with 20ng/ml human HGF (R&D), 20ng/ml human OSM (R&D), 0.1μM Dex (Sigma-Aldrich), 0.5μM A83-01(Tocris Bioscience) and 0.1μM Compound E (Tocris Bioscience), and the medium was changed every other day. For midHep differentiation, fHeps were cultured in 6C medium for 15 days, and 6C medium was changed every other day. 6C medium was prepared with HCM (without EGF, Lonza) supplemented with 0.2 μM MS-275, 0.1 μM Dex, 0.1 μM Compound E, 1 μM PD0325901, 0.5 μM A83-01, and 5 μM SB203580.  For aHep differentaition, midHeps were cultured with 4C medium for 60 days, and 4C medium was changed every three days.  4C medium was prepared with William’s E medium (Gibco), 1% GlutaMAXTM, 1% Non-Essential Amino Acid (Gibco), 1% penicillin-streptomycin, 10 mM nicotinamide (Sigma-Aldrich), 1.25 mM N-acetylcysteine (Sigma-Aldrich), 10 μM Y27632, 0.5 μM A83-01, 0.1 μM Dex and 30 μM  Forskolin (FSK, Selleck).  For aHep sorting, Single-cell suspensions of aHeps were obtained by Accutase™ (Gibco) digestion at 37 °C for 20 min, filtered through 40 μm strainers, and stained with PE-conjugated anti-human ASGR1 antibody (1:50; Miltenyi Biotec, 130-122-919) at 4 °C for 30 min in the dark. DAPI (1 μg/ml; Thermo Fisher) was added before flow cytometry to exclude dead cells.  Gating was performed based on FSC/SSC, DAPI exclusion, and PE fluorescence relative to PSC controls. For cell sorting, ASGR1⁺ aHeps were isolated on a BD Influx™ cell sorter (BD Biosciences). Sorted cells were collected in 4C medium for ATAC-seq.


title: APPLondon_3

description: Library name: Sample 49


title: Cc10-Cre;Rhoafl/fl+CRE1

description:
Library name: D1
KO+CRE1


title: Cc10-Cre+CRE3

description:
Library name: C3
WT+CRE3

value: RhoAWT


title: APPLondon_2

description: Library name: Sample 48


title: pure_aHep_222 ATAC-seq

description: Library name: sample2

value: H9 hESC


title: 6C-P_rep1 ATAC-seq

description: Library name: sample7

value: Pluripotent stem cells derived hepatocytes


title: ATACseq, DMSO, 30 min, VEH, 45 min

data_processing:
Tags were aligned to human genome (hg19) using Bowtie (version 1.2.0).
Genome tracks have been generated using bamCoverage (deepTools) to convert aligned reads to signal tracks (bigwig) using RPKM normalization (bin size of 50 bps and 300 bps read extension).
Assembly: hg19
Supplementary files format and content: bigWig (Coverage files)

extract_protocol:
Nuclei were isolated from MCF-7 cells (50000 cells) and subjected to transposition reaction with home made Tn5 loaded with primers for NextSeq library preparation.
Libraries were prepared using NEBNext HF Polymerase with indexing primers from Nextera and sequenced using Illumina NextSeq 500.

value: 30 min DMSO + 45 min EtOH


title: Cc10-Cre+CRE2

description:
Library name: C2
WT+CRE2


title: ERA ChIPseq, VEH, 45 min

value: 45 min EtOH


title: biopsy sample CTR-24 batch 3

city: Philadelphia

first: Yusen

last: Zhou

address: 3401 Civic Center Blvd

department: Department of Biomedical and Health Informatics

institute: Children's Hospital of Philadelphia

description:
Library name: Sample 69
10x Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggrefation were made using the 10X Cellranger 3.1.0
Assembly: GRCh38
Supplementary files format and content: Tab-separated values files and matrix files

source_name: gastrointestinal tract

extract_protocol:
For detail information please visit our protocol for human tissue: Morral C, Ghinnagow R, Karakasheva T, et al. Isolation of Epithelial and Stromal Cells from Colon Tissues in Homeostasis and Under Inflammatory Conditions. Bio Protoc. 2023;13:e4825. doi: 10.21769/BioProtoc.4825
Single cell RNA-seq libraries were generated using Chromium Next GEM Single Cell 3' GEM, Library & Gel Bead Kit v3.1 (10X GENOMICS INC) as per manufacturer’s instructions. Illumina NovaSeq 6000 was used to sequence libraries using parameters Read1: index5: index7:Read2:: 28:8:0:87 or 28:10:10:90

value: gastrointestinal tract

value: epithelial, immune and stromal


title: APPctrl_3

description: Library name: Sample 46


title: APPctrl_2

description: Library name: Sample 45


title: Cc10-Cre+CRE1

description:
Library name: C1
WT+CRE1


title: biopsy sample CTR-26 batch 3

description:
Library name: Sample 68
10x Genomics


title: Replicate1, SVFcells with DMSO treatment

description:
Library name: Sample1
DMSO1 column in FPKM_anno

value: Gonadal tissue

value: Stromal Vascular Fraction

value: Mature adipocyte

value: WT

value: DMSO


title: APPLondon_1

description: Library name: Sample 47


title: pure_aHep_221 ATAC-seq

description: Library name: sample1


title: Cc10-Cre;Rhoafl/fl+PBS3

description:
Library name: B3
KO+PBS3

value: Lung

value: RhoACKO

value: PBS


title: shNIT2_Input

first: Ziyang

state: Guangdong

address: 58 Zhongshan Second Road

institute: The First Affiliated Hospital, Sun Yat-sen University

data_processing:
Raw reads were filtered to obtain high-quality clean reads by removing sequencing adapters, short reads (length <35 bp) and low quality reads using Cutadapt (v1.9.1) and Trimmomatic (v0.35).
Then FastQC is used to ensure high reads quality.
The clean reads were mapped to the human genome (assembly hg38) using the Bowtie2 (v2.2.6) software.
Peak detection was performed using the MACS (v2.1.1)  peak finding algorithm with 0.01 set as the p-value cutoff.
Annotation of peak sites to gene features was performed using the ChIPseeker R package.
Assembly: hg38
Supplementary files format and content: bigWig, narrowPeak (except for Input sample)

growth_protocol: DMEM, 10% fetal bovine serum, 1x penicillin/streptomycin. Cells were cultured at 37C at 5% CO2.

extract_protocol:
Cells were fixed with 1% formaldehyde for 10 minutes. After quenching and cell lysis, chromatin was sonicated.
After reverse crosslinking, ChIP and input DNA fragments were end-repaired and A-tailed using the NEBNext End Repair/dA-Tailing Module (E7442, NEB) followed by adaptor ligation with the NEBNext Ultra Ligation Module (E7445, NEB). The DNA libraries were amplified for 15 cycles and sequenced using Illumina NextSeq 500 with single-end 1x75 as the sequencing mode.

value: Human gastric cancer cell

tag: chip antibody


title: biopsy sample CTR-22 batch 3

description:
Library name: Sample 67
10x Genomics


title: APPctrl_1

description: Library name: Sample 44


title: biopsy sample CTR-22 batch 2

description:
Library name: Sample 66
10x Genomics


title: shNIT2_ChIP

value: H3K14ac (Cat#AB_2793634, Active Motif).


title: ATACseq, DMSO, 30 min, E2, 45 min

first: Felipe

address: Melchor Fernández Almagro 3

institute: CNIO

value: ER positive breast cancer cell line

value: 30 min DMSO + 45 min 10 nM E2


title: HBMEC_3D_replicate_5

description: Library name: Sample 43

source_name: Brain

value: Brain


title: Cc10-Cre;Rhoafl/fl+PBS1

description:
Library name: B1
KO+PBS1


title: ATACseq, ICRF-187, 30 min, E2, 45 min

value: 30 min ICRF-187 + 45 min 10 nM E2


title: ATACseq, ICRF-187, 30 min, VEH, 45 min

value: 30 min ICRF-187 + 45 min EtOH


title: shNT_Input

value: shNT


title: biopsy sample CTR-22 batch 1

description:
Library name: Sample 65
10x Genomics

value: gastrointestinal tract

value: epithelial, immune and stromal


title: Cc10-Cre+PBS3

description:
Library name: A3
WT+PBS3

value: RhoAWT


title: shNT_ChIP


title: HBMEC_3D_replicate_3

description: Library name: Sample 41


title: biopsy sample CTR-21 batch 3

description:
Library name: Sample 64
10x Genomics


title: SC12, scRNAseq

city: Xiamen

first: Jing

state: Fujian

address: 668 Jimei Road

department: School of Medicine and School of Biomedical Sciences

institute: Huaqiao University

description: 10x Genomics

data_processing:
CellRanger was used to base-calling, alignment, filtering and generation of normalized abundance measurements.
Read 1: contains the 16bp 10x barcode and the 10bp UMI (bases 17-26).Index contains the sample barcode. Read 2 contains the cDNA information
Assembly: GRCh38
Supplementary files format and content: gzip files and raw count matrix files

source_name: spinal cord

extract_protocol:
The spinal cord tissue was first digested in 2 mg/ml collagenase IV and 10 U/μl DNase I in hibernate E medium and then in 1 mg/ml papain in hibernate E medium. Further pipetting was used to fully digest the tissue into single cells and analyzed using scRNAseq.
scRNA-seq libraries were prepared per the Single Cell 30 Reagent Kit User Guide v3.1 (10x Genomics). Cellular suspensions were loaded on a Chromium Controller instrument (10x Genomics) to generate single-cell gel bead-inemulsions (GEMs). GEM-reverse transcriptions (GEM-RTs) were performed in a Veriti 96-well thermal cycler. After RT, GEMs were harvested and the cDNAs were amplified and cleaned up with the SPRIselect Reagent Kit (Beckman Coulter). Indexed sequencing libraries were constructed using the Chromium Single-Cell 30 Library Kit (10x Genomics) for enzymatic fragmentation, end-repair, A-tailing, adaptor ligation, ligation cleanup, sample index PCR, and PCR cleanup. The barcoded sequencing libraries were quantified by quantitative PCR using the KAPA Library Quantification Kit (KAPA Biosystems). Sequencing libraries were loaded on a NextSeq500 (Illumina) with a custom sequencing setting (26 bp for read 1 and 98 bp for read 2) to obtain a sequencing depth of _80,000 reads per cell.

value: neuron

value: spinal cord

tag: age


title: HPAEC, 10dyne 60mmHg, rep 2

city: Seattle

first: Christian

middle: J

last: Mandrycky

state: WA

address: 850 Republican St

department: Bioengineering

institute: University of Washington

data_processing:
RNA-Seq reads were aligned to hg38 using STAR (two pass mapping strategy) and counts were generated using the featureCounts function of the subRead package
Assembly: hg38
Supplementary files format and content: tab delimited file with raw counts for each sample

molecule: polyA RNA

source_name: human pulmonary arterial endothelial cells

growth_protocol: HPAEC were maintained in endothelial growth media (EGM, Lonza), at 37C with 5% CO2

extract_protocol:
RNA was isolated by perfusion of channels with lysis buffer and RNA purified using Qiagen RNeasy micro kits
RNA quality was evaluated using an Agilent Tapestation where all samples had RINe scores ≥ 9.7. Libraries were prepared from RNA samples using SMART-Seq v4 Ultra Low Input (Takara) and Nextera XT DNA Library Preparation (Illumina) kits.

treatment_protocol: HPAEC were cultured in microfluidic channels under static conditions for 24 hours and then subject to the specified shear and pressure conditions for 24 hours. The perfusion media was EGM supplemented with 3.5% dextran to mimic blood viscosity.

value: endothelial cell

value: WT

tag: shear

tag: pressure

tag: culture format

value: channel


title: SC10, scRNAseq

description: 10x Genomics


title: Cc10-Cre+PBS1

description:
Library name: A1
WT+PBS1

value: Lung

value: PBS


title: Treg-aGalcer-2

city: Nanjing

first: Yingyu

last: Qin

address: Southeast University Dingjiaqiao NO.87

institute: Southeast University

description: Library name: aGC-CLP2_007_S4

data_processing:
bcl2fastq2 Conversion Software v2.20
This data utilizes fastp v0.23.2 tool for data filtering, following the recommended parameters by fastq software.
After removing low-quality sequences, the data was processed using sortmerna v4.3.4 to filter out ribosomal RNA and then aligned to the reference genome (GRCm39) using STAR v2.7.10a. Alignment quality assessment was subsequently performed using RSeQC v4.0.0, QualiMap v2.2.2, featureCounts v2.0.1, and Preseq v3.
Assembly: mm10
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample
Supplementary files format and content: csv files include FPKM values for each Sample

source_name: Spleen

extract_protocol:
The isolated Treg cells with a purity about 90% were subjected to TRIzol treatment, and total RNA was extracted according to the manufacturer’s protocol.
RNA libraries for RNA-seq were prepared using VAHTS Universal V8 RNA-seq Library Prep Kit following manufacturer's protocols.

value: Spleen

value: T cell

value: aGalcer


title: rBMEC_3D_replicate_5

description: Library name: Sample 38


title: SC9, scRNAseq

description: 10x Genomics


title: HBMEC_3D_replicate_1

description: Library name: Sample 39

value: Brain


title: HPAEC, 10dyne 20mmHg, rep 3

value: human pulmonary arterial endothelial cells


title: Cc10-Cre;Rhoafl/fl+PBS2

description:
Library name: B2
KO+PBS2

value: RhoACKO


title: SC8, scRNAseq

description: 10x Genomics


title: HBMEC_3D_replicate_4

description: Library name: Sample 42


title: Treg-pbs-2

description: Library name: P-CLP2_007_S2


title: Treg-aGalcer-1

description: Library name: aGC-CLP1_007_S0


title: Proximal Lung Organoid, GFP Negative, Pseudovirus Infected

city: La Jolla

first: Sandra

middle: L.

last: Leibel

address: 9500 Gilman Dr

department: Pediatrics

institute: University of California, San Diego

description:
PLO_GFPneg_Pvpos
iPSC

data_processing:
Demultiplexing, barcoded processing, and gene counting were performed using the Cell Ranger software v4.0.0 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger).
Assembly: hg38
Supplementary files format and content: 10x Genomics Cellranger output files: barcodes.tsv.gz, features.tsv.gz, matrix.mtx.gz.

source_name: proximal lung organoid

extract_protocol: 10X Genomics scRNA-seq 3’ v3.1 kit (10X Genomics) was used to generate the GEM, cDNA and sequencing library according to the manufacturer’s instructions (10X Genomics).

value: proximal lung organoid

value: pseudovirus infected


title: rBMEC_3D_replicate_4

description: Library name: Sample 37


title: Treg-pbs-1

description: Library name: P-CLP1_007_S1


title: Proximal Lung Organoid, GFP Positive, Pseudovirus Infected

description:
PLO_GFPpos_Pvpos
iPSC


title: HPAEC, 10dyne 60mmHg, rep 3


title: rBMEC_3D_replicate_2

description: Library name: Sample 35


title: rBMEC_3D_replicate_3

description: Library name: Sample 36


title: NOR1_R4

city: qingdao

first: dingwen

last: cao

state: shandong

address: Yan Erdao Road, South District

institute: Shandong Academy of Eye Disease Prevention and Therapy

description:
Library name: sample_8
control Group, replicate biosample 4

data_processing:
CLC Genomics Workbench v 11.0.1
Sequence reads were trimmed for adaptor sequence/low-quality sequence using CLC genomic benchwork (parameter- Quality limit: 0.05)
Trimmed sequence reads were mapped to GrCM38/mm10 using CLC genomic benchwork (parameters- mismath cost: 2 insertion cost: 3 deletion cost: 3 length fraction: 0.8 similarity fraction: 0.8)
Read count extraction and normalization were performed using CLC genomic benchwork
Assembly: mm10
Supplementary files format and content: tab-delimited text file includes gene counts for each sample

source_name: spleen

extract_protocol: RNA libraries for RNA-seq were prepared using SMARTER mRNA-Seq Library Prep Kit following manufacturer's protocols.

treatment_protocol: RNA was harvested using Rneasy mini plus kit (Qiagen). 1.3 ug of total RNA was used for the construction of sequencing libraries.

value: spleen


title: Cc10-Cre+PBS2

description:
Library name: A2
WT+PBS2

value: RhoAWT


title: HBMEC_3D_replicate_2

description: Library name: Sample 40


title: Proximal Lung Organoid, SARS-CoV-2 Infected, iPSC SPB Mutant, Replicate 1

description:
PLO_Infected_SPBmutant_Rep1
iPSC

data_processing:
Demultiplexing, barcoded processing, and gene counting were performed using the Cell Ranger software v5.0.1 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger).
Assembly: hg38
Supplementary files format and content: 10x Genomics Cellranger output files: barcodes.tsv.gz, features.tsv.gz, matrix.mtx.gz.

value: SARS-CoV-2 Infected


title: rBMEC_3D_replicate_1

description: Library name: Sample 34


title: HPAEC, 10dyne 0mmHg, rep 3


title: NOR1_R3

description:
Library name: sample_7
control Group, replicate biosample 3


title: HPAEC, 10dyne 60mmHg, rep 1


title: HPAEC, 10dyne 0mmHg, rep 2


title: NOR1_R2

description:
Library name: sample_6
control Group, replicate biosample 2


title: Healthy Control cfRRBS, Replicate 2

city: Dunedin

first: Aniruddha

last: Chatterjee

state: Otago

address: 270 Great king Street

department: Pathology

country: New Zealand

institute: University of Otago

description:
Library name: cfRRBS2
The standard reduced representation bisulfite sequencing (RRBS) enriches for CpG-rich regions by size-selecting fragments between 40 and 220 bp after restriction digestion with enzymes such as MspI. However, this size range overlaps with the average size of cfDNA (150 – 200 bp), complicating CpG enrichment in cfDNA samples. Cell-free reduced representation bisulfite sequencing (cfRRBS) addresses this limitation by dephosphorylating the 5’ ends of the DNA. This is followed by the ligation of a custom adaptor that differentially binds cfDNA with MspI cut sites at both ends, thus making it possible to isolate on-target (CpG-rich) from off-target regions in the sample.

library_source: other

data_processing:
The sequenced data for both library construction methods was processed identically using the following bioinformatics pipeline: quality control was performed using the FASTQC tool, and adaptor/quality trimming was carried out using TrimGalore. For the cfRRBS libraries, the –rrbs option was used to remove 2 bp from the 3' end of the reads. This ensures that the filled-in cytosines introduced during end-repair at MspI cut sites are excluded from downstream methylation calling. The sequencing reads were then aligned to the reference human genome (hg19) using Bismark with no mismatch allowed (-N 0). Methylation calling was performed with the Bismark methylation extractor, and unique CpG dyads were quantified using the coverage2cytosine module.
Assembly: GRCh37/hg19
Supplementary files format and content: .cov file (which can also be viewed as a text file). Each line represents the chromosome number, start position, end position, beta methylation value, number of unmethylated cytosines, number of methylated cytosines.

molecule: other

source_name: Plasma

extract_protocol:
Cell-free DNA was extracted from 2-5 mLs of plasma using the QIAamp MinElute ccfDNA Midi Kit according to the manufacturer's instructions. cfDNA was quantified using the Qubit 4 fluorometer according to the Qubit dsDNAhigh-sensitivity assay kit protocol. An Agilent 2100 Bioanalyser instrument was used to assess the cfDNA quality to rule out possible genomic DNA contamination.
For the cfRRBS technique, 10 ng of cfDNA was dephosphorylated using recombinant shrimp alkaline phosphatase (rSAP). This was followed by endonuclease digestion suing the MspI restriction enzyme, then enr-repair and adenylation of the 3' ends. Followiing the ligation of custom adapters, exonucleases were used to degrade unligated and partially ligated DNA fragments. This was followed by the cleavage of adaptor hairpin using antarctic thermolabile UDG and endonuclease VII, thus generating single-stranded DNA required for bisultte conversion. The DNA was bisulfite-converted twice using the Epitect plus bisulfite kit. This was followed by PCR amplification using the NEBNext Multiplex Oligos for Illumina with the following conditions: 95 °C for 5 minutes, 16 cycles for 98 oC for 20 seconds, 65 oC for 15 seconds, 72 oC for 45 seconds, followed by a final extension at 72 oC for 5 minutes. The amplified libraries were then pruified using a 2.5x Ampure bead: library ratio. The purified DNA was assessed for quality using a Qubit 4 fluorometer (Thermofisher Scientific, USA) and BioAnalyser (Agilent, USA). For the EM-Seq technique, only the control DNA was sheared (i.e., CpG methylated pUC19 and unmethylated lambda DNA) to 300 bp using the Covaris M220 focused-ultrasonicator with 130 L microtube AFA Fibre pre-slit snap-cap tubes. Furthermore, a 2x bead purification protocol was used to purify the adaptor-ligated DNA, then 1.8x, 2x, and 1x bead purification protocols for the TET2-converted, deaminated, and amplified DNA, respectively. Each library was amplified using the following conditions: 98 oC for 30 seconds, 10 cycles for 98 oC for 10 seconds, 62 oC for 30 seconds, 65 oC for 60 seconds and a final extension at 65 oC for 5 minutes.

value: Plasma


title: Healthy Control cfRRBS, Replicate 1

description:
Library name: cfRRBS1
The standard reduced representation bisulfite sequencing (RRBS) enriches for CpG-rich regions by size-selecting fragments between 40 and 220 bp after restriction digestion with enzymes such as MspI. However, this size range overlaps with the average size of cfDNA (150 – 200 bp), complicating CpG enrichment in cfDNA samples. Cell-free reduced representation bisulfite sequencing (cfRRBS) addresses this limitation by dephosphorylating the 5’ ends of the DNA. This is followed by the ligation of a custom adaptor that differentially binds cfDNA with MspI cut sites at both ends, thus making it possible to isolate on-target (CpG-rich) from off-target regions in the sample.


title: Proximal Lung Organoid, SARS-CoV-2 Infected, iPSC 31616, Replicate 1

description:
PLO_Infected_3161_Rep1
iPSC


title: HPAEC, 10dyne 0mmHg, rep 1

value: endothelial cell


title: Healthy Control EM-Seq, Replicate 2

description:
Library name: EM-Seq2
EM-Seq is a whole-genome approach that uses the APOBEC3A enzyme to selectively deaminate unmethylated cytosines to thymines. The methylated cytosines remain unconverted.

data_processing:
The sequenced data for both library construction methods was processed identically using the following bioinformatics pipeline: quality control was performed using the FASTQC tool, and adaptor/quality trimming was carried out using TrimGalore. For the cfRRBS libraries, the –rrbs option was used to remove 2 bp from the 3' end of the reads. This ensures that the filled-in cytosines introduced during end-repair at MspI cut sites are excluded from downstream methylation calling. The sequencing reads were then aligned to the reference human genome (hg19) using Bismark with no mismatch allowed (-N 0). Methylation calling was performed with the Bismark methylation extractor, and unique CpG dyads were quantified using the coverage2cytosine module.
Assembly: GRCh37/hg19
Supplementary files format and content: .cov file (which can also be viewed as a text file). Each line represents the chromosome number, start position, end position, beta methylation value, number of unmethylated cytosines, number of methylated cytosines.
Library strategy: EM-seq


title: HPAEC, 5dyne 60mmHg, rep 3

value: WT


title: HPAEC, 10dyne 20mmHg, rep 2

value: channel


title: HSK1_R4

description:
Library name: sample_4
Infection Group, replicate biosample 4

value: infection of herpes simplex virus-1


title: NOR1_R1

description:
Library name: sample_5
control Group, replicate biosample 1


title: HPAEC, 10dyne 20mmHg, rep 1


title: Proximal Lung Organoid, SARS-CoV-2 Infected, iPSC Hyro, Replicate 1

description:
PLO_Infected_Hyro_Rep1
iPSC


title: Distal Lung Organoid, Normal, Replicate 1

description:
DLO_Control_Rep1
iPSC

source_name: distal lung organoid

value: distal lung organoid

value: Normal


title: Proximal Lung Organoid, Normal, Replicate 2

description:
PLO_Control_Rep2
iPSC


title: HSK1_R3

description:
Library name: sample_3
Infection Group, replicate biosample 3


title: HPAEC, 5dyne 60mmHg, rep 2


title: HPAEC, 5dyne 60mmHg, rep 1


title: Healthy Control EM-Seq, Replicate 1

description:
Library name: EM-Seq1
EM-Seq is a whole-genome approach that uses the APOBEC3A enzyme to selectively deaminate unmethylated cytosines to thymines. The methylated cytosines remain unconverted.


title: day3, lenti_ETV6-R369W, Meg01-ETV6-KO#4

city: Amsterdam

first: Emile

last: van den Akker

address: Plesmanlaan 125

country: Netherlands

institute: Sanquin Research Amsterdam

description:
Library name: sample 18
KO_mu_3
I24-1085-10

data_processing:
In the trimming, Illumina adapter and poly-A sequences were removed from the reads
The trimmed reads were then aligned using HISAT2 (Kim et al, 2019)
After the HISAT2 alignment, SAMTools (Li et al, 2009) was used to sort and merge the alignments from multiple flow cells.
Quantification was performed using HT-seq count (Anders et al, 2015) after first sorting the alignments on readname using SAMTools.
Assembly: GRCh38
Supplementary files format and content: tab-delimited text file includes raw counts for each sample

source_name: hematopoietic

extract_protocol:
RNA was isolated using TRIzol RNA isolation reagents (ThermoFisher Scientific)
RNA-Seq library was prepared for analysis according to the Illumina TruSeq stranded mRNA protocol (www.illumina.com).

value: hematopoietic

value: leukemic


title: HSK1_R2

description:
Library name: sample_2
Infection Group, replicate biosample 2


title: Proximal Lung Organoid, Uninfected Control in BSL3 Lab, Replicate 1

description:
PLO_Control_Rep1
iPSC

value: Uninfected Control


title: HPAEC, 5dyne 20mmHg, rep 2

value: human pulmonary arterial endothelial cells


title: HPAEC, 5dyne 20mmHg, rep 3


title: Proximal Lung Organoid, wild-type, SARS-CoV-2 infected, 24hr, replicate3

data_processing:
We used Cutadapt v2.3 to trim Illumina Truseq adapters, polyA, and polyT sequences. Trimmed reads were first aligned to SARS-CoV-2 genome version NC_045512v2 using STAR aligner v2.7.0d_0221 with parameters according to ENCODE long RNA-seq pipeline (https://github.com/ENCODE-DCC/long-rna-seq-pipeline). Unaligned reads to SARS-CoV-2 genome were subsequently mapped to human genome hg38 using STAR and parameters as above. Gene expression levels were quantified using RSEM v1.3.1 and Gencode gene annotations v32 (Ensembl 98).
Assembly: hg38
Supplementary files format and content: TPM.txt: Tab-delimited file containing TPM (transcripts per millions) for each sample.

extract_protocol:
RNA was purified from TRIzol lysates using Direct-zol RNA Microprep kits (Zymo Research R2061) according to manufacturer recommendations that included DNase treatment.
RNA-seq assay was performed using an Illumina NEXTSeq 500 platform. Briefly, PolyA RNA was isolated using the NEBNext® Poly(A) mRNA Magnetic Isolation Module and barcoded libraries were made using the NEBNext® Ultra II™ Directional RNA Library Prep Kit for Illumina® (NEB, Ipswich MA). Libraries were pooled and single end sequenced (1X75) on the Illumina NextSeq 500 using the High output V2 kit (Illumina Inc., San Diego CA).

value: wild-type

value: SARS-CoV-2 infected, 24 hr


title: HSK1_R1

description:
Library name: sample_1
Infection Group, replicate biosample 1


title: day3, lenti_ETV6-R369W, Meg01-ETV6-KO#1

description:
Library name: sample 16
KO_mu_1
I24-1085-05


title: Proximal Lung Organoid, SARS-CoV-2 Infected, iPSC GM23450, Replicate 1

description:
PLO_Infected_GM23450_Rep1
iPSC

value: proximal lung organoid


title: Control oligodendrocyte progenitors (Acly knockout)

first: Patrizia

last: Casaccia

address: 85 St Nicholas Terrace

department: Neuroscience

institute: ASRC-CUNY

data_processing:
Illumina Casava 1.8.2 software used for basecalling.
Sequencing data was processed with 10X Cell Ranger Count (v.7.1.0) and aggregation of Cntrl and Acly CKO OPCs was performed with 10X Cell Ranger Aggr (v.7.1.0). 10,611 OPCs were collected from Cntrl sample with mean reads per cell of 72,834. 11,338 OPCs were collected from Acly CKO sample with mean reads per cell of 69,183. Downstream analyses were performed using 10X Loupe Browser (v.8.0). Barcodes with fewer than 1,350 genes, or greater than 10,000 genes, were removed from analyses. Barcodes with greater than 5% mitochondrial reads were eliminated.
tsv files include barcodes, features and matrix information
Assembly: mm39
Supplementary files format and content: Tab separated values and matrix files

source_name: PDGFRa+ oligodendrocyte progenitor cells

extract_protocol:
RNA is extracted usign Trizol from FACS sorted cells
The 10X library construction protocol was followed without alteration. Single-cell cDNA libraries from individual cells were pooled and sequenced for at least 50,000 reads per cell on a Illumina Novaseq 6000 sequencer.

treatment_protocol: Tamoxifen-injected pups

tag: strain

value: conditional Acly knockout

tag: developmental stage

value: postnatal day 6-8


title: Proximal Lung Organoid, wild-type, SARS-CoV-2 infected, 24hr, replicate2


title: HPAEC, 5dyne 20mmHg, rep 1


title: day3, lenti_ETV6-R369W, Meg01-ETV6-KO#2

description:
Library name: sample 17
KO_mu_2
I24-1085-06


title: Proximal Lung Organoid, wild-type, SARS-CoV-2 infected, 24hr, replicate1


title: day3, lenti_ETV6-WT, Meg01-ETV6-KO#4

description:
Library name: sample 15
KO_WT_3
I24-1085-12


title: Control oligodendrocyte progenitors (Control A)

value: PDGFRa+ oligodendrocyte progenitor cells

value: Control


title: HPAEC, 5dyne 0mmHg, rep 2

value: endothelial cell


title: day3, lenti_ETV6-WT, Meg01-ETV6-KO#1

description:
Library name: sample 13
KO_WT_1
I24-1085-04


title: Proximal Lung Organoid, wild-type, SARS-CoV-2 infected, 3 hr, replicate2

value: SARS-CoV-2 infected, 3 hr


title: Metaphase I, replicate 20, scRNAseq

first: yue

last: wang

address: NJMU

institute: Nanjing Medical University

data_processing:
The 8-nt cell barcode sequence from reads 2 of the sequencing read pairs was added to read 1 using the “extract” tool in UMI-tools. Subsequently, the template switch oligo (TSO) sequence, ployA tail,and low-quality bases in reads 1 were removed via custom script and “trimfq” command in seqtk.Cleaned read 1 sequences were then aligned to the GRCm38 reference genome using STAR, and uniquely mapped reads were counted with featureCounts. Gene expression levels were quantified based on raw counts.
Assembly: GRCm38 reference genome using STAR
Supplementary files format and content: Text files

source_name: Testis

extract_protocol:
Pachytene spermatocytes were fractionated from centrifugal elutriation and resuspended in MEM-α (Gibco, 12571063) supplemented with 10 mM sodium lactate (Sigma, L4263), 5% (v/v) FBS (ABW, AB-FBS-0050), 25 μM HEPES (Gibco, REF15630-080) and 1% penicillin–streptomycin sulfate (Gibco, 15140-122). They were then treated with 4 μM okadaic acid (Absin, abs810018-50 μg) for additional 5 h to induce meiotic progression to metaphase I.
The preparation of scRNA-seq library was performed using the modified STRT-seq method. In brief, samples were incubated at 72°C for 3 min after vortexing for 60 s. Then, the first-strand cDNA was reverse-synthesized using oligo (dT) anchored with cell-specific barcodes and template-switching oligonucleotides (TSO). After that, the second-strand cDNAs were synthesized, and the cDNAs were amplified by 20 cycles of PCR. The single-cell PCR products were then pooled and purified. Next, biotinylated pre-indexed primers were used to amplify the PCR product for an additional four cycles of PCR, introducing biotin tags to the 3′ ends of the amplified cDNAs. About 200 ng of cDNA was sheared using the Hieff NGS Fast Tagment DNA Library Prep Kit for Illumina (Yeasen), according to the manufacturer’s instructions. Dynabeads® MyOne Streptavidin C1 beads (Thermo Fisher) were used to enrich for the 3' terminal cDNAs. The RNA-seq library was then constructed using a Kapa Hyper Prep Kit (Kapa Biosystems) and subjected to 150 bp paired-end sequencing on the NovaSeq 6000 (Illumina).
library was performed according to the manufacter's  using the Hieff NGS Fast Tagment DNA Library Prep Kit for Illumina (Yeasen), following the provided instructions(Hieff NGS Fast Tagment DNA Library Prep Kit for Illumina (Yeasen))

value: Testis

value: 6-8 weeks old

value: Metaphase I spermatocytes


title: day3, lenti_EV, Meg01-ETV6-KO#4

description:
Library name: sample 12
KO_3
I24-1085-18


title: Metaphase I, replicate 19, scRNAseq


title: Metaphase I, replicate 18, scRNAseq


title: Proximal Lung Organoid, wild-type, Control, replicate2


title: HPAEC, 5dyne 0mmHg, rep 1

value: WT

value: channel


title: Proximal Lung Organoid, wild-type, SARS-CoV-2 infected, 3 hr, replicate1


title: HPAEC, static channel, rep 3


title: day3, lenti_EV, Meg01-ETV6-KO#2

description:
Library name: sample 11
KO_2
I24-1085-17

value: hematopoietic

value: leukemic


title: Metaphase I, replicate 17, scRNAseq


title: day3, lenti_EV, Meg01-ETV6-KO#1

description:
Library name: sample 10
KO_1
I24-1085-16


title: Metaphase I, replicate 16, scRNAseq


title: HPAEC, static channel, rep 2

value: human pulmonary arterial endothelial cells


title: Proximal Lung Organoid, SPB mutant, SARS-CoV-2 infected, 24 hr, replicate2

value: SPB mutant


title: day3, lenti_ETV6-R369W, Meg01-WT#4

description:
Library name: sample 9
WT_mu_3
I24-1085-03


title: HPAEC, static channel, rep 1


title: Metaphase I, replicate 15, scRNAseq


title: Proximal Lung Organoid, SPB mutant, SARS-CoV-2 infected, 24 hr, replicate1

value: SARS-CoV-2 infected, 24 hr


title: day3, lenti_ETV6-R369W, Meg01-WT#3

description:
Library name: sample 8
WT_mu_2
I24-1085-02


title: HPAEC, static well, rep 3

value: well


title: HPAEC, 5dyne 0mmHg, rep 3


title: Proximal Lung Organoid, SPB mutant, SARS-CoV-2 infected, 3 hr, replicate3

value: proximal lung organoid


title: day3, lenti_ETV6-WT, Meg01-ETV6-KO#2

description:
Library name: sample 14
KO_WT_2
I24-1085-11


title: Metaphase I, replicate 13, scRNAseq


title: Metaphase I, replicate 14, scRNAseq


title: HPAEC, static well, rep 1


title: HPAEC, static well, rep 2


title: Proximal Lung Organoid, SPB mutant, SARS-CoV-2 infected, 3 hr, replicate1


title: Osteogenic differentiation, Fibrinogen-GelMA microspheres, and co-culture with PMSCs, LMSCs-PMSCs-GFHA,rep3

city: Chang chun

first: huixin

last: Lv

address: 1500 Tsinghua Road

institute: School and Hospital of Stomatology, Jilin University

data_processing:
Fastp software was used to process raw reads in fastq format, and clean reads were obtained after removing low-quality reads for subsequent data analysis.
The clean reads were mapped to the reference genome using HISAT2.
Fragments Per Kilobase of exon model per Million fragments mapped (FPKM) of each gene was calculated.
The read counts of each gene were obtained through HTSeq-count.
Assembly: GRCh38.p13
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

source_name: human maxillary sinus membrane

growth_protocol: Mesenchymal stem cells were maintained in MEM α supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37℃.

extract_protocol:
RNA was harvested using RNAiso reagent (TAKARA, USA). RNA purity and quantification were evaluated using the NanoDrop2000 Spectrophotometer (Thermo Scientific, USA). RNA integrity was assessed using the Agilent2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA).
The transcriptome libraries were constructed using VAHTS Universal V5 RNA-seq Library Prep Kit according to the manufacturer’s instructions.

treatment_protocol:
Osteogenic differentiation was induced by treatment of hLMSCs and hPMSCs with Osteogenic Differentiation Kits (Oricell).
The cells were cultured with the microspheres in normal complete medium (NCM) on the first day. For osteogenic induction, the medium was replaced by differentiation induction medium on the next day. The renewing time of the medium was 3 days.

value: human maxillary sinus membrane

value: mesenchymal stem cells

value: osteogenic differentiation, Fibrinogen-GelMA microspheres, and co-culture with PMSCs loaded Fibrinogen-GelMA microspheres using transwells


title: Proximal Lung Organoid, SPB mutant, SARS-CoV-2 infected, 3 hr, replicate2


title: Osteogenic differentiation, Fibrinogen-GelMA microspheres, and co-culture with PMSCs, LMSCs-PMSCs-GFHA,rep2


title: Proximal Lung Organoid, SPB mutant, Control, replicate3

value: Control


title: Proximal Lung Organoid, wild-type, Control, replicate1

value: wild-type


title: Ncs2elp6hel2_1_di

city: Bern

first: Jie

last: Wu

state: Bern

address: Freiestrasse 3

country: Switzerland

institute: Department of Chemistry, Biochemistry and Pharmaceutical Sciences

data_processing:
*library strategy: Ribosome Profiling
Sequencing data from ribosome profiling was pre-processed by removing the adapter using the Fasx_toolkit. Four randomized linker nucleotides at the 3' end were trimmed. If the library was generated by dual randomization, three nucleotides at the 5’ end and six at the 3' end were trimmed. The quality of data was evaluated using FastQC (v0.11.7). Processed reads were mapped to non-coding RNA, including rRNAs, tRNAs, snoRNAs and other annotated lncRNAs using STAR (v2.5.3a) to remove non-protein-coding reads. Remaining reads were subsequently mapped to all annotated open reading frames in yeast using bowtie (v1.2.3) with unique mapping mode allowing at most one nucleotide mismatch with parameters "-v 1 -m 1 --norc --best --strata".
Disome profiling data were pre-processed like monosome profiling. 56-64-nt-long footprints are kept for analysis.
Unique mapped reads for each CDS were quantified using a custom script.
Assembly: sacCer3
Supplementary files format and content: raw count matrix

organism: Saccharomyces cerevisiae

source_name: MATa his3Δ1 leu2Δ0 ura3Δ0 ncs2Δ::HIS3MX elp6Δ::URA3 hel2Δ::LEU2

growth_protocol: Cells were grown in YPD at 30C and 200 RPM

extract_protocol:
Cell lysates were digested with Rnase I, layared on top of a sucrose gradient and run on an ultracentrifuge. Gradients were then fracrionated. RNA from sucrose fractions containing monosomes or disomes was extracted with acidic phenol.
Libraries were prepared according to (McGlincy & Ingolia, 2017)

value: MATa his3{delta}1 leu2{delta}0 ura3{delta}0 ncs2{delta}::HIS3MX elp6{delta}::URA3 hel2{delta}::LEU2


title: Ncs2elp6hel2_2_di


title: Metaphase I, replicate 12, scRNAseq

value: Testis

value: 6-8 weeks old


title: Metaphase I, replicate 10, scRNAseq

value: Metaphase I spermatocytes


title: Metaphase I, replicate 11, scRNAseq


title: Metaphase I, replicate 9, scRNAseq


title: Proximal Lung Organoid, SPB mutant, Control, replicate2


title: Ncs2elp6_1_di

source_name: MATa his3Δ1 leu2Δ0 ura3Δ0 ncs2Δ::HIS3MX elp6Δ::URA3

value: MATa his3{delta}1 leu2{delta}0 ura3{delta}0 ncs2{delta}::HIS3MX elp6{delta}::URA3


title: Osteogenic differentiation, Fibrinogen-GelMA microspheres, and co-culture with PMSCs, LMSCs-PMSCs-GFHA,rep1


title: Proximal Lung Organoid, SPB mutant, Control, replicate1


title: Metaphase I, replicate 8, scRNAseq


title: Hel2_2_di

source_name: MATa his3Δ1 leu2Δ0 ura3Δ0 hel2Δ::LEU2

value: MATa his3{delta}1 leu2{delta}0 ura3{delta}0 hel2{delta}::LEU2


title: MCF-7 cells_c-KIT_OE_+DOX+TAM_Day5_PROSeq_2

city: ITHACA

first: BROOKE

last: MARKS

state: NEW YORK

address: HUNGERFORD ROAD

institute: CORNELL UNIVERSITY

description: nascent RNA

data_processing:
sgRNA DNA: Genome index was made of the sgRNA DNA sequencing library using bwa index. Then DESeq2 was used to perform differential expression analysis of the number of sgRNAs in different conditions
PRO-seq: Differential expression analysis using DESeq2 was used to process data.
Supplementary files format and content: sgRNA DNA: Genome index was made of the sgRNA DNA sequencing library using bwa index
Supplementary files format and content: PRO-seq: hg38

growth_protocol: Cells were grown in Dulbecco’s Modified Eagle Medium (DMEM) supplemented using a specific lot (Seradigm; Lot # 335B15) of 5% fetal bovine serum (FBS) that tested negative for TET activity and 1X Antibiotic-Antimycotic (Gibco; Cat#15240-062).

extract_protocol:
sgRNA DNA sequencing: The extraction protocol to prepare genomic sgRNA DNA was performed following the “Illumina Sequencing Sample Preparation for use with CRISPRi/a-v2 Libraries” protocol (https://media.addgene.org/cms/filer_public/d3/bb/d3bb61d4-a453-4c65-903a-a7672ab71ae2/illuminasequencingsampleprep.pdf), with minor modifications described in our manuscript.
PRO-Seq: Nuclei were extracted and material was prepared following https://doi.org/10.1126/SCIENCE.1229386 and https://doi.org/10.1038/nprot.2016.086 protocols.
sgRNA DNA library construction was prepared followed in “Illumina Sequencing Sample Preparation for use with CRISPRi/a-v2 Libraries” protocol ((https://media.addgene.org/cms/filer_public/d3/bb/d3bb61d4-a453-4c65-903a-a7672ab71ae2/illuminasequencingsampleprep.pdf) with the minor modifications described in our manuscript.
PRO-seq RNA libraries were prepared for sequencing using standard Illumina protocols
sgRNA DNA sequencing and PRO-seq

treatment_protocol:
sgRNA DNA sequencing: Cells were then plated into four polystyrene CellSTACK 5-layer chambers (Corning, cat# 3319) at 106,000,000 cells per CellSTACK. DOX or vehicle control was added to each chamber. Then, TAM or vehicle control (with DOX or vehicle control) was added to the media after 12-24hrs. Media was replaced every 48hrs. Cells were treated with vehicle or DOX and with vehicle or TAM for 20 days.
PRO-Seq: Cells were treated with DOX or vehicle control for 24hrs, or with DOX or vehicle and TAM for 5 days. Media was replated every 48hrs.

value: Breast Cancer

value: Inducible c-KIT overexpressing

value: +DOX+TAM

tag: treatment time

value: 5 day treatment


title: day3, lenti_ETV6-R369W, Meg01-WT#2

description:
Library name: sample 7
WT_mu_1
I24-1085-01

value: hematopoietic

value: leukemic

value: WT


title: Osteogenic differentiation, Fibrinogen-GelMA microspheres, LMSCs-GFHA,rep2

value: human maxillary sinus membrane

value: mesenchymal stem cells

value: osteogenic differentiation, Fibrinogen-GelMA microspheres


title: Metaphase I, replicate 7, scRNAseq


title: Hel2_1_di


title: MCF-7 cells_c-KIT_OE_+DOX+TAM_Day5_PROSeq_1

description: nascent RNA


title: wt_2_di

source_name: MATa his3Δ1 leu2Δ0 ura3Δ0 met15Δ0

value: MATa his3{delta}1 leu2{delta}0 ura3{delta}0 met15{delta}0


title: Metaphase I, replicate 6, scRNAseq


title: Osteogenic differentiation, Fibrinogen-GelMA microspheres, LMSCs-GFHA,rep1


title: Ncs2elp6_2_di


title: wt_1_di


title: Osteogenic differentiation, Fibrinogen-GelMA microspheres, LMSCs,rep3


title: Metaphase I, replicate 5, scRNAseq


title: Ncs2elp6hel2_2_mono

value: MATa his3{delta}1 leu2{delta}0 ura3{delta}0 ncs2{delta}::HIS3MX elp6{delta}::URA3 hel2{delta}::LEU2


title: MCF-7 cells_c-KIT_OE_-DOX+TAM_Day5_PROSeq_1

description: nascent RNA

value: -DOX+TAM


title: Osteogenic differentiation, Fibrinogen-GelMA microspheres, LMSCs,rep2


title: Metaphase I, replicate 4, scRNAseq

value: Testis

value: 6-8 weeks old


title: MCF-7 cells_c-KIT_OE_+DOX_24hrs_PROSeq_2

description: nascent RNA

value: +DOX

value: 24hr treatment


title: Ncs2elp6hel2_1_mono


title: Osteogenic differentiation, Fibrinogen-GelMA microspheres, LMSCs,rep1


title: Osteogenic differentiation, Fibrinogen-GelMA microspheres, LMSCs-GFHA,rep3


title: Metaphase I, replicate 3, scRNAseq

value: Metaphase I spermatocytes


title: Osteogenic differentiation, GelMA microspheres, LMSCs-PMSCs,rep3

value: osteogenic differentiation, GelMA microspheres


title: MCF-7 cells_c-KIT_OE_+DOX_24hrs_PROSeq_1

description: nascent RNA

value: Breast Cancer

value: Inducible c-KIT overexpressing


title: MCF-7 cells_c-KIT_OE_-DOX_24hrs_PROSeq_2

description: nascent RNA

value: -DOX


title: Metaphase I, replicate 2, scRNAseq


title: Ncs2elp6_3_mono

value: MATa his3{delta}1 leu2{delta}0 ura3{delta}0 ncs2{delta}::HIS3MX elp6{delta}::URA3


title: Osteogenic differentiation, GelMA microspheres, LMSCs-PMSCs,rep2


title: Osteogenic differentiation, GelMA microspheres, LMSCs-PMSCs,rep1


title: MCF-7 cells_c-KIT_OE_-DOX_24hrs_PROSeq_1

description: nascent RNA


title: Ncs2elp6_2_mono


title: Metaphase I, replicate 1, scRNAseq


title: MCF7_NT2_RNAseq

city: Pittsburgh

first: Da

last: Yang

address: 308 Salk Pavilion

institute: University of Pittsburgh

data_processing:
Reads were aligned using STAR.
Gene expression quantification and differential expression analysis were done by cuffdiff.
Assembly: hg38
Supplementary files format and content: RNAseq_fpkm_cdk, comma-separated values file include gene expression analysis result

source_name: Mammary gland/Breast

extract_protocol:
Total RNA was isolated using RNeasy Mini Kit (Qiagen). 10 µg total RNA was treated with RNase-free DNase I (Promega) for 30 min at 37 °C and RNA cleanup was performed using the RNA Clean & Concentrator-5 columns (Zymo). 1 µg of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using KAPA RNA Hyper RiboErase HMR (96 rxn) following manufacturer's protocols.

value: Mammary gland/Breast

value: Human epithelial cell

value: nontargeting control2


title: Pachytene, replicate 20, scRNAseq

value: pachytene spermatocytes


title: Hel2_2_mono

value: MATa his3{delta}1 leu2{delta}0 ura3{delta}0 hel2{delta}::LEU2


title: MCF-7 cells_c-KIT_OE_-DOX+TAM_Day5_PROSeq_2

description: nascent RNA

value: 5 day treatment


title: Pachytene, replicate 19, scRNAseq


title: MCF-7 cells_+DOX+TAM_Day20_sgRNAlibrary_1

description: sgRNA DNA

value: Inducible sgRNA overexpressing

value: +DOX+TAM

value: 20 day treatment


title: MCF7_NT1_RNAseq

value: nontargeting control1


title: MCF-7 cells_+DOX+TAM_Day20_sgRNAlibrary_2

description: sgRNA DNA


title: Pachytene, replicate 17, scRNAseq

value: Testis

value: 6-8 weeks old


title: wt_3_mono

value: MATa his3{delta}1 leu2{delta}0 ura3{delta}0 met15{delta}0


title: Pachytene, replicate 18, scRNAseq


title: MCF7_ENSG226706_RNAseq

value: ENSG00000226706 activation


title: MCF-7 cells_+DOX-TAM_Day20_sgRNAlibrary_2

description: sgRNA DNA

value: Breast Cancer

value: +DOX-TAM


title: wt_2_mono


title: MCF7_LINC01117_RNAseq

value: LINC01117 activation


title: MCF-7 cells_-DOX+TAM_Day20_sgRNAlibrary_2

description: sgRNA DNA

value: -DOX+TAM


title: MCF7_TENM3as_RNAseq

value: Mammary gland/Breast

value: Human epithelial cell

value: TENM3-as1 activation


title: MCF-7 cells_+DOX-TAM_Day20_sgRNAlibrary_1

description: sgRNA DNA


title: Pachytene, replicate 16, scRNAseq

value: pachytene spermatocytes


title: MCF-7 cells_-DOX+TAM_Day20_sgRNAlibrary_1

description: sgRNA DNA


title: Ncs2elp6_1_mono

value: MATa his3{delta}1 leu2{delta}0 ura3{delta}0 ncs2{delta}::HIS3MX elp6{delta}::URA3


title: Ncs2elp6hel2_3_5p

data_processing:
*library strategy: 5P-seq
Adapter sequences were trimmed by cutadapt using parameters "-m 10 -a GATCGGAAGAGCACACGTCTGAACTCCAGTC". Untrimmed reads were also retained for downstream analysis due to the long insert size. The processed reads were mapped to non-coding RNA using STAR (v2.5.3a). The remaining reads were mapped to all annotated open reading frames in yeast using bowtie (v1.2.3) using the same parameters as for the analysis of ribosome profiling data. PCR duplicates were further removed using UMI-tools with 8 nt randomized barcodes at the 5' end of sequencing reads. The 3-nt periodicity of reads was also evaluated. Unique mapped reads were quantified using a custom script.
Assembly: sacCer3
Supplementary files format and content: 5P raw count matrix

extract_protocol:
Total RNA was extracted with acidic phenol
Libraries were prepared according to (Zhang & Pelechano, 2021)

value: MATa his3{delta}1 leu2{delta}0 ura3{delta}0 ncs2{delta}::HIS3MX elp6{delta}::URA3 hel2{delta}::LEU2


title: Pachytene, replicate 14, scRNAseq


title: MCF-7 cells_-DOX-TAM_Day20_sgRNAlibrary_2

description: sgRNA DNA

value: Inducible sgRNA overexpressing

value: -DOX-TAM


title: MCF-7 cells_-DOX-TAM_Day20_sgRNAlibrary_1

description: sgRNA DNA

value: 20 day treatment


title: Ncs2elp6hel2_1_5p


title: cdk1

data_processing:
MAGeCK (v0.5.9.4)  was used for sgRNA quantification and MAGeCK-mle algorithm was then used for the candidate gene selection with nontargeting control sgRNAs for normalization and generation of the null distribution.
Using the GENCODE v19 annotation, we re-annotated Human CRISPR lncRNA Activation Pooled Library originally built on the hg19.refGene.gtf and CabiliSuppDataSet1_lincRNAs_transcripts.gtf. Each sgRNA sequence was considered as a DNA motif and HOMER ‘find’ function was used to identify the loci of the sgRNAs. The transcripts with at least two sgRNAs mapped to their promoters (-1000 b to + 100 b of TSS) were considered as targets of the sgRNAs in the re-annotated library.
Assembly: hg19
Supplementary files format and content: totalcount_CDK_genomewide, comma-separated values file include sgRNA annotation and read count in five samples.
Supplementary files format and content: combine_mcf.count, comma-separated values file include sgRNA annotation and read count in six samples.
Library strategy: PCR amplified library

source_name: targeted screen condition: no drug treatment (4 weeks)

extract_protocol:
Genomic DNA was harvested from the survived cells after the screen maintained coverage of >500 cells expressing each sgRNA used the Zymo Research Quick-DNA Midiprep plus kit (Zymo Research, #FD4075) according to the manufacturer’s protocol.
The extracted genomic DNA was used for PCR using NEBNext High Fidelity 2 X PCR Master Mix (NEB, #M0541S). The NGS primers that amplify the sgRNA library were listed in the protocol.

value: Breast


title: cdk2

source_name: targeted screen condition: Palbociclib treatment


title: Ncs2elp6hel2_2_5p


title: Pachytene, replicate 13, scRNAseq

value: Testis

value: 6-8 weeks old


title: Pachytene, replicate 12, scRNAseq


title: Pachytene, replicate 10, scRNAseq


title: Ncs2elp6_3_5p


title: wt_1_mono

value: MATa his3{delta}1 leu2{delta}0 ura3{delta}0 met15{delta}0


title: Pachytene, replicate 15, scRNAseq


title: H2BW2 Stable HeLa cell_ChIP2

city: Hong Kong

first: Toyotaka

last: Ishibashi

address: Rm6260, Academic Building, HKUST, Clear Water Bay, Kowloon

department: Division of Life Science

country: Hong Kong

institute: The Hong Kong University of Science and Technology

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to hg19 whole genome using bowtie2 version 2.4.2  with default parameters in Galaxy.
Duplicate molecules were marked with MarkDuplicates with default paprameters.
Peak calling was achieved with MACS2 call peak Version 2.1.1.20160309 with default parameters.
Assembly: hg19
Supplementary files format and content: peak bed file

source_name: HeLa cell

growth_protocol: Flag-H2BFW2 stable expressed HeLa cell was maintained in DMEM with 10% (v/v) fetal bovine serum (FBS; GIBCO) and 1% Pen/Strep (GIBCO) in a 37 °C incubator under stable 5 % CO2 atmosphere

extract_protocol:
The ChIP-seq from formalin-fixed paraffin-embedded testes slides is as follows. Briefly, 20 human testis sections (10 µm) were deparaffinized and rehydrated. The tissue sections were then collected and washed by 600 µl wash buffer (1x PBS, 0.5% Tween 20), followed by a 30 mins treatment with 1 µg of RNAse (Invitrogen) and three-times wash with lysis buffer (0.2x PBS, 0.1% Tween 20, 40 mM Tris-HCl pH 7.5, 4 mM MgCl2, 1 mM CaCl2). After incubation, 600 µl of lysis buffer was added to the sample, and then it was treated with 0.5 units of MNase for 5 mins at 37 ℃. The reaction was stopped by adding EDTA to the final concentration of 15 mM, and 0.06 units of Thermolabile Proteinase K (NEB) were added with incubation at 37 ℃ for 30 mins. The proteinase K reaction was stopped by incubating at 65 ℃ for 20 mins, then the samples were sonicated until the DNA fragment size became around 150-300 bp. The sample was used to perform H2BW2 IP following standard IP method with homemade anti-H2BW2 antibody (peptide synthesis based polyclonal rabbit antibody, RGSRRRHANRRGDS). To elute the DNA, 2 μl of proteinase K (NEB) was added to the sample and incubated at 65℃ overnight and DNA was extracted with a regular PCR clean-up kit. The Flag-H2BW2 stable expression HeLa cell Ch-IP experiment was performed based on ANTI-FLAG® M2 Affinity Gel based on the manufacture’s instruction of Pierce™ Agarose ChIP Kit (Thermo Fisher Scientific).
The DNA library was prepared following the instruction mentioned in ThruPLEX DNA-Seq Kit (Takara) with pair-end primer.

treatment_protocol: Flag-H2BW2 expression was induced with 0.3ug/mL doxycycline for 12 hours. Medium was changed back to regular DMEM with 10% (v/v) fetal bovine serum (FBS; GIBCO) and 1% Pen/Strep (GIBCO) and keep for 12 hours.

value: cervical epithelial cell

value: HeLa CCL-2

tag: disease state

value: cervical carcinoma

value: ANTI-FLAG M2 Affinity Gel (Sigma, A2220)

value: 0.3ug/mL doxycycline for 12 hours


title: H2BW2 Stable HeLa cell_Input2

tag: cell line


title: H2BW2 Stable HeLa cell_Input1


title: p14b

tag: cell type

value: Human epithelial cell


title: cdk3


title: Pachytene, replicate 9, scRNAseq


title: Ncs2elp6_2_5p


title: H2BW2 Stable HeLa cell_ChIP1

tag: treatment


title: S5_genomewide

source_name: genome-wide screen condition: Palbociclib treatment


title: Hel2_1_mono

tag: genotype

value: MATa his3{delta}1 leu2{delta}0 ura3{delta}0 hel2{delta}::LEU2


title: Hel2_3_5p


title: S4_genomewide

tag: tissue


title: Pachytene, replicate 8, scRNAseq

value: pachytene spermatocytes


title: Hel2_2_5p


title: H2BW2_Input2

value: 30 years old

value: Donor with testicular cancer and tissue used within normal region.


title: Pachytene, replicate 7, scRNAseq


title: S3_genomewide

source_name: genome-wide screen condition: no drug treatment (4 weeks)


title: Pachytene, replicate 6, scRNAseq


title: H2BW2_ChIP2

value: custom antibody:Synthesized peptide using the H2BW2 peptide sequence (41-55 aa, RGSRRRHANRRGDS)


title: Hel2_1_5p


title: H2BW2_Input1

value: 18 years old


title: Pachytene, replicate 11, scRNAseq


title: p14a

source_name: targeted screen condition: no drug treatment (2 weeks)


title: p0

source_name: targeted screen condition: plasmid


title: S2_genomewide

source_name: genome-wide screen condition: no drug treatment (2 weeks)


title: Ncs2elp6_1_5p

value: MATa his3{delta}1 leu2{delta}0 ura3{delta}0 ncs2{delta}::HIS3MX elp6{delta}::URA3


title: Pachytene, replicate 5, scRNAseq


title: wt_2_5p


title: S1_genomewide

source_name: genome-wide screen condition: plasmid

value: Breast


title: Pachytene, replicate 4, scRNAseq

value: Testis


title: H2BW2_ChIP1


title: SUM159-R cells treated with dual compounds

data_processing:
Gene expression was defined by FPKM value (fragments per kilobase of exon per million fragments mapped) using RSEM software. Bioinformatics analysis was performed using Omicsmart, a dynamic and interactive online platform for data analysis (https://www.omicsmart.com). A log2 (fold change) >2 and a false discovery rate (FDR) < 0.01 were used as cut-off thresholds.
Assembly: hg38
Supplementary files format and content: FPKM

growth_protocol: SUM159 and its resistant derives were cultured in Ham’s F-12 Nutrient Mix medium with L-Glutamine (Gibco®) and supplemented with 5% FBS, 10mM HEPES (Gibco®), 5ng/ml Insulin, 1μg/ml hydrocortisone and 5000U/mL penicillin/streptomycin.The resistant cell lines were maintained in 150nM Paclitaxel

extract_protocol:
Total RNA was extracted using a mini-RNA isolation kit (cat. no.74106; Qiagen, Germany) and transcribed to cDNA with random primers.
The cDNA was ligated to Illumina sequencing adaptors and sequenced on the Illumina NovaSeq6000 by Gene Denovo Biotechnology Co. (Guangzhou, China).

treatment_protocol: Paclitaxel, 500nM,24h; Enzastaurin,2.5uM,24h; or dual compounds

value: paclitaxel-resistant TNBCs

value: WT

value: dual compounds


title: wt_3_5p

value: MATa his3{delta}1 leu2{delta}0 ura3{delta}0 met15{delta}0


title: wt_1_5p


title: LM-MEL-28-LPC-rep3

city: Melbourne

first: Pacman

last: Szeto

state: VIC

address: 89 Commercial Road

department: Medicine

country: Australia

institute: Monash University

data_processing:
FASTQ files were processed using Laxy (https://zenodo.org/record/3767372) which encompasses the RNAsik pipeline (https://joss.theoj.org/papers/10.21105/joss.00583). Briefly, GRCm38 reference genome was used for STAR alignment (PubmedID: 23104886)
Genome_build: GRCh38
Supplementary_files_format_and_content: Raw gene count matrix

source_name: melanoma

growth_protocol: The short-term human LM-MEL-28 patient-derived cell line was a kind gift from Dr Andreas Behren at the Olivia Newton-John Cancer Research Institute, and cultured in RPMI-1640 supplemented with 10% FBS and 1% penicillin/streptomycin.

extract_protocol:
Total cell RNA was extracted from FACS-purified LPC or HPC populations using the PureLink RNA Mini kit (ThermoFisher), according to the manufacturer’s instructions, including an on-column DNase treatment.
RNA was quantitated using Qubit RNA HS (Thermo Fisher Scientific) and 100 ng total RNA input was used for library preparation according to standard protocols (QuantSeq 3’ mRNA-Seq FWD, Lexogen). Indexed libraries were pooled and sequenced on a NextSeq 500 sequencer (Illumina).

value: human melanoma cell line

value: Low-pigmented


title: Pachytene, replicate 2, scRNAseq

source_name: Testis

value: 6-8 weeks old


title: LM-MEL-28-LPC-rep2


title: day3, lenti_ETV6-WT, Meg01-WT#3

description:
Library name: sample 5
WT_WT_2
I24-1085-08

source_name: hematopoietic

value: hematopoietic

value: leukemic


title: Pachytene, replicate 3, scRNAseq

value: pachytene spermatocytes


title: day3, lenti_ETV6-WT, Meg01-WT#4

description:
Library name: sample 6
WT_WT_3
I24-1085-09


title: LM-MEL-28-LPC-rep1


title: LM-MEL-28-HPC-rep3

value: High-pigmented


title: SUM159-R cells treated with DMSO

value: DMSO


title: LM-MEL-28-HPC-rep2


title: hepa1-6-soat1-ko-3

city: Shanghai

first: guangchuan

last: Wang

state: Shanghai

address: 320 Yue Yang Road

institute: Chinese Academy of Sciences

data_processing:
HISAT2
Assembly: tab-delimited text file includes raw counts for each sample
Supplementary files format and content: tab-delimited text file include RPKM values for each sample

source_name: cell

extract_protocol:
Total RNA was extracted using the TRIzol reagent (Invitrogen, CA, USA) according to the manufacturer’s protocol. RNA purity and quantification were evaluated using the NanoDrop 2000 spectrophotometer (Thermo Scientific, USA). RNA integrity was assessed using the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA).
the libraries were constructed using VAHTS Universal V6 RNA-seq Library Prep Kit according to the manufacturer’s instructions.

value: cell

value: Liver cancer cell

value: Soat1 knockdown

value: Normal culture


title: day3, lenti_EV, Meg01-WT#4

description:
Library name: sample 3
WT_4
I24-1085-15


title: hepa1-6-soat1-ko-2


title: LM-MEL-28-HPC-rep1


title: Pachytene, replicate 1, scRNAseq

value: Testis


title: A_SP-D_2

city: Odense M

first: Kim

last: Ravnskjaer

address: Campusvej 55

department: Department of Biochemistry and Molecular Biology

country: Denmark

institute: University of Southern Denmark

data_processing:
Initial filtering for high-quality reads was perfomed using CutAdapt. STAR (v. 2.7.0a) was used for alligning reads to the hg38 genome, and featureCounts (v.2.0.0)  for read annotation using the GRCh38 gtf file.
Assembly: hg38
Supplementary files format and content: raw count matrix

source_name: lung

growth_protocol: Non-small lung cancer cell line A549 was obtained from the ATCC (Middlesex, UK). All cells were cultured in RPMI-1640 medium, supplemented with 10% fetal bovine serum (FBS, 0010, ScienCell) and 1% penicillin-streptomycin (P/S, 0503, ScienCell).

extract_protocol:
Whole-cell RNA was extracted according to the manufacturer’s instructions by Trizol reagent (Ambion, Austin, TX). The Qubit 3.0 Fluorometer (Thermo Fisher Scientific) was used for RNA quantity measurement and RNA quality was measured by the Fragment Analyzer 5200 (Agilent, Santa Clara, CA).
According to the manufacture's protocol, libraries were constructed using the NEBNext Ultra RNA Library Prep Kit for Illumina and paired-end sequencing.

treatment_protocol: A549 cells were treated with recombinant human SP-D protein (10µg/ml) or vehicle for 48h. Vehicle treatment is the same volume of buffer used for elution of SP-D after purification.

value: lung

value: adenocarcinomic human alveolar basal epithelial cells

value: rhSP-D


title: A_SP-D_3


title: hepa1-6-soat1-ko-1


title: day3, lenti_EV, Meg01-WT#2

description:
Library name: sample 1
WT_2
I24-1085-13

value: WT


title: hepa1-6-vector-3


title: 6day_PCBP2_KD_b3

city: Fort Collins

first: Carol

last: Wilusz

state: Colorado

address: 1682 Campus Delivery

department: Microbiology, Immunology and Patholgy

institute: Colorado State University

data_processing:
Quality of sequence reads was assessed via FastQC v0.11.5.  Reads were trimmed of adaptor sequences and filtered for low-complexity or low-quality reads via Trimmomatic v0.32.  rRNA reads were filtered out using Bowtie2 v2.3.4.3 (Langmead and Salzberg, 2012) and a reference fasta file of mature 5S, 18S and 28S rRNA named mature_rRNA.fasta. Filtered reads were mapped to the hg19 genome using TopHat2 v2.0.12 (Kim et al., 2013) under default parameters.  The output .bam alignment files were converted to .bam.tdf format using igv-tools and read distributions were viewed on IGV v2.3.91.  RNA-seq alignment files in .sam format were utilized to calculate read counts associated with each transcript using HTSeq v0.11.1 (Anders et al., 2015), Samtools v1.9 (Li et al., 2009) and the hg19 genome feature file obtained from GENCODE (hg19, Ensembl 74).  The HTseq function htseq-count was used with the following options: --stranded=no --minaqual=20.  Raw counts generated by this analysis can be found in the documents 2day_raw_counts.txt and 6day_raw_counts.txt. Raw count data was filtered for detectable genes (> 30 total counts across all samples of a specified treatment), imported into R and analyzed using DESeq2 v1.22.1 (Love et al., 2014) under default parameters.  Results of the DESeq2 analysis can be found in the document 2day_DESeq_results.xlsx and 6day_DESeq_results.xlsx.
Genome_build: hg19
Supplementary_files_format_and_content: .tdf files: IGV-ready alignment files for individual samples.  *_HTseq_raw_counts.txt file: Tab-delimited text files of raw read counts generated by HTseq.   *_DESeq_results.xlsx: Excel files of DESeq2 results. hg19_gene_annotations.gtf.gz:  Gene annotation file used for calculating raw read counts with HTSeq. mature_rRNA.fasta.gz: Fasta file containing the mature rRNA sequences used for rRNA filtering.

source_name: induced pluripotent stem cell

growth_protocol: iPSCs (System Biosciences, #SC101A-iPSC, Lot #110415-01) were cultured on Matrigel (Corning #354277) in mTeSR1 media (STEMCELL Technologies, #85850) at 37°C in 5% CO2. Plates were coated with MatriGel in accordance with manufacturer protocols, MatriGel was diluted in DMEM/F12 (+ L-glutamine, + 15 mM HEPES, - phenol red; Gibco, #11039-021).

extract_protocol:
Total RNA extractions were performed in accordance with recommended protocols (Invitrogen, #15596026).
Libraries were constructed from 500 ng of total RNA using the SMARTer™ PCR cDNA Synthesis Kit (Clontech, #634926) and Advantage 2 PCR kit (Clontech, #639207) followed by Tn5-mediated tagmentation.

treatment_protocol: For 2 day knockdown, cells were grown for five days after passage before being transfected with an siRNA targeting PCBP2 or a negative scrambled control using Stemfect RNA Transfection kit (Stemgent, #00-0069). Transfection was repeated 24 hours later and cells were collected 24 hours after the second transfection. For 6 day knockdown samples, cells were grown for one day after passage before being transfected using the same protocol. Cells were transfected daily for five days and collected 24 hours after the last transfection. Cells were harvested in TRIzol Reagent (Invitrogen, #15596026) and stored at -80°C.

value: Fibroblast-derived stem cell

value: KD

tag: duration