title: Human breast cancer patient9

description:
Single-base extension was performed using hapten-labeled dideoxynucleotides, followed by multi-layered fluorescent staining with streptavidin-Cy3 and anti-DNP-Cy5 to detect incorporated labels.
Methylation analysis was performed of ER-positive tumors to identify tumor-intrinsic characteristics associated with immune responsiveness. The S04 epithelial cell state was associated with immune responsiveness while the S05 epithelial cell trate predicted immune evasion.
Illumina EPIC v1-0_B5 array
KAPE1_9472.v1_2R03C01


title: Human breast cancer patient10

status: Public on Jul 30 2025

type: genomic

city: Gothenburg

first: Axel

last: Stenmark Tullberg

address: Bla Straket

department: Department of Oncology

country: Sweden

institute: University of Gothenburg

description:
Single-base extension was performed using hapten-labeled dideoxynucleotides, followed by multi-layered fluorescent staining with streptavidin-Cy3 and anti-DNP-Cy5 to detect incorporated labels.
Methylation analysis was performed of ER-positive tumors to identify tumor-intrinsic characteristics associated with immune responsiveness. The S04 epithelial cell state was associated with immune responsiveness while the S05 epithelial cell trate predicted immune evasion.
Illumina EPIC v1-0_B5 array
KAPE1_10070.v1_2R05C01

hyb_protocol: Bisulfite-converted DNA was hybridized to the Illumina Infinium Methylation EPIC array (MethylationEPIC_v-1-0_B5) according to the manufacturer's standard Infinium HD Methylation Assay protocol.

scan_protocol: Illumina Infinium-compatible scanner

data_processing:
Raw intensity data (IDAT files) from the Illumina Infinium Methylation EPIC array were processed using GenomeStudio (v2011.1) from Illumina Inc. Data processing included background subtraction and normalization using GenomeStudio's 'Normalization Controls' feature, as per Illumina's recommendations. Samples were considered acceptable if their probe call rate exceeded 98% at a detection p-value of 0.01. Individual marker loci with a detection p-value > 0.01 were excluded. Processed data refers to Beta values mapped to Genome Build 37 (hg19). The final methylation profile is provided in a matrix format.
Processed values are reported as Beta values, representing the methylation level at each CpG site. Beta values range from 0 (completely unmethylated) to 1 (fully methylated).

label: Cy3 and Cy5

molecule: genomic DNA

organism: Homo sapiens

source_name: Breast cancer

label_protocol: Genomic DNA (250 ng per sample) underwent bisulfite conversion using the EZ DNA Methylation Kit (Zymo Research, Product No: D5004) according to the manufacturer's protocol. Bisulfite-converted DNA was eluted in 15µl, evaporated to a volume of <4µl, and then processed for the Illumina Infinium Methylation EPIC array.

growth_protocol: Samples were cryopreserved

extract_protocol: Genomic DNA was extracted from fresh-frozen or formalin-fixed paraffin-embedded samples using a standard spin-column based DNA extraction method, according to established laboratory protocols.

treatment_protocol: No treatment

tag: tissue

value: Breast cancer

tag: treatment

value: Pretreatment

value: Positive

tag: proliferativeindex

tag: immunescore


title: Human breast cancer patient12

description:
Single-base extension was performed using hapten-labeled dideoxynucleotides, followed by multi-layered fluorescent staining with streptavidin-Cy3 and anti-DNP-Cy5 to detect incorporated labels.
Methylation analysis was performed of ER-positive tumors to identify tumor-intrinsic characteristics associated with immune responsiveness. The S04 epithelial cell state was associated with immune responsiveness while the S05 epithelial cell trate predicted immune evasion.
Illumina EPIC v1-0_B5 array
KAPE1_7449.v2_3R01C01


title: Human breast cancer patient8

description:
Single-base extension was performed using hapten-labeled dideoxynucleotides, followed by multi-layered fluorescent staining with streptavidin-Cy3 and anti-DNP-Cy5 to detect incorporated labels.
Methylation analysis was performed of ER-positive tumors to identify tumor-intrinsic characteristics associated with immune responsiveness. The S04 epithelial cell state was associated with immune responsiveness while the S05 epithelial cell trate predicted immune evasion.
Illumina EPIC v1-0_B5 array
KAPE1_9828.v2_2R02C01


title: 0618-CiPS-2#

type: SRA

city: Beijing

first: Ruoqi

last: Cheng

state: Beijing

address: NO.5, Yiheyuan Road, Haidian District

department: School of Life Sciences

country: China

institute: Peking University

description: Library name: 0618-CiPS-2#

library_source: genomic

data_processing:
We followed the standard Bismark workflow to perform mapping, deduplication, and methylation extraction (https://github.com/FelixKrueger/ Bismark) for all our samples. Only CpG sites were used for further analysis.
Assembly: hg38
Supplementary files format and content: bw files for each sample

extract_protocol:
The genomic DNA were extracted using EasyPure Genomic DNA Kit (TransGen).
DNA were denatured and bisulﬁte converted using EZ DNA Methylation-GoldTM Kit (Zymo Research). The recovered bisulﬁte-converted DNAs were constructed into sequencing libraries. For each library, 90 Gb raw data was obtained by nova X plus sequencing (Novogene).

tag: cell line

tag: cell type

value: ADSC derived hCiPSC

tag: genotype

value: WT


title: 1217-CiPS-2#

description: Library name: 1217-CiPS-2#


title: 1217-CiPS-3#

description: Library name: 1217-CiPS-3#


title: Human breast cancer patient7

description:
Single-base extension was performed using hapten-labeled dideoxynucleotides, followed by multi-layered fluorescent staining with streptavidin-Cy3 and anti-DNP-Cy5 to detect incorporated labels.
Methylation analysis was performed of ER-positive tumors to identify tumor-intrinsic characteristics associated with immune responsiveness. The S04 epithelial cell state was associated with immune responsiveness while the S05 epithelial cell trate predicted immune evasion.
Illumina EPIC v1-0_B5 array
KAPE1_10991.v1_2R01C01


title: 0618-CiPS-1#

description: Library name: 0618-CiPS-1#


title: AraArabidopsis Thaliana, SR, treated, rep#2

city: Chicago

first: Cheng-Wei

last: Ju

state: Illinois

address: 929 East 57th Street, GCIS, Room E313

country: USA

institute: The University of Chicago

library_source: transcriptomic

data_processing:
The sequencing data were all trimmed with cutadapt tool (v4.8) to remove adapters and low-quality reads. PCR duplicates were removed with BBMap tool (v.38.73), 5-mer random barcodes at reads ends were trimmed and low-quality or short reads (less than 20 nt) were removed using cutadapt tool.
For tRNAs, remaining reads were aligned to tRNA sequence obtained from GtRNAdb (https://gtrnadb.ucsc.edu/) using hisat-3n (v.2.2.1-3n-0.0.3). Mitochondria and chloroplast tRNA sequences are obtained from published papers.
Meanwhile, we have also aligned remaining reads to hg38, mm10, or TAIR10 genome using hisat3n to investigate D sites in other RNA species.
The generated table from hisat-3n were parsed and analyzed by inhouse scripts. Internal mutation ratio at each D candidate site suggested by hisat-3n, was further confirmed by direct IGV visualization (v.2.8.0).
Assembly: mm10 (GRCm38.102), hg38 (GRCh38.107), TAIR10
Supplementary files format and content: For samples with cellular RNA, the mutation ratio at D sites in treated, input samples are shown. For samples with RNA probes, mutations at D sites are shown.
Library strategy: Chemical Reduction Assisted Cytosine Incorporation sequencing (CRACI)

molecule: total RNA

organism: Arabidopsis thaliana

source_name: SR

growth_protocol: Human HepG2 cell lines and mouse embryonic stem cells (mESC) used in this study were all purchased from ATCC (the American Type Culture Collection). HepG2 cell lines were maintained in DMEM (GIBCO, 11995), supplemented with 10% FBS and 1% 100X Pen/Strep (GIBCO). mESC cells were grown under a typical feeder-free culture condition: cells were cultured in DMEM (GIBCO, 11995), supplemented with 15% FBS, 1% Pen/Strep (GIBCO), 1X Glutamax (GIBCO), 1X non-essential amino acids (GIBCO), 1X 2-Mercaptoethanol (GIBCO), and 1000 U/ml leukemia inhibitory factor (Millipore, ESG1107), together with two inhibitors: 3 mM CHIR99021 (STEMCELL Technologies, dissolved in DMSO) and 1 mM PD0325901 (STEMCELL Technologies, dissolved in DMSO). mESC cells were distinctively cultured on gelatinized culture plates (0.2% Gelatin). The culture of mESC cells were passaged every 2 days. All cells were cultured at 37 Co under 5.0% CO2.

extract_protocol:
Generally, with harvesting cells as the first step, the media was aspirated, and the cells were washed once with proper volume of ice cold DPBS buffer for each plate. Then total RNA was isolated from cells with TRIzol reagent (Invitrogen) and then extracted following manufacturer’s protocol by isopropanol precipitation. Small RNA fraction was purified from total RNA with RNA Clean & Concentrator kit (Zymo Research) following manufacturer’s protocol. mRNA was extracted by two rounds of polyA+ purification with Dynabeads mRNA DIRECT kit (Ambion).
CRACI for D site detection Wild-type HepG2, mESC, and arabidopsis thaliana seedling cells (two replicates for each sample, one 10-cm plate per replicate); HepG2 siControl or DUS knockdown cells were prepared as described (two replicates for each sample, one 10-cm plate per replicate). After extracting the polyA+ RNA or small RNA from mammalian cells or plant cells, around 100 ng RNA was fragmented using RNA Fragmentation Reagents (catalog no. AM8740, Invitrogen) and heated at 70 °C for 14 min, followed by purification with Oligomer Clean and Concentrator (Zymo Research). 3′-End repair and 5′-phosphorylation were conducted with T4 polynucleotide kinase (PNK) (catalog no. EK0032, Thermo Fisher Scientific). RNA was mixed with 3 µL 10× T4 PNK reaction buffer (catalog no. B0201S, NEB) and 3 µl T4 PNK, diluted to a final volume of 30 µl, and incubated at 37 °C for 45 min; then 1.5 µl T4 PNK and 1.5 µl 10 mM ATP were added for another incubation at 37 °C for 45 min, followed by Oligomer Clean and Concentrator (Zymo Research) purification eluting with 10 µl RNase-free water.  To perform 3′-adapter ligation, 10 µl 3′-repaired and 5′-phosphorylated RNA fragments were incubated with 1.0 µl 20 µM RNA 3′ SR Adapter (5′App-NNNNNATCACG AGATCGGAAGAGCACACGTCT-3SpC3, with ATCACG as the inline barcode) at 70 °C for 2 mins and placed immediately on ice. Then, 2.5 µl 10× T4 RNA Ligase Reaction Buffer (catalog no. M0373L, NEB), 7.5 µl PEG8000 (50%), 1 µl SUPERase•In RNase Inhibitor and 2 µl T4 RNA Ligase 2 truncated KQ (catalog no. M0373L, NEB) were added to the RNA–adapter mixture48,49. The reaction was incubated at 25 °C for 2 h followed by 16 °C for 10 h. The reaction was further diluted to 47 µl with nuclease-free water, and the excessive adapters were removed with 2 µl 5′-deadenylase (catalog no. M0331S, NEB) at 30 °C for 45 min followed by adding 1 µl RecJf (catalog no. M0264L, NEB) for ssDNA digestion at 37 °C for 45 min. The 3′-end-ligated RNA was extracted by RNA Clean and Concentrator (Zymo Research) and eluted with 10 µl RNase-free water. The purified RNA was incubated with 1.2 µl 10 µM 5′ SR Adapter (5′-GUUCAGAGUUCUACAGUCCGACGAUC -3′) at 70 °C for 2 mins and placed immediately on ice. Then 2.5 µl 10× T4 RNA ligase reaction buffer, 1.0 µl 25 mM ATP, 10 µl PEG8000 (50%) and 1 µl T4 RNA Ligase 1 (high concentration, catalog no. M0437M, NEB) were added to the RNA–adapter mixture. The reaction was mixed well and incubated at 25 °C for 8 h, followed by RNA Clean and Concentrator (Zymo Research) purification, eluting with 12 µl RNase-free water.  A 2 µl aliquot of the purified RNA was saved for ‘Input1’ library construction, 2 µl aliquot of the purified RNA was saved for ‘Input2’ library construction, and the rest 6 µl was subjected to CRACI optimized reduction treatment, as the ‘Treated’ sample. The 6 µl RNA was mixed with 40 µl freshly prepared KBH4 (1 M KBH4, prepared by dissolving 54 mg KBH4 in 1000 µl RNase-free water) and Incubated the reaction mixture at 25 °C for 3 h, followed by purification with RNA Clean and Concentrator (Zymo Research) and elute with 10 µl H2O. ‘Input1’, ‘Input2’ and purified ‘Treated’ samples were diluted to 10 µl and mixed with 1.0 µl 2.0 µM SR RT primer (5′-AGACGTGTGCTCTTCCGATCT -3′) at 65 °C for 2 min and moved immediately onto ice. Then for ‘Input2’ and ‘Treated’ samples, a stock with 2 µl 10x AMV RT Buffer (New England BioLabs, cat. no. B0277AVIAL), 2 µl 1 mM dNTP Solution Mix (dilute from 10 mM dNTP Solution Mix, New England BioLabs, catalog no. N0447L), 2 µl 10mM dGTP (dilute from 100 mM dNTP Solution Mix, New England BioLabs, catalog no. N0442S), 1 µl RNaseOUT Recombinant Ribonuclease Inhibitor (catalog no. 10777019, Thermo Scientific) and 2 µl HIV RT (Worthington Biochemical, catalog no. LS05003) was added. For ‘Input1’ sample, a stock with 2 µl RNase-free water, 2 µl 10x AMV RT Buffer, 2 µl 10 mM dNTP Solution Mix (New England BioLabs, catalog no. N0447L), 1 µl RNaseOUT Recombinant Ribonuclease Inhibitor and 2 µl HIV RT was added.  The reaction mixture was heated at 70 °C for 5 min and then cDNA was purified using DNA Clean and Concentrator (Zymo Research). The eluted cDNAs (20 µl) were stored at –80 °C; 4 µl was used for each 15-cycle PCR amplification reaction, which was performed with the SR Primer for Illumina (NEB) and indexed primers (from NEBNext Multiplex Oligos for Illumina). All libraries were purified on a 3.5% low melting point agarose gel and sequenced on Illumina NovaSeqX with single-end 100 bp read length.

value: SR

tag: fraction

value: small RNA (<200 nt)


title: Human breast cancer patient6

description:
Single-base extension was performed using hapten-labeled dideoxynucleotides, followed by multi-layered fluorescent staining with streptavidin-Cy3 and anti-DNP-Cy5 to detect incorporated labels.
Methylation analysis was performed of ER-positive tumors to identify tumor-intrinsic characteristics associated with immune responsiveness. The S04 epithelial cell state was associated with immune responsiveness while the S05 epithelial cell trate predicted immune evasion.
Illumina EPIC v1-0_B5 array
KAPE1_11092.v1_1R08C01


title: Z0684-CiPS-4#

description: Library name: Z0684-CiPS-4#

value: EPC derived hCiPSC


title: Human breast cancer patient15

description:
Single-base extension was performed using hapten-labeled dideoxynucleotides, followed by multi-layered fluorescent staining with streptavidin-Cy3 and anti-DNP-Cy5 to detect incorporated labels.
Methylation analysis was performed of ER-positive tumors to identify tumor-intrinsic characteristics associated with immune responsiveness. The S04 epithelial cell state was associated with immune responsiveness while the S05 epithelial cell trate predicted immune evasion.
Illumina EPIC v1-0_B5 array
KAPE1_8905.v1_3R04C01


title: AraArabidopsis Thaliana, SR, treated, rep#1


title: Z0684-CiPS-1#

description: Library name: Z0684-CiPS-1#


title: YB3271-CiPS-7#

description: Library name: YB3271-CiPS-7#


title: Human breast cancer patient5

description:
Single-base extension was performed using hapten-labeled dideoxynucleotides, followed by multi-layered fluorescent staining with streptavidin-Cy3 and anti-DNP-Cy5 to detect incorporated labels.
Methylation analysis was performed of ER-positive tumors to identify tumor-intrinsic characteristics associated with immune responsiveness. The S04 epithelial cell state was associated with immune responsiveness while the S05 epithelial cell trate predicted immune evasion.
Illumina EPIC v1-0_B5 array
KAPE1_11018.v1_1R07C01


title: YB3271-CiPS-6#

description: Library name: YB3271-CiPS-6#


title: YB3272-CiPS-3#

description: Library name: YB3272-CiPS-3#


title: Human breast cancer patient3

description:
Single-base extension was performed using hapten-labeled dideoxynucleotides, followed by multi-layered fluorescent staining with streptavidin-Cy3 and anti-DNP-Cy5 to detect incorporated labels.
Methylation analysis was performed of ER-positive tumors to identify tumor-intrinsic characteristics associated with immune responsiveness. The S04 epithelial cell state was associated with immune responsiveness while the S05 epithelial cell trate predicted immune evasion.
Illumina EPIC v1-0_B5 array
KAPE1_5456.v1_1R05C01


title: Human breast cancer patient4

description:
Single-base extension was performed using hapten-labeled dideoxynucleotides, followed by multi-layered fluorescent staining with streptavidin-Cy3 and anti-DNP-Cy5 to detect incorporated labels.
Methylation analysis was performed of ER-positive tumors to identify tumor-intrinsic characteristics associated with immune responsiveness. The S04 epithelial cell state was associated with immune responsiveness while the S05 epithelial cell trate predicted immune evasion.
Illumina EPIC v1-0_B5 array
KAPE1_11153.v2_1R06C01


title: AraArabidopsis Thaliana, SR, input2, rep#1


title: 5034CBMC-CiPS-14#

description: Library name: 5034CBMC-CiPS-14#


title: AraArabidopsis Thaliana, SR, input1, rep#2


title: AraArabidopsis Thaliana, SR, input2, rep#2


title: 5034CBMC-CiPS-1#

description: Library name: 5034CBMC-CiPS-1#


title: Human breast cancer patient2

description:
Single-base extension was performed using hapten-labeled dideoxynucleotides, followed by multi-layered fluorescent staining with streptavidin-Cy3 and anti-DNP-Cy5 to detect incorporated labels.
Methylation analysis was performed of ER-positive tumors to identify tumor-intrinsic characteristics associated with immune responsiveness. The S04 epithelial cell state was associated with immune responsiveness while the S05 epithelial cell trate predicted immune evasion.
Illumina EPIC v1-0_B5 array
KAPE1_9114.v1_1R03C01


title: FOXO1-KO_LPS-3

city: Guangzhou

first: Yongjian

last: zhou

address: No.1, Pan Fu Road, Yuexiu District

institute: Guangzhou First People’s Hospital

description:
Library name: sample6
FOXO1-KO_LPS-3_fpkm

data_processing:
Reads obtained from the sequencing machines includes raw reads containing adapters or low quality bases which will affect the following assembly and analysis. Thus, to get high quality clean reads, reads were further filtered by fastp  (version 0.18.0).
Short reads alignment tool Bowtie2  (version 2.2.8) was used for mapping reads to ribosome RNA (rRNA) database. The rRNA mapped reads then will be removed. The remaining clean reads were further used in assembly and gene abundance calculation.
An index of the reference genome was built, and paired-end clean reads were mapped to the reference genome using HISAT2 2.1.0 and other parameters set as a default.
The mapped reads of each sample were assembled by using StringTie v1.3.1 in a reference_x0002_based approach. For each transcription region, a FPKM (fragment per kilobase of transcript per million mapped reads) value was calculated to quantify its expression abundance and variations, using RSEM software.
Assembly: Grch38
Supplementary files format and content: excel files include raw counts and FPKM values for each Sample

molecule: polyA RNA

source_name: liver

extract_protocol:
total RNA was extracted by Trizol(Life technologies)
The extracted mRNA is enriched using mRNA Capture Beads. After purification with beads, the mRNA is fragmented using high temperatures. The fragmented mRNA is then used as a template to synthesize the first strand of cDNA in a reverse transcription enzyme mixture system. While synthesizing the second strand of cDNA, end repair and A-tailing are completed. Next, adapters are ligated, and Hieff NGS® DNA Selection Beads are used for purification to select target fragments.

value: liver

value: Hepatocyte/Cancer cells

value: FoxO1 knockdown

value: LPS


title: FOXO1-KO_LPS-1

description:
Library name: sample4
FOXO1-KO_LPS-1_fpkm


title: Human breast cancer patient1

description:
Single-base extension was performed using hapten-labeled dideoxynucleotides, followed by multi-layered fluorescent staining with streptavidin-Cy3 and anti-DNP-Cy5 to detect incorporated labels.
Methylation analysis was performed of ER-positive tumors to identify tumor-intrinsic characteristics associated with immune responsiveness. The S04 epithelial cell state was associated with immune responsiveness while the S05 epithelial cell trate predicted immune evasion.
Illumina EPIC v1-0_B5 array
KAPE1_9002.v1_1R02C01


title: AraArabidopsis Thaliana, SR, input1, rep#1


title: FOXO1-KO_LPS-2

description:
Library name: sample5
FOXO1-KO_LPS-2_fpkm


title: Rdh10 KO input

city: La Jolla

first: Gregg

last: Duester

state: CA

address: 10901 North Torrey Pines Road

department: Center for Cardiovascular and Muscular Diseases

institute: Sanford Burnham Prebys Medical Discovery Institute

description: Library name: Rdh10_KO_input

data_processing:
Reads were trimmed using Cutadapt version 2.3. Trimmed reads were first aligned to mouse genome version mm10 chrM to remove mitochondrial reads using bowtie2 version 2.2.5 and parameters “--local -X 2000”. Unaligned reads were subsequently aligned to mouse genome version mm10 using bowtie2 and parameters “--very-sensitive --no-discordant -X 2000”. Low quality alignments were removed and properly aligned reads were retained using alignmentSieve version 3.4.3 with parameters “--ATACshift --minMappingQuality 30 --samFlagInclude 2”. Duplicate reads were removed using Picard MarkDuplicates version 2.22.0. ChIP-seq signal in bigwig format was generated using bamCoverage version 3.4.3 and parameters “--binSize 20 -p 12 --normalizeUsing CPM --extendReads --smoothLength 60”.
Assembly: mm10
Supplementary files format and content: ChIP-seq normalized signal in bigwig format

organism: Mus musculus

source_name: Embryonic craniofacial

extract_protocol:
For ChIP-seq we used trunk tissue from E10 wild-type or Rdh10-/- embryos dissected in modified PBS, i.e. phosphate-buffered saline containing 1X complete protease inhibitors (concentration recommended by use of soluble EDTA-free tablets sold by Roche #11873580001) and 10 mM  sodium butyrate as a histone deacetylase inhibitor (Sigma # B5887).
Samples were processed similar to previous methods (Berenguer et al., PLOS Biology 2020). Dissected face tissues were briefly centrifuged in 1.5 ml tubes and excess PBS dissection buffer was removed. For cross-linking of chromatin DNA and proteins, 500 ml 1% formaldehyde was added, the trunk samples were minced by pipetting up and down with a 200 ml pipette tip and then incubated at room temperature for 15 min. To stop the cross-linking reaction, 55 ml of 1.25 M glycine was added and samples were rocked at room temperature for 5 min. Samples were centrifuged at 5000 rpm for 5 min and the supernatant was carefully removed and discarded. A wash was performed in which 1000 ml of ice-cold modified PBS was added and mixed by vortex followed by centrifugation at 5000 rpm for 5 min and careful removal of supernatant that was discarded. This wash was repeated. Cross-linked trunk samples were stored at -80C until enough were collected to proceed, i.e. 100 wild-type trunks and 100 Aldh1a2-/- trunks to perform ChIP-seq with two antibodies in duplicate. Chromatin was fragmented by sonication. Cross-linked trunk samples were pooled, briefly centrifuged, and excess PBS removed. 490 ml lysis buffer (modified PBS containing 1% SDS, 10 mM EDTA, 50 mM Tris-HCl, pH 8.0) was added, mixed by vortexing, then samples were incubated on ice for 10 min. Samples were divided into four sonication microtubes (Covaris AFA Fiber Pre-Slit Snap-Cap 6x16 mm, #520045) with 120 ml per tube. Sonication was performed with a Covaris Sonicator with the following settings - Duty: 5%, Cycle: 200, Intensity: 4, #Cycles: 10, 60 sec each for a total sonication time of 14 min. The contents of the four tubes were re-combined by transfer to a single 1.5 ml microtube which was then centrifuged for 10 min at 13,000 rpm and the supernatants transferred to a fresh 1.5 ml microtube. These conditions were found to shear trunk DNA to an average size of 300 bp using a 5 ml sample for Bioanalyzer analysis. At this point 20 ml was removed for each sample (wild-type trunks and Aldh1a2-/- trunks) and stored at -20C to serve as input DNA for ChIP-seq. Each sample was divided into four 100 ml aliquots to perform immunoprecipitation with ChIP-grade antibodies for H3K27ac (Active Motif, Cat#39133) in triplicate. Immunoprecipitation was performed using the Pierce Magnetic ChIP Kit (Thermo Scientific, #26157) following the manufacturer’s instructions. The immunoprecipitated samples and input samples were subjected to reversal of cross-linking by adding water to 500 ml and 20 ml 5 M NaCl, vortexing and incubation at 65C for 4 hr; then addition of 2.6 ml RNase (10 mg/ml), vortexing and incubation at 37C for 30 min; then addition of 10 ml 0.5 M EDTA, 20 ml 1 M Tris-HCl, pH 8.0, 2 ml proteinase K (10 mg/ml), vortexing and incubation at 45C for 1 hr. DNA was extracted using ChIP DNA Clean & Concentrator (Zymo, # D5201 & D5205), After elution from the column in 50 ml of elution buffer, the DNA concentration was determine using 2 ml samples for Bioanalyzer analysis. The two input samples ranged from 16-20 ng/ml and the eight immunoprecipitated samples ranged from 0.1-0.2ng/ml (5-10 ng per 100 trunks). For ChIP-seq, 2 ng was used per sample to prepare libraries for DNA sequencing.

value: Embryonic craniofacial

value: Rdh10 KO


title: WT_LPS-2

description:
Library name: sample2
WT_LPS-2_fpkm


title: Space_methylation [206667650068_R06C01]

city: Montreal

first: Luda

last: Diatchenko

state: Quebec

address: 3775 Rue University

country: Canada

institute: McGill University

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

scan_protocol: Arrays were imaged using Illumina iScan system

data_processing:
Genomestudio v2011
Average Beta

source_name: Blood

label_protocol: Standard Illumina Protocol

extract_protocol: genomic DNA was extracted and purified from TMD samples using Qiagen Extraction Kit according to standard instructions

value: Blood


title: WT_LPS-1

description:
Library name: sample1
WT_LPS-1_fpkm


title: Rdh10 KO eye H3K27ac, rep2

description: Library name: Rdh10_KO_eye_H3K27ac_rep2


title: Space_methylation [206667650069_R05C01]


title: Space_methylation [206677660051_R03C01]


title: blood,Control,rep11

city: 河南

first: Li

last: Yusheng

state: 河南

address: 八号楼四楼

institute: 郑州大学第一附属医院

description: Library name: Control11

data_processing:
The raw data in Fastq format is first processed to remove sequences containing adapters, poly-N sequences, and low-quality reads to obtain clean data. The clean data is then aligned to the reference genome sequence. HISAT2 version 2.1.0 is used to align the sequences to the human reference genome GRCh38. Subsequently, StringTie is used to calculate the expression level of each gene, and the transcripts are quantified in terms of Fragments Per Kilobase of transcript per Million mapped reads (FPKM).
Assembly: HG38
Supplementary files format and content: csv files include FPKM values for each Sample

source_name: blood

extract_protocol:
The total RNA from animal tissues was extracted using TRlzol Reagent (Life Technologies, California, USA) according to the manufacturer’s instructions.1.3 ug of total RNA was used for the construction of sequencing libraries.
The total amount of starting material for each sample is 1 μg. Following the manufacturer's instructions, sequencing libraries are generated using the Hieff NGS Ultima Dual-mode mRNA Library Prep Kit for Illumina (Yeasen Biotechnology (Shanghai) Co., Ltd.), with an index added to the sequences of each sample. In brief, mRNA is isolated from total RNA using magnetic beads with oligo(dT). First-strand cDNA is synthesized, followed by second-strand cDNA synthesis. The blunt ends are repaired and converted to blunt ends through exonuclease and polymerase activities. After the DNA fragments are adenylated at the 3' end, they are ligated with NEBNext adapters that have a hairpin loop structure. Library fragments are purified using AMPure XP beads (Beckman Coulter, Beverly, USA). Then, 3 μl of USER Enzyme (NEB, USA) is added and incubated at 37°C for 15 minutes, followed by a 5-minute reaction at 95°C prior to PCR. PCR amplification is performed using high-fidelity DNA polymerase, universal PCR primers, and index (X) primers. Finally, PCR products are purified (AMPure XP beads) and the library quality is assessed using an Agilent Bioanalyzer 2100 system.

value: blood

tag: subject status

value: Control


title: blood,Control,rep10

description: Library name: Control10


title: YB3272-CiPS-4#

description: Library name: YB3272-CiPS-4#


title: blood,Control,rep9

description: Library name: Control9


title: blood,Control,rep8

description: Library name: Control8


title: Rdh10 KO eye H3K27ac, rep1

description: Library name: Rdh10_KO_eye_H3K27ac_rep1


title: blood,Control,rep7

description: Library name: Control7


title: WT eye input

description: Library name: WT_eye_input


title: Space_methylation [206667650062_R05C01]


title: WT_LPS-3

description:
Library name: sample3
WT_LPS-3_fpkm


title: blood,Control,rep5

description: Library name: Control5


title: Space_methylation [206667650093_R06C01]


title: WT eye H3K27ac, rep1

description: Library name: WT_eye_H3K27ac_rep1


title: blood,Control,rep6

description: Library name: Control6


title: blood,Control,rep4

description: Library name: Control4


title: blood,Control,rep3

description: Library name: Control3


title: WT eye H3K27ac, rep2

description: Library name: WT_eye_H3K27ac_rep2


title: blood,CAA,rep11

description: Library name: CAA11

value: CAA


title: control volunteer 006 [YSL]

city: Nanjing

first: Qiong

last: Li

state: Jiangsu

address: Dingjiaqiao Road 87#

institute: Southeast University

description: plasma cell free DNA from control volunteer

hyb_protocol: Hybridization protocolBisulphite converted DNA was amplified, fragmented and hybridised toIllumina Infinium MethylationEPIc Beadchip using standard Illumina protocol

scan_protocol: Arrays were imaged using Illumina iscan System using standardrecommended lllumina scanner setting

data_processing: IDAT files were processed using ChAMp R packages

label_protocol: Standard lllumina Protocol

extract_protocol: Genomic DNA from each cell line was extracted using the QIAamp DNA miniKit (Qiagen, Hilden, Germany)and quantified using Nanodrop (ThermoFisher).

value: plasma cell

value: plasma cell-free DNA


title: control volunteer 005 [XR]


title: blood,CAA,rep10

description: Library name: CAA10


title: blood,CAA,rep9

description: Library name: CAA9


title: 504838

type: protein

city: San Francisco

first: Denise

middle: M

last: Wolf

address: 2340 Sutter st

institute: University of California, San Francisco

data_processing: Samples from the Ganitumab arm, and a subset the control arm patients, were assayed on a new RPPA array (RPPA.4).  three different RPPA arrays (RPPA.1, RPPA.2 and RPPA.3) under GPL28470.  This RPPA array (containing over 100 samples across HR/HER2 subtypes) was standardized as follows: (1) sample w/out replacement 5000 times, maintaining a receptor subtype balance equal to that of the first ~1000 patients (HR+HER2-: 0.384, TN:0.368, HR+HER2+:0.158, HR-HER2+:0.09); (2) calculate the mean(mean) and mean(sd) for each RPPA endpoint over the samples; (3) standardize each endpoint of the array, as y=(x-mean(mean))/mean(sd).  These standardized data were then combined with controls assayed on RPPA arrays RPPA.1, RPPA.2, and RPPA.3, each normalized in the same way.  This procedure resulted in removal of batch effects, without 'warping' due to mismatches in subtype prevalence.

molecule: protein

source_name: primary breast cancer

value: primary breast cancer

tag: arm (short name)

tag: arm

value: Paclitaxel

tag: hr

tag: pcr


title: 987914


title: control volunteer 003 [JF]


title: blood,CAA,rep6

description: Library name: CAA6


title: blood,CAA,rep7

description: Library name: CAA7


title: blood,CAA,rep8

description: Library name: CAA8


title: control volunteer 004 [LQ]


title: blood,CAA,rep5

description: Library name: CAA5


title: 752372


title: control volunteer 002 [DY]


title: blood,CAA,rep4

description: Library name: CAA4


title: 679787


title: Space_methylation [206667650075_R07C01]


title: blood,CAA,rep3

description: Library name: CAA3


title: blood,CAA,rep2

description: Library name: CAA2


title: blood,Control,rep1

description: Library name: Control1


title: 409288


title: blood,CAA,rep1

description: Library name: CAA1


title: HAPE patient 006 [ZYY]

description: plasma cell free DNA from HAPE patient


title: iPSC, wild type, rep4

city: Tucson

first: Martha

last: Bhattacharya

state: AZ

address: 1040 E 4th Street

department: Neuroscience

institute: University of Arizona

description: Library name: WT_4

data_processing:
Raw data was received from Novogene after sequencing in the form of gzipped .fastq files. Raw files were assessed for quality using FastQC and it was determined there was an overabundance of Illumina adapter sequences in each file.
All raw files were trimmed for Illumina adapter sequences (TruSeq3-PE.fa:2:30:10:3:True) using Trimmomatic v0.39. Files were also trimmed in a quality filtering step (SLIDINGWINDOW:4:20) to remove the end of sequences with a Phred score below 20 within a given 4-base window.
Trimmed .fastq files were aligned to a transcriptome index for the human genome version 38 (sourced from refgenomes.databio.org) using Salmon v1.8.0.
Extraction and normalization of aligned read counts were performed on the quant.sf Salmon output files using DeSeq2.
Assembly: hg38 transcriptome index (salmon_partial_sa_index:default)
Supplementary files format and content: tab-delimited text file contains a single matrix with normalized counts as TPM (transcripts per million) for all samples by column

source_name: Coriell GM23476

extract_protocol:
RNA was harvested using Macherey-Nagel Nucleospin RNA purification kit following manufacturer's protocols.
Library construction was performed by a third party company (Novogene in Sacramento, CA) using a poly(A) enrichment protocol.

value: Coriell GM23476

value: Human iPSC

value: Wild type


title: control volunteer 001 [CXW]


title: 414844


title: iPSC, wild type, rep2

description: Library name: WT_2


title: iPSC, wild type, rep3

description: Library name: WT_3


title: HAPE patient 005 [WKY]

description: plasma cell free DNA from HAPE patient


title: iPSC, wild type, rep1

description: Library name: WT_1


title: 252748


title: HAPE patient 004 [TWZ]

description: plasma cell free DNA from HAPE patient


title: iPSC, Lys184Glu/Lys184Glu, rep4

description: Library name: Lys184Glu_homo4


title: iPSC, Lys184Glu/Lys184Glu, rep2

description: Library name: Lys184Glu_homo2


title: 712785


title: HAPE patient 003 [DJC]

description: plasma cell free DNA from HAPE patient


title: iPSC, Lys184Glu/Lys184Glu, rep1

description: Library name: Lys184Glu_homo1


title: 527320


title: iPSC, Lys184Glu/+, rep4

description: Library name: Lys184Glu_het4


title: 495440


title: HAPE patient 001 [CNS]

description: plasma cell free DNA from HAPE patient


title: iPSC, Lys184Glu/+, rep2

description: Library name: Lys184Glu_het2


title: 433144


title: iPSC, Lys184Glu/+, rep1

description: Library name: Lys184Glu_het1


title: S_pombe_WT_3

city: Sherbrooke

first: Michelle

middle: S

last: Scott

state: QC

address: 3201 Jean-Mignault

institute: Université de Sherbrooke

description:
Library name: Sample 13
small RNAs (<150 nt)

data_processing:
Base callings were converted to fastq using bcl2fastq v2.20.0 with the following parameters for S. pombe, S. cerevisiae and M. musculus: --minimum-trimmed-read-length 13 --mask-short-adapter-reads 13 --no-lane-splitting -p 32. Base callings were converted to fastq using bases2fastq v1.2.0 with the following parameters for G. gallus and M. mulatta: -p 36 –detect-adapters --filter-mask R1:N*-R2:N*.
Trimming of paired-end reads was performed using Trimmomatic v0.36 (parameters: ILLUMINACLIP:<fastaWithAdaptersEtc>:2:12:10:8, TRAILING:30, LEADING:30, MINLEN:20) in order to remove adapters and low-quality reads.
FastQC v0.11.5 was used before and after trimming to assess the quality of the reads.
Alignment of reads to the reference genome was performed using STAR v2.6.1a (parameters: --runMode alignReads, --outSAMunmapped None, --outSAMtype BAM SortedByCoordinates, outFilterScoreMinOverLread 0.3, --outFilterMatchNminOverLread 0.3, --outFilterMultimapNmax 100, --winAnchorMultimapNmax 100, --alignEndsProtrude 5 ConcordantPair). The index needed to align reads was generated using STAR v2.6.1a (parameters: --runMode genomeGenerate, --sjdbOverhang 74)
Gene expression normalized in transcript per million (TPM) was obtained using CoCo v0.2.1p4 (parameters: cc, --countType both, --strand 1 --paired)
Assembly: GRCg7b (G. gallus), Mmul_10 (M. mulatta), GRCm39 (M. musculus), R64-1-1 (S. cerevisiae), ASM294v2 (S. pombe)
Supplementary files format and content: A tab-separated (.tsv) file showing the gene id, gene name and abundance (in TPM) of all annotated genes for each sample in the given species.

organism: Schizosaccharomyces pombe

growth_protocol: Wild type 10H3 S. cerevisiae cultures were grown in Yeast Extract Peptone Dextrose (YEPD) rich media at 26°C. Wild type yAS99 S. pombe cultures were grown to mid-log phase in 25 mL of YES media at 32°C.

extract_protocol:
Phenol-chloroform RNA extraction was performed for M. musculus, S. cerevisiae and S. pombe, whereas no RNA extraction was needed for the Biochain-purchased RNA for G. gallus and M. mulatta.
TGIRT-Seq libraries were constructed as described previously (Boivin et al., RNA, 2018) using ribodepleted total RNA (S. cerevisiae and M. musculus) or gel-purified and size-selected small RNAs (S. pombe, M. mulatta and G. gallus).

value: WT


title: PGP1,DDX4-tdTomato/REC8-mGreenLantern,DDX4+,meiosis_day15

city: Boston

first: Merrick

middle: Pierson

last: Smela

state: MA

address: 3 Blackfan Circle

institute: Harvard University

data_processing:
NextFlow methylseq pipeline (https://nf-co.re/methylseq/), version 2.6.0 with default settings
Assembly: hg38 plus lambda phage and pUC19 spike-in controls
Supplementary files format and content: Methylation coverage (bismark output)

growth_protocol: Plasmids for constitutive expression of BCL2 and doxycycline-inducible expression of HOXB5, BOLL, and MEIOC were integrated into F2 D4TDZG, F3 D4TT2G, and PGP1 D4TR8G reporter hiPSCs. The iPSCs were seeded at 50,000 cells/cm2 on Matrigel-coated plates in mTeSR1 supplemented with 5 µM GSK3484862, 1 µg/mL doxycycline, and 10 µM Y-27632. For 6-well plates, 1.5 mL of medium was used per well. After one day, the media was replaced with APEL2 containing 5 µM GSK3484862 and 1 µg/mL doxycycline. A 50% media change was performed every 2 days, and GSK3484862 was withdrawn starting on day 7. Cells were harvested at each day from day 0 (hiPSC) to day 15.

extract_protocol:
Genomic DNA was extracted using the Qiagen DNeasy Micro kit from hiPSCs and cells from the meiosis induction at various time points. For some of the samples, DDX4+ and DDX4- cells were sorted prior to extraction (see sample information). Libraries were prepared from 200 ng DNA using the NEB Enzymatic Methyl-Seq kit (NEB #E7120) following the manufacturer’s instructions. Briefly, control DNA (methylated pUC19 and unmethylated λ phage) was spiked into each sample. Next, samples were sheared to ~300 bp using a Covaris S2 sonicator. Enzymatic methyl conversion was performed, and libraries were amplified using unique dual index primers. For the pilot experiment, 2 x 150 bp paired end sequencing was performed on an Illumina MiSeq. For the follow-up experiment, 2 x 150 bp paired end sequencing was performed on an Illumina NovaSeq.
Methyl-seq (NEB enzymatic kit)

treatment_protocol: Samples in the pilot experiment were fixed cells, and samples in the follow-up experiment were unfixed cells.


title: iPSC, Lys184Glu/Lys184Glu, rep3

description: Library name: Lys184Glu_homo3


title: S_pombe_WT_2

description:
Library name: Sample 12
small RNAs (<150 nt)


title: 963303


title: 172168


title: ATCC-BXS0116,DDX4-tdTomato/TFAP2C-mGreenLantern,DDX4-,meiosis_day15


title: ATCC-BXS0115,DDX4-tdTomato/DAZL-mGreenLantern,DDX4+,meiosis_day15


title: PGP1,DDX4-tdTomato/REC8-mGreenLantern,DDX4-,meiosis_day15


title: HAPE patient 002 [CYB]

description: plasma cell free DNA from HAPE patient


title: 970839


title: 711476


title: blood,Control,rep2

description: Library name: Control2


title: ATCC-BXS0116,DDX4-tdTomato/TFAP2C-mGreenLantern,DDX4+,meiosis_day15


title: ATCC-BXS0115,DDX4-tdTomato/DAZL-mGreenLantern,DDX4+,meiosis_day10


title: ATCC-BXS0115,DDX4-tdTomato/DAZL-mGreenLantern,DDX4-,meiosis_day10


title: 820348


title: snATAC-Seq - 1098_1

first: Jiekun

last: Yang

address: 32 Vassar Street

institute: MIT

description:
Library name: D21-194103
10x Genomics

library_source: genomic single cell

data_processing:
We received the sequences, mapped the reads against the GRCh38 human reference genome, and quantified the read counts using cellranger-atac-2.0.0 pipeline (10x Genomics).
Assembly: GRCh38
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Metastatic melanoma

extract_protocol:
We enzymatically digested and dissociated fresh tumor samples according to tissue dissociation kit protocols using the gentleMACS™ Dissociator (Miltenyi). Dissociated tissues were filtered, centrifuged, and the isolated cells were resuspended in 0.1% BSA in PBS and immediately processed for the generation of snATAC-seq libraries.
We performed snATAC-seq using the Chromium single cell ATAC v1 chemistry from 10x Genomics with the target of 5000 nuclei per sample. Then the libraries were profiled using the Novaseq S2 (Illumina) technology.

value: Metastatic melanoma

value: conventional dendritic cell


title: snATAC-Seq - 1098_3

description:
Library name: D19-9146
10x Genomics


title: ATCC-BXS0115,DDX4-tdTomato/DAZL-mGreenLantern,DDX4-,meiosis_day5


title: PGP1,DDX4-tdTomato/REC8-mGreenLantern,DDX4+,meiosis_day10


title: 688955


title: PGP1,DDX4-tdTomato/REC8-mGreenLantern,DDX4-,meiosis_day10


title: ATCC-BXS0116,DDX4-tdTomato/TFAP2C-mGreenLantern,DDX4+,meiosis_day5


title: PGP1,DDX4-tdTomato/REC8-mGreenLantern,Unsorted,meiosis_day2

value: Unsorted


title: ATCC-BXS0115,DDX4-tdTomato/DAZL-mGreenLantern,DDX4-,meiosis_day15


title: snATAC-Seq - 776-1

description:
Library name: D19-11972
10x Genomics


title: snATAC-Seq - 1009_1

description:
Library name: D19-11979
10x Genomics


title: snATAC-Seq - 620_2_rep2

description:
Library name: D21-194107
10x Genomics


title: snATAC-Seq - 620_2_rep1

description:
Library name: D21-194106
10x Genomics


title: ATCC-BXS0116,DDX4-tdTomato/TFAP2C-mGreenLantern,DDX4+,meiosis_day10


title: ATCC-BXS0116,DDX4-tdTomato/TFAP2C-mGreenLantern,DDX4-,meiosis_day10


title: ATCC-BXS0116,DDX4-tdTomato/TFAP2C-mGreenLantern,Unsorted,meiosis_day2


title: snATAC-Seq - 856_1

description:
Library name: D19-11980
10x Genomics


title: 421917


title: 896621


title: 741535


title: S_pombe_WT_1

description:
Library name: Sample 11
small RNAs (<150 nt)


title: PGP1,DDX4-tdTomato/REC8-mGreenLantern,DDX4+,meiosis_day5


title: iPSC, Lys184Glu/+, rep3

description: Library name: Lys184Glu_het3


title: ATCC-BXS0115,DDX4-tdTomato/DAZL-mGreenLantern,DDX4+,meiosis_day5


title: PGP1,DDX4-tdTomato/REC8-mGreenLantern,DDX4-,meiosis_day5


title: ATCC-BXS0116,DDX4-tdTomato/TFAP2C-mGreenLantern,DDX4-,meiosis_day5


title: 418593


title: ATCC-BXS0115,DDX4-tdTomato/DAZL-mGreenLantern,Unsorted,meiosis_day2


title: 522140


title: 103939


title: snATAC-Seq - 509_1

description:
Library name: D19-11973
10x Genomics


title: PGP1,DDX4-tdTomato/REC8-mGreenLantern,Unsorted,hiPSC

value: hiPSC


title: ATCC-BXS0116,DDX4-tdTomato/TFAP2C-mGreenLantern,Unsorted,hiPSC


title: ATCC-BXS0115,DDX4-tdTomato/DAZL-mGreenLantern,Unsorted,hiPSC


title: snATAC-Seq - 1098_4

description:
Library name: D19-11975
10x Genomics


title: 320538


title: snATAC-Seq - 452_2

description:
Library name: D19-11974
10x Genomics


title: a2WMLd71

city: Grand Rapids

first: Peter

middle: A

last: Jones

state: MI

address: 333 Bostwick Ave NE

department: Center of Epigenetics

institute: Van Andel Research Institute

hyb_protocol: Standard Illumina protocol

scan_protocol: Standard Illumina protocol

data_processing: SeSAMe R package on Bioconductor V1.24.0

label_protocol: Standard Illumina protocol

extract_protocol: Genomic DNA was extracted using Phenol-chloroform

value: liver

value: male


title: a2WMLbE6


title: a2WMLd74


title: snATAC-Seq - 1227_1

description:
Library name: D19-11985
10x Genomics


title: a2WMLbE1


title: a2WMLaE7


title: snATAC-Seq - 509_2

description:
Library name: D19-11988
10x Genomics


title: 355942


title: 462582


title: a2WMBbE9

value: brain


title: 654021

value: Control


title: a2WMBd74


title: snATAC-Seq - 1224_3_rep2

description:
Library name: D19-11984
10x Genomics


title: a2WMLaE6


title: a2WMBd71


title: snATAC-Seq - 1224_3_rep1

description:
Library name: D19-11983
10x Genomics


title: 901705


title: a2WMBbE6


title: a2WMBbE1


title: 843554


title: a2WMLbE9


title: CD45⁺CD3⁺ T cells, sorted from Isotype-treated PDTFs from lung cancer, BS-786, rep 2

city: Basel

first: DBM Bioinformatics

last: Core Facility

state: BS

address: Hebelstrasse 20

department: Departement of Biomedicine

country: Switzerland

institute: University of Basel

description:
Library name: BS786_DP47
CD45⁺CD3⁺ T cells

library_source: transcriptomic single cell

data_processing:
The fastq files were processed using Cell Ranger v5.0
Assembly: GRCh38
Supplementary files format and content: HDF5 10X Genomics file containing features, barcodes and sparse matrix of gene expression counts
Supplementary files format and content: Serialized R object containing Seurat object with analyzed data and metadata

source_name: PDTFs, lung tumor, NSCLC

extract_protocol:
Patient-derived tumor fragments (PDTFs) from three cancer patients with lung tumors were treated with either Isotype control (DP47), anti-PD1 (Pembrolizumab-PGLALA), Isotype-IL2v (DP47-IL2v), or PD1-IL2v for 48 hours. Subsequently, PDTFs were digested into a single cell suspension and CD45⁺CD3⁺ live T cells were sorted. Next, single cell RNA sequencing was performed using the 10x Genomics protocol for 3′ gene expression profiling with feature barcoding (CG000206, Rev A). TotalSeq B (Biolegend) anti-human Hashtag 2, 3, and 4 were used for feature barcoding.
The libraries were constructed according to10x Genomics protocol for 3′ gene expression profiling with feature barcoding (CG000206, Rev A), following the manufacturer’s instructions.

value: PDTFs, lung tumor, NSCLC

value: CD45+CD3+ T cells

tag: Sex

value: Isotype


title: CD45⁺CD3⁺ T cells, sorted from Isotype-IL2v-treated PDTFs from lung cancer, BS-786, rep 2

description:
Library name: BS786_DP47IL2v
CD45⁺CD3⁺ T cells


title: a2WMBaE6


title: a2WM3Ld6


title: CD45⁺CD3⁺ T cells, sorted from PD1-IL2v-treated PDTFs from lung cancer, BS-786, rep 2

description:
Library name: BS786_PD1IL2v
CD45⁺CD3⁺ T cells


title: a2WM3Bd6


title: 580541

value: primary breast cancer


title: CD45⁺CD3⁺ T cells, sorted from Pembrolizumab-PGLALA-treated PDTFs from lung cancer, BS-786, rep 2

description:
Library name: BS786_PembroPGLALA
CD45⁺CD3⁺ T cells

value: Pembrolizumab-PGLALA


title: 532183

value: Paclitaxel


title: a2WM3Ld2


title: a2WMBaE7


title: CD45⁺CD3⁺ T cells, sorted from PD1-IL2v-treated PDTFs from lung cancer, BS-788, rep 2

description:
Library name: BS788_PD1IL2v
CD45⁺CD3⁺ T cells

value: female


title: 587604


title: a2WM3Bd2


title: a2WFLbE0


title: a2WFBbE0


title: CD45⁺CD3⁺ T cells, sorted from Isotype-IL2v-treated PDTFs from lung cancer, BS-788, rep 1

description:
Library name: BS788_DP47IL2v
CD45⁺CD3⁺ T cells


title: a2WFBaE5


title: a2WFLbE7


title: a2WFLaE5


title: a2WFBbE7


title: CD45⁺CD3⁺ T cells, sorted from Pembrolizumab-PGLALA-treated PDTFs from lung cancer, BS-788, rep 1

description:
Library name: BS788_PembroPGLALA
CD45⁺CD3⁺ T cells


title: a2WF3Lc8


title: CD45⁺CD3⁺ T cells, sorted from Isotype-treated PDTFs from lung cancer, BS-788, rep 1

description:
Library name: BS788_DP47
CD45⁺CD3⁺ T cells


title: a2WF3Lc6


title: 241998


title: 607843


title: a2WF3Lc4


title: CD45⁺CD3⁺ T cells, sorted from Isotype-IL2v-treated PDTFs from lung cancer, BS-723, rep 1

description:
Library name: BS723_D47IL2v
CD45⁺CD3⁺ T cells


title: 136536


title: 748611


title: a2WF3Lb4


title: a2WF3Bc8


title: CD45⁺CD3⁺ T cells, sorted from PD1-IL2v-treated PDTFs from lung cancer, BS-723, rep 1

description:
Library name: BS723_PD1IL2v
CD45⁺CD3⁺ T cells


title: a2WF3L61


title: 796558


title: a2WF3Bc6


title: a2WF3Lb3


title: Vδ1 T cells, PBMC, People living with HIV-1, subject 5

city: Toulouse

first: Pierre

last: Delobel

address: CHU Purpan – BP 3028

country: France

institute: Infinity

description: Library name: 8550

data_processing:
Data were processed using CellRanger v.7.0.1
Cell filtering, PCA, UMAP and clustering were performed using Seurat v.5.0.1
Assembly: Homo sapiens GRCh38 reference genome and Ensembl annotation v.110
Supplementary files format and content: barcodes, features and matrix files were generated using CellRanger from 10X Genomics. They contain respectively cell barcodes, gene names and raw counts for each sample.
Supplementary files format and content: scdata.rds file was generated using Seurat v.5.0.1

extract_protocol:
Single-cell libraries were generated using the Chromium iX Single-Cell Instrument and Chromium Next GEM Single Cell 3′ Kit v3.1, Chip G Single Cell kit, Dual Index kit TT Set A and NT set A, and 3’ Feature Barcode kit (10x Genomics).
Single-cell libraries were generated using the Chromium iX Single-Cell Instrument and Chromium Next GEM Single Cell 3′ Kit v3.1, Chip G Single Cell kit, Dual Index kit TT Set A and NT set A, and 3’ Feature Barcode kit (10x Genomics).

value: Blood

value: Vδ1 T cells

tag: disease

tag: batch


title: a2HMLbX


title: Vδ1 T cells, PBMC, People living with HIV-1, subject 4

description: Library name: 8549


title: Vδ1 T cells, PBMC, People living with HIV-1, subject 6

description: Library name: 8552


title: a2HMLbE7


title: a2WF3Bb4

value: WT


title: a2HMLbE2


title: Vδ1 T cells, PBMC, People living with HIV-1, subject 3

description: Library name: 8547


title: 520258


title: 771813


title: 219545


title: 808714


title: 293142


title: Vδ1 T cells, PBMC, People living with HIV-1, subject 2

description: Library name: 8533


title: a2HMLbE10


title: a2HMBbX


title: Vδ1 T cells, PBMC, People living with HIV-1, subject 1

description: Library name: 8508


title: a2WF3Bc4


title: a2WF3B61


title: a2HMBbE7


title: a2WF3Bb3


title: a2HMBbE2


title: Vδ1 T cells, PBMC, uninfected control, subject 6

description: Library name: 3134


title: 689076


title: a2HMBbE10


title: 879224


title: a2HM3Lc9


title: 929391


title: Vδ1 T cells, PBMC, uninfected control, subject 5

description: Library name: 3132


title: Vδ1 T cells, PBMC, uninfected control, subject 3

description: Library name: 3110


title: a2HM3Lc0


title: a2HM3Bd4


title: a2HM3Bd5


title: Vδ1 T cells, PBMC, uninfected control, subject 4

description: Library name: 3119


title: 885590


title: a2HM3Bc9


title: Vδ1 T cells, PBMC, uninfected control, subject 2

description: Library name: 3109


title: a2HM3Bc0


title: 405717


title: a2HM3Ld4


title: Vδ1 T cells, PBMC, uninfected control, subject 1

description: Library name: 3105


title: a2HFLbE5


title: 328160


title: 197942


title: 752469


title: a2HM3Ld5


title: a2HFBbE5


title: 916645


title: fCLIP input rep2

city: Seoul

first: Sunghan

last: Lee

state: South Korea

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

department: School of Biological Sciences

country: South Korea

institute: Seoul National University

description:
Library name: Sample2
fCLIP-seq

library_source: other

data_processing:
Sequencing reads were first mapped to the combined human-SARS-CoV-2 genome using STAR with options accommodating non-canonical viral junctions. Only uniquely mapped reads were used in the downstream analysis. Peak calling analysis was conducted using Piranha with the options -s -n -l -z 50. Adjacent peaks were merged, and those showing enrichment with an FDR < 0.05 in both replicates were selected for further analyses.
Assembly: STAR index were built using concatenated genome of human genome (GRCh38.primary_assembly) and SARS-CoV-2 genome (NC_045512.2).
Supplementary files format and content: Tab-delimited text file include the fCLIP-seq peak calling results generated by Piranha.
Supplementary files format and content: Comma-delimited csv file include the coverage of fCLIP reads on SARS-CoV-2 genome.
Library strategy: fCLIP-seq

molecule: other

source_name: human lung

extract_protocol: Cells were fixed with 0.1% formaldehyde, quenched and lysed. After IP with specific antibodies, RNAs were extracted by ethanol precipitation. RNAs were ligated with 3' adapter. After gel cut, RNAs were ligated with 5' adapter followed by reverse transcription and PCR amplifcation.

value: human lung

value: human lung cancer cell line


title: a2HFLaE4


title: 809037


title: a2HFBaE4


title: a2HF3Lc3


title: fCLIP input rep1

description:
Library name: Sample1
fCLIP-seq


title: a2HF3Lb6


title: a2HF3L58


title: a2HF3La3


title: 460776


title: a2HF3Bb6


title: a2HF3Bc3


title: 198891


title: a2HF3Ba3


title: 0.5 mM DFMO treated for 14 days

city: Cambridge

first: Pushkal

last: Sharma

address: 455 Main Street

institute: Whitehead Institute

description: Library name: DFMO14

data_processing:
Sequencing reads were mapped to the reverse complimentary of the sgRNA library using the read_count_CRISPR_guides.pl script available in our GitHub repository (https://github.com/whitehead/barc/tree/main/Perl). The differential sgRNA abundance between DFMO-treated and untreated samples was identified using the Robust Rank Aggregation (RRA) algorithm implemented in the “test” command of MAGeCK (v0.5.9.3).
Assembly: sgRNAs_seq.txt
Supplementary files format and content: tab delimited text file with raw counts for each guide per sample

source_name: K562 cells

extract_protocol:
Genomic DNA (gDNA) was extracted from cell pellets of 20 x 106 cells using the Blood genomicPrep Mini Spin Kit (Cytiva # 28904264) or 60 × 106 cells using the QIAamp DNA Blood Maxiprep Kit (Qiagen # 51192) according to manufacturer’s instructions with minor modifications: Cytiva and QIAGEN Protease were replaced with a 10 mg/mL solution of ProteinaseK (MilliporeSigma # 3115879001) in water; cells were lysed overnight; centrifugation steps after Qiagen Buffer AW1 and AW2 were performed for 2 minutes and 5 minutes, respectively;  2 x 30 µL (Cytiva) or 1 mL (Qiagen) of water preheated to 70 °C was used to elute gDNA (1- or 5-minute incubation), followed by centrifugation for 1 or 5 minutes (Cytiva or Qiagen extractions, respectively). gDNA was quantified using the Qubit dsDNA HS Assay kit (Thermo Fisher Scientific #Q32851).
All PCR reactions were performed in 50 µL reactions using ExTaq Polymerase (Takara Bio #RR001B). For all samples, 1, 3, or 6 µg of gDNA was initially amplified for 28 cycles in 50 µL test PCR reactions. Subsequently, an additional 50 µL reactions were performed using 6 µg per reaction (140 µg gDNA). Reactions were pooled and 100 µL of each sample was purified using HighPrep PCR beads (MagBio Genomics #AC-60005), eluted with 20 µL water, and quantified using the Qubit dsDNA HS Assay kit before sequencing for 26 cycles on an Illumina NovaSeq.

value: K562 cells

value: DFMO


title: Control cells

description: Library name: untreatd14

value: control


title: a2HF3B58

value: brain


title: a2E7HM136L

value: liver

value: male


title: 782334

value: Control


title: D7_CD36_KMT5A_3

city: Rochester

first: Laurie

last: Steiner

state: NY

address: 601 Elmwood Ave

department: Pediatrics

institute: University of Rochester

description:
Library name: D7_CD36_KMT5A_3
CUT&RUN

data_processing:
Bowtie2 alignment to Hg38 genome
Picard dupliate removal
bamCoverage RPKM normalization
Assembly: Hg38
Supplementary files format and content: bigWig
Library strategy: CUT&Run

source_name: CD34 HSPC

growth_protocol: Human CD34 HSPCs were provided by the Yale Cooperative Center of Excellence in Hematology, and subjected to erythroid culture using semi synchronous CD36+ selection culture system, as previously described (Gautier). Early basophilic erythroblasts (Day 7), approximately 500,000 cells per replicate were collected for CUT&RUN

extract_protocol:
CUT&RUN assays were performed using the Epicypher CUTANA CUT&RUN protocol v1.6.
Libraries were generated using the NEBNext Ultra II DNA Library Prep kit (NEB). For KMT5A, size selection was optimized for small fragments (end prep for 20C for 30 minutes followed by 50C for 60 minutes, ligation AMPure XP cleanup at 1.75X, annealing temperature of 65C for library amplification, and library AMPure XP cleanup using 1st round negative selection at 0.8X followed by a 2nd round positive selection at 1.2X). Libraries were sequenced with illumina HiSeq, paired end 150 bp length reads.

value: CD34 HSPC

value: Erythroblast

value: wt

value: Day7_Early basophilic


title: a2E7HM136B


title: 357017

value: primary breast cancer

value: Paclitaxel


title: D7_CD36_KMT5A_2

description:
Library name: D7_CD36_KMT5A_2
CUT&RUN


title: 942017


title: a2E7HF150B

value: female


title: a2E7HF150L


title: D7_CD36_KMT5A_1

description:
Library name: D7_CD36_KMT5A_1
CUT&RUN


title: a2E4HM150L


title: 581648


title: a2E4HM150B


title: D7_CD36_CNR_H4K20me1_3

description:
Library name: D7_CD36_CNR_H4K20me1_3
CUT&RUN


title: a2E4HF154L


title: D7_CD36_CNR_H4K20me1_2

description:
Library name: D7_CD36_CNR_H4K20me1_2
CUT&RUN


title: 698094


title: a2E2WM154L

value: WT


title: 373672


title: a2E2WM154B


title: D7_CD36_CNR_H4K20me1_1

description:
Library name: D7_CD36_CNR_H4K20me1_1
CUT&RUN


title: a2E1HF154L


title: a2E1HF154B


title: BC-3, MPH, induced, Rep3

first: Eva

middle: Henriette

last: Gottwein

state: IL

address: 320 E Superior St., Tarry building, Room 6-752

department: Microbiology-Immunology

institute: Northwestern University

description: Library name: Sample 12

data_processing:
RNA-seq data were processed using the nf-core/rnaseq pipeline (v3.18.0). Gene annotations derived from Gencode v36.
Assembly: GRCh38.d1.vd1
Supplementary files format and content: tab deliminated text file including normalized counts for each gene and each sample.

source_name: Hematopoietic/lymphoid tissue

extract_protocol:
TRIzol according to protocol.
polyA selection and stranded RNA-seq through Genewiz (Azenta Life Sciences). 150bp stranded PE Illumina.

value: Hematopoietic/lymphoid tissue

value: Primary Effusion Lymphoma

value: MPH Transduced

value: Doxycycline induction


title: a1WMLd74


title: 615873


title: a1WMLd71


title: BC-3, MPH, induced, Rep2

description: Library name: Sample 11


title: a1WMLbE9


title: 614044


title: BC-3, MPH, induced, Rep1

description: Library name: Sample 10


title: BC-3, MPH, uninduced, Rep3

description: Library name: Sample 9


title: a2E4HF154B


title: a1WMLaE6


title: BC-3, MPH, uninduced, Rep2

description: Library name: Sample 8


title: a1WMBd74


title: a1WMBd71


title: 282082


title: a1WMBbE9


title: a1WMBbE1


title: 800710


title: 327133


title: 151481


title: 273745


title: BC-3, MPH, uninduced, Rep1

description: Library name: Sample 7


title: a1WMBaE6


title: a1WMLbE1


title: 363669


title: a1WM3Ld6


title: BC-3, hrGFPii, Dox induced, Rep3

description: Library name: Sample 6

value: hrGFPii transduced


title: a1WM3Bd6

value: brain


title: BC-3, hrGFPii, Dox induced, Rep2

description: Library name: Sample 5


title: a1WM3Bd2


title: a1WM3Ld2

value: liver


title: 517446


title: BC-3, hrGFPii, Dox induced, Rep1

description: Library name: Sample 4


title: Sen_3

first: Alexander

middle: Quinn

last: Wixom

state: MN

address: 200 1st St SW

department: Quantitative Health Sciences

institute: Mayo Clinic

description:
Library name: Sample 9
Cultured cells

data_processing:
MAPRseq 3.1.3 was used to process and align reads to hg38 genome, counts and FPKM values were generated.
Assembly: hg38
Supplementary files format and content: tsv file containing all samples raw counts (one column per sample, one gene per row)
Supplementary files format and content: tsv file containing all samples RPKM values (one column per sample, one row per gene)

source_name: Biliary epithelia

growth_protocol: NHCs were stably transfected with a p16-promoter driven green fluorescent protein (GFP) reporter (p16-GFP-NHC) and cultured in H69 media in the presence or absence of the cellular stressor LPS in our in vitro model of experimentally induced NHC senescence.

extract_protocol:
RNA was isolated using Rneasy Mini Kit (Qiagen)
RNA libraries for RNA seq were prepared using Truseq stranded mRNA library preparation, LibTruSeqStrmRNAv2(TSMRN), according to manufacturer's protocol

treatment_protocol: The cells were collected and standard fluorescence activated cell sorting (FACS) analysis was performed. We then performed RNA sequencing analysis on the non-senescent (GFP-) and senescent (GFP+) cell populations.

value: Biliary epithelia

value: NHC

value: Cholangiocyte

value: LPS 10 days (GFP+)


title: a1WFLc40


title: BC-3, hrGFPii, uninduced, Rep3

description: Library name: Sample 3


title: 845663

value: Control


title: a1WFLbE7


title: a1WFLbE0


title: BC-3, hrGFPii, uninduced, Rep1

description: Library name: Sample 1


title: a1WFLa21


title: Sen_2

description:
Library name: Sample 8
Cultured cells


title: Bulk RNA-seq hESF untreated Repeat 2

city: Shenzhen

first: Andrew

middle: P

last: Hutchins

address: 1088 Xueyuan Rd

department: Bioinformatics

institute: Southern University of Science and Technology

description:
Library name: Bulk RNA-seq hESF untreated Repeat 2
hESF_expression_TPM.tsv.gz
hESF_expression_count.tsv.gz
Hs_hesf_untreated.rp2

data_processing:
The short read sequences were first filtered with fastp. The filtered SR sequences were then used for quantification using STAR and RSEM.
For short read quantification, RSEM STAR references were made using the assembled transcripts.
Assembly: hg38
Supplementary files format and content: TSV files containing transcript counts or TPMs are provided. Each TSV is assembled against the cell type-specific GTF, or against the combined_assembly of all transcripts in all four cell types. Where a transcript matches a known GENCODE transcript it will have an ENST, ENSG and SYMBOL accession. Where a transcript has any matching exon nucleotide, it will be annotated with the matching ENSG and SYMBOL. Where a transcript has no match to GENCODE it will not have ant accession number.

source_name: hESF

growth_protocol: We used human embryonic skin fibroblasts, hESF (CCC-ESF-1; BNCC100546; RRID:CVCL_6884) to investigate the influence of differentiation inducing factors on the transcriptional landscape to establish that the expression patterns were due to the actual change in expression patterns, and not just reflection of different factor treatments. The initial hESF cells were grown in 90% DMEM-H basal medium supplemented with 10% fetal bovine serum (FBS, NATOCOR). The medium was changed every day. We cultured the cell lines in endoderm and mesoderm media for five days with the normal differentiation-inducing factors, mimicking the differentiation process from the PSCs. As a control, hESFs were also cultured in the normal hESF medium for five days. At the end of the fifth day, RNA was extracted and sequenced on short-read platforms. Transcript quantification was done as for PSC-derived cell lines. Cell clustering analyses were then done using DESeq2.

extract_protocol:
RNA was isolated using RNAzol RT (MRC, RN190) according to the manufacturer’s protocol. Samples for short-read RNA-Seq was prepared for sequencing with RNA-seq NEB Next Ultra RNA Library Prep Kit (NEB, #7530). Short-read RNA sequencing was performed on Illumina Novaseq 6000 platform.
Samples for short-read RNA-Seq was prepared for sequencing with RNA-seq NEB Next Ultra RNA Library Prep Kit (NEB, #7530).

treatment_protocol: For endoderm differentiation cells were cultured for 120 h, in RPMI medium (Life Technologies) supplemented with 100 ng/ml Activin A (PEPROTECH, 120-14E-100), 50 nM/ml WNT3A (MedChemExpress, HY-P70453A), 0.5% FBS (BIOWEST, S1580), 2X GlutaMax (Thermo Fisher, 35050061), 0.2x MEM Non-Essential Amino Acids Solution (Thermo Fisher,11140050), and 55 µM β-mercaptoethanol (BBI, A600194). For mesoderm differentiation, the cells were cultured in DMEM/F12 supplemented with 2X GlutaMax, 0.2X MEM Non-Essential Amino Acids Solution, 55µM b-mercaptoethanol, 0.5% FBS, 100ng/ml VEGF (PEPROTECH,100-20-50), 100ng/ml BMP4 (PEPROTECH, 120-05ET), 10 ng/ml bFGF (PEPROTECH, 100-18B-100), and 100ng/ml Activin A. From 24 to 120 h of mesoderm differentiation, Activin A was removed from the culture medium.

value: hESF

value: fibroblast

value: Untreated


title: SR_2

description:
Library name: Sample 5
Cultured cells

value: LPS 10 days (GFP-)


title: 477816

value: primary breast cancer

value: Paclitaxel


title: SR_3

description:
Library name: Sample 6
Cultured cells


title: BC-3, hrGFPii, uninduced, Rep2

city: Chicago

description: Library name: Sample 2

value: Hematopoietic/lymphoid tissue

value: Primary Effusion Lymphoma


title: SR_1

description:
Library name: Sample 4
Cultured cells


title: Sen_1

description:
Library name: Sample 7
Cultured cells


title: 318438


title: a1WFBbE7

value: WT

value: female


title: Bulk RNA-seq hESF untreated Repeat 1

description:
Library name: Bulk RNA-seq hESF untreated Repeat 1
hESF_expression_TPM.tsv.gz
hESF_expression_count.tsv.gz
Hs_hesf_untreated.rp1


title: Ctrl_3

description:
Library name: Sample 3
Cultured cells

value: No treatment


title: a1WFBc40

value: brain


title: a1WFBbE0


title: 579881


title: 264678


title: a1WFBa21


title: 507198


description:
Library name: Bulk RNA-seq hESF treated with mesoderm-inducing medium Repeat 1
hESF_expression_TPM.tsv.gz
hESF_expression_count.tsv.gz
Hs_hesf_mesoderm.rp1

value: mesoderm differentiation medium


title: Ctrl_2

description:
Library name: Sample 2
Cultured cells

value: Biliary epithelia

value: NHC


title: 202539


title: 709559


title: Ctrl_1_R

description:
Library name: Sample 1
Cultured cells

value: Cholangiocyte


description:
Library name: Bulk RNA-seq hESF treated with endoderm-inducing medium Repeat 2
hESF_expression_TPM.tsv.gz
hESF_expression_count.tsv.gz
Hs_hesf_endoderm.rp2

value: endoderm differentiation medium


title: 602943

value: Control


title: a1WF3Lm4

value: liver


description:
Library name: Bulk RNA-seq hESF treated with endoderm-inducing medium Repeat 1
hESF_expression_TPM.tsv.gz
hESF_expression_count.tsv.gz
Hs_hesf_endoderm.rp1

value: hESF

value: fibroblast


title: a1WF3Lm1


title: C42_DMSO_72h

city: Houston

first: Daniel

last: Frigo

state: TX

address: 1515 HOLCOMBE BLVD

institute: MD Anderson Cancer

data_processing:
Fastq files were trimmed by Trimmomatic (0.39) and then aligned to the GRCh38 assembly using STAR (2.7.0f) two-pass alignment. The transcripts abundance was counted using HT-seq (0.11.0). Differentially expressed genes were determined using the R package DESeq2 (1.30.1) with the following filters: absolute log fold change (LFC) >=1 and adjust p value (padj) <= 0.01 unless otherwise noted. R package biomaRT was used for ID conversion and annotation. R package NMF, RColorBrewer and Venn were used for visualization.
Assembly: hg38
Supplementary files format and content: csv files with normalized counts

growth_protocol: C4-2 cells were cultured in IMEM supplemented with fetal bovine serum (5%).

extract_protocol:
RNA for RNA-sequencing (RNA-seq) was isolated using RNeasy Plus Kits according to the manufacturer’s instructions. After extraction, RNA quality and quantity were determined by Tapestation 4200 (Agilent) with High Sensitivity RNA ScreenTape Assay (Agilent) and Qubit fluorometer with Qubit RNA HS Assay Kit respectively. The RNA integrity number (RIN) for all RNA-seq samples was greater than 8
RNA-seq libraries were prepared using KAPA RNA HyperPrep Kits with Ribo Erase (Roche). Total RNA input for each library preparation was 500 ng quantified by Qubit, and PCR amplification was set with 8 cycles. The quality control of each RNA-seq library was tested by Qubit fluorometer and Tapestation 4200 before pooling. Nine libraries with different KAPA dual-indexed adaptors were multiplexed as one pool and sequenced on one lane of the Illumina HiSeq 4000 sequencing platform (Illumina) at the MDACC Advanced Technology Genomics Core (ATGC) with 5% PhiX spike-in and read format of 76-8-8-76, paired-end.

treatment_protocol: C4-2 cells were seeded on 10 cm dishes and grown in IMEM-FCS without phenol red for 48 hours. Cells were treated with DMSO (vehicle) or 500 nM 666-15  for 72 hours prior to RNA extraction.

value: Prostate Cancer

value: vehicle 72h


title: 803514

value: primary breast cancer

value: Paclitaxel


title: a1WF3Bm4

value: WT


title: TDP43 Experiment (TDP43-knockdown) sample 5, Soma Fraction

city: Rockville

first: Veronica

last: Ryan

state: MD

address: 9000 Rockville Pike

department: Center for Alzheimer's and Related Dementias, Alzheimer's and Related Dementias Independent Scholar

institute: National Institute on Aging

description: Library name: TDP43.20

data_processing:
WT sample reads were deduplicated based on the entire read sequence; RBP KD samples were deduplicated using the 8-nt UMI at the start of R2. Following deduplication, the remaining 6 nt linker on R2 was then trimmed. Reads were aligned using STAR v2.7.11b  to GENCODE release 45 with primary assembly annotation. Optical duplicates were marked using picardtools MarkDuplicates v3.2.0. Gene counts were quantified using the featureCounts module of subread v 2.0.6 with the following parameters: counting paired-end reads as a single entity instead of fragments (-p --countReadPairs); ignoring marked duplicates (--ignoreDup); including multimapping reads with fractional count assignment (-M --fraction); assign to exon features (-t exon); summarize at gene-level meta feature (-g gene_id). Fractional read counts were rounded to the nearest integer.
Assembly: hg38 GENCODE v45
Supplementary files format and content: csv, ENSEMBL gene-level feature counts per sample

growth_protocol: iPSCs were grown as established in Essential 8 media. As appropriate, sgRNAs were transduced and iPSCs were selected for cells with successful transduction. Cells were split with accutase and replated in doxycyline-containing induction media to initiate neuronal differentation, as established. on d3 post dox induction, neurons were split to PLO and laminin coated 6-well cell culture inserts with 1 µm pore size transparent PET membranes. On day 17 post dox induction, neurons were harvested.

extract_protocol:
RNA was collected using the Qiagen RNeasy Miniprep kit following manufacterers instructions.
10 ng of RNA per sample was used with the Takara Total RNA-seq Kit v2 - Pico Input Mammalian (634413) for WT samples and Takara Total RNA-seq Kit v3 - Pico Input Mammalian (634485) for RBP KD samples and followed manufacturer instructions.

value: Soma


description:
Library name: Bulk RNA-seq hESF treated with mesoderm-inducing medium Repeat 2
hESF_expression_TPM.tsv.gz
hESF_expression_count.tsv.gz
Hs_hesf_mesoderm.rp2


title: TDP43 Experiment (TDP43-knockdown) sample 4, Soma Fraction

description: Library name: TDP43.19


title: a1WF3Bm1

value: female


title: 819622


title: C42_addback_CREB_S133A

value: CREB1 KO

value: no treatment


title: C42_addback_CREB_WT


title: a1HMLd76

value: male


title: 677915


title: TDP43 Experiment (TDP43-knockdown) sample 3, Soma Fraction

description: Library name: TDP43.18


title: C42_DKO_S2

value: CREB1 and ATF1 KO


title: TDP43 Experiment (TDP43-knockdown) sample 2, Soma Fraction

description: Library name: TDP43.17


title: a1HMLd73


title: a1HMLd72


title: C42_66615_72h


title: C42_ATF1_KO_S2

value: ATF1 KO


title: C42_DKOS1


title: a1HMLd70


title: 229144


title: C42_ATF1_KO_S1


title: TDP43 Experiment (TDP43-knockdown) sample 1, Soma Fraction

description: Library name: TDP43.16


title: TDP43 Experiment (TDP43-knockdown) sample 5, Neurite Fraction

description: Library name: TDP43.15

value: Neurite


title: TDP43 Experiment (TDP43-knockdown) sample 4, Neurite Fraction

description: Library name: TDP43.14


title: 749097

value: Control


title: 299364


title: C42_CREB_KO_S2


title: a1HMLbE3

value: liver


title: a1HMLbE2


title: TDP43 Experiment (TDP43-knockdown) sample 3, Neurite Fraction

description: Library name: TDP43.13


title: 906042


title: C42_CREB_KO_S1


title: 932200


title: 349225


title: a1HMLaE7


title: 794428


title: TDP43 Experiment (TDP43-knockdown) sample 2, Neurite Fraction

description: Library name: TDP43.12


title: a1HMBd76

value: brain


title: TDP43 Experiment (TDP43-knockdown) sample 1, Neurite Fraction

description: Library name: TDP43.11


title: C42_CAMKK2_KO_S3

value: CAMKK2 KO


title: C42_Cas9

value: Prostate Cancer


title: TDP43 Experiment (nontargeting-sgRNA) sample 6, Soma Fraction

description: Library name: TDP43.10

value: nontargeting-sgRNA


title: C42_CAMKK2_KO_S2


title: TDP43 Experiment (nontargeting-sgRNA) sample 5, Soma Fraction

description: Library name: TDP43.9


title: 834418

value: primary breast cancer


title: C42_CAMKK2_KO_S1


title: a1HMBd70


title: a1HMBd72


title: TDP43 Experiment (nontargeting-sgRNA) sample 4, Soma Fraction

description: Library name: TDP43.8


title: C42_CAMKK2_Cas9_S3


title: TDP43 Experiment (nontargeting-sgRNA) sample 2, Soma Fraction

description: Library name: TDP43.7


title: 517870

value: Paclitaxel


title: a1HMBbE3


title: C42_CAMKK2_Cas9_S2

value: WT


title: 491526


title: TDP43 Experiment (nontargeting-sgRNA) sample 1, Soma Fraction

description: Library name: TDP43.6

value: Soma


title: a1HMBd73


title: 724384


title: C42_CAMKK2_Cas9_S1


title: 238790


title: a1HMBaE7


title: a1HFLc44

value: female


title: TDP43 Experiment (nontargeting-sgRNA) sample 6, Neurite Fraction

description: Library name: TDP43.5


title: 706169


title: D10_CD36_H4K20me1_2

description: CUT&Tag

data_processing:
Bowtie2 alignment to Hg38 genome
Picard dupliate removal
bamCoverage RPKM normalization
Assembly: Hg38
Supplementary files format and content: bigWig

growth_protocol: Human CD34 HSPCs were provided by the Yale Cooperative Center of Excellence in Hematology, and subjected to erythroid culture using semi synchronous CD36+ selection culture system, as previously described (Gautier). Early basophilic erythroblasts (Day 7) or orthochromatic erythroblasts (Day 10) were collected for CUT&Tag (approximately 100,000 cells per replicate)

extract_protocol:
CUT&Tag was performed following the Bench top V.1 protocol (Kaya-Okur et al, 2019) Briefly, cells were bound to Concanavalin A beads, and incubated in primary antibodies overnight at 4 degrees, secondary antibodies for 1h at RT, and pA-Tn5 adapter complex for 1h at RT.
Tagmentation was induced for 1h, and DNA was extracted with phenol-chloroform-isomyl alcohol. Libraries were amplified using NEBNext HiFi 2X Master mix, pooled, and cleaned up using 1.3X vol. SPRI beads.

value: CD34 HSPC

value: Erythroblast

value: wt


title: TDP43 Experiment (nontargeting-sgRNA) sample 5, Neurite Fraction

description: Library name: TDP43.4


title: a1HFLbE4


title: 938719

data_processing: Samples from the Ganitumab arm, and a subset the control arm patients, were assayed on a new RPPA array (RPPA.4).  three different RPPA arrays (RPPA.1, RPPA.2 and RPPA.3) under GPL28470.  This RPPA array (containing over 100 samples across HR/HER2 subtypes) was standardized as follows: (1) sample w/out replacement 5000 times, maintaining a receptor subtype balance equal to that of the first ~1000 patients (HR+HER2-: 0.384, TN:0.368, HR+HER2+:0.158, HR-HER2+:0.09); (2) calculate the mean(mean) and mean(sd) for each RPPA endpoint over the samples; (3) standardize each endpoint of the array, as y=(x-mean(mean))/mean(sd).  These standardized data were then combined with controls assayed on RPPA arrays RPPA.1, RPPA.2, and RPPA.3, each normalized in the same way.  This procedure resulted in removal of batch effects, without 'warping' due to mismatches in subtype prevalence.


title: a1HMBbE2

value: male


title: D10_CD36_H4K20me1_1

description: CUT&Tag


title: TDP43 Experiment (nontargeting-sgRNA) sample 1, Neurite Fraction

description: Library name: TDP43.1


title: 116603


title: a1HFLaE3


title: D7_CD36_H4K20me1_2

description: CUT&Tag

value: Day7_Early basophilic


title: a1HFLaE1


title: 152090


title: D10_CD36_H4K20me1_3

description: CUT&Tag


title: hnRNPA1 Experiment (hnRNPA1-knockdown) sample 6, Soma Fraction

description: Library name: hnRNPA1.24


title: hnRNPA1 Experiment (hnRNPA1-knockdown) sample 5, Soma Fraction

description: Library name: hnRNPA1.23


title: 408692


title: D7_CD36_H4K20me1_1

description: CUT&Tag


title: a1HFLa23


title: TDP43 Experiment (nontargeting-sgRNA) sample 4, Neurite Fraction

description: Library name: TDP43.3

value: Neurite


title: hnRNPA1 Experiment (hnRNPA1-knockdown) sample 4, Soma Fraction

description: Library name: hnRNPA1.22


title: SALL4 Morpholino 3

city: Minneapolis

first: Micah

last: Gearhart

address: 6-160 Jackson Hall, 321 Church St.

department: Genetics, Cell Biology and Development

institute: University of Minnesota

description:
Library name: Sall4 MO 3
Sall4 MO 3

data_processing:
Reads were mapped to the GRCz11 genome using STAR (2.7.10a). Gene level abundance was calculated using Danio rerio annotations (Ensembl Release 99) with the RSubread package
Differential expression was calculated using DESeq2 (1.38.3)
Assembly: GRCz11
Supplementary files format and content: Raw counts and normalized FPKM values

organism: Danio rerio

source_name: Tissue posterior to the last somite collected at 16 hpf

growth_protocol: Zebrafish were maintained under standard conditions at approximately 28ºC with a 14-hour light and 10-hour dark cycle.

extract_protocol:
Tissues were stored in Trizol (15596026, Invitrogen) at -80oC. Total RNA was purified using the RNeasy micro kit (74004, Qiagen).
Strand-specific RNA-seq libraries were created by the Illumina Library Creation System with 500 ng of RNA

treatment_protocol: see above

value: sall4 morpholino injected (Harvey and Logan, 2006)


title: a1HFLa22

value: liver


title: TDP43 Experiment (nontargeting-sgRNA) sample 2, Neurite Fraction

description: Library name: TDP43.2


title: a1HFLaE5


title: SALL4 Morpholino 2

description:
Library name: Sall4 MO 2
Sall4 MO 2

value: Tissue posterior to the last somite collected at 16 hpf


title: 885871

first: Denise

last: Wolf

address: 2340 Sutter st

institute: University of California, San Francisco

value: Control


title: a1HFBc44

value: brain


title: 706639


title: D7_CD36_H4K20me1_3

description: CUT&Tag


title: SALL4 Morpholino 1

description:
Library name: Sall4 MO 1
Sall4 MO 1


title: a1HFBbE4


title: 104268


title: Control Sample 3

description:
Library name: Control 3
Control 3

value: non-injected


title: hnRNPA1 Experiment (hnRNPA1-knockdown) sample 2, Soma Fraction

description: Library name: hnRNPA1.20


title: 734997

value: primary breast cancer


title: 689452

value: Paclitaxel


title: 294739


title: hnRNPA1 Experiment (hnRNPA1-knockdown) sample 1, Soma Fraction

description: Library name: hnRNPA1.19


title: a1HFBaE5


title: Control Sample 2

description:
Library name: Control 2
Control 2


title: a1HFBaE3


title: hnRNPA1 Experiment (hnRNPA1-knockdown) sample 3, Soma Fraction

description: Library name: hnRNPA1.21


title: 913527


title: hnRNPA1 Experiment (hnRNPA1-knockdown) sample 6, Neurite Fraction

description: Library name: hnRNPA1.18


title: a1HFBaE1


title: Control Sample 1

description:
Library name: Control 1
Control 1

value: scrambled morpholino injected


title: 139973


title: hnRNPA1 Experiment (hnRNPA1-knockdown) sample 5, Neurite Fraction

description: Library name: hnRNPA1.17


title: hnRNPA1 Experiment (hnRNPA1-knockdown) sample 4, Neurite Fraction

description: Library name: hnRNPA1.16


title: a1HFBa23


title: 233191


title: 653927


title: 783427


title: a1HFBa22


title: hnRNPA1 Experiment (hnRNPA1-knockdown) sample 3, Neurite Fraction

description: Library name: hnRNPA1.15


title: hnRNPA1 Experiment (hnRNPA1-knockdown) sample 2, Neurite Fraction

description: Library name: hnRNPA1.14


title: QX492

city: Lausanne

first: Xiaoxu

last: Li

address: Station 15 - CH

institute: EPFL

description: Library name: G6

data_processing:
FastQC (default parameters) was used to verify the quality of the reads. No low-quality reads were present and no trimming was needed.
Alignment was performed against worm genome (WBcel235 sm-toplevel) following the STAR (version 2.73a) manual guidelines
Counts for each sample features (outputed by STAR) where read into R
Assembly: WBcel235 sm-toplevel
Supplementary files format and content: processed_data_GEO_upload.xlsx

organism: Caenorhabditis elegans

source_name: Caenorhabditis elegans

growth_protocol: For both the RIAILs and wild-type N2 validation experiments, 5–10 L4-stage worms were transferred onto RNAi plates (containing 2 mM IPTG and 25 µg/mL carbenicillin) seeded with E. coli HT115, with 15 µg/mL doxycycline (Dox; Sigma, Cat. D9891). Once F1 progeny reached the L4 stage, worms were transferred to corresponding plates supplemented with 10 µM 5-fluoro-2’-deoxyuridine (5FU) to prevent progeny production. The L4 stage was defined as day 2 of life

extract_protocol:
On the day of the extraction, 1 mL of TriPure Isolation Reagent was added to each tube. The samples were then frozen and thawed quickly eight times with liquid nitrogen and 37ºC water bath to rupture cell membranes. RNA was then extracted by using a column-based kit from Macherey-Nagel.
BGISeq-500 library construction Protocol

value: Caenorhabditis elegans

value: Doxycycline


title: QX491

description: Library name: G4


title: a1HF3Lm5

value: female


title: QX494

description: Library name: G8


title: hnRNPA1 Experiment (hnRNPA1-knockdown) sample 1, Neurite Fraction

description: Library name: hnRNPA1.13


title: a1HF3Bm5


title: N2_batch4

description: Library name: G34


title: hnRNPA1 Experiment (nontargeting-sgRNA) sample 6, Soma Fraction

description: Library name: hnRNPA1.12

value: Soma

value: nontargeting-sgRNA


title: 367682


title: 1241WT_Sperm

source_name: Sperm from fetile mouse

value: sperm

value: WT


title: QX572

description: Library name: G32


title: 515565


title: 395379


title: hnRNPA1 Experiment (nontargeting-sgRNA) sample 5, Soma Fraction

description: Library name: hnRNPA1.11


title: QX568

description: Library name: G30


title: hnRNPA1 Experiment (nontargeting-sgRNA) sample 4, Soma Fraction

description: Library name: hnRNPA1.10


title: 1238KO_Sperm


title: CB4856_batch4

description: Library name: G2


title: 549172


title: QX537

description: Library name: G28


title: 255078


title: 775346


title: hnRNPA1 Experiment (nontargeting-sgRNA) sample 3, Soma Fraction

description: Library name: hnRNPA1.9


title: QX519

description: Library name: G26


title: 1229WT_Sperm


title: hnRNPA1 Experiment (nontargeting-sgRNA) sample 2, Soma Fraction

description: Library name: hnRNPA1.8


title: 395076


title: 1228KO_Sperm


title: QX508

description: Library name: G22


title: hnRNPA1 Experiment (nontargeting-sgRNA) sample 1, Soma Fraction

description: Library name: hnRNPA1.7


title: QX515

description: Library name: G24


title: hnRNPA1 Experiment (nontargeting-sgRNA) sample 6, Neurite Fraction

description: Library name: hnRNPA1.6

value: Neurite


title: hnRNPA1 Experiment (nontargeting-sgRNA) sample 5, Neurite Fraction

description: Library name: hnRNPA1.5


title: QX503

description: Library name: G20


title: 899692


title: 1239KO_Sperm


title: 489504


title: hnRNPA1 Experiment (nontargeting-sgRNA) sample 4, Neurite Fraction

description: Library name: hnRNPA1.4


title: QX501

description: Library name: G16


title: QX498

description: Library name: G14


title: 1235WT_Sperm


title: 138027

value: Ganitumab

value: Paclitaxel + Ganitumab


title: Donor 2

type: RNA

city: Madison

first: Rithvik

last: Turaga

state: WI

address: Suite 3000, 1111 Highland Ave

institute: University of Wisconsin-Madison, Dept of Dermatology

description: Test

data_processing:
The normalization and all the data analysis were performed according to the manufacturers instructions using their web-based software package: https://geneglobe.qiagen.com/us/my-geneglobe/analysis
For the normalization it uses the average of five housekeeping genes: B2M,  GAPDH, HPRT1, RPLP0, HGDC. Target gene signals normalized to housekeeping genes; 2^-deltaCt, where deltaCt = (Ct_Target − Ct_HKG)]

label: SYBR Green

source_name: Whole blood derived differentiated memory-like NK cells

label_protocol: PCR assays were performed using the Human Glucose Metabolism RT2 Profler PCR Array (Qiagen) following the Manufacturer’s instructions. Reverse transcription was performed from total RNA using the RT2 First Strand Kit (Qiagen). Quantitative real-time PCR were performed (Light Cycler 480, Roche).

growth_protocol: Memory-like NK cells were cultured for one day in the presence of interleukin-12 (IL-12, 200µg/mL ), interleukin-15 (IL-15, 200µg/mL ) and interleukin-18 (IL-18, 200µg/mL ). After  24hrs media was changed to media containing only inteleukin-15 (IL-15, 200µg/mL). Cell were allowed to remain in culture for 6 days.

extract_protocol: Total RNA was extracted using Qiagen RNAEasy Plus Micro Kit

value: Memory-like NK cells

tag: group

value: Group 2


title: Donor 3

description: Test

value: Group 3


title: QX497

description: Library name: G12

tag: tissue


title: 628823

city: San Francisco


title: Donor 1

description: Test

value: Group 1


title: hnRNPA1 Experiment (nontargeting-sgRNA) sample 2, Neurite Fraction

description: Library name: hnRNPA1.2

tag: treatment


title: hnRNPA1 Experiment (nontargeting-sgRNA) sample 1, Neurite Fraction

description: Library name: hnRNPA1.1


title: QX496

description: Library name: G10


title: 820807

value: primary breast cancer


title: Donor 4

description: Control

value: Control group


title: QX533

description: Library name: F8


title: WT Experiment (no-sgRNA) sample 7, Soma Fraction

description: Library name: soma.7

value: no-sgRNA


title: 866660

value: Control

value: Paclitaxel


title: QX532

description: Library name: F6

value: Caenorhabditis elegans

value: Doxycycline


title: QX527

description: Library name: F4


title: 559021


title: N2_batch3

description: Library name: F42


title: WT Experiment (no-sgRNA) sample 5, Soma Fraction

description: Library name: soma.5

value: Soma


title: QX598

description: Library name: F40


title: hnRNPA1 Experiment (nontargeting-sgRNA) sample 3, Neurite Fraction

description: Library name: hnRNPA1.3

value: nontargeting-sgRNA


title: 182346


title: 362150


title: WT Experiment (no-sgRNA) sample 7, Neurite Fraction

description: Library name: neurite.7


title: WT Experiment (no-sgRNA) sample 6, Neurite Fraction

description: Library name: neurite.6


title: 618860


title: QX596

description: Library name: F36


title: 221686


title: 330134


title: 683457


title: QX595

description: Library name: F34


title: QX591

description: Library name: F32


title: WT Experiment (no-sgRNA) sample 6, Soma Fraction

description: Library name: soma.6


title: WT Experiment (no-sgRNA) sample 4, Neurite Fraction

description: Library name: neurite.4


title: QX587

description: Library name: F30


title: 535779


title: 122795


title: 429220


title: CB4856_batch3

description: Library name: F2


title: Pooled_snRNA-seq_Human2_1

city: Leuven

first: Llewelyn

last: Roderick

address: Herestraat 49

department: Department of Cardiovascular Sciences

country: Belgium

institute: KU Leuven

description:
Library name: Human heart tissue - Pooled 1
10x Genomics

data_processing:
The sequencing reads of the human dataset were aligned to the GRCh38 reference genome and processed with 10x Genomics Cell Ranger 7.0.0
Species-mixed (human and sheep) data were separately mapped to both the human genome (GRCh38) and the sheep genome (ARS-UI_Ramb_v2.0), whereas 4-sample-multiplexed human data were mapped to the human genome (GRCh38) only.
Assembly: GRCh38, ARS-UI_Ramb_v2.0
Supplementary files format and content: tab-delimited value files and matrix files

molecule: nuclear RNA

source_name: heart ventricle

extract_protocol:
Nuclei were isolated from heart tissue by mechanical disruption, followed by centrifugation through sucrose and purification from debris by FACS. In brief, frozen heart tissue (~100 mg) was suspended in 5 ml of lysis buffer and thawed on wet ice. When samples were pooled for 10x RNA-Seq (multiple human samples, or sheep and human), samples were either combined after (human real-world dataset) or prior to homogenization (human application dataset and sheep-human species-mixed dataset), where equivalent weights of each tissue sample were pooled. Next, samples were homogenized using a gentleMACS dissociator (Miltenyi) with gentleMACS M tubes and the Protein_01_01 protocol. 5 ml of lysis buffer containing NP-40 was added to the homogenate and incubated on wet ice for 15 min. Then, the suspension was filtered through a 30 μM cell strainer (Miltenyi). Residual nuclei were recovered by washing the M tube and filter with 2 ml of lysis buffer containing NP-40, which was then combined with the remainder of the homogenate. The homogenate was centrifuged in a swinging-bucket centrifuge (Eppendorf, 5920R) at 1000 g for 5 min (4 ℃, ramp speed 4/4). The supernatant was carefully removed and the pellet containing nuclei was resuspended in 2 ml of sucrose buffer, which was then layered on top of 2 ml of sucrose buffer. The sample was then centrifuged at 500 g for 5 min (Eppendorf, 5920R; 4 ℃, ramp speed of 4/4) to recover nuclei. The supernatant was removed and the pellet was resuspended in 500 μl of wash buffer and centrifuged at 500 g for 5 min (Eppendorf, 5920R; 4 ℃, ramp speed of 4/4). The supernatant was carefully removed and stained with 1 ml of staining buffer containing DAPI (1:1000; 7406). DAPI-positive nuclei were separated from cell debris by flow sorting using a SONY sorter instrument (SONY MA900) and collected into 50 μl of collection buffer. Sorted nuclei were then collected by centrifugation at 1000 g for 5 min (Eppendorf, 5920R; 4°C, ramp speed of 4/4), and the concentration was adjusted to 1,000 nuclei/µl targeted for predicted capture 10,000.
Nuclear suspensions were loaded on a 10x Chromium Controller (10x Genomics) and processed with 10x Chromium Single Cell 3’ Reagent Kit v3 (10x Genomics) according to the manufacturer’s protocol. Cell-RT mix was prepared, targeting 10,000 cells per sample. Library quantification and quality assessment were performed using the Bioanalyzer Agilent 2100 with a High Sensitivity DNA chip (Agilent Genomics). Indexed libraries were pooled equimolarly and sequenced on an Illumina NovaSeq 6000 by GenomeScan using paired-end 26x98-bp reads as the sequencing mode. Libraries were sequenced on the NovaSeq 6000 (Illumina) at 30,000 reads per nuclei resolution.

value: heart ventricle


title: Pooled_snRNA-seq_Human2_2

description:
Library name: Human heart tissue - Pooled 2
10x Genomics


title: QX586

description: Library name: F28


title: 467686


title: 547892


title: 950742


title: WT Experiment (no-sgRNA) sample 5, Neurite Fraction

description: Library name: neurite.5

value: Neurite


title: Individual_snRNA-seq_Donor_6

description:
Library name: Human heart tissue - Donor 6
10x Genomics


title: QX585

description: Library name: F26


title: Individual_snRNA-seq_Donor_5

description:
Library name: Human heart tissue - Donor 5
10x Genomics


title: QX584

description: Library name: F24


title: Individual_snRNA-seq_Donor_4

description:
Library name: Human heart tissue - Donor 4
10x Genomics


title: 766967

value: Ganitumab


title: Pooled_snRNA-seq_Human4_3

description:
Library name: Human heart tissue - Pooled 3
10x Genomics

source_name: heart atria

value: heart atria


title: Individual_snRNA-seq_Donor_3

description:
Library name: Human heart tissue - Donor 3
10x Genomics


title: QX580

description: Library name: F22


title: QX579

description: Library name: F20


title: 239910

value: Paclitaxel + Ganitumab


title: Individual_snRNA-seq_Donor_2

description:
Library name: Human heart tissue - Donor 2
10x Genomics


title: QX567

description: Library name: F18


title: 172366


title: 966016


title: QX565

description: Library name: F16


title: Heart_bulkRNA-seq_Donor_6

description: Library name: Human heart tissue - Donor6

data_processing:
Sequencing reads from bulk RNA-seq were trimmed by Trim Galore! and aligned with STAR to the same reference genome used for the single-nucleus RNA-seq.
Gene expression was quantified at the transcript level using Salmon, with the validatMappings and -gcBias parameters switched on, to the homo sapiens transcriptome.
Assembly: GRCh38
Supplementary files format and content: tab-delimited value files

extract_protocol:
Total RNA was isolated using the RNeasy Micro Kit (Qiagen) from homogenised frozen left ventricular human cardiac according to the manufacturer’s protocol.
From 1 μg of RNA, RNA-seq libraries were prepared with the TruSeq RNA Sample Preparation Kit following the manufacturer's manual. Sequencing was performed on Illumina NovaSeq 6000 (2x150 bp paired-end reads).


title: QX561

description: Library name: F14


title: Heart_bulkRNA-seq_Donor_5

description: Library name: Human heart tissue - Donor5


title: Heart_bulkRNA-seq_Donor_4

description: Library name: Human heart tissue - Donor4


title: Heart_bulkRNA-seq_Donor_3

description: Library name: Human heart tissue - Donor3


title: 430441


title: QX545

description: Library name: F12


title: QX534

description: Library name: F10


title: QX493

description: Library name: E6


title: Heart_bulkRNA-seq_Donor_2

description: Library name: Human heart tissue - Donor2


title: QX490

description: Library name: E4


title: 115987


title: Heart_bulkRNA-seq_Donor_1

description: Library name: Human heart tissue - Donor1


title: 120422


title: 460642


title: Individual_snRNA-seq_Donor_1

description:
Library name: Human heart tissue - Donor 1
10x Genomics


title: 209967


title: QX577

description: Library name: E30


title: 802308


title: 465008


title: S1D8

city: Beijing

first: Ruoqi

last: Cheng

state: Beijing

address: NO.5, Yiheyuan Road, Haidian District

institute: Peking University

description:
Library name: S1D8
10x Genomics

data_processing:
The clean single-cell RNA-seq reads were mapped to human reference genome hg38 using Cell Ranger v5.0.1.
Assembly: hg38
Supplementary files format and content: gz archives contain Cell Ranger output (barcodes.tsv, features.tsv, matrix.mtx).

source_name: human blood cells during chemical reprogramming

extract_protocol:
Cells were collected at the indicated time points during chemical reprogramming and resuspended at a concentration of 1 × 10 6  cells per ml in PBS with 0.04% bovine serum albumin. Using the Single Cell 3′ Library and Gel Bead kit V3.1 (10x Genomics, 1000075) along with the Chromium Single Cell B Chip kit (10x Genomics, 1000074), the cell suspension containing 300–600 viable cells per ml was loaded onto the Chromium single-cell controller (10x Genomics) to create single-cell gel beads in emulsion (GEMs) following the manufacturer’s instructions.
The captured cells were lysed, and the released RNA was barcoded through reverse transcription in individual GEMs, performed on a S1000TM Touch Thermal Cycler (Bio-Rad) at 53 °C for 45 min followed by 85 °C for 5 min and incubation at 4 °C. scRNA-seq libraries were constructed using a Single Cell 3′ Library and Gel Bead kit V3.1 (10x Genomics) and sequenced on an Illumina NovaSeq 6000 sequencer, with a sequencing depth of no less than 1 × 10 5  reads per cell with paired-end 150-bp reads (PE150).

treatment_protocol: blood cells were treatment by the chemical reprogramming protocol

value: self-derived S1D8

value: WT


title: 327917

state: CA

source_name: primary breast cancer


title: S1D6

description:
Library name: S1D6
10x Genomics

value: human blood cells during chemical reprogramming

value: self-derived S1D6


title: QX576

description: Library name: E28


title: S1D3

description:
Library name: S1D3
10x Genomics

value: self-derived S1D3


title: QX575

description: Library name: E26


title: 345483

value: primary breast cancer


title: S1D1

description:
Library name: S1D1
10x Genomics

value: self-derived S1D1


title: QX574

description: Library name: E24


title: 798604


title: PBMC EPC

description:
Library name: PBMC EPC
10x Genomics

source_name: human blood cells

value: human blood cells

value: Z0684 PBMC EPC

value: erythroid progenitor cells (EPC)


title: QX573

description: Library name: E22

value: Caenorhabditis elegans

value: Doxycycline


title: QX571

description: Library name: E20


title: QX570

description: Library name: E18


title: 515281


title: Z0684_CiPSC-4 rep1

description:
Library name: Z0684_CiPSC-4 rep1
column name in counts.csv: Z0684_CiPSC-4#-1

data_processing:
Sequenced reads were trimmed for adaptor sequence, and masked for low quality data by Trimmomatic v0.39, then mapped to hg38 whole genome using STAR v2.7.10b and annotated using gencode v47 gtf file.
sam file generated by STAR was converted to bam and counts were generated using featureCounts v2.0.6.
Assembly: hg38
Supplementary files format and content: csv file with raw gene counts for every gene and every sample.

source_name: induced from EPC

extract_protocol:
Total RNA was extracted utilizing the TGuide S32 Blood/Cell/Tissue RNA kit in conjunction with the TGuide S32 nucleic acid extractor.
For the preparation of RNA-seq libraries, the NEBNext Ultra RNA Library Prep Kit for Illumina (provided by New England BioLabs, catalog number E7775) was used. The resultant libraries, comprising fragmented and randomly primed RNA molecules, were sequenced as paired-end reads of 2 x 150 base pairs

value: induced from EPC

value: EPC derived hCiPSC


title: Z0684-EPC rep1

description:
Library name: Z0684-EPC rep1
column name in counts.csv: Z0684-EPC-1