title: cervicothoracic SCDH-INs_1

city: Madison

first: Randolph

middle: S

last: Ashton

state: WI

address: 330 N Orchard St.

department: Biomedical Engineering and Wisconsin Institute for Discovery

institute: University of Wisconsin-Madison

description:
Library name: Sample 1
120 hrs of HOX propagation (7 days), followed by 3 days of RA/SB/LDN treatment to generate pCNSPs, then 4 days of RA treatment to generate dorsal horn progenitors. Cultures were matured for 5 days with DAPT before MPS seeding. Cells were aggregated into spheroids and cultured in the MPS for 5 weeks together with Anatomic Nociceptor spheroids.

data_processing:
Single cell RNAseq data were analyzed by the UW Bioinformatics Resource Center. Experiment data were demultiplexed using the Cell Ranger Single Cell Software Suite, mkfastq command wrapped around Illumina's bcl2fastq. The MiSeq balancing run was quality controlled using calculations based on UMI-tools (Smith et al, 2017). Samples libraries were balanced for the number of estimated reads per cell and run on an Illimina NovaSeq system. Cell Ranger software was then to perform demultiplexing, alignment, filtering, barcode counting, UMI counting, and gene expression estimation for each sample according to the 10x Genomics documentation (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger). The gene expression estimates from each sample were then aggregated using Cellranger (cellranger aggr) to compare experimental groups with normalized sequencing-depth and expression data. Smith, T.S., Heger, A., & Sudbery, I. UMI-tools: Modelling sequencing errors in Unique Molecular Identifiers to improve quantification accuracy. Genome Res. 2017, 491-499 (2017).
Assembly: GRCh38
Supplementary files format and content: Tab-separated values files and matrix files

source_name: iPS(IMR90)-4 + Anatomic Inc. RealDRG

growth_protocol: hPSCs were maintained at 37°C in 5% CO2 in Essential 8 (E8) medium on 35 mm Matrigel (WiCell) coated tissue culture-treated plates and were passaged when 70-80% confluent. Briefly, cells were washed once with phosphate buffered saline (PBS, Invitrogen), then incubated at 37°C in Versene (Invitrogen) for 5 minutes. Versene was aspirated, the cells were gently dissociated from the well with fresh E8, and re-plated at a  1:12 seeding ratio. Media was replenished daily (Lippmann et. al. 2014).

extract_protocol:
Cell spheroids were manually removed from the MPS devices and singularized for scRNAseq by dissociation with Papain (Worthington). Using sterilized forceps, cell spheroids were removed from the PEG hydrogel mold, transferred to a conical tube containing PBS, and allowed to settle for 10 minutes. The spheroids were then resuspended in Papain solution containing DNase and incubated for 1.5 hours at 37° C on an orbital shaker. Cells were then triturated vigorously, centrifuged for 5 minutes at 300g, and quenched in ovomucoid solution containing DNase. Quenched cells were centrifuged, gently resuspended in PBS containing 0.2% BSA and 10 μM Y27632, then passed through a 40 mm cell strainer (Mitenyi Biotec) to remove debris. Cells were quantified and diluted to 700 cells/mL for sequencing.  Cells were kept on ice before being quantified and diluted for sequencing.
Transcriptomic profiling was performed using the Chromium Single Cell Gene Expression system (10X Genomics), according to the manufacturer’s recommendations using the Single Cell 30 Reagent v2/v3 kits (10X Genomics). Post-GEM-RT and post-cDNA amplification cleanup were performed using Dynabeads MyOne silane beads (Thermofisher) and SPRIselect (Beckman Coulter) kits respectively. Successful library preparation was confirmed using an Agilent Bioanalyzer (High Sensitivity DNA kit) and Qubit Fluorometer (High Sensitivity dsDNA kit).  Samples libraries were balanced for the number of estimated reads per cell and run on a NovaSeq 6000 system.

treatment_protocol: HOX PROPAGATION: To initiate neuromesodermal progenitor (NMP) differentiation, hESCs were washed once with PBS, incubated at 37°C in Accutase (Invitrogen) for 5 mins, singularized by gentle trituration, and quenched with 1 volume E8 media. Following centrifugation for 5 mins at 300g, hESCs were replated onto 35 mm Matrigel-coated plates at a density of 1.5 x 105 cells/cm2 in E8 medium with 10 μM ROCK inhibitor (Y27632, Tocris). The media was replaced with Essential 6 (E6) medium (Lippmann et al., 2014) on the following day (Day 0), and then changed to E6 supplemented with 200 ng/mL FGF8b (Peprotech) 24 hours later (Day 1). On Day 2, Hox propagation was initiated by activation of Wnt signaling using NMP media comprised of E6 medium supplemented with 200 ng/mL FGF8b and 3 μM CHIR99021 (Tocris). This constitutes the “Hox timepoint” of 0hrs. First, cells were sub-cultured at a 2:3 ratio. Briefly, cells were washed once with PBS, incubated in Accutase for 1.5-2 mins, and removed from the surface by gentle pipetting. After centrifugation, cells were gently resuspended in NMP Medium containing 10 μM Y27632 and seeded on 35 mm Matrigel-coated plates. Media was replenished on Day 4. Cells were sub-cultured again at a 2:3 ratio on Day 5. pCNSPs were differentiated after 120hrs.  pCNSP DIFFERENTIATION: NMPs were cultured for 1 day in pCNSP media, comprising of E6 media supplemented with 1 µM retinoic acid (RA; Sigma), 10 µM SB-431542 (Abcam), and 100 nM µL LDN-193189 (Stemgent). Cells were singularized and replated at 5 x 105 cells/cm2 in pCNSP media containing 10 μM Y27632 for an additional 2 days. Media was replenished daily. DORSAL DIFFERENTIATION: pCNSPs were differentiated to dorsal horn progenitors by culturing in E6 media containing 1 uM RA for 4 days. Media was replenished daily.  NEURONAL DIFFERENTIATION: To differentiate neurons, progenitors were cultured in maturation media, with daily media changes for 5 days. Maturation media consisted of E6 containing 1x N2 Supplement (Thermofisher), 50x B27 Supplement (Thermofisher), 1 µM cAMP (Sigma), 10 ng/mL GDNF, 10 ng/mL BDNF, 10 ng/mL NT-3 (Peprotech), and 10 µM DAPT (Tocris). Post-mitotic neurons were cryopreserved prior to MPS seeding. MPS SEEDING AND CULTURE: Cells were thawed and plated onto wells of a 6-well plate in human cocolture media (Neurobasal media containing containing 2% B27 supplement, 1% N2 suppement, 1% anti-anti, 1% glutamax, 10ng/mL BDNF, 10ng/mL GDNF, 20ng/mL NGF, 10ng/mL NT3, 1uM dibutyrl-cAMP). After 24 hours, cells were singularized and seeded at 25k cells per well into 96 well round-bottom, low attachment plates and centrifuged at 500g for 5 minutes. Plates were then incubated for 48 hours for spheroid aggregation. The same method was used to create spheroids from RealDRG™ Nociceptors purchased from Anatomic Inc. One hPSC derived dorsal horn spheroid and one Anatomic Nociceptor spheroid were seeded into the MPS with Corning® Matrigel diluted 1:1 with human coculture media. The MPS devices were cultured in human coculture media for 5 weeks with media changes every other day.

value: iPS(IMR90)-4 + Anatomic Inc. RealDRG

value: hiPSC derived dorsal horn neurons + hPSC derived DRG Sensory Neurons


title: LV5-NID1-3

status: Public on Aug 01 2025

type: SRA

city: jinan

first: liu

last: jialiang

address: wenhuaxi road

country: China

institute: shandong university

description:
NID-3
processed data file2.txt

library_source: transcriptomic

data_processing:
SOAPnuke (V2.1.0) was used to filter the sequencing data as follows:  (1) Reads containing sequencing joints were removed;  (2) Reads with N ratio greater than 0.5% were removed;  (3) Removal of low-quality reads (those with Qphred≤20 bases accounting for more than 50% of the length of the entire reads).  Clean reads are obtained after filtering
Assembly: HISAT2 (V2.1.0) was used to compare clean reads with the reference genome,  and Bowtie2  (V2.3.5) was used to align the quality controlled sequence to the  reference transcription sequence.
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample

molecule: total RNA

organism: Homo sapiens

extract_protocol:
Total RNA was extracted using the Trizol(Invitrogen, CA, USA), RNA purity and integrity was monitored by NanoDrop 2000 spectrophotometer (NanoDrop Technologies, Wilmington, DE, USA) and a Bioanalyzer 2100 system (Agilent  Technologies, CA, USA). RNA contamination was assessed by 1.5% agarose gel.
Oligo(dT)-attached magnetic beads were used to purify mRNA. Purified mRNA  was fragmented into small pieces with fragment buffer at appropriate temperature. Then  First-strand cDNA was generated using random hexamer-primed reverse transcription,  followed by a second-strand cDNA synthesis and purified using AMPure XP Beads.  Afterwards, A-Tailing Mix and RNA Index Adapters were added by incubating to end  cDNA repair. The cDNA fragments obtained from previous steps were amplified by  PCR, and products were purified by Ampure XP Bead, get the final library. After the library was constructed, Qubit 2.0 was used for preliminary  quantification, and the library was diluted to 1.5 ng/μL. Then Agilent 2100 BioAnalyzer  was used to detect the insert size of the library. Qrt-pcr was used to accurately quantify the effective concentration of the library to ensure the quality of the library.

tag: cell line

tag: cell type

value: human colon cancer cells


title: patient_A4__bb21217 CAR T cells__DoseCohort_150x10^6 cells

city: Seattle

first: Daniel

last: Zak

state: WA

address: 188 East Blaine Street, Suite 300

country: USA

institute: Regeneron

description:
Library name: A4
75bp PE

data_processing:
Sequences were aligned to the human genome using STAR aligner (Dobin et al., 2013).
Gene features were only determined for uniquely mapped reads and these were annotated with the GENCODE version 29 gene transfer format (gtf) file using RNA-Seq by Expectation Maximization (RSEM) (Li & Dewey, 2011). For each gene feature, RSEM provides read counts and transcripts per million reads.
Assembly: human genome: GRCh38, GENCODE version 29; gene annotations: GENCODE version 29 gene transfer format (gtf) file.
Supplementary files format and content: Three processed data files include comma-delimited text files that contain (1) RSEM TPMs, (2) RSEM expected counts, and (3) batch corrected RSEM expected counts for each sample.  The batch corrected counts were used in the WGCNA analyses.

source_name: autologous CAR T cells manufactured from PBMCs obtained from leukapheresis

growth_protocol: bb21217 Drug Product (DP) was manufactured by transducing autologous T cells with an anti-BCMA02 CAR lentiviral vector as described by Friedman et al. and culturing in the presence of bb007.    DP T cells were otherwise untreated.

extract_protocol:
Total RNA was isolated using the Qiagen 96-well RNeasy Prep Kit.
RNA was extracted from each sample containing 1–2 × 106 cells and quality was assessed using the Agilent 2200 TapeStation system with High Sensitivity RNA ScreenTape Assay (Agilent, Santa Clara, CA). Samples with at least 5 ng/μL of RNA and an RNA integrity number score >7 were used in the library preparation following the exact protocol in the Kapa RNA HyperPrep Kit with RiboErase (Roche, Pleasanton, CA). Final libraries with a concentration greater than 4 nM and an average fragment size between 300 and 500 bases were pooled in equimolar ratio and volume to make a final sample of 4 nM.
The pooled library was sequenced on a NextSeq 500/550 sequencer (Illumina, San Diego, CA) using a High Output Kit providing 150 cycles with 75 base pair paired-end reads to a minimum depth of 20 million reads per sample.

tag: tissue

tag: disease state

value: relapsed/refractory multiple myeloma

value: bb21217 CAR T cells

tag: transgene

value: anti-BCMA02 CAR

tag: treatment

value: manufactured by transducing autologous T cells with an anti-BCMA02 CAR lentiviral vector as described by Friedman et al. (2018) and culturing in the presence of bb007

tag: dose cohort

tag: randomized id


title: S462 cell line, 10 nM trametinib 48h, replicate 3

city: Select

first: Angelina

middle: V.

last: Vaseva

state: Oregon

address: Pediatrics

institute: Oregon Health Science University

description:
Library name: GSM250722035
T3_S4

data_processing:
Trim Galore was applied to raw sequencing data to remove the adapter and poor-quality reads.
STAR were used to align DNA and RNA sequencing data to the reference genome.
To remove mouse-derived reads in PDXs, we mapped the sequencing data to the human (GRCh38, GENCODE v29) and mouse (GRCm38, GENCODE vM19) reference genomes. Disambiguate was then employed on the BAM files to remove mouse reads. RSEM5 was applied to calculate raw read counts.
Assembly: GRCh38
Supplementary files format and content: Expression Matrix, in TPM

growth_protocol: cells were plated in tissue culture dishes in RPMI medium supplemented with 10% FBS

extract_protocol:
RNA was isolated using RNeasy Mini Kit (QIAGEN). The quality of Total RNA was checked by Agilent Fragment Analyzer (Agilent Technologies, Santa Clara, CA), and only high-quality RNA samples (RQN >7) were used for mRNA-seq library preparation and sequencing.
Following the Illumina TruSeq stranded mRNA sample preparation guide, we used approximately 500ng Total RNA for RNA-seq library preparation. fter RNA-seq libraries were quantified, they were pooled and subsequently loaded for 101bp paired read sequencing run on the Illumina NovaSeq 6000 platform.

treatment_protocol: Treatment was done the next next day after plating. Cells were treated with either 250 nM LXH254, 10 nM trametinib, or 250 nM LXH254 + 10 nM trametinib for 48 hours. Each treatment was done in triplicate. Three MPNST cell lines were used: ST8814, S462, and NF90.8

value: MPNST

value: 10 nM trametinib 48h


title: NF90.8 cell line, 10 nM trametinib 48h, replicate 3

description:
Library name: GSM250722034
T3_908


title: LV5-NID1-2

description:
NID-2
processed data file2.txt


title: MDA-MB-231/tet-off/EV clone H3_biol_rep_2

city: Baltimore

first: Julia

middle: L

last: Rutherford

address: 108 N Greene St

institute: University of Maryland, Baltimore

description: Library name: TTP-H3-2

data_processing:
Data was processed by Azenta Biosciences according to established protocols.
Sequenced reads were trimmed using Trimmomatic v.0.36.
Trimmed reads were mapped to the Homo sapiens GRCh38 reference genome using STAR aligner v.2.5.2b.
Unique gene hit counts were calculated using featureCounts from the Subread package v.1.5.2.
Differential expression analysis was performed using DESeq2.
Assembly: GRCh38
Supplementary files format and content: csv file including ENSEMBL ID, gene symbol, log2(fold change) values, p-values, adjusted p-values, and raw counts

growth_protocol: All cells were maintained in DMEM, 10% FBS, 100 IU/mL pencillin, 100 ug/mL streptomycin, 400 ug/mL G418 sulfate, and 100 ug/mL Hygromycin B. 2 ug/mL doxycycline was added to cells expressing TTP.

extract_protocol:
RNA was extracted using the NucleoSpin RNA kit (Macherey-Nagel)
Libraries were constructed by Azenta Biosciences using the NEBNext Ultra II RNA library preparation kit.

treatment_protocol: Before experiements, selection agents and doxycycline were washed out for at least 24 hours to allow expression of TTP.

value: TNBC cell line


title: patient_E4__bb21217 CAR T cells__DoseCohort_450x10^6 cells

description:
Library name: E4
75bp PE

value: autologous CAR T cells manufactured from PBMCs obtained from leukapheresis


title: RNA_B16_F10_PBS_rep1

city: Beijing

first: Jie

last: Liang

address: beiyitiao 11, zhognguancun, beijing

institute: National Center for Nanoscience and Technology, Chinese Academy of Sciences

data_processing:
Quality control, raw data (raw reads) of fastq format were firstly processed through in-house perl scripts.
Reads mapping to the reference genome,paired-end clean reads were aligned to the reference genome using Hisat2 v2.0.5.
Novel transcripts prediction were assembled by StringTie and quantification of gene expression level were obtained using featureCounts v1.5.0-p3.
Differential expression analysis
Assembly: GRCm38
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

organism: Mus musculus

source_name: tumor

extract_protocol:
RNA was harvested using TRIzol and RNA integrity was assessed using the RNA Nano 6000 Assay Kit.
RNA libraries for RNA-seq were prepared using NEBNext mRNA-Seq Library Prep Kit following manufacturer's protocols.

value: tumor

value: tumor-associated macrophages

tag: genotype

value: WT

value: PBS


title: LV5-NID1-1

description:
NID-1
processed data file2.txt


title: MDA-MB-231/tet-off/EV clone H3_biol_rep_1

description: Library name: TTP-H3-1


title: cervicothoracic SCDH-INs_2

description:
Library name: Sample 2
120 hrs of HOX propagation (7 days), followed by 3 days of RA/SB/LDN treatment to generate pCNSPs, then 4 days of RA treatment to generate dorsal horn progenitors. Cultures were matured for 5 days with DAPT before MPS seeding. Cells were aggregated into spheroids and cultured in the MPS for 5 weeks together with Anatomic Nociceptor spheroids.

library_source: transcriptomic single cell

molecule: polyA RNA


title: patient_A6__bb21217 CAR T cells__DoseCohort_450x10^6 cells

description:
Library name: A6
75bp PE


title: LV5-3

description:
480-3
processed data file2.txt


title: MDA-MB-231/tet-off/EV clone E11_biol_rep_4

description: Library name: TTP-E11-4


title: ST8814 cell line, 10 nM trametinib 48h, replicate 2

description:
Library name: GSM250722033
T2_ST


title: patient_Z1__bb21217 CAR T cells__DoseCohort_450x10^6 cells

description:
Library name: Z1
75bp PE


title: P19, shUbe2t #2, S9.6

city: Jinan

first: Yongze

last: Yu

email: lwyyzsdu@163.com, lwyyzsdu@hotmail.com

state: Shandong

address: 文化西路44号国家辅助生殖与优生工程技术研究中心

institute: Shandong University

library_source: genomic

data_processing:
library strategy:CUT&Tag
The library preparations were sequenced on Illumina Novaseq platform at Novogene Science and Technology Co., Ltd (Beijing, China) and 150bp paired-end reads were generated
The read sequences produced by the Illumina pipeline in FASTQ format were pre-processed through Trimmomatic software, and all low-quality reads and PCR adapters were removed
CUT&Tag reads were aligned to the UCSC mm10 genome using Bowtie v0.7.12.
All peak calling was performed with MACS2 v2.1.2 using ‘macs2 -q 0.05 --call-summits --nomodel --shift -100 --extsize 200 --keep-dupall’.
bigWig files were generated using the genomicRanges R package. narrowPeak files were generated using MACS v2.1.2 with default settings.
Assembly: mm10
Supplementary files format and content: bigWig, narrowPeak

molecule: genomic DNA

source_name: embryo

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

extract_protocol:
The genome DNA were extracted by the Hyperactive Universal CUT&Tag Assay Kit for Illumina (Vazyme Biotech, China; TD903).
CUT&Tag libraries were prepared using the Hyperactive Universal CUT&Tag Assay Kit for Illumina (Vazyme Biotech, China; TD903). Libraries were amplified using 11 cycles on the thermocycler. Libraries were purified with the AMPure beads and library quality was assessed on the Agilent Bioanalyzer 2100 system.

value: embryo

value: Mouse embryo carcinoma

value: Ube2t knockdown

value: Knockdown with shUbe2t #2 adenovirus, S9.6 antibody used


title: LV5-2

description:
480-2
processed data file2.txt

value: human colon cancer cells


title: NF90.8 cell line, 10 nM trametinib 48h, replicate 2

description:
Library name: GSM250722031
T2_908


title: patient_F9__bb21217 CAR T cells__DoseCohort_450x10^6 cells

description:
Library name: F9
75bp PE

value: relapsed/refractory multiple myeloma


title: patient_X1__bb21217 CAR T cells__DoseCohort_450x10^6 cells

description:
Library name: X1
75bp PE

value: bb21217 CAR T cells


title: patient_G7__bb21217 CAR T cells__DoseCohort_450x10^6 cells

description:
Library name: G7
75bp PE

value: anti-BCMA02 CAR


title: MDA-MB-231/tet-off/EV clone H3_biol_rep_3

description: Library name: TTP-H3-3


title: LV5-1

description:
480-1
processed data file2.txt


title: MDA-MB-231/tet-off/EV clone E11_biol_rep_2

description: Library name: TTP-E11-2


title: MDA-MB-231/tet-off/TTP clone E11_biol_rep_1

description: Library name: TTP-E11-1


title: EV-XP-NID1-LX-2-3

description:
SOE3
processed data file3.txt

value: Human Hepatic Stellate Cells


title: patient_J3__bb21217 CAR T cells__DoseCohort_300x10^6 cells

description:
Library name: J3
75bp PE

value: manufactured by transducing autologous T cells with an anti-BCMA02 CAR lentiviral vector as described by Friedman et al. (2018) and culturing in the presence of bb007


title: S462 cell line, 10 nM trametinib 48h, replicate 1

description:
Library name: GSM250722029
T1_S4

value: MPNST

value: 10 nM trametinib 48h


title: MDA-MB-231/tet-off/EV clone B_biol_rep_4

description: Library name: EV-B-4

value: TNBC cell line


title: EV-XP-NID1-LX-2-2

description:
SOE2
processed data file3.txt


title: EV-XP-NID1-LX-2-1

description:
SOE1
processed data file3.txt


title: NF90.8 cell line, 10 nM trametinib 48h, replicate 1

description:
Library name: GSM250722028
T1_908


title: patient_S6__bb21217 CAR T cells__DoseCohort_150x10^6 cells

description:
Library name: S6
75bp PE

value: autologous CAR T cells manufactured from PBMCs obtained from leukapheresis


title: MDA-MB-231/tet-off/EV clone E11_biol_rep_3

description: Library name: TTP-E11-3


title: patient_G2__bb21217 CAR T cells__DoseCohort_300x10^6 cells

description:
Library name: G2
75bp PE


title: patient_K6__bb21217 CAR T cells__DoseCohort_150x10^6 cells

description:
Library name: K6
75bp PE


title: S462 cell line, 250 nM LXH254 + 10 nM trametinib 48h, replicate 3

description:
Library name: GSM250722026
LT3_S4

value: 250 nM LXH254 + 10nM trametinib 48h


title: MDA-MB-231/tet-off/EV clone B_biol_rep_1

description: Library name: EV-B-1


title: EV-XP-LX-2-3

description:
SWT3
processed data file3.txt


title: MDA-MB-231/tet-off/EV clone B_biol_rep_3

description: Library name: EV-B-3


title: S462 cell line, 10nM trametinib 48h, replicate 2

description:
Library name: GSM250722032
T2_S4


title: ST8814 cell line, 250 nM LXH254 + 10 nM trametinib 48h, replicate 3

description:
Library name: GSM250722027
LT3_ST


title: EV-XP-LX-2-2

description:
SWT2
processed data file3.txt


title: EV-XP-LX-2-1

description:
SWT1
processed data file3.txt


title: MDA-MB-231/tet-off/EV clone A_biol_rep_4

description: Library name: EV-A-4


title: ST8814 cell line, 10nM trametinib 48h, replicate 1,

description:
Library name: GSM250722030
T1_ST


title: MDA-MB-231/tet-off/EV clone B_biol_rep_2

description: Library name: EV-B-2


title: NF90.8 cell line, 250 nM LXH254 + 10nM trametinib 48h, replicate 3

description:
Library name: GSM250722025
LT3_908


title: patient_Z3__bb21217 CAR T cells__DoseCohort_450x10^6 cells

description:
Library name: Z3
75bp PE


title: ST8814 cell line, 250 nM LXH254 + 10 nM trametinib 48h, replicate 2

description:
Library name: GSM250722024
LT2_ST


title: patient_M6__bb21217 CAR T cells__DoseCohort_150x10^6 cells

description:
Library name: M6
75bp PE


title: patient_H4__bb21217 CAR T cells__DoseCohort_450x10^6 cells

description:
Library name: H4
75bp PE


title: MDA-MB-231/tet-off/EV clone A_biol_rep_3

description: Library name: EV-A-3


title: Normal_group2

city: kunming

first: Xiao

last: Kuang

state: yunnan

address: 374 Dianmian Avenue, Kunming, Yunnan

institute: The Second Affiliated Hospital of Kunming Medical University

data_processing:
Total RNA was purified by electrophoretic separation on a 15% urea denaturing polyacrylamide gel electrophoresis (PAGE) gel and small RNA regions corresponding to the 18–30 nt bands in the marker lane (14-30 ssRNA Ladder Marker, TAKARA) were excised and recovered. Then the 18–30 nt small RNAs were ligated to adenylated 3’ adapters annealed to unique molecular identifiers (UMI), followed by the ligation of 5’adapters. The adapter-ligated small RNAs were subsequently transcribed into cDNA by SuperScript II Reverse Transcriptase (Invitrogen, USA) and then several rounds of PCR amplification with PCR Primer Cocktail and PCR Mix were performed to enrich the cDNA fragments. The PCR products were selected by agarose gel electrophoresis with target fragments 110~130 bp, and then purified by QIAquick Gel Extraction Kit (QIAGEN, Valencia, CA). The library was quality and quantitated in two methods:check the distribution of the fragments size using the Agilent 2100 bioanalyzer, and quantify the library using real-time quantitative PCR.
The final ligation PCR products were sequenced on the BGISEQ-500 platform (BGI, Shenzhen, China).
Small RNA expression levels were calculated by counting the absolute number of molecules using unique molecular identifiers.(Kivioja, et al., 2011) Differential expression analysis was performed using DEGseq,(Wang, et al., 2010) Q value ≤ 0.001, and the absolute value of Log2Ratio ≥ 1 as the default threshold to judge the significance of expression differences.
The final mRNA library was amplified with phi29 (Thermo Fisher Scientific, Waltham, MA, USA) into DNA nanoballs, where one molecule had more than 300 copies. The DNA nanoballs were loaded into patterned nanoarrays to generate reads of 100 bases on the opposite end of the BGISEQ500 platform (BGI ).
Assembly: mm10

source_name: Blood plasma

extract_protocol:
Total RNA was extracted from the blood using RNAiso Blood (Takara) according to the manufacturer’s instructions. The final RNA concentrations for all specimens ranged from 150 to 250 ng/µL, the A260/A280 values ranged from 1.98 to 2, and the RNA integrity number (RIN) values ranged from 6.7 to 8.0.
RNA libraries for RNA-seq were prepared using SMARTER mRNA-Seq and miRNA Library Prep Kit following manufacturer's protocols.

value: healthy control

tag: gender

value: Male

tag: age

value: Blood plasma


title: S462 cell line, 250 nM LXH254 + 10 nM trametinib 48h, replicate 2

description:
Library name: GSM250722023
LT2_S4


title: MDA-MB-231/tet-off/EV clone A_biol_rep_2

description: Library name: EV-A-2


title: NF90.8 cell line, 250 nM LXH254 + 10 nM trametinib 48h, replicate 2

description:
Library name: GSM250722022
LT2_908


title: patient_E7__bb21217 CAR T cells__DoseCohort_450x10^6 cells

description:
Library name: E7
75bp PE


title: MDA-MB-231/tet-off/EV clone A_biol_rep_1

description: Library name: EV-A-1


title: patient_T8__bb21217 CAR T cells__DoseCohort_450x10^6 cells

description:
Library name: T8
75bp PE


title: patient_A3__bb21217 CAR T cells__DoseCohort_450x10^6 cells

description:
Library name: A3
75bp PE


title: Normal_group1

value: Female


title: ST8814 cell line, 250 nM LXH254 + 10 nM trametinib 48h, replicate 1,

description:
Library name: GSM250722021
LT1_ST


title: Disease_group3

value: cirrhosis


title: patient_O9__bb21217 CAR T cells__DoseCohort_450x10^6 cells

description:
Library name: O9
75bp PE


title: RNA-seq, srcap mutation b, differentiated

city: Evanston

first: Stephenie

last: Droll

state: IL

address: Hogan 2-100 2205 Tech Drive

department: Molecular Biosciences

institute: Northwestern University

description: Library name: library_H

data_processing:
quality control by FASTQC
adaptor trimming by Trimgalore
alignment to hg38 by STAR
quantification gene expression by Salmon using the counts per gene option
Assembly: hg38
Supplementary files format and content: DESEQ2 outputs in .csv format

source_name: skin epidermis

growth_protocol: Keratinocytes were maintained in SFM and Medium 154 with human keratinocyte growth supplement, antimycotic, and penicillin streptomycin. Progenitor cells were cultured at < 50% confluency. Differentiation was induced by seeding at confluency with 1.2 mM caclium chloride for four days. Incubator maintained set at 37 C, 5% CO2.

extract_protocol:
Quick-RNA Miniprep Kit with DNase treatment
NEBNext Poly(A) mRNA Magnetic Isolation Module and NEBNext Ultra II Directional RNA Library Prep Kit

treatment_protocol: Keratinocytes were centrifuged for one hour at 1250 RMP at 32 degrees Celsius with emptry vector or SRCAP-mutatio - lentivirus. Cells were selected for 24 hours with puromycin. Cells were harvested for RNA or seeded for differentiation 72 hours after transduction.

value: skin epidermis

value: keratinocyte

value: srcap mutation

value: differentiated


title: RNA-seq, srcap mutation a, differentiated

description: Library name: library_G


title: patient_U4__bb21217 CAR T cells__DoseCohort_300x10^6 cells

description:
Library name: U4
75bp PE

value: relapsed/refractory multiple myeloma

value: bb21217 CAR T cells

value: anti-BCMA02 CAR


title: Disease_group1


title: Disease_group2


title: S462 cell line, 250 nM LXH254 + 10 nM trametinib 48h, replicate 1

description:
Library name: GSM250722020
LT1_S4

value: MPNST


title: RNA-seq, control b, differentiated

description: Library name: library_F

value: empty vector


title: NF90.8 cell line, 250 nM LXH254 + 10nM trametinib 48h, replicate 1

description:
Library name: GSM250722019
LT1_908


title: Normal_group3


title: patient_M1__bb21217 CAR T cells__DoseCohort_450x10^6 cells

description:
Library name: M1
75bp PE

value: manufactured by transducing autologous T cells with an anti-BCMA02 CAR lentiviral vector as described by Friedman et al. (2018) and culturing in the presence of bb007


title: S462 cell line, 250 nM LXH254 48h , replicate 3

description:
Library name: GSM250722017
L3_S4


title: ST8814 cell line, 250 nM LXH254 48h, replicate 3

description:
Library name: GSM250722018
L3_ST


title: RNA-seq, control a, differentiated

description: Library name: library_E


title: C-Mo-TSN-siIL1A

city: Guangzhou

first: Yonghao

last: Ruan

address: 135 Xin Gang Xi Road, Guangzhou, China

institute: Sun Yat-sen University

description: Library name: sample6

data_processing:
Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts. In this step, clean data (clean reads) were obtained by removing reads containing adapter, reads containing poly-N and low quality reads from raw data. At the same time, Q20, Q30 and GC content the clean data were calculated. All the downstream analyses were based on the clean data with high quality.
Index of the reference genome was built using Bowtie v2.0.6 and paired-end clean reads were aligned to the reference genome using TopHat v2.0.12.
The FPKM of each gene was calculated based on the length of the gene and number of reads count mapped to this gene was calculated.
Assembly: ftp://ftp.ensembl.org/pub/release-80/fasta/anas_platyrhychos/dna/
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

source_name: blood

extract_protocol:
Four polyA mRNA-seg libraries, include two from si-NC monocyte samples and two from si-IL1A monocyte samples. RNA was harvested using Trizol reagent. DNBSEQ stamdard kits was used with 3 ug of total RNA for the construction of Sequencing.
RNA libraries were prepared for sequencing using standard DNBSEQ-T7 protocols.

value: blood

value: monocyte

value: myeloid


title: C-Mo-TSN-siNC

description: Library name: sample5

value: siNC


title: patient_J2__bb21217 CAR T cells__DoseCohort_150x10^6 cells

description:
Library name: J2
75bp PE

value: autologous CAR T cells manufactured from PBMCs obtained from leukapheresis


title: patient_D6__bb21217 CAR T cells__DoseCohort_450x10^6 cells

description:
Library name: D6
75bp PE


title: RNA-seq, srcap mutation a

description: Library name: library_C

value: none, progenitor


title: NF90.8 cell line, 250 nM LXH254 48h, replicate 3

description:
Library name: GSM250722016
L3_908


title: ST8814 cell line, 250 nM LXH254 48h, replicate 2

description:
Library name: GSM250722015
L2_ST


title: patient_S4__bb21217 CAR T cells__DoseCohort_450x10^6 cells

description:
Library name: S4
75bp PE


title: B-Mo-TSN-siNC

description: Library name: sample3


title: patient_X5__bb21217 CAR T cells__DoseCohort_450x10^6 cells

description:
Library name: X5
75bp PE


title: RNA-seq, control b

description: Library name: library_B


title: S462 cell line, 250 nM LXH254 48h, replicate 2

description:
Library name: GSM250722014
L2_S4


title: RNA-seq, control a

description: Library name: library_A


title: NF90.8 cell line, 250 nM LXH254 48h, replicate 2

description:
Library name: GSM250722013
L2_908


title: patient_F4__bb21217 CAR T cells__DoseCohort_300x10^6 cells

description:
Library name: F4
75bp PE


title: A-Mo-TSN-siNC

description: Library name: sample1


title: srcap mutation b, differentiated

description:
Library name: library_Z
H2A.Z, Active Motif 39943

data_processing:
Read quality control by FastQC
Adaptor trimming by Trimgalore
Aligned to hg38 with BWA-MEM, default parameters
Peak calling by MACS2, narrowPeak. q < 0.001 for H2A.Z peak calling
Assembly: hg38
Supplementary files format and content: MACS2 peaks in .narrowPeak format

extract_protocol:
Keratinocytes were fixed for 10 minutes in 1% formaldehyde, quenched with glycine, nuclei extracted, and sonicated with a Bioruptor Pico (Diagenode).
NEBNext Ultra II DNA Library Prep Kit for Illumina


title: sgRNA Bmal1,replicate 3

first: Dandan

last: Zong

address: No.106, Zhongshan 2nd Road

institute: Guangdong Provincial People’s Hospital

data_processing:
Raw RNA-seq reads contaminated with adapters and reads with low-quality bases were discarded to obtain the clean reads, and then clean reads were mapped against UCSC human reference hg38 using fastp (V0.20.1), and uniquely mapped reads were counted using HISAT2 (hisat2-2.0.4). Gene expression levels were quantified with RPKM (reads per kilobase million).
Assembly: hg38
Supplementary files format and content: Tab-separated text files

source_name: thyroid

growth_protocol: Htoris3.1 cells were transfected with BMAL1-targeting siRNA (RIBOBIO) using Lipofectamine 3000 (Thermo, L3000015). Cells were exposed to 50 nM siRNAs for 6 hours and then grown in RMI1640 with 10% FBS for an additional 24 hours. Htoris3.1 cells were also transfected with CRISPR-Cas9 targeting BMAL1(WZ Biosciences Inc). Cells were co-incubated with the CRISPR-Cas9 virus for 12 hours, then placed in RMI1640 with 10% FBS for 24 hours, and after 48 hours of screening using the antibiotic puromycin, single clones were selected and cells were collected for knockout validation using western blot.

extract_protocol:
Total RNA was exacted with TRIzol Reagent (Invitrogen).
After assessing the concentration of RNA with Qubit TM dsDNA HS Assay Kit (Thermo), 1 μg per sample were constructed into libraries through VAHTS Universal V6 RNA-seq Library Prep Kit for MGI (Vazyme Biotech, NRM604-01) following manufacturer’s manuals. And enrichment of fragments of interest via VAHTSTM DNA Clean Beads (Vazyme Biotech, N411-03). Sequencing data were generated on DNBSEQ-T7 platform with 150-bp paired-end read length by MGI.

treatment_protocol: To induce cell senescence, cells were exposed to Etoposide (2 μM, MedChemExpress) for 24 h.

value: thyroid

value: normal thyroid cell line

value: BMAL1 knock out

value: Etoposide treatment for 12 hours


title: patient_G4__bb21217 CAR T cells__DoseCohort_300x10^6 cells

description:
Library name: G4
75bp PE


title: A-Mo-TSN-siIL1A

description: Library name: sample2


title: srcap mutation a, differentiated

description:
Library name: library_Y
H2A.Z, Active Motif 39943

value: skin epidermis

value: keratinocyte

value: srcap mutation

value: differentiated


title: ST8814 cell line, 250 nM LXH254 48h, replicate 1,

description:
Library name: GSM250722012
L1_ST

value: MPNST


title: B-Mo-TSN-siIL1A

description: Library name: sample4


title: S462 cell line, 250 nM LXH254 48h, replicate 1

description:
Library name: GSM250722011
L1_S4


title: NF90.8 cell line, 250 nM LXH254 48h, replicate 1

description:
Library name: GSM250722010
L1_908


title: sgRNA Bmal1,replicate 2


title: control a, differentiated

description:
Library name: library_W
H2A.Z, Active Motif 39943

value: empty vector


title: ST8814 cell line, control, replicate 3

description:
Library name: GSM250722009
C3_ST


title: RNA-seq, srcap mutation b

description: Library name: library_D


title: patient_I7__bb21217 CAR T cells__DoseCohort_150x10^6 cells

description:
Library name: I7
75bp PE

value: relapsed/refractory multiple myeloma

value: bb21217 CAR T cells

value: anti-BCMA02 CAR

value: manufactured by transducing autologous T cells with an anti-BCMA02 CAR lentiviral vector as described by Friedman et al. (2018) and culturing in the presence of bb007


title: patient_E1__bb21217 CAR T cells__DoseCohort_150x10^6 cells

description:
Library name: E1
75bp PE


title: control b, differentiated

description:
Library name: library_X
H2A.Z, Active Motif 39943


title: DOX_IFN3

city: Essen

first: Florian

last: Rambow

department: IKIM

country: Germany

institute: University Hospital Essen

data_processing:
were then mapped to the human genome (hg19) using STAR (2.4.1b) and quantified with Subread (1.4.6-p2).
Assembly: hg19
Supplementary files format and content: MaMel65_sf_log2+1.txt
Supplementary files format and content: RNAseq libraries were size-factor-normalized and +1 log2 transformed

source_name: melanoma

growth_protocol: Human melanoma cell lines and HCmel12 cells were cultured in RPMI 1640 medium (Life Technologies, Carlsbad, CA) supplemented with 10% fetal bovine serum (FCS, Biochrome, Berlin, Germany), 1mM Sodium Pyruvate (Gibco), 2 mM L-glutamine, 10 mM non-essential amino acids, 1 mM HEPES, 100 U/mL penicillin and 100 μg/mL streptomycin (all from Life Technologies) and 20 μM 2-mercaptoethanol (Sigma, St. Louis, MO). All cell lines were cultured in a humidified incubator with 5% CO2 at 37oC. For cytokine stimulations, cells were treated with indicated concentrations of either human IFNα-2A (Roche) or mouse IFNβ (Sigma).

extract_protocol:
Total RNA was extracted as described above using the NucleoSpin RNA kit (Macherey Nagel, cat. no. 740955). The RNA integrity was monitored using Bioanalyzer analysis (Agilent, RIN: 9.7–10).
About 500 pg of RNA per sample was reversetranscribed and amplified using a modified SMARTseq2 protocol (Rambow et al. 2018). Prior to generating sequencing libraries using the NexteraXT kit (Illumina, cat. no. FC-131-10), cDNA profiles were monitored using the Bioanalyzer. Sequencing was performed on a Nextseq500 platform

treatment_protocol: Subconfluent, adherent cultures of the MM65-tetON-MITF-eGFP cell line were treated with 1 µg/mL doxycycline for 24h to induce the expression of fluorophore tagged MITF. The induction was verified with fluorescence microscopy and the cells were treated either with vehicle, a protective dose of 100 U/mL IFNα. 5h later some of the cell cultures were infected with type I IFN sensitive oncolytic SFV virus38 and cell survival was analyzed in crystal violet cell survival assay 72h later as described above

value: melanoma

value: tumor

value: Dox+IFNa


title: sgRNA Bmal1,replicate 1

value: thyroid


title: control,replicate 3

value: normal thyroid cell line

value: wild type


title: srcap mutation b

description:
Library name: library_V
H2A.Z, Active Motif 39943

value: none, progenitor


title: DOX_IFN2


title: control,replicate 2

value: Etoposide treatment for 12 hours


title: NF90.8 cell line, control replicate 3

description:
Library name: GSM250722007
C3_908

value: control


title: srcap mutation a

description:
Library name: library_U
H2A.Z, Active Motif 39943

value: skin epidermis

value: keratinocyte

value: srcap mutation


title: control,replicate 1


title: control b

description:
Library name: library_T
H2A.Z, Active Motif 39943

value: empty vector


title: IFN-3

value: Dox+Vehicle


title: DOX_IFN1


title: PBMCs,  IL-15/IL-15Ra, 24h, 35826

city: Minneapolis

first: Michael

last: Gale

state: Minnesota

address: 689 23rd Ave SE

department: Microbiology and Immunology

institute: University of Minnesota

description:
Library name: G042_O17_35826_IL15_24h_GEMS1_cDNA1_LIB1
!0x Genomics

data_processing:
demuliplexed and aligned data using CellRanger v6.0.1 to the Rhesus macaque genome (Mmul 10)
Assembly: Rhesus macaque genome v10 (Mmul) Ensembl annotation version 100
Supplementary files format and content: barcode, features and matrix files

organism: Macaca mulatta

source_name: PBMCs

extract_protocol:
10x extraction protocol
Chromium Next GEM Single Cell 3’ Reagent Kits v3.1 ; 10X Genomics

treatment_protocol: Ex-vivo PBMCs from Rhesus macaques were treated with IL-15/IL-15Ra (40ng/ml)

value: PBMCs

tag: time

tag: Sex

value: male

tag: animal id

tag: dose

value: 40 ng/ml


title: IFN-2

value: melanoma


title: control a

description:
Library name: library_S
H2A.Z, Active Motif 39943


title: S462 cell line, control, replicate 2

description:
Library name: GSM250722005
C2_S4

value: MPNST


title: ST8814 cell line, control, replicate 2

description:
Library name: GSM250722006
C2_ST


title: DF H2A.Z, SRCAP shRNA 3

description: Library name: library_208

data_processing:
Read quality control by FastQC
Adaptor trimming by Trimgalore
Aligned to hg38 with BWA-MEM, default parameters
Peak calling by MACS2, narrowPeak. q < 0.001 for H2A.Z peak calling
Assembly: hg38
Supplementary files format and content: .csv peak lists, MACS2 output

growth_protocol: Human primary epidermal keratinocytes pooled from a minimum of six donors were maintained at 37 degrees Celsius in a 1:1 mixture of Keratinocyte-SFM and Medium 154 at a confluency between 10-50% for the progenitor state. For differentiation, keratinocytes were seeded at confluency with 1.2 mM calcium chloride.

extract_protocol:
For ChIP, Keratinocytes were fixed with 1% formaldehyde for 10 minutes and quenched with 0.125 M glycine. Nuclei were extracted, lysed in RIPA buffer, and sonicated with a Bioruptor Pico. After H2A.Z IP, DNA was purified with the ChIP DNA Clean & Concentrator Kit from Zymo Research. For Cut&Run, progenitor keratinocytes were processed with the EpiCypher CUTANA ChIC/CUT&RUN Kit.
NEBNext Ultra II DNA Library Prep Kit

treatment_protocol: Keratinocytes were centrifuged for one hour at 1250 RMP at 32 degrees Celsius with control- or shRNA- lentivirus. Cells were selected for 24 hours with puromycin. To induce differentiation, keratinocytes were seeded at 100% confluency with 1.2 mM CaCl2 for four days then ChIP-seq was performed.

value: primary keratinocyte

value: SRCAP shRNA

value: differentiation, day 4

tag: batch

value: H2A.Z Active Motif 39943


title: ST8814 cell line, control, replicate 1,

description:
Library name: GSM250722003
C1_ST


title: DF H2A.Z, SRCAP shRNA 1

description: Library name: library_207


title: DOX-3

value: tumor

value: Vehicle+IFNa


title: DF H2A.Z, control 2

description: Library name: library_202

value: control


title: PBMCs,  IL-15/IL-15Ra, 24h, 35811

description:
Library name: G039_O17_35811_IL15_24h_GEMS1_cDNA1_LIB1
!0x Genomics


title: DOX-2


title: IFN-1


title: NF90.8 cell line, control replicate 2

description:
Library name: GSM250722004
C2_908


title: PBMCs,  IL-15/IL-15Ra, 24h, 35816

description:
Library name: G040_O17_35816_IL15_24h_GEMS1_cDNA1_LIB1
!0x Genomics


title: S462 cell line, control, replicate 3

description:
Library name: GSM250722008
C3_S4


title: NF90.8 cell line, control replicate 1,

description:
Library name: GSM250722001
C1_908


title: S462 cell line, control, replicate 1

description:
Library name: GSM250722002
C1_S4


title: PBMCs,  IL-15/IL-15Ra, 24h, 33523

description:
Library name: G038_O17_33523_IL15_24h_GEMS1_cDNA1_LIB1
!0x Genomics


title: DOX-1


title: PBMCs,  IL-15/IL-15Ra, 24h, 32275

description:
Library name: G037_O17_32275_IL15_24h_GEMS1_cDNA1_LIB1
!0x Genomics


title: SRSF12_GFP_cJL310_rep3

city: Cambridge

first: Jimmy

last: Ly

state: Massachusetts

address: 455 main street

department: Biology

institute: Whitehead Institute

description:
Library name: SRSF12_GFP_cJL310_rep3
Illumina NovaSeq (was not an option)

data_processing:
Samples were demultiplexed with bcl2fastq v2.20 to generate fastq files.
Reads were aligned using STAR v2.7.1.a with options ---runThreadN 6 --runMode alignReads --outFilterMultimapNmax 1 --outFilterType BySJout --outSAMattributes All --outSAMtype BAM SortedByCoordinate for RIP-seq; --runThreadN 2 --limitBAMsortRAM 10000000000 --runMode alignReads --outFilterMultimapNmax 5000 --winAnchorMultimapNmax 1000 --outFilterType BySJout --outSAMattributes All --outSAMtype BAM SortedByCoordinate for rRNA analysis.
Transcript counts were quantified using Htseq-count
Dfferential expression analysis was performed using DEseq2
Assembly: Human genome: hg38 (gencode v25) and Mouse genome: m38 (gencode v24)
Supplementary files format and content: Transcript counts are stored in tab-delimited files with one row per transcript, quantification done using Htseq-count.

source_name: HeLa

growth_protocol: HeLa cells were maintained in DMEM supplemented with 10% fetal bovine serum, 2 mM L-glutamine, and 100 U/mL penicillin/streptomycin

extract_protocol:
Cells in 6 well plates were washed once with 1x PBS then lysed in 400uL Trizol on plate. To the TRI Reagent lysate, 120 µL of chloroform was added, followed by shaking and centrifugation at 21,000 x g for 15 minutes at 4°C to achieve phase separation. The upper aqueous phase, was carefully transferred to a new tube, mixed with an equal volume of chloroform, and centrifuged again at 21,000 x g for 1 minute at 4°C. RNA was then precipitated by adding 300 mM NaCl and 30 µg of GlycoBlue (AM9516), along with an equal volume of isopropanol, and incubating the mixture overnight at -20°C. The RNA pellet was centrifuged at 21,000 x g for 15 minutes at 4°C, washed with 70% ethanol, and resuspended in RNase-free water. For the last replicate of SRSF12 overexpression analysis, we used Phasemaker tubes to extract RNA.
With one exeption (below), all RNA was prepped with the Watchmaker genomics kit with rRNA depletion according to manufacturer's instructions. For the third replicate of SRSF12 overexpression transcriptome analysis, rRNA depletion and library preparation were carried out with the KAPA RNA HyperPrep Kit with RiboErase (HMR) (Roche KK8560) according to manufacturer’s instructions.

treatment_protocol: GFP transgene expression was induced with 1 ug/mL doxycycline for 2 days and cells were harvested for RNA-sequencing

value: HeLa

value: doxycycline


title: NT-3

value: Vehicle+Vehicle


title: DF SRCAP sh4

description: Library name: library_517

data_processing:
Read quality control by FastQC
Adaptor trimming by Trimgalore
Alignment to hg38 with STAR
Gene expression quantification with Salmon
Differential expression calculated by DESeq2
Assembly: hg38
Supplementary files format and content: .csv,  DESeq2 output

growth_protocol: Human primary epidermal keratinocytes pooled from a minimum of six donors were maintained at 37 degrees Celsius in a 1:1 mixture of Keratinocyte-SFM and Medium 154 at a confluency between 10-50% for progenitors. Differentiation was induced by seeding at confluency with 1.2 mM calcium for four days.

extract_protocol:
Quick-RNA MiniPrep Kit by Zymo Research with Dnase I digestion according to manufacturer's instructions
NEBNext Poly(A) mRNA Magnetic Isolation Module followed by NEBNext Ultra II Directional RNA Library Prep Kit

treatment_protocol: Keratinocytes were centrifuged for one hour at 1250 RMP at 32 degrees Celsius with control- or shRNA- lentivirus. RNA was collected after differentiation

value: skin epidermis

value: SRCAP knockdown

value: differentiated day 4


title: PBMCs, control, 24h, 35826

description:
Library name: G036_O17_35826_C_24h_GEMS1_cDNA1_LIB1
!0x Genomics

value: PBMCs

value: male

value: 0 ng/ml


title: GFP_cJL220_rep3

description:
Library name: GFP_cJL220_rep3
Illumina NovaSeq (was not an option)

value: GFP


title: NT-2

value: melanoma


title: PBMCs,  IL-15/IL-15Ra, 24h, 35824

description:
Library name: G041_O17_35824_IL15_24h_GEMS1_cDNA1_LIB1
!0x Genomics

value: 40 ng/ml


title: YDBSFR_92

city: Zhengzhou

first: Yilin

last: Zhang

address: Zhengdong New District

institute: The First Affiliated Hospital of Henan University of Chinese Medicine

description: Library name: Sample 129

data_processing:
Preliminary quantification was performed using Qubit 2.0 Fluorometer. After dilution, insert size was detected by Agilent 2100 bioanalyzer, and the effective library concentration (>2 nM) was accurately quantified by qRT-PCR to ensure the library quality.
Libraries were pooled according to the effective concentration and target downstream data volume, then sequenced on Illumina NovaSeq 6000 to generate 150 bp paired-end reads to obtain the sequence information of the fragments to be tested.
Image data of sequencing fragments were obtained from high-throughput sequencer and converted to sequence data (reads) by CASAVA base recognition. After filtering, reads with undetermined base information, reads with splice, and reads with Qphred≤20 bases accounting for ≥50% of the whole read length were removed. Q20, Q30 and GC contents of cleaned data were calculated to obtain high-quality dataset.
Reference genome and gene annotation files were downloaded from genome website. HISAT2 v2.0.5 was used to build genome index and align the paired-end clean reads with the reference genome.
Quantification of gene expression levels: Feature Counts (1.5.0-p3) was used to calculate the reads mapped to each gene. FPKM (fragments per kilobase of transcript per million mapped reads) was calculated based on gene length to estimate gene expression levels.
The number of genes in the samples was normalized using DESeq2 software (1.20.0) , and the fold change (FC) was calculated. The P-values were adjusted to control the false discovery rate using the method of Benjamini and Hochberg.
Assembly: hg38
Supplementary files format and content: Txt files include FPKM values for each Sample

source_name: whole blood

extract_protocol:
Total RNA was extracted using PAXgene Blood miRNA Kit.
Library construction: Using total RNA as starting material, polyA-tailed mRNA was enriched by Oligo(dT) magnetic beads. The enriched mRNA was randomly fragmented by divalent cations in Fragmentation Buffer. In the M-MuLV reverse transcriptase system, random oligonucleotides were used as primers to synthesize the first-strand cDNA with fragmented mRNA as template, and the RNA strand was degraded using RNaseH. Subsequently, the second cDNA strand was synthesized using dNTPs as raw materials in DNA polymerase I system. About 370~420 bp of purified double-stranded cDNA was screened by using AMPure XP beads after end repair, A-tail addition and sequencing junction ligation steps, and further amplified by PCR, and then the PCR product was purified again by using AMPure XP beads, and the library was finally obtained.

value: whole blood


title: PBMCs, control, 24h, 35824

description:
Library name: G035_O17_35824_C_24h_GEMS1_cDNA1_LIB1
!0x Genomics


title: DF SRCAP sh3

description: Library name: library_516

value: primary keratinocyte


title: NT-1

value: tumor


title: DF H2A.Z, control 1

description: Library name: library_201

value: differentiation, day 4

value: H2A.Z Active Motif 39943


title: DF SRCAP sh1

description: Library name: library_515


title: YDBSFR_6

description: Library name: Sample 128


title: HUVEC batch 416Z042, EMT

city: Frankfurt

first: Simonida

last: Zehr

state: Hesse

address: Theodor-Stern-Kai 7

department: Institute for Cardiovascular Physiology

institute: Goethe University, Frankfurt am Main, Germany,

data_processing:
Nuclear RNA sequencing reads were aligned to the hg38 (GENCODE v43) genome assembly using STAR [22] (v2.7.10) with the parameters –outSAMtype BAM Sort[1]edByCoordinate –quantMode GeneCounts.
Differential gene expression analysis was performed using DESeq2 (v1.40.2), with the respective donor per sample included in the experimental design.
Assembly: hg38 (GENCODE v43)
Supplementary files format and content: nucRNA_CTL_N1_ReadsPerGene.out.tab: Tab-delimited STAR output file with 4 columns which correspond to different strandedness options. column 1: gene ID; column 2: counts for unstranded RNA-seq; column 3: counts for the 1st read strand aligned with RNA (htseq-count option -s yes); column 4: counts for the 2nd read strand aligned with RNA (htseq-count option -s reverse)
Supplementary files format and content: nucRNA_CTL_N2_ReadsPerGene.out.tab: Tab-delimited STAR output file with 4 columns which correspond to different strandedness options. column 1: gene ID; column 2: counts for unstranded RNA-seq; column 3: counts for the 1st read strand aligned with RNA (htseq-count option -s yes); column 4: counts for the 2nd read strand aligned with RNA (htseq-count option -s reverse)
Supplementary files format and content: nucRNA_CTL_N3_ReadsPerGene.out.tab: Tab-delimited STAR output file with 4 columns which correspond to different strandedness options. column 1: gene ID; column 2: counts for unstranded RNA-seq; column 3: counts for the 1st read strand aligned with RNA (htseq-count option -s yes); column 4: counts for the 2nd read strand aligned with RNA (htseq-count option -s reverse)
Supplementary files format and content: nucRNA_EndMT_N1_ReadsPerGene.out.tab: Tab-delimited STAR output file with 4 columns which correspond to different strandedness options. column 1: gene ID; column 2: counts for unstranded RNA-seq; column 3: counts for the 1st read strand aligned with RNA (htseq-count option -s yes); column 4: counts for the 2nd read strand aligned with RNA (htseq-count option -s reverse)
Supplementary files format and content: nucRNA_EndMT_N2_ReadsPerGene.out.tab: Tab-delimited STAR output file with 4 columns which correspond to different strandedness options. column 1: gene ID; column 2: counts for unstranded RNA-seq; column 3: counts for the 1st read strand aligned with RNA (htseq-count option -s yes); column 4: counts for the 2nd read strand aligned with RNA (htseq-count option -s reverse)
Supplementary files format and content: nucRNA_EndMT_N3_ReadsPerGene.out.tab: Tab-delimited STAR output file with 4 columns which correspond to different strandedness options. column 1: gene ID; column 2: counts for unstranded RNA-seq; column 3: counts for the 1st read strand aligned with RNA (htseq-count option -s yes); column 4: counts for the 2nd read strand aligned with RNA (htseq-count option -s reverse)
Supplementary files format and content: EndMT_nucRNA-seq_results.txt: Tab-delemited DeSeq2 results with 8 columns: baseMean, log2FoldChange, lfcSE, pvalue, padj, GeneID, Symbol, Biotype

molecule: nuclear RNA

source_name: Human umbilical vein

growth_protocol: Human umbilical vein endothelial cells (HUVEC, batches 405Z013, 408Z014, 416Z042, Lonza) were cultured on 0.2 % gelatin-coated dishes in endothelial growth medium (EGM, Pelo Biotech). EGM was supplemented with 8 % fetal calf serum (FCS, Sigma[1]Aldrich), 50 U/mL penicillin (Gibco) and 50 µg/mL streptomycin (Gibco). The cells were thawed freshly and passaged once on a 10 cm dish (Sarstedt). Experiments were performed with passage 3. Cells were incubated at 37 ◦C with 5 % CO2. If not stated otherwise, three batches of HUVECs were used for the experiments. All media used were pre-warmed at 37°C

extract_protocol:
To isolate nuclear extract, medium was aspirated and cells were washed once with cold Hank’s solution. Harvesting was performed by scraping cells twice in 500 µL Hank’s solution and centrifuging (1 min, 13 000 rpm at 4 ◦C). The supernatant was removed and the pellet resuspended in 600 µL buffer A. After incubation on ice for 15 minutes, 45 µL 10 % Nonidet (Sigma Aldrich) were added to lyse the cytosolic membrane, the cells were vortexed for 10 seconds and centrifuged (1 min, 13 000 rpm at 4 ◦C). The supernatant, containing the cytosolic fraction, was removed and the pellet resuspended in 150 µL buffer C. To lyse the nuclei, the resuspended pellet was incu[1]bated in a shaker for 15 minutes at 1400 rpm and 4 ◦C. To remove insoluble debris, the lysate was centrifuged (5 min, 13 000 rpm at 4 ◦C) and the supernatant was transferred into a new 1.5 mL tube
RNA isolation was performed according to Bio&SELL RNA isolation kit manual. If not otherwise stated, RNA was eluted in 30 µL at 13 000 rpm for 1 minute at room temperature. RNA concentration was measured with the NanoDrop ND-1000. Library preparation was carried out using the SMARTer® Stranded Total RNA-Seq Kit v2 – Pico input mammalian. Libraries were sequenced on an Illumina NextSeq 500 sequencer with single-end, 75 bp read length and to an average depth of 30 million reads.

treatment_protocol: Endothelial-to-mesenchymal transition (EndMT) was induced according to Monteiro et al 2021. HUVECs were seeded in EGM (Pelo Biotech) with a density of 6900 cells/cm2 in 0.2 % gelatin-coated dishes one day prior to induction on a 15 cm dish (Sarstedt). Medium was changed every 24 h for a total of 5 days. To induce EndMT, differentiation medium (DM) was used, which consisted of endothelial basal medium (EBM, Pelo Biotech) supplemented with 8 % FCS (Sigma-Aldrich), 50 U/mL penicillin (Gibco), 50 µg/mL streptomycin (Gibco) and L-glutamine (Gibco). 10 ng/mL TGF-β2 (Peprotech) and 1 ng/mL IL-1β(Peprotech) were added freshly to pre-warmed DM medium.

value: Human umbilical vein

value: HUVEC

value: Mesenchymal-like cell

value: IL-1β + TGF-β


title: DF control 2 - srcap

description: Library name: library_514

value: skin epidermis

value: control


title: PBMCs, control, 24h, 35816

description:
Library name: G034_O17_35816_C_24h_GEMS1_cDNA1_LIB1
!0x Genomics

value: PBMCs


title: HUVEC batch 408Z014, EMT


title: PBMCs, control, 24h, 35811

description:
Library name: G033_O17_35811_C_24h_GEMS1_cDNA1_LIB1
!0x Genomics

value: male


title: YDBSFR_3

description: Library name: Sample 126


title: YDBSFR_56

description: Library name: Sample 127


title: DF control 1 - srcap

description: Library name: library_513

value: differentiated day 4


title: DF H2AZ2 sh4

description: Library name: library_512

value: H2AZ2 knockdown


title: HUVEC batch 405Z013, EMT


title: PBMCs,  IL-15/IL-15Ra, 12h, 35826

description:
Library name: G030_O17_35826_IL15_12h_GEMS1_cDNA1_LIB1
!0x Genomics


title: PBMCs, control, 24h, 33523

description:
Library name: G032_O17_33523_C_24h_GEMS1_cDNA1_LIB1
!0x Genomics

value: 0 ng/ml


title: DF SRCAP sh5

description: Library name: library_518

value: SRCAP knockdown


title: YDBSFR_239

description: Library name: Sample 124

value: whole blood


title: HUVEC batch 408Z014, CTL

value: Endothelial cell


title: HUVEC batch 416Z042, CTL


title: PBMCs,  IL-15/IL-15Ra, 12h, 35824

description:
Library name: G029_O17_35824_IL15_12h_GEMS1_cDNA1_LIB1
!0x Genomics

value: 40 ng/ml


title: DF H2AZ2 sh2

description: Library name: library_510

value: primary keratinocyte


title: YDBSFR_38

description: Library name: Sample 125


title: YDBSFR_234

description: Library name: Sample 123


title: HUVEC batch 405Z013, CTL


title: YDBSFR_231

description: Library name: Sample 122


title: PBMCs,  IL-15/IL-15Ra, 12h, 35816

description:
Library name: G028_O17_35816_IL15_12h_GEMS1_cDNA1_LIB1
!0x Genomics


title: HUVEC batch 416Z042, EMT

data_processing:
Reads were aligned to the hg38 genome assembly (GENCODE v43) using Bowtie2 (2.4.5) with the parameters –local and –very-sensitive. Normalized read coverage tracks were generated using bamCoverage (v3.5.3) with the parameter –normalizeUsing set to CPM.
Peaks were called using MACS (3.0.0), with the parameter –format set to BAMPE.
Peaks were compared between conditions using MACS bdgdiff, with appropriate summed sequencing depths per condition.
Assembly: hg38 (GENCODE v43)
Supplementary files format and content: EndMT_ATAC_CTL_H13.bw: normalised peaks per sample
Supplementary files format and content: EndMT_ATAC_CTL_H14.bw: normalised peaks per sample
Supplementary files format and content: EndMT_ATAC_CTL_H42.bw: normalised peaks per sample
Supplementary files format and content: EndMT_ATAC_TRT_H13.bw: normalised peaks per sample
Supplementary files format and content: EndMT_ATAC_TRT_H14.bw: normalised peaks per sample
Supplementary files format and content: EndMT_ATAC_TRT_H42.bw: normalised peaks per sample

extract_protocol:
5x104 HUVEC for CTL and EndMT each were washed once with 50µL ice-cold PBS and lysed in 50µL cold ATAC lysis buffer. Cells were incubated for 3min on ice and filled up with ATAC wash buffer to 1mL and inverted three times. Nuclei were pelleted by centrifugation (10min, 500xg, 4°C). Supernatants were removed and nuclei were resuspended in 50µL ATAC transposition reaction mix. After incubation (37°C, 1,000rpm, 30min), the DNA was purified using the Qiagen MinElute kit and eluted in 10µL Elution buffer.
The library was prepared with the ATAC library amplification reaction mix as described in Buenrostro et al. (2013). The library was sequenced paired-end (2x75bp) on an Illumina NextSeq 500 to an average depth of 20 million reads.


title: DF H2AZ2 sh1

description: Library name: library_509


title: PBMCs,  IL-15/IL-15Ra, 12h, 35811

description:
Library name: G027_O17_35811_IL15_12h_GEMS1_cDNA1_LIB1
!0x Genomics


title: PBMCs, control, 24h, 32275

description:
Library name: G031_O17_32275_C_24h_GEMS1_cDNA1_LIB1
!0x Genomics


title: DF control 2 - h2az2

description: Library name: library_508


title: HUVEC batch 408Z014, EMT


title: YDBSFR_230

description: Library name: Sample 121


title: PBMCs,  IL-15/IL-15Ra, 12h, 32275

description:
Library name: G025_O17_32275_IL15_12h_GEMS1_cDNA1_LIB1
!0x Genomics


title: DF H2AZ1 sh4

description: Library name: library_506

value: H2AZ1 knockdown


title: PBMCs,  IL-15/IL-15Ra, 12h, 33523

description:
Library name: G026_O17_33523_IL15_12h_GEMS1_cDNA1_LIB1
!0x Genomics


title: HUVEC batch 416Z042, CTL

value: Human umbilical vein


title: YDBSFR_227

description: Library name: Sample 120


title: HUVEC batch 405Z013, EMT

value: HUVEC


title: DF H2AZ2 sh3

description: Library name: library_511


title: DF control 1 - h2az2

description: Library name: library_507


title: PBMCs, control, 12h, 35826

description:
Library name: G024_O17_35826_C_12h_GEMS1_cDNA1_LIB1
!0x Genomics


title: YDBSFR_217

description: Library name: Sample 119


title: DF H2AZ1 sh3

description: Library name: library_505


title: HUVEC batch 408Z014, CTL


title: PBMCs, control, 12h, 35824

description:
Library name: G023_O17_35824_C_12h_GEMS1_cDNA1_LIB1
!0x Genomics


title: DF H2AZ1 sh2

description: Library name: library_504


title: PBMCs, control, 12h, 35816

description:
Library name: G022_O17_35816_C_12h_GEMS1_cDNA1_LIB1
!0x Genomics


title: YDBSFR_211

description: Library name: Sample 118


title: DF H2AZ1 sh1

description: Library name: library_503


title: HUVEC batch 405Z013, RNA, EMT

description:
Ligation-based sequencing of intracting RNA & DNA
SS_RADICL_N1_EMT_FA_RADIAnT_results.txt

data_processing:
Control and EndMT RADICL-seq data were analysed using the RADIAnT Snake_x0002_make pipeline, using the hg38 genome assembly and 5 kb genomic bins. Significant RNA-DNA interactions were those with a RADIAnT p value < 0.05. RNA biotypes were assigned to populations of interacting RNAs as annotated in GENCODE release 43. Interaction proportions per RNA were calculated per condition by taking the number of significant interactions per RNA divided by the total number of significant interactions in the condition. Circular genome plots were made using ggplot2 (v3.5.0).
Assembly: hg38 (GENCODE v43)
Supplementary files format and content: SS_RADICL_N1_CTL_FA_RADIAnT_results.txt: Tab-delimited RADIAnT result file describing RNA-DNA interactions in  control (endothelial) condition with columns: JoinColumn,  Symbol,  Bin, BinChr, BinCentre, GeneChr, GeneLeft, GeneRight, ReadCount, ExpectedCount, Method, OriginalMethod, P, Padj
Supplementary files format and content: SS_RADICL_N1_EMT_FA_RADIAnT_results.txt: Tab-delimited RADIAnT result file describing RNA-DNA interactions in mesenchymal-like condition with columns: JoinColumn,  Symbol,  Bin, BinChr, BinCentre, GeneChr, GeneLeft, GeneRight, ReadCount, ExpectedCount, Method, OriginalMethod, P, Padj
Library strategy: RADICL-sequencing

extract_protocol:
To isolate nuclear extract, medium was aspirated and cells were washed once with cold Hank’s solution. Harvesting was performed by scraping cells twice in 500 µL Hank’s solution and centrifuging (1 min, 13 000 rpm at 4 ◦C). The supernatant was removed and the pellet resuspended in 600 µL buffer A. After incubation on ice for 15 minutes, 45 µL 10 % Nonidet (Sigma Aldrich) were added to lyse the cytosolic membrane, the cells were vortexed for 10 seconds and centrifuged (1 min, 13 000 rpm at 4 ◦C). The supernatant, containing the cytosolic fraction, was removed and the pellet resuspended in 150 µL buffer C. To lyse the nuclei, the resuspended pellet was incu[1]bated in a shaker for 15 minutes at 1400 rpm and 4 ◦C. To remove insoluble debris, the lysate was centrifuged (5 min, 13 000 rpm at 4 ◦C) and the supernatant was transferred into a new 1.5 mL tube
RADICL-seq was performed on control HUVECs and HUVECs subjected to EndMT. For each condition, 4 million cells were washed once with PBS, trypsinated and spun down (1200 rpm, 4 minutes). The cell pellet was resuspended in 5 mL PBS and the cells were counted using a Neubauer counting chamber and Trypan blue staining. 2 million cells were cross-linked in 2 mL fresh 1 % formaldehyde for 10 minutes at room temperature. Crosslinking was stopped by adding 715 µL of freshly prepared 1 mol/L glycine in double-distilled water. Cells were centrifuged (100 ×g, 5 minutes, 4 ◦C), and the cell pellet was washed once with 5 mL ice-cold PBS and spun down again (100 ×g, 5 minutes, 4 ◦C). Pellets were shock-frozen in liquid nitrogen and stored at −80 ◦C. Thereon, the RADICL-seq protocol was carried out as described by Bonetti et al. [8]. Final library concentrations were measured by Qubit fluorometer and library quality and size was determined by a Bioanalyzer High Sensitivity DNA Analysis according to manufacturer’s protocol (Agilent). Paired-end sequencing with 150 bp read length was carried out using an Illumina NextSeq 500 sequencer with a sequencing depth of 125 million reads per condition

value: Mesenchymal-like cell


title: YDBSFR_204

description: Library name: Sample 116


title: PBMCs, control, 12h, 35811

description:
Library name: G021_O17_35811_C_12h_GEMS1_cDNA1_LIB1
!0x Genomics


title: YDBSFR_202

description: Library name: Sample 115


title: HUVEC batch 405Z013, DNA, EMT

value: IL-1β + TGF-β


title: PBMCs, control, 12h, 33523

description:
Library name: G020_O17_33523_C_12h_GEMS1_cDNA1_LIB1
!0x Genomics


title: DF control 1 - h2az1

description: Library name: library_501

value: skin epidermis


title: PBMCs, control, 12h, 32275

description:
Library name: G019_O17_32275_C_12h_GEMS1_cDNA1_LIB1
!0x Genomics

value: control


title: HUVEC batch 405Z013, RNA, CTL

description:
Ligation-based sequencing of intracting RNA & DNA
SS_RADICL_N1_CTL_FA_RADIAnT_results.txt


title: YDBSFR_199

description: Library name: Sample 113


title: YDBSFR_196

description: Library name: Sample 112


title: YDBSFR_193

description: Library name: Sample 111


title: shcircFUT8_3

city: Chongqing

first: Huang

last: Wu

state: Chongqing

address: 10 Changjiang Access Road

department: Department of Blood Transfusion

institute: Daping Hospital, Army Medical University

data_processing:
Basecalls performed using CASAVA(version 1.8).
RNA-seq reads were  processed using FastP (version 0.20.0) and mapped to hg38 using HISAT2 (version 2.0.5).
FPKM (fragments per kilobase of transcript per million mapped reads)  were used for estimating gene expression levels.
Differential expression analysis was performed using the DESeq2 R package (1.16.1).
Assembly: hg38
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

source_name: umbilical cord blood CD34+ cells

growth_protocol: CD34+ cells cultured in StemSpan™ SFEM II Medium with antibiotics in humidified atmosphere with 5% CO2 at 37C.

extract_protocol:
Total RNAs were extracted using Trizol Reagent. PolyA RNA was isolated with oligo dT magnetic beads and fragmented with divalent cations.
RNA-Seq libraries preparation with NEBNext® Ultra™ RNA Library Prep Kit for Illumina (NEB #E7770) according to the manufacturer's instructions.

treatment_protocol: megakaryocyte differentiation was induced by treatment  25 ng/ml stem cell factor (SCF) and 20 ng/ml thrombopoietin (TPO). Media was changed on days 3, 6 and 9; days 6 and 9 had no SCF and TPO was increased to 50 ng/mL.

value: Day 13

value: umbilical cord blood CD34+ cells

value: hematopoietic stem cell

value: megakaryocyte differentiation


title: PBMCs,  IL-15/IL-15Ra, 6h, 35826

description:
Library name: G018_O17_35826_IL15_6h_GEMS1_cDNA1_LIB1
!0x Genomics

value: PBMCs

value: male


title: YDBSFR_205

description: Library name: Sample 117

value: whole blood


title: MCF7_Hexn_input

city: New York

first: Douglas

last: Barrows

state: NY

address: 1230 York Ave

institute: Rockefeller University

data_processing:
ChIP-seq reads were aligned using Rsubread’s align method and predicted fragment lengths were calculated by the ChIPQC R Bioconductor package. Normalized, fragment extended signal bigWigs were created using the rtracklayer R Bioconductor package. Peak calls were made using the MACS2 software.
Assembly: hg38
Supplementary files format and content: bigwig files
Supplementary files format and content: narrowPeak files from MACS2

extract_protocol:
Post-confluent cells were fixed with 1% formaldehyde for 10 min, followed by quenching with 125mM glycine and washed with cold TBS (20mM Tris-HCl, 150mM NaCl, pH 7.4) twice. Cells were lysed in cell lysis buffer (10mM Tris-HCl, 10mM NaCl, 0.5% NP-40, pH7.5) and then incubated on ice for 10 mins. Lysates spinned down and resuspended in 500 μl MNase digestion buffer (20mM Tris-HCl, 15mM NaCl, 60mM KCl, 1mM CaCl2, pH 7.5) with MNase (New England, M0247S, 0.25U/1000 cells). After 20 minutes of incubation at 37°C with continuous mixing, digestion was stopped by addition of 500 μl of 2X STOP/ChIP buffer (100mM Tris-HCl, 20mM EDTA, 200mM NaCl, 2% Triton X-100, 0.2% sodium deoxycholate, pH8.1). Samples were sonicated for 7 cycles (30 secs on/30 secs off) with 40% amplitude (Branson Digital Sonifier) and then centrifuged at 12,000rpm for 15min at 4°C to remove insoluble debris. Apart from input samples (1% volume for each ChIP reaction) kept for reverse-crosslinking, lysates were incubated with antibodies (antibody information: see table attached) at 4°C overnight. Antibody-bound complexes were then captured by incubation with Protein A sepharose CL-4B beads (Amersham) for rabbit antibodies or Protein G sepharose 4B beads (Invitrogen) for mouse antibodies (both 20μl per 1mL lysate) for 4 hr at 4 °C. The beads were washed sequentially with STOP/ChIP buffer (50mM Tris-HCl, 10mM EDTA, 100mM NaCl, 1% Triton X-100, 0.1% sodium deoxycholate, pH8.1), high salt buffer (50mM Tris-HCl, 10mM EDTA, 500mM NaCl, 1% Triton X-100, 0.1% sodium deoxycholate, pH8.1), LiCl2 buffer (10mM Tris-HCl, 0.25M LiCl2, 0.5% NP-40, 0.5% sodium deoxycholate, 1 mM EDTA, pH8.0), and TE buffer (50mM Tris-HCl, 10mM EDTA, pH 8.0) (twice). Bound DNA was eluted and reverse-crosslinked at 65°C overnight in ChIP elution buffer (10mM Tris-HCl, 150mM NaCl, 10mM EDTA, 5mM DTT, 1% SDS, pH 8.0). After treatment with RNase A (0.2mg/ml, 37°C, 1h) and proteinase K (2mg/ml, 37°C, 2h), DNA used for sequencing was purified using a MiniElute PCR purification kit (Qiagen), and DNA used for qPCR was purified using a QIAquick PCR purification kit (Qiagen). DNA quality was assessed using an Agilent Bioanalyzer, and quantified using a Qubit Fluorometer (Invitrogen).
ChIP-seq libraries were generated using DNA SMART ChIP-seq kits (Takara Bio) according to the manufacturer's instructions. After size selection (for 250-600bp) by AMPure XP beads (Beckman Coulter), the library was quality was evaluated using the Bioanalyzer and sequenced on Illumina NovaSeq SP (100bp two ends) and Illumina NextSeq High (75 bp single end).

value: breast cancer cell line

value: original

tag: chip antibody


title: PBMCs,  IL-15/IL-15Ra, 6h, 35824

description:
Library name: G017_O17_35824_IL15_6h_GEMS1_cDNA1_LIB1
!0x Genomics

value: 40 ng/ml


title: NC3

tag: cell line

value: Negative control (scr)


title: ERKi B

data_processing:
Read quality control by FastQC
Adaptor trimming by Trimgalore
Aligned to hg38 with BWA-MEM, default parameters
Peak calling by MACS2, narrowPeak, q 0.001
Assembly: hg38
Supplementary files format and content: MACS2 called peaks in .csv format

source_name: foreskin epidermis

growth_protocol: differentiated to day 4

extract_protocol:
Keratinocytes were fixed with 1% formaldehyde for 10 minutes and quenched with 0.125 M glycine. Nuclei were extracted, lysed in RIPA buffer, and sonicated with a Bioruptor Pico. After H2A.Z IP, DNA was purified with the ChIP DNA Clean & Concentrator Kit from Zymo Research.
NEBNext Ultra II DNA Library Prep Kit

treatment_protocol: Keratinocytes were centrifuged for one hour at 1250 RMP at 32 degrees Celsius with control- or shRNA- lentivirus. Cells were selected for 24 hours with puromycin; DNA was harvested ~72 hours after transduction. To induce differentiation, keratinocytes were seeded at 100% confluency with 1.2 mM CaCl2 for four days. Small molecule inhibitors were added to cell culture media for 48 hours.

value: foreskin epidermis

tag: cell type

value: primary keratinocyte


title: ERKi A

tag: tissue


title: HUVEC batch 405Z013, CTL

value: Human umbilical vein

value: HUVEC

value: Endothelial cell


title: MCF7_Hexn_PolII

value: anti Pol II RPB1 (CTD4H8) (Santa Cruz SC-47701)


title: YDBSFR_184

description: Library name: Sample 110


title: PBMCs,  IL-15/IL-15Ra, 6h, 35816

description:
Library name: G016_O17_35816_IL15_6h_GEMS1_cDNA1_LIB1
!0x Genomics


title: PBMCs,  IL-15/IL-15Ra, 6h, 35811

description:
Library name: G015_O17_35811_IL15_6h_GEMS1_cDNA1_LIB1
!0x Genomics


title: MEKi B

value: 10 uM RDEA119


title: DF control 2 - h2az1

description: Library name: library_502

value: skin epidermis

value: control

value: differentiated day 4


title: YDBSFR_175

description: Library name: Sample 109


title: YDBSFR_201

description: Library name: Sample 114


title: MCF7_MED1WT_ER

source_name: MCF7 MED1 WT

extract_protocol:
Post-confluent cells were fixed with 1% formaldehyde for 10 min, followed by quenching with 125mM glycine and washed with cold TBS (20mM Tris-HCl, 150mM NaCl, pH 7.4) twice. Cells were lysed in cell lysis buffer (10mM Tris-HCl, 10mM NaCl, 0.5% NP-40, pH7.5) and then incubated on ice for 10 mins. Lysates spinned down and resuspended in 500 μl MNase digestion buffer (20mM Tris-HCl, 15mM NaCl, 60mM KCl, 1mM CaCl2, pH 7.5) with MNase (New England, M0247S, 0.25U/1000 cells). After 20 minutes of incubation at 37°C with continuous mixing, digestion was stopped by addition of 500 μl of 2X STOP/ChIP buffer (100mM Tris-HCl, 20mM EDTA, 200mM NaCl, 2% Triton X-100, 0.2% sodium deoxycholate, pH8.1). Samples were sonicated for 7 cycles (30 secs on/30 secs off) with 40% amplitude (Branson Digital Sonifier) and then centrifuged at 12,000rpm for 15min at 4°C to remove insoluble debris. Apart from input samples (1% volume for each ChIP reaction) kept for reverse-crosslinking, lysates were incubated with antibodies (antibody information: see table attached) at 4°C overnight. Antibody-bound complexes were then captured by incubation with Protein A sepharose CL-4B beads (Amersham) for rabbit antibodies or Protein G sepharose 4B beads (Invitrogen) for mouse antibodies (both 20μl per 1mL lysate) for 4 hr at 4 °C. The beads were washed sequentially with STOP/ChIP buffer (50mM Tris-HCl, 10mM EDTA, 100mM NaCl, 1% Triton X-100, 0.1% sodium deoxycholate, pH8.1), high salt buffer (50mM Tris-HCl, 10mM EDTA, 500mM NaCl, 1% Triton X-100, 0.1% sodium deoxycholate, pH8.1), LiCl2 buffer (10mM Tris-HCl, 0.25M LiCl2, 0.5% NP-40, 0.5% sodium deoxycholate, 1 mM EDTA, pH8.0), and TE buffer (50mM Tris-HCl, 10mM EDTA, pH 8.0) (twice). Bound DNA was eluted and reverse-crosslinked at 65°C overnight in ChIP elution buffer (10mM Tris-HCl, 150mM NaCl, 10mM EDTA, 5mM DTT, 1% SDS, pH 8.0). After treatment with RNase A (0.2mg/ml, 37°C, 1h) and proteinase K (2mg/ml, 37°C, 2h), DNA used for sequencing was purified using a MiniElute PCR purification kit (Qiagen), and DNA used for qPCR was purified using a QIAquick PCR purification kit (Qiagen). DNA quality was assessed using an Agilent Bioanalyzer, and quantified using a Qubit Fluorometer (Invitrogen).
ChIP-seq libraries were generated using DNA SMART ChIP-seq kits (Takara Bio) according to the manufacturer's instructions. After size selection (for 250-600bp) by AMPure XP beads (Beckman Coulter), the library was quality was evaluated using the Bioanalyzer and sequenced on Illumina NovaSeq SP (100bp two ends) and Illumina NextSeq High (75 bp single end).
ChIP-seq / HiCAR-seq

value: MCF7 MED1 WT

value: anti ER-alpha (D8H8) (Cell signaling #8644S)


title: PBMCs,  IL-15/IL-15Ra, 6h, 33523

description:
Library name: G014_O17_33523_IL15_6h_GEMS1_cDNA1_LIB1
!0x Genomics

value: PBMCs

value: male


title: MEKi A


title: MCF7_MED1KR_input

source_name: MCF7 MED1 6KR

value: MCF7 MED1 6KR

value: breast cancer cell line


title: PBMCs,  IL-15/IL-15Ra, 6h, 32275

description:
Library name: G013_O17_32275_IL15_6h_GEMS1_cDNA1_LIB1
!0x Genomics

value: 40 ng/ml


title: HUVEC batch 405Z013, DNA, CTL


title: EGFRi B

value: foreskin epidermis


title: YDBSFR_171

description: Library name: Sample 107

value: whole blood


title: MCF7_MED1KR_PolII


title: PBMCs, control, 6h, 35826

description:
Library name: G012_O17_35826_C_6h_GEMS1_cDNA1_LIB1
!0x Genomics


title: DMSO B

value: primary keratinocyte


title: YDBSFR_167

description: Library name: Sample 106


title: MCF7_MED1KR_ER


title: EGFRi A


title: MCF7_MED1WT_input


title: YDBSFR_160

description: Library name: Sample 105


title: PBMCs, control, 6h, 35824

description:
Library name: G011_O17_35824_C_6h_GEMS1_cDNA1_LIB1
!0x Genomics


title: MCF7_MED1KR_MED17

value: anti MED17 (Aviva OAGA04959)


title: PBMCs, control, 6h, 35811

description:
Library name: G009_O17_35811_C_6h_GEMS1_cDNA1_LIB1
!0x Genomics

value: 0 ng/ml


title: DMSO A


title: MCF7_MED1WT_PolII

value: anti Pol II RPB1 (CTD4H8) (Santa Cruz SC-47701)


title: PBMCs, control, 6h, 35816

description:
Library name: G010_O17_35816_C_6h_GEMS1_cDNA1_LIB1
!0x Genomics


title: YDBSFR_149

description: Library name: Sample 103


title: SRCAP shRNA5

value: SRCAP knockdown


title: YDBSFR_143

description: Library name: Sample 102


title: PBMCs, control, 6h, 33523

description:
Library name: G008_O17_33523_C_6h_GEMS1_cDNA1_LIB1
!0x Genomics


title: MCF7_MED17_input

value: original


title: SRCAP shRNA3


title: YDBSFR_14

description: Library name: Sample 104


title: MCF7_MED1_input


title: YDBSFR_134

description: Library name: Sample 100


title: PBMCs, control, 0h, 35826

description:
Library name: G006_O17_35826_C_0h_GEMS1_cDNA1_LIB1
!0x Genomics

value: control


title: EP400 shRNA2

value: EP400 knockdown


title: MCF7_MED1WT_MED17

value: MCF7 MED1 WT


title: MCF7_H3K27ac_input


title: YDBSFR_172

description: Library name: Sample 108


title: YDBSFR_142

description: Library name: Sample 101


title: Control 2

value: control 2


title: PBMCs, control, 0h, 35824

description:
Library name: G005_O17_35824_C_0h_GEMS1_cDNA1_LIB1
!0x Genomics

value: PBMCs


title: MCF7_H3K4me_H3K4me3_PolII_input


title: YDBSFR_125

description: Library name: Sample 99


title: PBMCs, control, 0h, 35816

description:
Library name: G004_O17_35816_C_0h_GEMS1_cDNA1_LIB1
!0x Genomics

value: male


title: PBMCs, control, 0h, 35811

description:
Library name: G003_O17_35811_C_0h_GEMS1_cDNA1_LIB1
!0x Genomics


title: MCF7_PolII


title: Control 1

value: control 1


title: YDBS_98

description: Library name: Sample 96


title: PBMCs, control, 0h, 33523

description:
Library name: G002_O17_33523_C_0h_GEMS1_cDNA1_LIB1
!0x Genomics


title: Differentiated, d4 B

value: differentiated to day 4


title: PBMCs, control, 6h, 32275

description:
Library name: G007_O17_32275_C_6h_GEMS1_cDNA1_LIB1
!0x Genomics


title: PBMCs, control, 0h, 32275

description:
Library name: G001_O17_32275_C_0h_GEMS1_cDNA1_LIB1
!0x Genomics


title: YDBSFR_105

description: Library name: Sample 97


title: progenitor B


title: EP400 shRNA4


title: MCF7_MED1

value: breast cancer cell line

value: anti MED1 (bethyl A300-793A)


title: Differentiated, d4 A

value: foreskin epidermis


title: YDBS_96

description: Library name: Sample 95

value: whole blood


title: Whole blood, RhCMV 68-1 Gag/RTN/Pol, day 455, 35896

description: Library name: G518_O07_ABL3_35896_D455

data_processing:
Trimgalorev0.6.4 used to remove low quality reads and bases
Filtered out globin and rRNA reads using bowtie2v2.4.2
Aligned reads with STARv2.710b
Assembly: Rhesus macaques version10 Ensembl annoation v111
Supplementary files format and content: text file of counts for each sample

source_name: Whole blood

extract_protocol:
Isolation of RNA from Whole Blood Using the RNAdvance Blood Kit – for NHP samples
mRNA Library Prep for RNA from Whole Blood using KAPA HyperPrep Reagents

treatment_protocol: A prime and boost of one of the 3 modified RhCMV/SIV vectors were given to female rhesus macaques

value: Whole blood

value: RhCMV 68-1 Gag/RTN/Pol

value: day 455

value: female

tag: treatment outcome

value: Protected


title: YDBSFR_10

description: Library name: Sample 98


title: MCF7_MED17

value: original

value: anti MED17 (Aviva OAGA04959)


title: progenitor A

value: primary keratinocyte


title: YDBS_93

description: Library name: Sample 94


title: MCF7_H3K27ac

value: anti H3K27ac (D5E4) (Cell signaling #8173)


title: H2AZ1 shRNA4 + H2AZ2 shRNA4 [RNA-seq]

description:
sh4_plus_sh4
library_24
H2AZ1_H2AZ2_knockdown.csv

data_processing:
Read quality control by FastQC
Adaptor trimming by Trimgalore
Alignment to hg38 with STAR
Gene expression quantification with Salmon
Differential expression calculated by DESeq2
Assembly: hg38
Supplementary files format and content: .csv file with gene expression data, log2fold-change, and statistics for all genes

growth_protocol: Human primary epidermal keratinocytes pooled from a minimum of six donors were maintained at 37 degrees Celsius in a 1:1 mixture of Keratinocyte-SFM and Medium 154 at a confluency between 10-50%.

treatment_protocol: Keratinocytes were centrifuged for one hour at 1250 RMP at 32 degrees Celsius with control- or shRNA- lentivirus. For double knockdown, transductions were performed serially on the same day. Cells were selected for 24 hours with puromycin. RNA was extracted ~72 hours post-transduction.

value: H2AZ1+2 knockdown


title: MCF7_H3K4me

value: anti H3K4me (Abcam ab8895)


title: YDBS_87

description: Library name: Sample 93


title: H2AZ1 shRNA3 + H2AZ2 shRNA3 [RNA-seq]

description:
sh3_plus_sh3
library_23
H2AZ1_H2AZ2_knockdown.csv


title: Whole blood, RhCMV 68-1 Gag/RTN/Pol, day 455, 35887

description: Library name: G516_O07_ABL3_35887_D455

value: Uninfected


title: YDBS_85

description: Library name: Sample 92


title: Whole blood, RhCMV 68-1 Gag/RTN/Pol, day 455, 32607

description: Library name: G515_O07_ABL3_32607_D455


title: H2AZ1 shRNA2 + H2AZ2 shRNA2 [RNA-seq]

description:
sh2_plus_sh2
library_22
H2AZ1_H2AZ2_knockdown.csv


title: YDBS_5

description: Library name: Sample 91


title: HL-60 DRB-Treated Input ChIP-Seq

city: Boston

first: Annalisa

last: Di Ruscio

address: 3 Blackfan Circle, Center of Life Science, Room 407

institute: Beth Israel Deaconess Medical Center, Harvard Medical School

data_processing:
Raw reads were trimmed using fastp with the flags: “LeadMinTrimQual: 3 TrailMinTrimQual: 3 avgMinQual: 15 minReadLength: 40 palindromeClipTreshold: 30 seedMisMatches: 2 simpleClipThreshold: 10 windowSize: 4”. After cleanup, reads were aligned to hg38 using bowtie2 (v2.4.2) with the flags set to: “--no-mixed –no-discordant”. Bam file sorting and indexing was performed using samtools (v1.12). For read filtering both samtools and bamtolls were used. Samtools optiond: "-b -F 0x004 -q 10 -G 0x009 -f 0x001" bamtools was run allowing an edit distance of maximum 4 (NM <= 4) and an absolute insert size of maximum 2000. Peak Calling was performed with MACS3 (v3.0) with options set to “--broad --broad-cutoff 0.1 -g hs --SPMR --qvalue 0.05 --keep-dup all -B" -f BAMPE”. Begraph files generated by MACS were converted into the binary fomrat using the bedgraphToBigWig kent’s utility.   Peak files were annotated using Homer (v4.11) with default parameters with the exception of the gtf option that was set to a custom GTF file coming from our de novo transcript discovery analysis. Bam coverage maps were generated using bamCompare from deeptools (v3.5.1) with options set to: “--operation log2 --ignoreDuplicates --scaleFactorsMethod None --normalizeUsing RPKM --effectiveGenomeSize 2913022398 --extendReads --binSize 6 --exactScaling --skipNAs --smoothLength 18 –ignoreDuplicates”.
Assembly: hg38
Supplementary files format and content: bigwig, peak

growth_protocol: The human leukemia cell line HL-60 was obtained from ATCC and grown in glutamine containing medium in the absence of antibiotics, at 37 °C in a humidified atmosphere with 5% CO2.

extract_protocol: Nascent RNA/DNA capture was performed using Click-iT® Nascent RNA Capture Kit (ThermoFisher) according to the manufacturer’s instructions with minor modifications. Briefly, 1. Labeling the cells with EU/EdU. 200 mM EU or 30 mM EdU stock solutions were added to the cells, to a final concentration 0.5 mM or 30 uM, respectively. 2. Incubation. The cells were incubated for 1 or 2 hours. 3. RNA/DNA isolation. The cells were harvested and the RNA/DNA were isolated and dissolved in 14 uL of H2O. 4. Biotinylation of RNA/DNA by Click reaction. Click-iT reaction cocktail (50 uL per reaction) was prepared accordingly to manufacturer’s instructions: a mixture containing 1x Click-iT EU buffer; 2 mM CuSO4; 1 mM Biotin azide; 13.25 uL of the isolated RNA; 10 mM Click-iT® reaction buffer additive 1; 12 mM Click-iT reaction buffer additive 2 was prepared. After adding each component, the reaction cocktail was gently mixed by vortexing. The addition of the Click-iT reaction buffer additive 1 stock initiates the click reaction between the EU-RNA/EdU-DNA and biotin azide. Afterwards the Click-iT reaction buffer additive 2 is added and incubated for 30 minutes with gentle vortexing. 5. RNA/DNA precipitation. 1 uL of UltraPure Glycogen, 55 uL of 7 M ammonium acetate, and 750 uL of chilled 100% ethanol were added to the click reaction, incubated at –70°C for at least 30 minutes and after centrifugation the pellet was dissolved in 125 uL of H2O. 6. Binding biotinylated RNA/DNA to Dynabeads MyOne Streptavidin T1 magnetic beads. The RNA/DNA binding reaction mixture included: 125 uL 2xClick-iT RNA binding buffer; 2 uL Ribonuclease Inhibitor or 2 uL of water for DNA; 125 uL of the isolated biotinylated RNA/DNA. The RNA binding reaction mixture was heated at 68–70°C for 5 minutes and 50 uL of bead suspension added into the heated RNA binding reaction mixture. The tube containing the RNA/DNA binding reaction was incubated at r.t. for 30 min while gently vortexing to prevent the beads from settling. The beads were immobilized using the magnet and washed 5 times with 500 uL of Click-iT reaction wash buffer 1 and 5 times with 500 uL of Click-iT reaction wash buffer 2. Finally, the beads were resuspended in 50 uL of Click-iT reaction wash buffer 2 and the captured RNA immediately processed to cDNA synthesis. The captured DNA was released into 50 uL of boiling water and used in qPCR analyses. RIP-Seq - Immunoprecipitated RNA were processed for sequencing as described by Di Ruscio et al.(Di Ruscio et al., 2013) with some modifications. RNAs were depleted of ribosomal RNA with Ribo-ZeroTM Magnetic Gold Kit. Double stranded cDNA libraries were constructed using ScriptSeq v2 RNA-Seq Library Preparation Kit. The libraries were subjected to final size-selection in 3% agarose gels. 250-500 bp fragments were excised and recovered using the Qiaquick Gel Extraction Kit (Qiagen). RNA-Seq - RNA was extracted with TRI Reagent (MRC). RNA samples were treated with DNase I (10 U of DNase I (Roche) per 3 ug of total RNA; 37ºC for one hour; in the presence of RNase A inhibitor).   RIP-Seq - Immunoprecipitated RNA were processed for sequencing as described by Di Ruscio et al.(Di Ruscio et al., 2013) with some modifications. RNAs were depleted of ribosomal RNA with Ribo-ZeroTM Magnetic Gold Kit. Double stranded cDNA libraries were constructed using ScriptSeq v2 RNA-Seq Library Preparation Kit. The libraries were subjected to final size-selection in 3% agarose gels. 250-500 bp fragments were excised and recovered using the Qiaquick Gel Extraction Kit (Qiagen). RNA-Seq - RNA was extracted with TRI Reagent (MRC). RNA samples were treated with DNase I (10 U of DNase I (Roche) per 3 ug of total RNA; 37ºC for one hour; in the presence of RNase A inhibitor). RNAs were depleted of ribosomal RNA with Ribo-Zero Magnetic Gold Kit. Double stranded cDNA libraries were constructed using ScriptSeq v2 RNA-Seq Library Preparation Kit. The libraries were subjected to final size-selection in 3% agarose gel. 250-500 bp fragments were excised and recovered using the Qiaquick Gel Extraction Kit (Qiagen). Libraries were sequenced on a Hi-Seq-2000 Illumina. ChIP-Seq – ChIP libraries’ construction was performed as described (Mikkelsen et al., 2008) and paired-end sequenced on NextSeq500 platform, at a reading length of 36 nucleotides.

treatment_protocol: Double Thymidine block (early S-phase block) was carried out as described (Di Ruscio et al., 2013). Briefly, HL-60 cells were grown overnight to 70-80% confluence, washed twice with 1xPBS and cultured in DMEM (10% FCS) + 2.5 mM Thymidine for 18 h (first block). Thymidine was washed out with 1xPBS and cells were grown in DMEM (10% FCS). After 8 hrs cells were cultured in the presence of thymidine for 18 h (second block) and then released as described (Di Ruscio et al., 2013). Synchrony was monitored by flow cytometry analysis of propidium iodide-stained cells using a LSRII flow cytometer (BD Biosciences) at the Harvard Stem Cell Institute/Beth Israel Deaconess Center flow cytometry facility. DRB and Actinomycin D treatments were carried out as described (Di Ruscio et al., 2013). Briefly, after release from double thymidine block, HL-60 cells were treated with 100 μM of 5,6-Dichlorobenzimidazole 1-β–D-ribofuranoside (DRB)(Mitchell and Fraser, 2008) (Sigma Aldrich) or 0.8 μM of Actinomycin D (Sigma Aldrich) as indicated at each time point.

value: Human Caucasian promyelocytic leukaemia

value: DRB

value: none (input)


title: HL-60 DRB-Treated H2A.Z ChIP-Seq

value: H2A.Z (Abcam ab4174)


title: Whole blood, RhCMV 68-1 Gag/RTN/Pol, day 455, 31687

description: Library name: G514_O07_ABL3_31687_D455


title: YDBS_4

description: Library name: Sample 89

value: whole blood


title: Whole blood, RhCMV 68-1 Gag/RTN/Pol, day 455, 31670

description: Library name: G507_O07_ABL3_31670_D455

value: Whole blood


title: Whole blood, RhCMV 68-1 Gag/RTN/Pol, day 455, 31450

description: Library name: G505_O07_ABL3_31450_D455

value: RhCMV 68-1 Gag/RTN/Pol


title: HL-60 DMSO-Treated Input ChIP-Seq

value: DMSO


title: HL-60 DRB-Treated acH2A.Z ChIP-Seq


title: H2AZ1 shRNA1 + H2AZ2 shRNA1 [RNA-seq]

description:
sh1_plus_sh1
library_21
H2AZ1_H2AZ2_knockdown.csv

value: foreskin epidermis


title: YDBS_243

description: Library name: Sample 88


title: Control 1d [RNA-seq]

description:
control_1d
library_19
H2AZ1_H2AZ2_knockdown.csv

value: control for H2AZ1+2 knockdown


title: Whole blood, RhCMV 68-1 Gag/RTN/Pol, day 455, 35895

description: Library name: G517_O07_ABL3_35895_D455

value: day 455

value: female

value: Protected


title: H2AZ2 shRNA4 [RNA-seq]

description:
H2AZ2_sh4
library_18
H2AZ2_knockdown.csv

value: primary keratinocyte

value: H2AZ2 knockdown


title: HL-60 DMSO-Treated H2A.Z ChIP-Seq


title: Whole blood, RhCMV 68-1 Gag/RTN/Pol, day 455, 31432

description: Library name: G504_O07_ABL3_31432_D455

value: Nonprotected


title: MCF7_H3K4me3

value: breast cancer cell line

value: original

value: anti H3K4me3 (Abcam ab8580)


title: H2AZ2 shRNA3 [RNA-seq]

description:
H2AZ2_sh3
library_17
H2AZ2_knockdown.csv


title: Whole blood, RhCMV 68-1 Gag/RTN/Pol, day 455, 30653

description: Library name: G503_O07_ABL3_30653_D455


title: HL-60 DMSO-Treated acH2A.Z ChIP-Seq

value: Human Caucasian promyelocytic leukaemia


title: YDBS_241

description: Library name: Sample 86


title: HL-60 ACTD-Treated Input ChIP-Seq

value: Actinomycin D

value: none (input)


title: Whole blood, RhCMV 68-1 HLAE supertope Rh156,108 miR126, day 455, 33705

description: Library name: G472_O07_ABL3_33705_D455

value: Whole blood


title: YDBS_236

description: Library name: Sample 85

value: whole blood


title: H2AZ2 shRNA2 [RNA-seq]

description:
H2AZ2_sh2
library_16
H2AZ2_knockdown.csv


title: YDBS_57

description: Library name: Sample 90


title: Control 2d [RNA-seq]

description:
control_2d
library_20
H2AZ1_H2AZ2_knockdown.csv


title: Whole blood, RhCMV 68-1 HLAE supertope Rh156,108 miR126, day 455, 33495

description: Library name: G471_O07_ABL3_33495_D455


title: H2AZ2 shRNA1 [RNA-seq]

description:
H2AZ2_sh1
library_15
H2AZ2_knockdown.csv


title: HL-60 ACTD-Treated H2A.Z ChIP-Seq

value: H2A.Z (Abcam ab4174)


title: YDBS_242

description: Library name: Sample 87


title: YDBS_233

description: Library name: Sample 83


title: Whole blood, RhCMV 68-1 HLAE supertope Rh156,108 miR126, day 455, 32931

description: Library name: G470_O07_ABL3_32931_D455


title: Control 1c [RNA-seq]

description:
control_1c
library_13
H2AZ2_knockdown.csv

value: foreskin epidermis

value: control for H2AZ2 knockdown


title: Whole blood, RhCMV 68-1 HLAE supertope Rh156,108 miR126, day 455, 32751

description: Library name: G468_O07_ABL3_32751_D455

value: day 455


title: YDBS_225

description: Library name: Sample 81


title: YDBS_229

description: Library name: Sample 82


title: Whole blood, RhCMV 68-1 HLAE supertope Rh156,108 miR126, day 455, 32886

description: Library name: G469_O07_ABL3_32886_D455

value: female


title: H2AZ1 shRNA4 [RNA-seq]

description:
H2AZ1_sh4
library_12
H2AZ1_knockdown.csv

value: H2AZ1 knockdown


title: T3_FPKM

city: Taipei

first: Yen-Sung

last: Huang

address: Academia Sinica, No.128, Sec2,

department: Institute of Biomedical Sciences

country: Taiwan

institute: Academia Sinica

data_processing:
The sequences generated went through a filtering process to obtain qualified reads. Trimmomatics was implemented to trim or remove the reads according to the quality score.
Qualified reads after filtering low-quality data were analyzed using TopHat/Cufflinks(1) for gene expression estimation.
The gene expression level was calculated as FPKM (Fragments Per Kilobase of transcript per Million mapped reads). For differential expression analysis, CummeRbund was employed to perform statistical analyses of gene expression profiles.
The reference genome and gene annotations were retrieved from Ensembl database.
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample

source_name: plasma

extract_protocol:
Total RNA was extracted from plasma using TRIzol LS (Life Technologies, Carlsbad, USA) and NucleoSpin RNA XS (Macherey Nagel, Duren, Germany).
All procedures were carried out according to the manufacture's protocol from Illumina. Library construction of all samples were used by Agilent's SureSelect Strand Specific RNA Library Preparation Kit for 75SE (Single-End or Paired-End) sequencing on Solexa platform. The sequence was directly determined using sequencing-by-synthesis technology via the TruSeq SBS Kit. Raw sequences were obtained from the Illumina Pipeline software bcl2fastq v2.0 and expected to generate 20M (million reads or Gb) per sample.

tag: condition

value: traumatic brain injury


title: H2AZ1 shRNA3 [RNA-seq]

description:
H2AZ1_sh3
library_11
H2AZ1_knockdown.csv

value: primary keratinocyte


title: H2AZ1 shRNA2 [RNA-seq]

description:
H2AZ1_sh2
library_10
H2AZ1_knockdown.csv


title: T4_FPKM


title: T1_FPKM


title: YDBS_198

description: Library name: Sample 79


title: Whole blood, RhCMV 68-1 HLAE supertope Rh156,108 miR126, day 455, 32319

description: Library name: G466_O07_ABL3_32319_D455

tag: treatment

value: Protected


title: Male adult, Abx Morphine 5

city: Winston-Salem

first: Rebecca

last: Hofford

state: NC

address: 115 S Chestnut St

department: Translational Neuroscience

institute: Wake Forest School of Medicine

description:
Library name: AbxD5
Sample names in column (minus "ReadsPerGene.out")

data_processing:
Reads were removed if they contained adaptor contamination, when nucleotides were uncertain for 10% or more of the read, or the base quality was less than 5 for 50% of the reads.
Aligned using STAR v2.7.10a
Normalized using DESeq2
Differential expression of genes using ExpressAnalyst
Assembly: mm10
Supplementary files format and content: HoffordZeroMale.csv (Read counts for all male samples)

source_name: Brain

extract_protocol:
Rneasy Mini Kit (Qiagen)
Fast RNA-seq Library Prep Kit V2 (abclonal Technology)

value: Brain

value: All

value: wild type

value: Male

tag: developmental stage

value: adult

value: Abx morphine


title: YDBS_207

description: Library name: Sample 80


title: YDBS_235

description: Library name: Sample 84


title: HL-60 ACTD-Treated acH2A.Z ChIP-Seq

value: Human Caucasian promyelocytic leukaemia

value: Actinomycin D


title: Whole blood, RhCMV 68-1 Rh156,108 miR126 Gag/RTN/Pol, day 455, 35907

description: Library name: G464_O07_ABL3_35907_D455

value: Whole blood

value: RhCMV 68-1 Rh156,108 miR126 Gag/RTN/Pol

value: Nonprotected


title: Control 2b [RNA-seq]

description:
control_2b
library_8
H2AZ1_knockdown.csv

value: foreskin epidermis

value: control for H2AZ1 knockdown


title: YDBS_180

description: Library name: Sample 77

value: whole blood


title: YDBS_185

description: Library name: Sample 78


title: Whole blood, RhCMV 68-1 Rh156,108 miR126 Gag/RTN/Pol, day 455, 35908

description: Library name: G465_O07_ABL3_35908_D455

value: day 455

value: female


title: H2AZ1 shRNA1 [RNA-seq]

description:
H2AZ1_sh1
library_9
H2AZ1_knockdown.csv

value: primary keratinocyte

value: H2AZ1 knockdown


title: Control 2c [RNA-seq]

description:
control_2c
library_14
H2AZ2_knockdown.csv

value: control for H2AZ2 knockdown


title: Male adult, Abx Morphine 3

description:
Library name: AbxD3
Sample names in column (minus "ReadsPerGene.out")

value: Brain

value: All

value: wild type