title: BMAC scRNA OA - 88

description: Library name: BMAC_03_025


title: BMAC scRNA OA - 86

status: Public on Feb 25 2026

type: SRA

city: Atlanta

first: Krishnendu

last: Roy

state: Georgia

address: 345 ferst drive NW, marcus nanotechnology building, room no 3102B, 3rd floor

department: IBB

country: USA

institute: Georgia tech

description: Library name: BMAC_03_019

library_source: transcriptomic single cell

data_processing:
R, Cellranger, Linux server commndline, Bash, Python
Assembly: grch38
Supplementary files format and content: tab delimited barcode, feature and count matrices

molecule: total RNA

organism: Homo sapiens

source_name: knee - OA

extract_protocol:
3' mRNA was barcoded using 10x Genomics Chromium instrument
10x Genomics 3' GEX kitwas used as per manufacturer's manual

tag: tissue

value: Bone Marrow

tag: cell type

value: BMAC


title: BMAC scRNA OA - 89

description: Library name: BMAC_03_029


title: BMAC scRNA OA - 87

description: Library name: BMAC_03_020


title: BMAC scRNA OA - 84

description: Library name: BMAC_03_012


title: BMAC scRNA OA - 90

description: Library name: BMAC_03_031


title: BMAC scRNA OA - 81

description: Library name: BMAC_02_163


title: BMAC scRNA OA - 80

description: Library name: BMAC_02_161


title: BMAC scRNA OA - 78

description: Library name: BMAC_02_156


title: BMAC scRNA OA - 79

description: Library name: BMAC_02_160


title: BMAC scRNA OA - 91

description: Library name: BMAC_03_032


title: BMAC scRNA OA - 76

description: Library name: BMAC_02_150


title: BMAC scRNA OA - 82

description: Library name: BMAC_03_008


title: BMAC scRNA OA - 77

description: Library name: BMAC_02_155


title: BMAC scRNA OA - 72

description: Library name: BMAC_02_137


title: BMAC scRNA OA - 68

description: Library name: BMAC_02_114


title: BMAC scRNA OA - 83

description: Library name: BMAC_03_011


title: BMAC scRNA OA - 74

description: Library name: BMAC_02_143


title: BMAC scRNA OA - 73

description: Library name: BMAC_02_138


title: BMAC scRNA OA - 75

description: Library name: BMAC_02_148


title: BMAC scRNA OA - 70

description: Library name: BMAC_02_118


title: BMAC scRNA OA - 71

description: Library name: BMAC_02_121


title: BMAC scRNA OA - 85

description: Library name: BMAC_03_014


title: BMAC scRNA OA - 67

description: Library name: BMAC_02_112


title: BMAC scRNA OA - 69

description: Library name: BMAC_02_117


title: BMAC scRNA OA - 63

description: Library name: BMAC_02_092


title: BMAC scRNA OA - 64

description: Library name: BMAC_02_102


title: BMAC scRNA OA - 61

description: Library name: BMAC_02_087


title: BMAC scRNA OA - 65

description: Library name: BMAC_02_104


title: BMAC scRNA OA - 58

description: Library name: BMAC_02_075


title: BMAC scRNA OA - 60

description: Library name: BMAC_02_083


title: BMAC scRNA OA - 59

description: Library name: BMAC_02_078


title: BMAC scRNA OA - 56

description: Library name: BMAC_02_068


title: BMAC scRNA OA - 66

description: Library name: BMAC_02_108


title: BMAC scRNA OA - 53

description: Library name: BMAC_02_058


title: BMAC scRNA OA - 54

description: Library name: BMAC_02_061


title: BMAC scRNA OA - 51

description: Library name: BMAC_02_047


title: BMAC scRNA OA - 49

description: Library name: BMAC_02_038


title: BMAC scRNA OA - 48

description: Library name: BMAC_02_034


title: BMAC scRNA OA - 55

description: Library name: BMAC_02_066


title: BMAC scRNA OA - 47

description: Library name: BMAC_02_027


title: BMAC scRNA OA - 45

description: Library name: BMAC_02_022


title: BMAC scRNA OA - 42

description: Library name: BMAC_01_160


title: BMAC scRNA OA - 44

description: Library name: BMAC_02_013


title: BMAC scRNA OA - 46

description: Library name: BMAC_02_026


title: BMAC scRNA OA - 57

description: Library name: BMAC_02_073


title: BMAC scRNA OA - 39

description: Library name: BMAC_01_155


title: BMAC scRNA OA - 52

description: Library name: BMAC_02_055


title: BMAC scRNA OA - 41

description: Library name: BMAC_01_159


title: BMAC scRNA OA - 38

description: Library name: BMAC_01_148


title: BMAC scRNA OA - 40

description: Library name: BMAC_01_158


title: BMAC scRNA OA - 33

description: Library name: BMAC_01_133


title: BMAC scRNA OA - 50

description: Library name: BMAC_02_043


title: BMAC scRNA OA - 28

description: Library name: BMAC_01_109


title: BMAC scRNA OA - 32

description: Library name: BMAC_01_129


title: BMAC scRNA OA - 35

description: Library name: BMAC_01_140


title: BMAC scRNA OA - 37

description: Library name: BMAC_01_144


title: BMAC scRNA OA - 31

description: Library name: BMAC_01_120


title: BMAC scRNA OA - 25

description: Library name: BMAC_01_100


title: BMAC scRNA OA - 34

description: Library name: BMAC_01_136


title: BMAC scRNA OA - 27

description: Library name: BMAC_01_102


title: BMAC scRNA OA - 29

description: Library name: BMAC_01_114


title: BMAC scRNA OA - 24

description: Library name: BMAC_01_095


title: BMAC scRNA OA - 23

description: Library name: BMAC_01_092


title: BMAC scRNA OA - 14

description: Library name: BMAC_01_045


title: BMAC scRNA OA - 30

description: Library name: BMAC_01_118


title: BMAC scRNA OA - 22

description: Library name: BMAC_01_083


title: BMAC scRNA OA - 15

description: Library name: BMAC_01_054


title: BMAC scRNA OA - 20

description: Library name: BMAC_01_075


title: BMAC scRNA OA - 21

description: Library name: BMAC_01_079


title: BMAC scRNA OA - 18

description: Library name: BMAC_01_070


title: BMAC scRNA OA - 26

description: Library name: BMAC_01_101


title: BMAC scRNA OA - 19

description: Library name: BMAC_01_071


title: BMAC scRNA OA - 17

description: Library name: BMAC_01_062


title: BMAC scRNA OA - 16

description: Library name: BMAC_01_061


title: BMAC scRNA OA - 12

description: Library name: BMAC_01_038


title: BMAC scRNA OA - 11

description: Library name: BMAC_01_032


title: BMAC scRNA OA - 9

description: Library name: BMAC_01_027


title: BMAC scRNA OA - 13

description: Library name: BMAC_01_041


title: BMAC scRNA OA - 10

description: Library name: BMAC_01_031


title: BMAC scRNA OA - 6

description: Library name: BMAC_01_016


title: BMAC scRNA OA - 4

description: Library name: BMAC_01_012


title: BMAC scRNA OA - 5

description: Library name: BMAC_01_015


title: BMAC scRNA OA - 8

description: Library name: BMAC_01_026


title: BMAC scRNA OA - 2

description: Library name: BMAC_01_004


title: BMAC scRNA OA - 3

description: Library name: BMAC_01_006


title: BMAC scRNA OA - 1

description: Library name: BMAC_01_003


title: WT.2_ATAC

city: Memphis

first: Mitchell

last: Weiss

state: TN

address: 262 Danny Thomas Place, MS #341 Memphis, TN   38105

department: Department of Hematology

institute: St. Jude Children’s Research Hospital

description:
10X Genomics
PD_thal2_ATAC
fig2.hudep2.rds

library_source: genomic single cell

data_processing:
Single-cell RNA-seq data was analyzed using cellranger count (v7.0.0) with default parameters. Single-cell RNA-seq and ATAC-seq data was analyzed using cellranger-arc count (v2.0.0). The transcriptome database was based on cellranger GRCh38-2020-A_build, with HBG1 and HBA1 masked: chr11:5248267-5250324,chr16:176670-177535. Novel transcripts that overlapped with HBG1 and HBG2 were removed from the gtf file: ENSG00000284931, ENSG00000239920.
Seurat v5.0.1 was used for the downstream analysis. The reticulocyte cells were filtered by nFeature_RNA between 100 and 5000, MT content <=10% and nCount_RNA <=50000. T he Hudep2 cells were filtered by nFeature_RNA between 200 and 5000, MT content <=20% and nCount_RNA <=50000.
Cell clustering and annotation were done using the BoneMarrowMap: https://github.com/andygxzeng/BoneMarrowMap
Assembly: hg38
Supplementary files format and content: R data format

molecule: genomic DNA

source_name: cell line

growth_protocol: All human subjects research studies were approved by the Institutional Review Board (SCCRIP: Sickle Cell Research and Intervention Program) at St. Jude Children’s Research Hospital. Reticulocytes were sorted directly from the primary blood draw. HUDEP-2 cells were maintained at 0.3x10^6 cells/mL in SFEM supplemented with 50 ng/mL SCF, 3 U/mL EPO, 10 ug/mL doxycycline, 1 uM dexamethasone, and 1X penicillin.streptomycin

extract_protocol:
Reticulocytes were sorted from primary blood draws through the gating strategy hCD45-/hCD71+/Thiazole Orange+ for library preparation. Undifferentiated (not sorted) HUDEP-2 cells were used for library preparation. Cells were processed using 10X Genomics reagents according to manufacturer’s protocol.
For reticulocytes, gel beads-in-emulsion (GEM) generation, cDNA amplification, and library construction were performed following the protocol of Chromium Next GEM Single Cell 3′ Reagent Kits v3.1 (Dual Index, 10x Genomics) with target recovery of 8,000–10,000 cells per library or sample. Libraries derived from HUDEP-2 cells were prepared following the 10X Genomics Single Cell Multiome ATAC + Gene Expression suggested protocol.

treatment_protocol: Reticulocytes were not exposed to treatment. HUDEP-2 cells with the specific deletions were generated through Cas9-mediated homology-directed repair

value: cell line

tag: cell line

tag: genotype

value: WT


title: HPFH1.2_ATAC

description:
10X Genomics
PD2_ATAC
fig2.hudep2.rds


title: WT.1_ATAC

description:
10X Genomics
PD_thal1_ATAC
fig2.hudep2.rds


title: WT.2_mRNA

description:
10X Genomics
PD_thal2_RNA
fig2.hudep2.rds

molecule: polyA RNA


title: HPFH1.1_ATAC

description:
10X Genomics
PD1_ATAC
fig2.hudep2.rds


title: Agdb-thal.1_ATAC

description:
10X Genomics
PD3_ATAC
fig2.hudep2.rds

value: Agdb-thal


title: BMAC scRNA OA - 7

description: Library name: BMAC_01_022


title: Agdb-thal.2_mRNA

description:
10X Genomics
PD5_RNA
fig2.hudep2.rds


title: HPFH1.2_mRNA

description:
10X Genomics
PD2_RNA
fig2.hudep2.rds


title: HbS/Agdb-thal.2

description:
10X Genomics
TB11134_HbSAgdbthal_retics_S31
fig1.retics.rds

source_name: blood

value: blood

value: Human CD45-/CD71+/Thiazole Orange+

value: HbS/Agdb-thal


title: HbS/Agdb-thal.1

description:
10X Genomics
TB09311_HbSAgdbthal_retics_S21
fig1.retics.rds


title: HPFH1.1_mRNA

description:
10X Genomics
PD1_RNA
fig2.hudep2.rds


title: Agdb-thal.1_mRNA

description:
10X Genomics
PD3_RNA
fig2.hudep2.rds


title: HbS/HPFH.3

description:
10X Genomics
TB2400297retics_S15
fig1.retics.rds

value: HbS/HPFH


title: HbS/HPFH.2

description:
10X Genomics
TB2400296Retics_S14
fig1.retics.rds


title: BMAC scRNA OA - 62

description: Library name: BMAC_02_089


title: HbS/HPFH.1

description:
10X Genomics
TB2400292retics_S13
fig1.retics.rds


title: WildType_3

city: Bethesda

first: Caroline

last: Esnault

state: md

address: 9000 Rockville Pike,

institute: NICHD NIH

library_source: transcriptomic

data_processing:
Raw sequence reads were processed using the same methods described below for ChIPseq sequence reads with the following parameter differences: cutadapt parameters “-a AGATCGGAAGAGCACACGTCTGAACTCCAGTCA -A AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT -q 20 –minimum-length=25” for paired-end reads; PCR duplicates were flagged with picard MarkDuplicates with parameter “VALIDATION_STRINGENCY=LENIENT”; trimmed reads were mapped to the genome with hisat2 v 2.2.1 with the parameters “--no-unal -S”; Bigwig files were generated with deeptools bamCoverage with parameters “--minMappingQuality 20 --ignoreDuplicates --smoothlength”. Gene expression was then quantified using the subread featureCounts v2.0.1 with default parameters with the uniquely aligned reads and the reference annotation v19_GRCh37.87_merged_transcripts. The Gencode human reference genome release_19 GRCh37.p13 was used, along with the corresponding Gencode v19 GRCh37.87 GTF annotation. The annotation was further processed by filtering for transcript entries, and merging transcripts per gene with the R GenomicRanges reduce function, which we refer as v19_GRCh37.87_merged_transcripts.
Assembly: hg19
Supplementary files format and content: featurecounts.txt file contains raw counts in genes.

source_name: Human cell line (HEK293T)

growth_protocol: HEK293T cells were propagated in Dulbecco’s modified Eagle’s media supplemented to contain fetal bovine serum (10%) and penicillin-streptomycin (1%; 100 U/ml) (DMEM). Cells were grown at 37 °C in humified tissue culture cell incubators.

extract_protocol:
RNA was extracted from HEK293T and LEDGF KO cells with RNeasy Plus Mini kit (Qiagen) following manufacturer’s instructions.
Approximately 1 µg of total RNA per sample was purified with PolyA extraction, and then purified mRNAs were used to make RNA-Seq libraries with specific barcodes using Illumina TruSeq Stranded mRNA Library Prep Kit. All the RNA-Seq libraries were pooled together and sequenced using illumina NovaSeq 6000 to generate approximately ∼40 million 2×100 paired-end reads for each sample. The raw data were demultiplexed and analyzed further.

treatment_protocol: HEK293T cells were modified with CRIPSR to prevent expression of both the p52 and p75 isoforms of LEDGF. Cas9 with two sgRNAs targeting exon 2 of PSIP1 generated a clone with one allele encoding a frameshift after amino acid 30 adding seven additional amino acids and a second allele with a stop codon at amino acid 24.

value: Human cell line (HEK293T)

value: control


title: Agdb-thal.2_ATAC

description:
10X Genomics
PD5_ATAC
fig2.hudep2.rds


title: WildType_4


title: WT.1_mRNA

description:
10X Genomics
PD_thal1_RNA
fig2.hudep2.rds


title: LEDGF-KO_4

value: LEDGF-KO


title: LEDGF-KO_3


title: LEDGF-KO_2


title: Anti-MBD1

city: Nanchang

first: Yi

last: Sang

state: Jiangxi

address: No.128,Xiangshan North Road

country: China

institute: Nanchang University

library_source: genomic

data_processing:
Raw reads in fastq format were processed to remove contaminating adapter sequences using Trimmomatics
Quality distribution plot and base content distribution were generated by FASTQC
CUT&Tag reads were aligned to the hg38 genome using BWA（0.7.13-r1126） . Only uniquely mapping reads with at most two mismatches were retained.
Peaks were called uing MACS v2.1.2 with the significance cut-off q-value <=0.05
bigWig files were generated using the deeptools. Peak files were generated using MACS v2 with default settings.
Assembly: hg38
Supplementary files format and content: bigWig
Library strategy: CUT&Tag

source_name: Lung cancer

extract_protocol:
CUT&Tag assay was carried out using the NovoNGS CUT&Tag 3.0 High Sensitivity Kit (Novoprotein, N259-YH01) according to manufacturer’s instructions. Briefly, 100000 lung cancer cells were incubated with ConA magnetic beads for 10min at room temperature.
To amplify libraries, 35μL DNA was mixed with 2.5μL of a universal i5 and auniquely barcoded i7 primer. A volume of 10 μL 5× AmpliMix was added and mixed. The sample was placed in a Thermocycler with a heated lid using the following cycling conditions: 72 °C for 3 min (gap filling); 98 °C for 30 s; 18 cycles of 98 °C for 15 s, 60 °C for 20 s and 72°C for 10 s; final extension at 72 °C for 10 s and hold at 10 °C. libraried clean-up was performed NovoNGS DNA Clean beads.

value: Lung cancer

tag: antibody


title: WildType_1


title: LN95 cells, BU3-12, - androgen, biol rep 2

city: Vancouver

first: Marianne

last: Sadar

state: BC

address: 675 West 10th Ave

department: Genome Sciences Centre

country: Canada

institute: BC Cancer Research Institute

data_processing:
STAR[1] (version 2.5.2b) was used to align RNA-Seq data to the genome reference (hg38);  RSEM[2] (version 1.3.0) was used to quantify gene and isoform expression; Ensembl 100 gene annotation GTF[3] was used to build the RSEM reference and to add gene and transcript specific information to the output files, such as gene name, transcript name, and chromosomal coordinates. Differential expression (DE) analysis was performed using R[4] (version R-4.0.2) and DESeq[5] package (version 1.39.1) with raw read count (gene-level abundances) as input data. When applying DESeq, the functions estimate SizeFactors and nbinomTest were used.
Assembly: hg38
Supplementary files format and content: tab-deliminated text file contains FPKM for each sample
Supplementary files format and content: tab-deliminated text file contains transcript abundance for each sample

growth_protocol: LNCaP95 cells were maintained in RPMI 1640 supplemented with 10% charcoal-stripped fetal bovine serum (CSS) in humidified atmosphere with 5% C02 at 37C.

extract_protocol:
Cells were harvested in 1mL Trizol and total RNA was purified using the PureLink RNA mini kit (Invitrogen). 0.9 ug of RNA was used for library construction.
Polyadenylated (PolyA+) RNA was purified using the NEBNext Poly(A) mRNA Magnetic  Isolation Module (E7490L, New England Biolabs) from 500 ng total RNA. First-strand cDNA was synthesized from heat-denatured purified mRNA using a Maxima H Minus First Strand cDNA Synthesis kit (Thermo-Fisher, USA) and random hexamer primers at a concentration of 200 ng/µL along with a final concentration of 40 ng/µL Actinomycin D, followed by PCR Clean DX (Aline Biosciences) bead purification on a Microlab NIMBUS robot (Hamilton Robotics, USA). The second strand cDNA was synthesized following the NEBNext Ultra Directional Second Strand cDNA Synthesis protocol (New England Biolabs) that incorporates dUTP in the dNTP mix, allowing the second strand to be digested using USERTM enzyme (NEB) in the post-adapter ligation reaction and thus achieving strand specificity.  cDNA was fragmented to by Covaris LE220 sonication to achieve 250-300 bp average fragment lengths. The paired-end sequencing library was prepared following the BC Cancer Genome Sciences Centre strand-specific, plate-based library construction protocol on a Microlab NIMBUS robot (Hamilton Robotics, USA).

treatment_protocol: Cells were treated with DMSO vehicle, enzalutamide (5uM), EPI-002 (35uM) or BU3-12 (5uM) for 48 hr  in RPMI 1640 containing 1.5% CSS

tag: treatment

value: BU3-12, no androgen


title: LN95 cells, BU3-12, - androgen, biol rep 3


title: LEDGF-KO_1


title: WildType_2


title: LN95 cells, EPI-002, - androgen, biol rep 1

value: EPI-002, no androgen


title: LN95 cells, ENZA, - androgen, biol rep 3

value: ENZA, no androgen


title: LN95 cells, ENZA, - androgen, biol rep 2


title: LN95 cells, BU3-12, - androgen, biol rep 1


title: BMAC scRNA OA - 43

description: Library name: BMAC_01_164


title: LN95 cells, ENZA, - androgen, biol rep 1


title: LN95 cells, EPI-002, - androgen, biol rep 3


title: LN95 cells, VEH, - androgen, biol rep 2

value: VEH, no androgen


title: RNA from bacterial cell, LS2 medium, 30 degree celsius, 90 hour, replicate 2

city: Khlong Luang

first: Wuttichai

last: Mhuantong

state: Pathum Thani

address: National Center for Genetic Engineering and Biotechnology (BIOTEC)

country: Thailand

institute: BIOTEC

description:
Library name: H90_3
RNA-Seq from bacterial cell, LS2 medium, 30 degree celsius, 90 hour, replicate 2

data_processing:
To be updated.
Assembly: Actinoplanes siamensis TBRC 4237
Supplementary files format and content: Comma-separated values (CSV) for read_count.csv

organism: Actinoplanes siamensis

source_name: Bacterial cell pellet from liquid cultivation

growth_protocol: A. siamensis TBRC 4237 was cultured on ISP3 agar and incubated at 30°C for 15–22 days. The agar cultures were cut by cork borer and inoculated into 50 mL of LS2 using 250-mL baffled flask. Cells were harvested by vacuum filtration from the cultures at 66, 72, and 90 h cultivation for RNA extraction.

extract_protocol:
RNA of A. siamensis TBRC 4237 was extracted using RiboPure™ RNA Purification Kit, bacteria (Invitrogen, U.S.A.). Cells were harvested from 250–600 microliter cultures in LS2 medium by centrifugation and resuspended with 300 microliter RNAwiz solution. Then, RNA extraction was performed following the kit protocol. RNA eluted from the kit columns were treated with DNaseI. Concentration and quality of RNA was measured by using nanodrop and 0.8% agarose gel electrophoresis, respectively. Approximately 6 microgram RNA of each samples was submitted for RNAseq analysis service at NovogeneAIT Genomics, Singapore. The integrity of RNA samples was analyzed by using Agilent 2100 bioanalyzer. The RNA sequencing was performed on Illumina NovaSeq 6000 with paired end 150 bp and acquired 3 GB data per samples.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: No treatment to bacterial cells before RNA extraction.

value: Bacterial cell

value: bacterial cell cultured in LS2 medium at 30 degree celsius for 90 hour


title: LN95 cells, VEH, - androgen, biol rep 3


title: RNA from bacterial cell, LS2 medium, 30 degree celsius, 90 hour, replicate 1

description:
Library name: H90_2
RNA-Seq from bacterial cell, LS2 medium, 30 degree celsius, 90 hour, replicate 1


title: RNA from bacterial cell, LS2 medium, 30 degree celsius, 90 hour, replicate 3

description:
Library name: H90_4
RNA-Seq from bacterial cell, LS2 medium, 30 degree celsius, 90 hour, replicate 3


title: LN95 cells, VEH, - androgen, biol rep 1


title: LNCaP cells, BU3-12, + androgen, biol rep 3

source_name: LNCaP

growth_protocol: LNCaP cells were maintained in RPMI 1640 supplemented with 5% fetal bovine serum (FBS) in humidified atmosphere with 5% C02 at 37C.  24 hrs prior to treatment, media was replaced with RPMI 1640 without serum.

extract_protocol:
Cells were harvested in 1mL Trizol and total RNA was purified using the PureLink RNA mini kit (Invitrogen) according to manufacturer's instruction.
Polyadenylated (PolyA+) RNA was purified using the NEBNext Poly(A) mRNA Magnetic  Isolation Module (E7490L, New England Biolabs) from 500 ng total RNA. First-strand cDNA was synthesized from heat-denatured purified mRNA using a Maxima H Minus First Strand cDNA Synthesis kit (Thermo-Fisher, USA) and random hexamer primers at a concentration of 200 ng/µL along with a final concentration of 40 ng/µL Actinomycin D, followed by PCR Clean DX (Aline Biosciences) bead purification on a Microlab NIMBUS robot (Hamilton Robotics, USA). The second strand cDNA was synthesized following the NEBNext Ultra Directional Second Strand cDNA Synthesis protocol (New England Biolabs) that incorporates dUTP in the dNTP mix, allowing the second strand to be digested using USERTM enzyme (NEB) in the post-adapter ligation reaction and thus achieving strand specificity.  cDNA was fragmented to by Covaris LE220 sonication to achieve 250-300 bp average fragment lengths. The paired-end sequencing library was prepared following the BC Cancer Genome Sciences Centre strand-specific, plate-based library construction protocol on a Microlab NIMBUS robot (Hamilton Robotics, USA).

treatment_protocol: Cells were pre-treated with DMSO vehicle, enzalutamide (5uM) EPI-002 (35uM), BU3-12 (5uM) for 1 hr under serum-free conditions.  Cells were then stimulated with R1881 (1nM) or EtOH control in serum-free conditions for 24 hr prior to harvest.

value: LNCaP

value: BU3-12, + androgen


title: RNA from bacterial cell, LS2 medium, 30 degree celsius, 72 hour, replicate 4

description:
Library name: H72_4
RNA-Seq from bacterial cell, LS2 medium, 30 degree celsius, 72 hour, replicate 4

value: bacterial cell cultured in LS2 medium at 30 degree celsius for 72 hour


title: RNA from bacterial cell, LS2 medium, 30 degree celsius, 72 hour, replicate 3

description:
Library name: H72_3
RNA-Seq from bacterial cell, LS2 medium, 30 degree celsius, 72 hour, replicate 3


title: RNA from bacterial cell, LS2 medium, 30 degree celsius, 72 hour, replicate 2

description:
Library name: H72_2
RNA-Seq from bacterial cell, LS2 medium, 30 degree celsius, 72 hour, replicate 2


title: LNCaP cells, BU3-12, + androgen, biol rep 1

value: WT


title: LNCaP cells, BU3-12, + androgen, biol rep 2


title: RNA from bacterial cell, LS2 medium, 30 degree celsius, 66 hour, replicate 4

description:
Library name: H66_4
RNA-Seq from bacterial cell, LS2 medium, 30 degree celsius, 66 hour, replicate 4

value: bacterial cell cultured in LS2 medium at 30 degree celsius for 66 hour


title: LNCaP cells, EPI-002, + androgen, biol rep 2

value: EPI-002, + androgen


title: LNCaP cells, ENZA, + androgen, biol rep 3

value: ENZA, + androgen


title: RNA from bacterial cell, LS2 medium, 30 degree celsius, 66 hour, replicate 2

description:
Library name: H66_2
RNA-Seq from bacterial cell, LS2 medium, 30 degree celsius, 66 hour, replicate 2


title: RNA from bacterial cell, LS2 medium, 30 degree celsius, 72 hour, replicate 1

description:
Library name: H72_1
RNA-Seq from bacterial cell, LS2 medium, 30 degree celsius, 72 hour, replicate 1


title: RNA from bacterial cell, LS2 medium, 30 degree celsius, 66 hour, replicate 3

description:
Library name: H66_3
RNA-Seq from bacterial cell, LS2 medium, 30 degree celsius, 66 hour, replicate 3


title: LNCaP cells, EPI-002,  androgen, biol rep 3


title: LNCaP cells, EPI-002, + androgen, biol rep 1


title: RNA from bacterial cell, LS2 medium, 30 degree celsius, 66 hour, replicate 1

description:
Library name: H66_1
RNA-Seq from bacterial cell, LS2 medium, 30 degree celsius, 66 hour, replicate 1


title: LNCaP cells, VEH, + androgen, biol rep 3

value: VEH, + androgen


title: LNCaP cells, ENZA, + androgen, biol rep 1


title: LNCaP cells, VEH, + androgen, biol rep 2


title: DcdxBDrogADGTA rep 1

city: Norwich

first: Tung

last: Le

address: Colney Lane

department: Molecular Microbiology

country: United Kingdom

institute: John Innes Centre

description: Library name: TLE22

data_processing:
All data processing was done in the Galaxy platform.
Sequencing reads were checked for quality using FastQC.
Reads were then mapped to the NA1000 reference genome using Hisat2
Mapped reads were assigned to gene IDs using htseq-count
Assembly: Caulobacter crescentus NA1000 reference genome (NC_011916.1)
Supplementary files format and content: Tab-delimited text files containg raw read counts generated by htseq-count. One per sample.

organism: Caulobacter vibrioides

source_name: bacterial cell

growth_protocol: Caulobacter crescentus cells were grown for 20h at 30 C, then back-diluted to an OD600 of 0.1 and grown for a further 20h to stationary phase.

extract_protocol:
Total RNA was purified using the Direct-zol RNA miniprep kit (Zymo Research) and 10 μg was digested with 20 units of Turbo DNaseI (Invitrogen) at 37 °C for 1 h. DNaseI was removed using the RNA clean and concentrator-25 kit (Zymo Research).
Purified RNA samples were shipped to GeneWiz where bacterial rRNA depletion was performed with an NEBNext rRNA Depletion Kit (Cat. No. E7850X). Libraries were prepared by GeneWiz.

tag: strain

value: bacterial cell

value: DrogBDrogADGTA


title: DcdxBDrogADGTA rep 3

description: Library name: TLE24


title: DcdxBDrogADGTA rep 2

description: Library name: TLE23


title: LNCaP cells, ENZA, + androgen, biol rep 2


title: DrogADGTA rep 2

description: Library name: TLE17

value: DrogADGTA


title: LNCaP cells, VEH, + androgen, biol rep 1


title: DrogADGTA rep 3

description: Library name: TLE18


title: LNCaP cells, VEH, - androgen, biol rep 2


title: LNCaP cells, VEH, - androgen, biol rep 3


title: LNCaP cells, VEH, - androgen, biol rep 1


title: DcdxB rep 3

description: Library name: TLE09

value: DrogB


title: HCT116 cells, SON-depletion, 4sU-pulse RNA rep2

city: Berlin

first: IBRAHIM

middle: AVSAR

last: ILIK

state: Berlin

address: Ihnestraße 63-73

country: Germany

institute: Max-Planck-Institut für molekulare Genetik

data_processing:
Illumina base calling, demultiplexing and FASTQ conversion
Read alignment to the human genome (GRCh38 assembly) using STAR 2.7.9a
Reads counted on GENCODE release 29 gene models using STAR 2.7.9a
Read alignments (.bam files) converted to bigWigs using bamCoverage 3.5.1
Assembly: hg38
Supplementary files format and content: RPKM normalized RNA-seq coverage in bigWig format

extract_protocol:
Total RNA was extracted from cells with Quick-RNA MicroPrep kit (Zymo) after fractionation.
ribo-depleted RNA
Strand-specific libraries were generated using KAPA Stranded RNA-seq Library Preparation Kit (Roche)

value: SON-HaloTag


title: Wildtype rep 3

description: Library name: TLE03

value: Wildtype


title: DcdxB rep 2

description: Library name: TLE08


title: HCT116 cells, control, 4sU-pulse RNA rep1

value: control


title: DcdxB rep 1

description: Library name: TLE07


title: DrogADGTA rep 1

description: Library name: TLE16


title: HCT116 cells, control, 4sU-pulse RNA rep2


title: Wildtype rep 2

description: Library name: TLE02


title: HCT116 cells, SONdepletion_SF3B1_rep1

data_processing:
Illumina base calling, demultiplexing and FASTQ conversion
Merging with bbmerge v. 38.72
Demultiplexing with flexbar v. 3.5.0
UMI extraction with umi_tools extract v. 1.0.0
Alignment to human (hg38)
bigWig generation using bamCoverage 3.3.1
Assembly: hg38
Supplementary files format and content: Raw RNA-seq coverage in bigWig format, separate files for plus and minus strands

extract_protocol:
Cells were crosslnked with 0.199 mj/cm2 UV-C light,  after nuclei isolation lysed with 1xNLB buffer, 1H4 or a rabbit polyclonal Ab against SF3B1 was used to IP targets proteins, co-purifying RNA isolated with proteinase K digestion and purified with Oligo clean and concentrator-5 columns (Zymo).
RNAseI digested RNA
Custom library prep, described in Ilik et al., 2020. Isolated RNA is ligated to s-oligo on beads, reverse-transcribed, RNaseH digested, circularized with CircLigase and PCR amplified.
FLASH-seq (Ilik et al., 2020)

tag: group

value: PROTAC


title: HCT116 cells, SONdepletion_SF3B1_rep2


title: HCT116 cells, SON-depletion, 4sU-pulse RNA rep1


title: Wildtype rep 1

description: Library name: TLE01


title: HCT116 cells, SONdepletion_1H4_rep2


city: Stanford

first: Adit

last: Naor

state: CA

address: 300 Pasteur Drive Stanford, D305 Fairchild Building

institute: Stanford

description: Library name: In vivo_Experiment_In-vitro_MDBK-adapted_1

data_processing:
Raw reads were uploaded onto the CLC Genomics Workbench 8.0 (Qiagen) platform for independent alignments against the human genomes (Ensembl.org/ hg19) and Toxoplasma Type II ME49 strain (ToxoDB-24). All parameters were left at their default values. The number of total reads mapped to each genome was used to determine the RPKM (Reads Per Kilobase of transcript per Million mapped reads).
Assembly: ToxoDB-24
Supplementary files format and content: Excel containing RPKM for all samples

organism: Toxoplasma gondii ME49

source_name: Parasites from an infected tissue culture

extract_protocol:
RNA Sequencing was performed exactly as previously described (Panas et al., 2019). The only change was that the samples were collected 18 hpi from infected HFF or MDBK monolayers, as indicated
Multiplex sequencing libraries were generated with RNA Sample Prep Kit (Illumina)

value: Toxoplasma gondii ME49 and Madin-Darby bovine kidney


title: HCT116 cells, control_SF3B1_rep1

value: DMSO


description: Library name: In vivo_Experiment_In-vitro_MDBK-adapted_3

value: Parasites from an infected tissue culture


description: Library name: In vivo_Experiment_In-vitro_HFF-adapted_3

value: Toxoplasma gondii ME49 and Human foreskin fibroblast


title: HCT116 cells, control_SF3B1_rep2


description: Library name: In vivo_Experiment_In-vivo_MDBK-adapted_3

source_name: Parasites from an infected mouse peritoneum

value: Toxoplasma gondii ME49


description: Library name: In vivo_Experiment_In-vitro_MDBK-adapted_2


title: HCT116 cells, SON+SRRM2, pA(+) RNA rep3

data_processing:
Illumina base calling, demultiplexing and FASTQ conversion
Read alignment to the human genome (GRCh38 assembly) using STAR 2.7.9a
Read alignments (.bam files) converted to bigWigs using bamCoverage 3.5.1
Assembly: hg38
Supplementary files format and content: RPKM normalized RNA-seq coverage in bigWig format

extract_protocol:
Total RNA was extracted from cells with Quick-RNA MicroPrep kit (Zymo) after fractionation. Polyadenylated RNA was then isolated using Dynabeads™ mRNA Purification Kit. Purification was done twice to increase purity.
Strand-specific libraries were generated using KAPA Stranded RNA-seq Library Preparation Kit (Roche)

value: SON-HaloTag SRRM2-dTAG


description: Library name: In vivo_Experiment_In-vivo_MDBK-adapted_2

value: Parasites from an infected mouse peritoneum


description: Library name: In vivo_Experiment_In-vitro_HFF-adapted_1


title: HCT116 cells, control_1H4_rep1


title: HCT116 cells, control_1H4_rep2


title: HCT116 cells, SONdepletion_1H4_rep1


title: HCT116 cells, SON+SRRM2, pA(+) RNA rep1


title: HCT116 cells, SON+SRRM2, pA(+) RNA rep2


description: Library name: In vivo_Experiment_In-vivo_MDBK-adapted_1


title: LN95 cells, EPI-002, - androgen, biol rep 2

value: WT

value: EPI-002, no androgen


description: Library name: In vivo_Experiment_In-vivo_HFF-adapted_3


title: In vivo_Experiment_350th_pass_on_MDBK_3

description: Library name: In vivo_Experiment_350th_pass_on_MDBK_3


title: HCT116 cells, SON, pA(+) RNA rep2


title: HCT116 cells, SON, pA(+) RNA rep1


description: Library name: In vivo_Experiment_In-vivo_HFF-adapted_1


title: HCT116 cells, SRRM2, pA(+) RNA rep3


title: In vivo_Experiment_350th_pass_on_HFF_3

description: Library name: In vivo_Experiment_350th_pass_on_HFF_3


title: HCT116 cells, SRRM2, pA(+) RNA rep2


title: In vivo_Experiment_350th_pass_on_MDBK_2

description: Library name: In vivo_Experiment_350th_pass_on_MDBK_2


title: In vivo_Experiment_350th_pass_on_HFF_2

description: Library name: In vivo_Experiment_350th_pass_on_HFF_2


title: In vivo_Experiment_350th_pass_on_MDBK_1

description: Library name: In vivo_Experiment_350th_pass_on_MDBK_1


description: Library name: Short Passage_Pass_360_on_HFF_and_2_pass_on_MDBK_2


description: Library name: In vivo_Experiment_In-vivo_HFF-adapted_2


description: Library name: Short Passage_Pass_360_on_HFF_and_2_pass_on_MDBK_1


title: In vivo_Experiment_350th_pass_on_HFF_1

description: Library name: In vivo_Experiment_350th_pass_on_HFF_1


title: HCT116 cells, SRRM2, pA(+) RNA rep1


title: HCT116 cells, SON-depleted, total RNA rep3

tag: fraction

value: total RNA


title: HCT116 cells, control, pA(+) RNA rep3


title: HCT116 cells, SON-depleted, total RNA rep1


title: HCT116 cells, control, pA(+) RNA rep2


title: Short Passage_Pass_360_on_HFF_1

description: Library name: Short Passage_Pass_360_on_HFF_1


title: HCT116 cells, control, pA(+) RNA rep1


title: HCT116 cells, SON-depleted, total RNA rep2


title: HCT116 cells, control, total RNA rep3


title: Short Passage_Pass_360_on_HFF_2

description: Library name: Short Passage_Pass_360_on_HFF_2


description: Library name: Short Passage_Pass_40_on_HFF_and_2_pass_on_MDBK_2


description: Library name: Short Passage_Pass_40_on_HFF_and_2_pass_on_MDBK_1


title: Short Passage_Pass_40_on_HFF_2

description: Library name: Short Passage_Pass_40_on_HFF_2


title: HCT116 cells, control, total RNA rep2


title: Short Passage_Pass_40_on_HFF_1

description: Library name: Short Passage_Pass_40_on_HFF_1


title: HCT116 cells, SON-depleted, cytoplasmic RNA rep3

value: cytoplasmic RNA


title: 2nd Experiment_ 100th_pass_on_MDBK_2

description: Library name: 2nd Experiment_ 100th_pass_on_MDBK_2


title: HCT116 cells, control, total RNA rep1


title: HCT116 cells, SON-depleted, cytoplasmic RNA rep2


title: 2nd Experiment_ 100th_pass_on_MDBK_1

description: Library name: 2nd Experiment_ 100th_pass_on_MDBK_1


title: 2nd Experiment_ 100th_pass_on_HFF_2

description: Library name: 2nd Experiment_ 100th_pass_on_HFF_2


title: HCT116 cells, control, cytoplasmic RNA rep3


title: 2nd Experiment_ 100th_pass_on_HFF_1

description: Library name: 2nd Experiment_ 100th_pass_on_HFF_1


title: 2nd Experiment_ 2nd_pass_on_MDBK_2

description: Library name: 2nd Experiment_ 2nd_pass_on_MDBK_2


title: HCT116 cells, SON-depleted, nuclear RNA rep2

value: nuclear RNA


title: 2nd Experiment_ 2nd_pass_on_HFF_2

description: Library name: 2nd Experiment_ 2nd_pass_on_HFF_2


title: HCT116 cells, SON-depleted, cytoplasmic RNA rep1


title: HCT116 cells, SON-depleted, nuclear RNA rep1


title: 2nd Experiment_ 2nd_pass_on_MDBK_1

description: Library name: 2nd Experiment_ 2nd_pass_on_MDBK_1


title: 2nd Experiment_ In_vivo_2

description: Library name: 2nd Experiment_ In_vivo_2

source_name: Parasites from an infected mouse brain

value: Parasites from an infected mouse brain


title: HCT116 cells, SON-depleted, nuclear RNA rep3

value: SON-HaloTag


title: 2nd Experiment_ In_vivo_1

description: Library name: 2nd Experiment_ In_vivo_1


title: 2nd Experiment_ 2nd_pass_on_HFF_1

description: Library name: 2nd Experiment_ 2nd_pass_on_HFF_1


title: HCT116 cells, control, nuclear RNA rep3


title: HCT116 cells, control, cytoplasmic RNA rep2


title: HCT116 cells, control, cytoplasmic RNA rep1


title: HCT116 cells, SON-depleted, RNAPIIser2p CUT & RUN, rep3

data_processing:
Illumina base calling, demultiplexing and FASTQ conversion
Read alignment to the human genome (GRCh38 assembly) using bowtie2
Read alignments (.bam files) converted to bigWigs using bamCoverage 3.5.1
Assembly: hg38
Supplementary files format and content: RPKM normalized coverage in bigWig format
Library strategy: CUT&RUN

extract_protocol:
The activation of concA beads, the binding of the cells to the beads, and the binding of the antibody were carried out following the EpiCypher CUTANA™ CUT&RUN Protocol v2.1  (https://www.epicypher.com/content/documents/protocols/cutana-cut&run-protocol-2.1.pdf) with few minor changes. 500,000 cells per replicate were spun 5min at 800g at RT. Buffers have the same composition, with the addition of 1x phosStop (Roche, cat. no. 0490683700)
The library was prepared according to NEBNext® Ultra™ II DNA Library Prep Kit for Illumina® (NEB #E7645S/L) with the following modifications.The end-repair was performed in a thermal cycler, with the heated lid set to ≥ 75°C, and with the following program: 30min 20°C, 1h 50C, hold at 4°C. The two bead clean-ups were carried out using AMPure beads (Beckman coulter, cat. no. A63881), with a ratio of 1.1x and 0.9x respectively pre- and post- PCR amplification.


title: 1st Experiment_250th_pass_on_MDBK_2

description: Library name: 1st Experiment_250th_pass_on_MDBK_2


title: HCT116 cells, control, nuclear RNA rep2


title: HCT116 cells, control, nuclear RNA rep1


title: HCT116 cells, control, RNAPIIser2p CUT & RUN, rep3


title: 1st Experiment_70th_pass_on_MDBK_3

description: Library name: 1st Experiment_70th_pass_on_MDBK_3


title: 1st Experiment_250th_pass_on_MDBK_1

description: Library name: 1st Experiment_250th_pass_on_MDBK_1


title: 1st Experiment_250th_pass_on_HFF_2

description: Library name: 1st Experiment_250th_pass_on_HFF_2


title: HCT116 cells, SON-depleted, RNAPIIser2p CUT & RUN, rep2


title: 1st Experiment_250th_pass_on_HFF_1

description: Library name: 1st Experiment_250th_pass_on_HFF_1


title: 1st Experiment_70th_pass_on_MDBK_1

description: Library name: 1st Experiment_70th_pass_on_MDBK_1


title: HCT116 cells, control, RNAPIIser2p CUT & RUN, rep2


title: 1st Experiment_70th_pass_on_MDBK_2

description: Library name: 1st Experiment_70th_pass_on_MDBK_2


title: HCT116 cells, SON-depleted, RNAPIIser2p CUT & RUN, rep1


title: HCT116 cells, SON-depleted, H3K27me3 CUT & RUN, rep1


title: HCT116 cells, control, RNAPIIser2p CUT & RUN, rep1


title: HCT116 cells, SON-depleted, H3K27me3 CUT & RUN, rep3


title: HCT116 cells, SON, pA(+) RNA rep3


title: HCT116 cells, SON-depleted, H3K27me3 CUT & RUN, rep2


title: 1st Experiment_70th_pass_on_HFF_2

description: Library name: 1st Experiment_70th_pass_on_HFF_2


title: 1st Experiment_70th_pass_on_HFF_3

description: Library name: 1st Experiment_70th_pass_on_HFF_3


title: 1st Experiment_35th_pass_MDBK_2

description: Library name: 1st Experiment_35th_pass_MDBK_2


title: 1st Experiment_70th_pass_on_HFF_1

description: Library name: 1st Experiment_70th_pass_on_HFF_1


title: HCT116 cells, control, H3K27me3 CUT & RUN, rep2


title: 1st Experiment_35th_pass_on_HFF_2

description: Library name: 1st Experiment_35th_pass_on_HFF_2


title: 1st Experiment_35th_pass_MDBK_3

description: Library name: 1st Experiment_35th_pass_MDBK_3


title: HCT116 cells, control, H3K27me3 CUT & RUN, rep1


title: 1st Experiment_35th_pass_MDBK_1

description: Library name: 1st Experiment_35th_pass_MDBK_1


title: HCT116 cells, SON-depleted, H3K9me3 CUT & RUN, rep2


title: BMAC scRNA OA - 36

description: Library name: BMAC_01_142

value: Bone Marrow

value: BMAC


title: 1st Experiment_35th_pass_on_HFF_1

description: Library name: 1st Experiment_35th_pass_on_HFF_1


title: HCT116 cells, control, H3K27me3 CUT & RUN, rep3

value: control


title: HCT116 cells, SON-depleted, H3K9me3 CUT & RUN, rep1


title: 1st Experiment_35th_pass_on_HFF_3

description: Library name: 1st Experiment_35th_pass_on_HFF_3


title: HCT116 cells, control, H3K9me3 CUT & RUN, rep3


title: HCT116 cells, SON-depleted, H3K9me3 CUT & RUN, rep3


title: 1st Experiment_2nd_pass_on_MDBK

description: Library name: 1st Experiment_2nd_pass_on_MDBK

value: Toxoplasma gondii ME49 and Madin-Darby bovine kidney


title: HCT116 cells, control, H3K9me3 CUT & RUN, rep1


title: 1st Experiment_2nd_pass_on_HFF_1

description: Library name: 1st Experiment_2nd_pass_on_HFF_1


title: 1st Experiment_In_vivo

description: Library name: 1st Experiment_In_vivo


title: HCT116 cells, SON-depletion, 4sU-chase RNA rep2


title: Rad52 KO1, olaparib, replicate 3

city: St. Louis

first: Dineo

last: Khabele

state: Missouri

address: 425 S. Euclid Avenue, CB 8064

department: Obstetrics and Gynecology

institute: Washington University in St. Louis

description: Library name: sample.KO1_ola3

data_processing:
Base-calling and demultiplexing were performed using Illumina’s bcl2fastq software, with a maximum of one mismatch allowed in the index read.
RNA-seq reads were aligned to the mouse reference genome (Ensembl GRCm39.113) using STAR (v2.7.11b).
Gene-level counts were derived from uniquely aligned fragments using Subread:featureCount (v2.0.8).
Isoform expression was quantified with Salmon (v1.10.0).
Post-alignment quality control metrics, including ribosomal fraction, junction saturation, and read distribution, were assessed using RSeQC (v5.04).
Assembly: Ensembl GRCm39.113
Supplementary files format and content: The final processed data file is a tab-delimited text file
Supplementary files format and content: The columns include: raw counts, TPM, and FPKM values for each gene.

organism: Mus musculus

growth_protocol: ID8-OR cells were maintained in DMEM supplemented with 4 % fetal bovine serum (FBS), 1 x ITS, penicillin/streptomycin in humidified atmosphere with 5% CO2 at 37C.

extract_protocol:
Total RNA was harvested from cells using the RNeasy Mini Kit (Qiagen), including an on-column DNase treatment. A total of 5 to 10 µg of total RNA was used for the construction of a sequencing library.
Total RNA integrity was determined using an Agilent Bioanalyzer or 4200 Tapestation. Library preparation was performed with 5 to 10µg of total RNA with a RIN score greater than 8.0. Ribosomal RNA was depleted by poly-A selection using Oligo-dT beads (mRNA Direct kit, Life Technologies). The mRNA was then fragmented, reverse transcribed to yield cDNA using SuperScript III RT enzyme and random hexamers, and converted to ds-cDNA. The cDNA was blunt-ended, an A-base was added to the 3' ends, and Illumina sequencing adapters were ligated. Ligated fragments were then amplified for 12-15 cycles using primers incorporating unique dual index tags. Libraries were sequenced on an Illumina NovaSeq X Plus using 2x150bp paired-end reads.

treatment_protocol: One day after plating, cells were treated for 24 hours with either 1 µM Olaparib (AZD2281, Selleck Chemicals) dissolved in DMSO or with vehicle (DMSO, Sigma) alone.

value: PARP inhibitor-resistant, BRCA2-deficient mouse ovarian cancer

value: RAD52 knockout

value: olaparib

tag: batch


title: HCT116 cells, control, 4sU-chase RNA rep2


title: Rad52 KO1, olaparib, replicate 2

description: Library name: sample.KO1_ola2


title: HCT116 cells, control, 4sU-chase RNA rep1


title: HCT116 cells, SON-depletion, 4sU-chase RNA rep1


title: Scramble, olaparib, replicate 2

description: Library name: sample.Scr_ola2


title: Scramble, olaparib, replicate 3

description: Library name: sample.Scr_ola3


title: HCT116 cells, control, rep3 (re-analysis)


title: HCT116 cells, control, H3K9me3 CUT & RUN, rep2


title: Rad52 KO1, vehicle, replicate 3

description: Library name: sample.KO1_UT_3

value: DMSO


title: Rad52 KO1, vehicle, replicate 2

description: Library name: sample.KO1_UT_2


title: HCT116 cells, TRA2AB-depleted, pA(+) RNA rep2

value: TRA2A+TRA2B siRNA


title: HCT116 cells, TRA2AB-depleted, pA(+) RNA rep3


title: HCT116 cells, TRA2AB-depleted, pA(+) RNA rep1


title: HCT116 cells, control, rep1 (re-analysis)


title: HCT116 cells, control, rep2 (re-analysis)


title: Scramble, vehicle, replicate 2

description: Library name: sample.Scr_UT_2


title: Scramble, vehicle, replicate 3

description: Library name: sample.Scr_UT_3


title: Long-read RNA-seq of Cephalotaxus harringtonia: pooled young inner needles, young stem, old needles, old stem, root tips

first: Yaereen

last: Dho

address: 443 Via Ortega, Shriram Center for Biological and Chemical Engineering Room 271

department: Chemistry

institute: Stanford University

description: Library name: PacBio_pooled

data_processing:
For processing of Illumina data, the quality of raw Illumina sequencing reads was evaluated using FastQC (Babraham Bioinformatics, Babraham Institute). These reads were processed to remove adapters, barcodes, and low-quality sequences using Trimmomatic68, using the following parameters: <ILLUMINACLIP:TruSeq3-PE-2.fa:2:30:10 LEADING:5 TRAILING:5 SLIDINGWINDOW:4:5 MINLEN:50>. The trimmed reads were then re-assessed with FastQC to confirm quality. These processed Illumina sequencing reads were used to quantify each transcript abundance against PacBio Iso-Seq transcriptome.
For PacBio Iso-Seq data, the raw data were processed using the Iso-Seq 3 pipeline in SMRT® Link software (PacBio) with default settings, resulting in generation of 357,877 high quality transcript isoforms. The quality of the Iso-seq transcriptome was assessed by mapping short read Ilumina short reads to the long read transcriptome assembly using bowtie2 and through BUSCO analysis for completeness. Peptide sequences, with longest ORF identified for each transcript, were then predicted using Transdecoder, resulting in 349,712 contigs. Redundant contigs were removed using CD-HIT-EST with a cut-off at 99% identity, yielding a final PacBio Iso-Seq transcriptome of 29,163 unique transcripts. Then this final processed PacBio Iso-seq transcriptome was annotated with best-hit Pfam terms, followed by all subsequent (lower-ranked) Pfam hits. Annotations also included the best Basic Local Alignment Search Tool (BLAST) hit from Arabidopsis thaliana proteomes (via UniProt), Taxus chinensis proteomes, and Cephalotaxus hainanensis proteomes, using BLASTP. Quantification of processed Illumina reads against the processed PacBio transcriptome was performed using Kallisto with default parameters. For all downstream expression analysis, log2-transformed, TMM-normalized CPM expression values were used.
Assembly: How the transcriptome was processed is described above in data processing step.
Supplementary files format and content: csv file includes expression values for all 36 samples, represented as TMM-normalized, log2-transformed counts per million.
Supplementary files format and content: fasta file includes 29,163 unique transcripts from processed PacBio Iso-Seq data.

organism: Cephalotaxus harringtonia

growth_protocol: The plants were purchased from Forest Farms (forestfarm.com). They were grown in pots with soil, watered approximately once every week. Growth conditions consisted of ambient laboratory temperature and lighting.

extract_protocol:
Various tissues from C. harringtonia var. Fastigiata were excised from the whole plant using ethanol-sterilized scissors. For young inner needles (YIN), actively growing inner young light-green yellowish needles of 0.5-2 cm in length were harvested. Young outer needles (YON) were actively growing outer light-green needles, 1.5-3 cm in length. For young stems (YSt), light-green stems with YIN and YON of 2-3 cm in length from the tip of the stem (meristem) was harvested; all the surrounding needles were removed using a sterile scalpel. Old needles (ON) were mature, dark green needles (≥1-2 years old), 4-7 cm in length. For old stems (OSt), at least 1-2 year-old mature dark green stems (4-5 cm in length) with ON removed were collected. Before harvesting root tips (Rt), they were thoroughly washed with water, quickly rinsed with 30% ethanol, and washed again with water as a final washing step. Then, roots of 5-8 cm in length from the root tip, including the root meristem, were collected. Needles and roots, due to their thin structure, were latitudinally split into equally sized sections for paired metabolomics (feeding experiments) and transcriptomics (RNA-seq). Stems were longitudinally sectioned into equal halves for the same paired analyses. All the tissues were immediately flash frozen in liquid nitrogen and were homogenized to a fine powder under liquid nitrogen using a chilled mortar and pestle that were pre-treated with RNAse Zap RNAse Decontamination Solution (Thermo Fisher Scientific). RNA from the powdered tissue samples were extracted using RNeasy Plant Mini Kit (Qiagen) with on-column DNase digestion. RLC buffer was used as the lysis buffer. For root samples, the extracted RNA was further cleaned up using the same kit. RNA concentration and purity were measured using a NanoDrop and Qubit (Qubit® 2.0 Fluorometer), and quality was further assessed using an Agilent 2100 Bioanalyzer.
Library preparation for Illumina NovaSeq 6000 (S4 Flow cell – PE150) sequencing was performed using the NEBNext® Ultra™ II RNA Library Prep Kit for Illumina® (non-directional; New England Biolabs), as per the manufacturer instructions. Individual libraries were barcoded with internal index sets at Novogene. For fragmentation, Diagenode Bioruptor Pico was used, and inserts were size selected with NEBNext beads to have an average insert size of 150-200 bp. The PCR products were purified (AMPure XP system). The quality and size distribution of each library were confirmed with analysis using a High Sensitivity DNA chip on a 2100 Bioanalyzer (Agilent). Each library was quantified using Qubit (Qubit® 2.0 Fluorometer) and real-time PCR (Kapa). Equimolar amounts of libraries for each sample (36 total, from May 2023 feeding experiments) were pooled for paired-end sequencing within a single Novaseq 6000 lane (S4 Flow cell – PE150). For PacBio Iso-Seq libraries, only a subset of tissues from the 36 total samples was sequenced: Rt1 (root tips), Rt6 (root tips), an equal combination of Rt4 and Rt8 (root tips), an equal combination of YIN3 and YIN4 (young inner needles), an equal combination of YSt3 and OSt3 (young and old stems), and an equal combination of ON1 and ON2 (old needles). Inclusion of Rt1, Rt,6 and Rt8—tissues with active CET biosynthesis—ensured that the transcriptome contained CET biosynthetic genes. Additional tissues were included to represent all other major tissue types beyond root tips, enabling capture of complete transcripts from C. harringtonia. PacBio SMRT library preparation and sequencing were performed by QB3 Genomics, UC Berkeley, Berkeley, CA (RRID: SCR_022170) on the PacBio Sequel II System using the Sequel II 3.1 binding kit with a 30-hour movie time. RNA concentration was adjusted to <5 ng/μL using the Qubit HS RNA Kit, and RNA quality was assessed via capillary electrophoresis on an Agilent Bioanalyzer 2100 using the Eukaryotic Total RNA Pico Assay, as per the manufacturer instructions, with a 2 min denaturation at 70 C followed by a 2 min cold shock on ice in a freezer. PacBio SMRT sequencing library was prepared as described in the Iso-Seq™ Template Preparation for Sequel® Systems manual using the NEBNext® Single Cell/Low Input cDNA Synthesis & Amplification Module and the Pacific Biosciences Iso-Seq Express Oligo Kit with the barcoded primers provided in the manufacturer’s protocol for first-strand cDNA synthesis (standard purification) and PCR amplification. Barcoded cDNAs from six representative samples (containing 10 unique tissue samples as discussed above) were pooled in equimolar amounts, and a single library was prepared from this pooled cDNA using the SMRTbell Prep Kit 3.0 following the standard protocol.


title: Rad52 KO1, olaparib, replicate 1

description: Library name: sample.KO1_ola1


title: HB27, DhqSR (input)2

city: Wuhan

first: Bu

last: xuying

address: Shizishan Street

institute: Huazhong agricultural university

description: Library name: HB27 , INPUT2

data_processing:
enriched peaks identified with MACS and visualized in Integrative Genome Viewer (IGV).
Assembly: hg38
Supplementary files format and content: bigWig

organism: Thermus thermophilus HB27

growth_protocol: TB medium

extract_protocol:
DhqR protein was incubated with HB27 genomic DNA fragment and 1% methanal at 65 °C for 10 min.
Libraries were sequenced on an Illumina HiSeq 2000.

value: bacterial cell


title: HB27, DhqSR (ChIP)2

description: Library name: HB27 65, ChIP2


title: Scramble, vehicle, replicate 1

description: Library name: sample.Scr_UT_1

value: WT


title: RD6_RFL_HTO_lib3

first: Sivaranjani

last: Namasivayam

address: 33 North Drive

department: NIAID

institute: NIH

description:
Library name: Grp5_HTO_lib3
10X Genomics

data_processing:
Basecalling and demultiplexing was performed using RTA 3.4.4 a d Bc12fasrq2.20
Alignment, tagging, gene and transcript counting, and clustering analysis was performed using Cellranger 6.0.2
Assembly: Mmul_10
Supplementary files format and content: Tab separated tsv file and matrix table with gene counts for each gene and sample

organism: Macaca mulatta

source_name: Granuloma

extract_protocol:
Single cell suspensions of the granulomas were generated. Samples were filtered, hashtagged iwht BioLegend's TotalSeq A antibodies, pooled, sorted for live cells and washed prior to single cell generation
Single cell GEMs were generated using the 10X Chromium Controller and libraries were prepared according to the 10X Genomics v3.1 protocol

value: Granuloma

value: primary cells


description: Library name: In vivo_Experiment_In-vitro_HFF-adapted_2

value: Parasites from an infected tissue culture

value: Toxoplasma gondii ME49 and Human foreskin fibroblast


title: RD6_RFL_HTO_lib1

description:
Library name: Grp5_HTO_lib1
10X Genomics


title: Rad52 KO1, vehicle, replicate 1

description: Library name: sample.KO1_UT_1


title: lightorgan_SYPC_rep4

type: RNA

city: Pasadena

first: Vera

last: Beilinson

address: 1200 E. California Blvd

department: Biology and Bioengineering

institute: Caltech

hyb_protocol: standard protocol

scan_protocol: standard protocol

data_processing:
The raw data was imported into R for statistical analysis using NanoStringDiff. Normalized counts where retrieved from nSolver
The normalized_data.txt contains normalized counts form nSolver

label: not provided

organism: Euprymna scolopes

source_name: light organ, sypC

label_protocol: standard protocol

growth_protocol: Hatchling squid where exopsed for 24hr to either no bacteria (APO), wild-type (WT/SYM) bacteria, or muant bacteria (sypC)

extract_protocol: total light-organ RNA was isolated using an RNeasy Mini Kit (Qiagen, Germantown, MD, #74106) and Qiagen QIAshredder according to the manufacturer’s instructions. Samples were treated with TURBO DNase (Thermo Fisher Scientific, #AM1907) to remove DNA contamination.

treatment_protocol: At 24 hrs post exoposure, squid where preserved in RNALater at 4C overnight then at -80C until extraction.

value: light organ

value: muant bacteria (sypC)


title: RHG_RCD_HTO_lib3

description:
Library name: Grp4_HTO_lib3
10X Genomics


title: lightorgan_SYPC_rep2


title: RHG_RCD_HTO_lib2

description:
Library name: Grp4_HTO_lib2
10X Genomics


title: lightorgan_SYPC_rep3


title: lightorgan_SYPC_rep1


title: RHG_RCD_HTO_lib1

description:
Library name: Grp4_HTO_lib1
10X Genomics


title: HB27, DhqSR (input)1

description: Library name: HB27 , INPUT1


title: RED_RJH_HTO_lib3

description:
Library name: Grp3_HTO_lib3
10X Genomics


title: RD6_RFL_HTO_lib2

description:
Library name: Grp5_HTO_lib2
10X Genomics


title: lightorgan_WT_rep4

source_name: light organ, WT

value: wild-type (WT/SYM) bacteria


title: lightorgan_WT_rep3


title: lightorgan_WT_rep2


title: RED_RJH_HTO_lib2

description:
Library name: Grp3_HTO_lib2
10X Genomics


title: RML_RCK_HTO_lib2

description:
Library name: Grp2_HTO_lib2
10X Genomics


title: lightorgan_APO_rep4

source_name: light organ, APO

value: no bacteria (APO)


title: lightorgan_APO_rep3


title: HB27, DhqSR (ChIP)1

description: Library name: HB27 65, ChIP1


title: RML_RCK_HTO_lib3

description:
Library name: Grp2_HTO_lib3
10X Genomics


title: lightorgan_WT_rep1


title: RB9_RC7_HTO_lib3

description:
Library name: Grp1_HTO_lib3
10X Genomics


title: RB9_RC7_HTO_lib2

description:
Library name: Grp1_HTO_lib2
10X Genomics


title: RB9_RC7_HTO_lib1

description:
Library name: Grp1_HTO_lib1
10X Genomics


title: RD6_RFL_cDNA_lib3

description:
Library name: Grp5_cDNA_lib3
10X Genomics


title: RHG_RCD_cDNA_lib3

description:
Library name: Grp4_cDNA_lib3
10X Genomics


title: RD6_RFL_cDNA_lib1

description:
Library name: Grp5_cDNA_lib1
10X Genomics


title: RED_RJH_HTO_lib1

description:
Library name: Grp3_HTO_lib1
10X Genomics


title: RHG_RCD_cDNA_lib1

description:
Library name: Grp4_cDNA_lib1
10X Genomics


title: RD6_RFL_cDNA_lib2

description:
Library name: Grp5_cDNA_lib2
10X Genomics


title: lightorgan_APO_rep2


title: lightorgan_APO_rep1


title: Severe_MalariaSample_Thrombocytopenia_2

city: Bangalore

first: Genotypic

last: technology

state: Karnataka

address: 259, Apoorva 4th cross,80 feet Road,RMV 2ND STAGE

country: India

institute: Genotypic Technology

hyb_protocol: Labeled cRNA samples were fragmented at 60°C and hybridized onto an Agilent Custom Plasmodium falciparum Gene Expression Microarray 8X60K using the Gene Expression Hybridization kit (Agilent Technologies, In situ Hybridization kit, Part Number 5190-0404)

scan_protocol: The hybridized slides were scanned using the Agilent Microarray Scanner (Agilent Technologies, Part Number G2600D)

data_processing: Data extraction from Images was done using Feature Extraction software  and Normalization of the data was done in GeneSpring GX  : 75th percentile shift  method .

organism: Plasmodium falciparum

source_name: Total RNA, Test Group 3, Sample 2

label_protocol: Samples were labeled using an Agilent Quick-Amp labeling Kit (p/n5190-0442). Total RNA was reverse transcribed at 40°C using an oligo dT primer tagged to a T7 polymerase promoter and converted to double-stranded cDNA. Synthesized double-stranded cDNA was used as the template for cRNA generation. cRNA was generated by in vitro transcription, and the dye Cy3 CTP(Agilent) was incorporated during this step. The cDNA synthesis and in vitro transcription steps were carried out at 40°C.

growth_protocol: Clinical samples collected from malaria patients

extract_protocol: RNA from enriched blood was isolated using TRIzol as per manufacture's protocols.

treatment_protocol: Total RNA was extracted from venous blood samples collected from malaria patients. The patients exhibited symptoms categorized as un-complicated (n =6), hepatic dysfunction (n=12), cerebral malaria (n=4) and thrombocytopenia (n=6).

value: Enriched blood sample

tag: clinical complication

value: Severe malaria - Thrombocytopenia


title: RML_RCK_HTO_lib1

description:
Library name: Grp2_HTO_lib1
10X Genomics


title: Severe_MalariaSample_Thrombocytopenia_3

source_name: Total RNA, Test Group 3, Sample 3


title: RED_RJH_cDNA_lib1

description:
Library name: Grp3_cDNA_lib1
10X Genomics


title: Severe_MalariaSample_Thrombocytopenia_1

source_name: Total RNA, Test Group 3, Sample 1


title: RHG_RCD_cDNA_lib2

description:
Library name: Grp4_cDNA_lib2
10X Genomics


title: RED_RJH_cDNA_lib2

description:
Library name: Grp3_cDNA_lib2
10X Genomics


title: Severe_MalariaSample_Thrombocytopenia_5

source_name: Total RNA, Test Group 3, Sample 5


title: RML_RCK_cDNA_lib2

description:
Library name: Grp2_cDNA_lib2
10X Genomics


title: Scramble, olaparib, replicate 1

description: Library name: sample.Scr_ola1

value: PARP inhibitor-resistant, BRCA2-deficient mouse ovarian cancer


title: RML_RCK_cDNA_lib3

description:
Library name: Grp2_cDNA_lib3
10X Genomics


title: Severe_MalariaSample_Thrombocytopenia_6

source_name: Total RNA, Test Group 3, Sample 6


title: Severe_MalariaSample_Thrombocytopenia_4

source_name: Total RNA, Test Group 3, Sample 4


title: RML_RCK_cDNA_lib1

description:
Library name: Grp2_cDNA_lib1
10X Genomics


title: Severe_MalariaSample_CerebralMalaria_1

source_name: Total RNA, Test Group 2, Sample 1

value: Severe malaria - Cerebral Malaria


title: RED_RJH_cDNA_lib3

description:
Library name: Grp3_cDNA_lib3
10X Genomics


title: RB9_RC7_cDNA_lib3

description:
Library name: Grp1_cDNA_lib3
10X Genomics


title: Severe_MalariaSample_HepaticDysfunction_11

source_name: Total RNA, Test Group 1, Sample 11

value: Severe malaria - Hepatic Dysfunction


title: Severe_MalariaSample_CerebralMalaria_4

source_name: Total RNA, Test Group 2, Sample 4


title: RB9_RC7_cDNA_lib2

description:
Library name: Grp1_cDNA_lib2
10X Genomics


title: Severe_MalariaSample_CerebralMalaria_3

source_name: Total RNA, Test Group 2, Sample 3


title: Severe_MalariaSample_HepaticDysfunction_12

source_name: Total RNA, Test Group 1, Sample 12


title: Severe_MalariaSample_CerebralMalaria_2

source_name: Total RNA, Test Group 2, Sample 2


title: RB9_RC7_cDNA_lib1

description:
Library name: Grp1_cDNA_lib1
10X Genomics


title: Sample_91_Gran55 ,DI5X_rmIFNγR1-IgG

city: Salvador

first: Artur

middle: Trancoso Lopo

last: Queiroz

address: Rua Waldemar Falcão, 121

country: Brazil

institute: Instituto Gonçalo Moniz

description: Library name: Sample_91_Gran55

data_processing:
bcl2fastq software (Illumina inc.)
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence with trimmomatic, then mapped to genome Mmul_10 version using STAR
Assembly: Mmul_10
Supplementary files format and content: tab-delimited text files include counts values for each Sample and Matrix table with raw gene counts for every gene and every sample

source_name: granuloma

extract_protocol:
RNA was isolated using the RNeasy Plus Mini Kit (50) (cat# 74134) according to the manufacturers’ recommendation (QIAGEN).
The library preparation was done using the QIAseq RNA Library Kit (QIAGEN). A total of 5ul total RNA was converted into RNA NGS libraries. Adapters containing UMIs were ligated to the RNA. Then RNA was converted to cDNA. The cDNA was amplified using PCR (22 cycles) and during the PCR indices were added. After PCR, the samples were purified. Library preparation QC was performed using either Bioanalyzer 2100 (Agilent) or TapeStation 4200 (Agilent).

value: granuloma

tag: Sex

value: M

tag: infection

value: Mtb infected


title: Severe_MalariaSample_HepaticDysfunction_9

source_name: Total RNA, Test Group 1, Sample 9


title: flox_om

city: Changchun

first: zhenhua

last: zhu

address: Xinmin  Street 71#

institute: The First Hospital of Jilin University

description:
Library name: Sample2
10× Genomics

data_processing:
Raw fastqs data were processed with CellRanger (v7.1.0) for alignment and unique molecular identifier (UMI) counting. Cells failing quality control thresholds were eliminated according to: mitochondrial gene percentage < 20% and detected genes per cell = 500–5000. Scrublet (v3.0.0) was used for doublet removal.
Assembly: Mouse mm10
Supplementary files format and content: Tab separated values files

source_name: Bone marrow

extract_protocol:
After a 2-week period, mice were humanely sacrificed, and their femurs were extracted. Bone marrow isolation via Dulbecco's Modified Eagle's Medium (DMEM) flushing yielded single-cell suspensions for downstream scRNA-seq analysis.
The Chromium Single Cell 3' Reagent Kit of the Chromium platform (10X Genomics, Pleasanton, CA) was used for sequencing in reference to the manual. The library preparation was carried out and the sequencing was executed on the Illumina NextSeq 500 system (Illumina, San Diego, CA, USA).

value: Bone marrow

value: WT

value: S. aureus


title: Sample_95_Gran59 ,DI5X_rmIFNγR1-IgG

description: Library name: Sample_95_Gran59


title: Sample_92_Gran56 ,DI5X_rmIFNγR1-IgG

description: Library name: Sample_92_Gran56


title: Severe_MalariaSample_HepaticDysfunction_6

source_name: Total RNA, Test Group 1, Sample 6


title: flox_ctrl

description:
Library name: Sample1
10× Genomics

value: PBS


title: Sample_90_Gran54 ,DI5X_rmIFNγR1-IgG

description: Library name: Sample_90_Gran54


title: Mouse E10.5 forelimbs, Tbx5 ChIP-Seq replicate 2

city: Athens

first: Douglas

last: Menke

address: 500 DW Brooks Drive

department: Genetics

institute: University of Georgia

description: Library name: mm10_E10.5_Tbx5_ChIP_R2

data_processing:
The quality of sequenced reads were evaluated with FastQC.
ENCODE Transcription Factor and Histone ChIP-Seq processing pipeline was used to identify highly reproducible (conservative) peak sets with an irreproducible discovery rate (IDR) cutoff of 0.05
Assembly: mm10
Supplementary files format and content: tab-delimited text file containing IDR peaks

source_name: forelimbs

growth_protocol: Forelimbs were collected from the E10.5 mice (outbred ICR; Envigo)

extract_protocol:
Forelimb samples were crosslinked with 1% formaldehyde, and the tissues were pre-disrupted with a probe sonicator (Branson 450) before shearing in a Bioruptor.
Sheared chromatin was incubated in Protein G Agarose Columns (Active Motif) with a human/mouse TBX5 polyclonal antibody (R&D Systems AF5918)
ChIP-seq libraries were prepared using the NEBNext Ultra II Library Prep Kit
Sera-Mag SpeedBeads were utilized to perform size selection and to remove primer and adapter fragments
Libraries were sequenced by the Georgia Genomics and Bioinformatics Core to generate single-end 75 bp reads.

value: forelimbs

value: ICR

value: E10.5 embryonic cells

value: wild type


title: Severe_MalariaSample_HepaticDysfunction_4

source_name: Total RNA, Test Group 1, Sample 4


title: cko_om

description:
Library name: Sample3
10× Genomics

value: Trim59 knock out


title: Severe_MalariaSample_HepaticDysfunction_3

source_name: Total RNA, Test Group 1, Sample 3

value: Enriched blood sample


title: Sample_96_Gran60 ,DI5X_rmIFNγR1-IgG

description: Library name: Sample_96_Gran60


title: Mouse E10.5 forelimbs, Input replicate 2

description: Library name: mm10_E10.5_Input_R2


title: Mouse E10.5 forelimbs, Tbx5 ChIP-Seq replicate 1

description: Library name: mm10_E10.5_Tbx5_ChIP_R1


title: Severe_MalariaSample_HepaticDysfunction_5

source_name: Total RNA, Test Group 1, Sample 5


title: Sample_89_Gran53 ,DI5X_rmIFNγR1-IgG

description: Library name: Sample_89_Gran53


title: Sample_88_Gran52 ,DI5X_rmIFNγR1-IgG

description: Library name: Sample_88_Gran52


title: Severe_MalariaSample_HepaticDysfunction_2

source_name: Total RNA, Test Group 1, Sample 2


title: Mouse E10.5 forelimbs, Input replicate 1

description: Library name: mm10_E10.5_Input_R1


title: WT Ipsilateral 3

city: Muenster

first: Lydia

last: Sorokin

address: Waldeyerstr. 15

institute: University of Muenster

description: Library name: WT3IL

data_processing:
FASTQ files were generated using bcl2fastq software (version v2.17.1.14 Illumina). Subsequent analysis was performed using the Galaxy program. Quality control was performed using FASTQC (version 0.72+galaxy1). The last 10 low quality reads were trimmed away. The trimmed reads (70 bp) were mapped with RNA STAR (version 2.6.0-b1) to mouse genome (mm10) with gencode vM22 gene annotation. Reads were counted with featureCounts tool (version 1.6.4). The raw counts were normalized using DESeq2 package in R program. Differentially expressed genes were detected using unadjusted p value (Wald’s test) and log2 fold change.
Assembly: mm10
Supplementary files format and content: bulk_rnaseq_raw_counts.xlsx
Supplementary files format and content: bulk_rnaseq_norm_assorted.xlsx

source_name: Brain hemisphere (without cerebellum)

extract_protocol:
Mice were transcardially perfused with ice-cold PBS. Brains were removed, the olfactory bulb and cerebellum removed, and ipsilateral and contralateral brain hemispheres were homogenized in TRIzol Reagent (Life Technologies). Brains from 2 mice per group were pooled. Differential centrifugation and washing were employed to remove blood and associated immune cells and a chloroform/phenol extraction was employed to extract RNA/DNA.
Libraries were prepared according to the manufacturer’s instructions using Chromium Single Cell 3’ Library & Gel Bead Kit v3 (10X Genomics)

value: Brain hemisphere (without cerebellum)

tag: brain hemisphere

value: Ipsilateral


title: Severe_MalariaSample_HepaticDysfunction_10

source_name: Total RNA, Test Group 1, Sample 10


title: Severe_MalariaSample_HepaticDysfunction_8

source_name: Total RNA, Test Group 1, Sample 8


title: WT Ipsilateral 2

description: Library name: WT2IL


title: Sample_87_Gran51 ,DI5X_rmIFNγR1-IgG

description: Library name: Sample_87_Gran51


title: Severe_MalariaSample_HepaticDysfunction_7

source_name: Total RNA, Test Group 1, Sample 7


title: WT Contralateral 2

description: Library name: WT2CL

value: Contralateral


title: Sample_86_Gran50 ,DI5T_rmIFNγR1-IgG

description: Library name: Sample_86_Gran50


title: WT Ipsilateral 1

description: Library name: WT1IL


title: Uncomplicated_MalariaSample_5

source_name: Total RNA, Control Sample 5

value: Uncomplicated Malaria


title: WT Contralateral 3

description: Library name: WT3CL


title: WT Contralateral 1

description: Library name: WT1CL


title: Severe_MalariaSample_HepaticDysfunction_1

source_name: Total RNA, Test Group 1, Sample 1

value: Severe malaria - Hepatic Dysfunction


title: Lama4-/- Contralateral 3

description: Library name: KO3CL


title: Sample_84_Gran48 ,DI5T_rmIFNγR1-IgG

description: Library name: Sample_84_Gran48

value: granuloma

value: M


title: Lama4-/- Ipsilateral 3

description: Library name: KO3IL


title: Uncomplicated_MalariaSample_3

source_name: Total RNA, Control Sample 3


title: Lama4-/- Ipsilateral 1

description: Library name: KO1IL


title: smad1-cKO_PGC_15-somite

city: Beijing

first: Tao

last: Zheng

state: Beijing

address: Medical Building, Tsinghua University

institute: Tsinghua University

description:
Library name: smad1-cKO_PGC_15-somite
Sheet name in samples_quantification_summary.xlsx: smad1-cKO_PGC_15-somite

data_processing:
Sequencing reads were analyzed using CRISPResso2 (v2.3.2) in “CRISPRessoPooled” mode (Clement et al., 2019), with default parameters and substitutions excluded. Notably, the parameter --min_paired_end_reads_overlap was set to 0 to retain paired-end reads even if they lacked any overlapping region. This adjustment was critical because the gRNA target sites were deliberately designed near one end of each amplicon rather than centrally, ensuring that either the forward (R1) or reverse (R2) read alone would confidently cover the target site for editing analysis.
Assembly: smad1_gRNA_target#1: gcgccacaatgaatgtcacctcactcttttccttcaccagcccggcggtcaaacgactgctgggctggaagcaaggggatgaagaagagaagtgggcagagaaggcggtggatgcactggtcaagaagttgaagaagaagaagggcgctatggaggaactagagagggcactcagctgccccggtcagccaagcaattgtgtcactatcccacgctcactggatgggaggcttcaagtatcacaccgaaaggggcttcctcacgtcatctactgccgtgtgtggcgatggcccgacctgcaatcgcaccatgagctcaaggccctagagtgctgtgagtttcct smad1_gRNA_target#2: tcctatgtaattgtgcaagtcaatgcagaatatttagtatatcctactggacatagaatagttatgtataaacaaagcaaaccttttccgatgtgacgccgggtgttttcgatggttgagttccggttgacatttgacagcagacccaggcagaagcggttgcggttgttggatgggtcagtaaagccatccacgagtacactggtggatgaggccagaaaggcttcacccacacgattattcagctcatagtacacaatggagcaccagtgcttgggttcctgataggccacaggatgaacatctgcaca smad1_gRNA_target#3: ttccaggtaaaccttgtgttcatcttgtgtacagtagcttacctttacaaaactcatgcggatggtgcacatcttggtgagttcatagacagcttcaaaaccgtgattgactgactgtgccaagagctctgcaaactcctggttgttgaagatcttgaggctgcagcgactggggatcttgcatacggtggtggggtggaaaccatggtggtaattgcagttgcggctctggacaaagatactgctgtcgctcaaacattcggcatacacctctcctcccacatagtacaaatggactcctgcagaatgtat
Supplementary files format and content: xlsx file includes quantification summary for each sample

organism: Danio rerio

source_name: PGC

growth_protocol: Zebrafish embryos were maintained in Holtfreter's water. PGCs and somatic cells were sorted using a MoFlo Astrios EQ Cell Sorter from transgenic embryos expressing fluorescent protein-labeled PGCs at desired stages.

extract_protocol:
Approximately 300 PGCs or somatic cells were isolated by FACS from 15-somite stage smad1-cKO and control sibling embryos. Genomic DNA was extracted and subjected to WGA using the Discover-sc Single Cell Kit (Vazyme, catalog no. N601-01) according to the manufacturer’s instructions. The amplified genome DNA was diluted and used as a template for PCR with Phanta Max Super-Fidelity DNA Polymerase (Vazyme, catalog no. P505) to amplify three target regions of smad1 gRNAs per sample (Primer sequences are listed in Supplementary Table 5). PCR products were purified by gel extraction.
For each group (sibling somatic cells, sibling PGCs, smad1-cKO somatic cells, and smad1-cKO PGCs), the three PCR products were pooled in equimolar amounts and used for library preparation with the NEBNext Ultra II DNA Library Prep Kit (NEB, catalog no. E7645S).

value: PGC

value: Holtfreter's water


title: Uncomplicated_MalariaSample_4

source_name: Total RNA, Control Sample 4


title: Lama4-/- Ipsilateral 2

description: Library name: KO2IL


title: Uncomplicated_MalariaSample_2

source_name: Total RNA, Control Sample 2


title: smad1-cKO_soma_15-somite

description:
Library name: smad1-cKO_soma_15-somite
Sheet name in samples_quantification_summary.xlsx: smad1-cKO_soma_15-somite

source_name: Somatic cells

value: Somatic cells


title: Sample_94_Gran58 ,DI5X_rmIFNγR1-IgG

description: Library name: Sample_94_Gran58

source_name: granuloma

value: Mtb infected


title: Lama4-/- Contralateral 2

description: Library name: KO2CL


title: Uncomplicated_MalariaSample_1

source_name: Total RNA, Control Sample 1


title: Sample_82_Gran46 ,DI5T_rmIFNγR1-IgG

description: Library name: Sample_82_Gran46


title: Tek-Cre:Lama5-/- cortex sample 2

description:
Library name: a5cx2
10x Genomics

data_processing:
The Cellranger (10x genomics) pipeline was followed to demultiplex the sequencing data, to align it to the mouse reference genome (mm10), to count the reads, and to aggregate the resulting cell-gene matrices according to sample replicates. Subsequent data analysis was performed with R package Seurat (version 3.1).
Assembly: mm10
Supplementary files format and content: matrix

source_name: Brain cortical plate

extract_protocol:
Brains were removed, minced into small pieces in ice cold DMEM (Sigma-Aldrich) and digested for 60 min at 37ºC in 30 U/ml papain (LK003153; Worthington Biochemical), 40 µg/ml DNase type IV (LS006331; Worthington Biochemical) and 0.125 mg/ml Liberase TM (5401119001; Sigma-Aldrich) in DMEM. Myelin was removed by centrifugation at 1000 x g for 10 min through 22% BSA.
Libraries were prepared according to the manufacturer’s instructions using Chromium Single Cell 3’ Library & Gel Bead Kit v3 (10X Genomics)

value: Brain cortical plate


title: Lama4-/- Contralateral 1

description: Library name: KO1CL


title: control_soma_15-somite

description:
Library name: control_soma_15-somite
Sheet name in samples_quantification_summary.xlsx: control_soma_15-somite

value: WT


title: Sample_81_Gran45 ,DI5T_rmIFNγR1-IgG

description: Library name: Sample_81_Gran45


title: Tek-Cre:Lama5-/- cortex sample 1

description:
Library name: a5cx1
10x Genomics


title: Sample_83_Gran47 ,DI5T_rmIFNγR1-IgG

description: Library name: Sample_83_Gran47


title: Sample_80_Gran44 ,DI5T_rmIFNγR1-IgG

description: Library name: Sample_80_Gran44


title: Lama4-/- cortex sample1

description:
Library name: a4_cx1
10x Genomics


title: smad1-KD_PGC_75%-epiboly_rep2

description:
Library name: smad1-KD_PGC_75-epiboly_rep2
Column name in control-MO_smad1-KD_PGC_75%-epiboly_TPM.csv:smad1-KD_PGC_75%-epiboly_rep2

data_processing:
The cleaned reads were then aligned to the zebrafish reference genome  (danRer11) using STAR (version 2.7.10b).
StringTie (version 2.2.1) was used to calculate TPM (Transcripts Per Million) values with the following parameters: stringtie -e -B -G Danio_rerio.GRCz11.108.gtf.
Assembly: Danio_rerio.GRCz11.dna.primary_assembly.fa
Supplementary files format and content: csv files include TPM values for each sample

growth_protocol: Zebrafish embryos were maintained in Holtfreter's water. PGCs were sorted using a MoFlo Astrios EQ Cell Sorter from transgenic embryos expressing fluorescent protein-labeled PGCs at desired stages.

extract_protocol:
Full-length cDNA from FACS-sorted PGCs was generated using the Single Cell Full Length mRNA-Amplification Kit (Vazyme, catalog no. N712), according to the manufacturer's manual.
For library preparation, 1 ng of cDNA was processed with the TruePrep DNA Library Prep Kit V2 (Vazyme, TD503), where adaptors were inserted via transposase reaction and tagged fragments were amplified.

value: smad1-MO injected/Holtfreter's water


title: WT cortex sample 2 (as a control for Tek-Cre:Lama5-/- mice)

description:
Library name: wt1cx2
10x Genomics


title: Lama4-/- cortex sample2

description:
Library name: a4_cx2
10x Genomics


title: control_PGC_15-somite

description:
Library name: control_PGC_15-somite
Sheet name in samples_quantification_summary.xlsx: control_PGC_15-somite


title: WT cortex sample 1 (as a control for Tek-Cre:Lama5-/- mice)

description:
Library name: wt1cx1
10x Genomics


title: smad1-KD_PGC_75%-epiboly_rep1

description:
Library name: smad1-KD_PGC_75-epiboly_rep1
Column name in control-MO_smad1-KD_PGC_75%-epiboly_TPM.csv:smad1-KD_PGC_75%-epiboly_rep1


title: Sample_79_Gran43 ,DI5T_rmIFNγR1-IgG

description: Library name: Sample_79_Gran43


title: Sample_78_Gran42 ,DI5T_rmIFNγR1-IgG

description: Library name: Sample_78_Gran42


title: control-MO_PGC_75%-epiboly_rep2

description:
Library name: control-MO_PGC_75-epiboly_rep2
Column name in control-MO_smad1-KD_PGC_75%-epiboly_TPM.csv:control-MO_PGC_75%-epiboly_rep2

value: control-MO injected/Holtfreter's water


title: SC123_HTO

city: Birmingham

first: Yong

last: Wang

state: AL

address: 1918 University Blvd

department: Cell, Developmental and Integrative Biology

institute: University of Alabama at Birmingham

description:
Library name: SC123 _HTO
10x Genomics

library_source: other

data_processing:
Raw base call files were demultiplexed into FASTQ files. Sequencing files were processed and mapped to mm10, and count matrices were extracted using the Cell Ranger Single Cell Software (v 7.1.0) .
Assembly: Mouse mm10
Supplementary files format and content: h5 files

molecule: protein

source_name: SC

extract_protocol:
Mononuclear cells were isolated for sequencing as described above with 3 CB or SC pooled per sample and sorted for CD45+CD11b+ live cells on a BD FACsAria. Sorted CD45+CD11b+ cells were resuspended in DPBS supplemented with 0.04% w/v BSA.
Single Cell 3′ Reagent Kit V3.1 was used in conjunction with TotalSeqB antibodies to generate 3' gene expression library and HTO library. Single cells and beads containing barcoded DNA oligos were captured into oil droplets to generate the gel bead-in-emulsion (GEM) by 10x Chromium controller. The poly-A RNA from the cell lysate in GEM was reverse-transcripted to cDNA. Libraries were constructed according to the manufacturer’s instructions. TotalSeq-B0301 anti mouse Hashtag1, TotalSeq-B0302 anti mouse Hashtag2, and TotalSeq-B0303 anti mouse Hashtag3 were used for Ly6GN, BT_04C, CB123, SC123 samples.

value: SC

value: CD45+CD11b+ cells

value: Socs3_Del_Ly6G  mice

value: EAE


title: SC123_GEX

description:
Library name: SC123_mRNA
10x Genomics


title: WT cortex sample 1 (as a control for Lama4-/-)

description:
Library name: cont_cx1
10x Genomics


title: Sample_77_Gran41 ,DI5T_rmIFNγR1-IgG

description: Library name: Sample_77_Gran41


title: CB123_HTO

description:
Library name: CB123_HTO
10x Genomics

source_name: CB

value: CB


title: CB123_GEX

description:
Library name: CB123_mRNA
10x Genomics

value: CD45+Cd11b+ cells


title: control-MO_PGC_75%-epiboly_rep1

description:
Library name: control-MO_PGC_75-epiboly_rep1
Column name in control-MO_smad1-KD_PGC_75%-epiboly_TPM.csv:control-MO_PGC_75%-epiboly_rep1


title: Sample_76_Gran40 ,DI3P_rmIFNγR1-IgG

description: Library name: Sample_76_Gran40


title: smad1-KD_PGC_1dpf_rep2

description:
Library name: smad1-KD_PGC_1dpf_rep2
Column name in control-MO_smad1-KD_PGC_1dpf_TPM.csv:smad1-KD_PGC_1dpf_rep2


title: BT_04C_HTO

description:
Library name: BT_04C_HTO
10x Genomics

value: Ly6G_pos_neg  mice


title: Ly6GN_HTO

description:
Library name: Ly6GN_HTO
10x Genomics

source_name: SC and CB

value: SC and CB

value: Ly6G_pos_neg and  Socs3_Del_Ly6G  mice  mice

value: naïve


title: Sample_75_Gran39 ,DI3P_rmIFNγR1-IgG

description: Library name: Sample_75_Gran39

value: granuloma

value: M


title: Ly6GN_GEX

description:
Library name: Ly6GN_mRNA
10x Genomics

value: Ly6G_pos_neg and  Socs3_Del_Ly6G  mice


title: smad1-KD_PGC_1dpf_rep1

description:
Library name: smad1-KD_PGC_1dpf_rep1
Column name in control-MO_smad1-KD_PGC_1dpf_TPM.csv:smad1-KD_PGC_1dpf_rep1

value: PGC


title: Sample_74_Gran38 ,DI3P_rmIFNγR1-IgG

description: Library name: Sample_74_Gran38

value: Mtb infected


title: Erbb2_OE_Corpus_3

city: Zurich

first: Genome

last: Informatics

address: Winterthurerstrasse 190

department: Functional Genomics Center Zurich (FGCZ)

country: Switzerland

institute: ETH ZURICH / University of Zurich

description: Library name: JH187_3_2

data_processing:
RNA-seq reads were aligned with STAR-aligner using the genome build GENCODE Mus musculus GRCm39 Release M31
Gene expression values were computed with the function featureCounts from the R package Rsubread.
Assembly: GENCODE Mus musculus GRCm39 Release M31
Supplementary files format and content: tab-delimited .txt files include 2 columns: ensemble feature identifier and count number.

source_name: Stomach corpus

extract_protocol:
Extracted using QIAGEN Rneasy mini kit following manufacturer's protocols
RNA libraries were prepared using standard Illumina protocols

value: Stomach corpus

value: Erbb2 Overexpression


title: control-MO_PGC_1dpf_rep1

description:
Library name: control-MO_PGC_1dpf_rep1
Column name in control-MO_smad1-KD_PGC_1dpf_TPM.csv:control-MO_PGC_1dpf_rep1

value: WT

value: control-MO injected/Holtfreter's water


title: control-MO_PGC_1dpf_rep2

description:
Library name: control-MO_PGC_1dpf_rep2
Column name in control-MO_smad1-KD_PGC_1dpf_TPM.csv:control-MO_PGC_1dpf_rep2


title: Erbb2_OE_Corpus_2

description: Library name: JH187_2_2


title: Ctrl_Corpus_3

description: Library name: JH187_3_1

value: Control


title: Ctrl_Corpus_2

description: Library name: JH187_2_1


title: Sample_72_Gran36 ,DI3P_rmIFNγR1-IgG

description: Library name: Sample_72_Gran36


title: Sample_73_Gran37 ,DI3P_rmIFNγR1-IgG

description: Library name: Sample_73_Gran37


title: Sample_93_Gran57 ,DI5X_rmIFNγR1-IgG

description: Library name: Sample_93_Gran57


title: Erbb2_OE_Corpus_1

description: Library name: JH187_1_2


title: Sample_71_Gran35 ,DI3P_rmIFNγR1-IgG

description: Library name: Sample_71_Gran35


title: smad1-cKO_PGC_75%-epiboly_rep3

description:
Library name: smad1-cKO_PGC_75-epiboly_rep3
Column name in control_smad1-cKO_PGC_75%-epiboly_TPM.csv: smad1-cKO_PGC_75%-epiboly_rep3

value: Holtfreter's water


title: RYBP phase disruption, rep1

city: Guangzhou

first: Chao

last: Wei

address: No.74 Zhongshan Rd.2

institute: Sun Yat-Sen University

description: Library name: Sample 47

data_processing:
The Fastq data underwent quality checking using trim_galore
subsequent alignment of paired-end reads to the MM9 reference genome was performed using STAR
Gene-specific read counts were generated using Htseq-count
Assembly: mm9
Supplementary files format and content: tab-delimited txt and bigwig files
Supplementary files format and content: tab-delimited txt and bigwig files

source_name: embryonic stem cell

growth_protocol: ESCs were cultured in ESC medium containing DMEM (Hyclone), 15% (v/v) fetal bovine serum (FBS, Hyclone), 0.1 mM β-mercaptoethanol (Sigma), 2 mM L-glutamine (Thermo Fisher), 0.1 mM nonessential amino acids (Thermo Fisher), 1% (v/v) nucleoside mix (Sigma), 1000 U/mL recombinant LIF (Millipore) in 37 C, 5% CO2 incubator.

extract_protocol:
Total RNA was extracted from cells using Trizol reagent
RNA library for RNA-seq was performed according the manufacture's protocol

treatment_protocol: Mouse Rybp-floxed ESCs (Rybp+/+) were cultured in ESC medium, RYBP-depleted ESCs (Rybp-/-) were generated by supplementing the medium with 5 μM 4-hydroxytamoxifen (4-OHT, Sigma) for 4 days.

value: embryonic stem cell


title: RYBP phase disruption, rep2

description: Library name: Sample 48


title: WT.RYBP, rep2

description: Library name: Sample 46

value: RYBPfl/fl Rosa26::CreERT2::WT RYBP overexpression


title: Sample_70_Gran34 ,DI3P_rmIFNγR1-IgG

description: Library name: Sample_70_Gran34


title: smad1-cKO_PGC_75%-epiboly_rep1

description:
Library name: smad1-cKO_PGC_75-epiboly_rep1
Column name in control_smad1-cKO_PGC_75%-epiboly_TPM.csv: smad1-cKO_PGC_75%-epiboly_rep1


title: Sample_69_Gran33 ,DI3P_rmIFNγR1-IgG

description: Library name: Sample_69_Gran33


title: Ctrl_Corpus_1

description: Library name: JH187_1_1


title: TF-AA mutation,rep2

description: Library name: Sample 44

value: TF-AA mutation


title: control_PGC_75%-epiboly_rep3

description:
Library name: control_PGC_75-epiboly_rep3
Column name in control_smad1-cKO_PGC_75%-epiboly_TPM.csv: control_PGC_75%-epiboly_rep3


title: smad1-cKO_PGC_75%-epiboly_rep2

description:
Library name: smad1-cKO_PGC_75-epiboly_rep2
Column name in control_smad1-cKO_PGC_75%-epiboly_TPM.csv: smad1-cKO_PGC_75%-epiboly_rep2


title: WT ESC,rep2

description: Library name: Sample 42

value: control


title: Tet.RYBP.DOX,rep2

description: Library name: Sample 40

value: Tet on.RYBP

value: DOX


title: Sample_67_Gran31 ,DI3P_rmIFNγR1-IgG

description: Library name: Sample_67_Gran31

value: granuloma


title: WT ESC,rep1

description: Library name: Sample 41


title: control_PGC_75%-epiboly_rep1

description:
Library name: control_PGC_75-epiboly_rep1
Column name in control_smad1-cKO_PGC_75%-epiboly_TPM.csv: control_PGC_75%-epiboly_rep1


title: control_PGC_75%-epiboly_rep2

description:
Library name: control_PGC_75-epiboly_rep2
Column name in control_smad1-cKO_PGC_75%-epiboly_TPM.csv: control_PGC_75%-epiboly_rep2


title: WT.RYBP, rep1

description: Library name: Sample 45


title: Tet.RYBP.vehicle,rep2

description: Library name: Sample 38

value: vehicle


title: Sample_66_Gran30 ,DI6N_Control IgG

description: Library name: Sample_66_Gran30

value: M


title: TF-AA mutation,rep1

description: Library name: Sample 43


title: Tet.RYBP.DOX,rep1

description: Library name: Sample 39


title: Sample_68_Gran32 ,DI3P_rmIFNγR1-IgG

description: Library name: Sample_68_Gran32


title: smad1-cKO_PGC_1dpf_rep3

description:
Library name: smad1-cKO_PGC_1dpf_rep3
Column name in control_smad1-cKO_PGC_1dpf_TPM.csv: smad1-cKO_PGC_1dpf_rep3

value: PGC


title: Tet.RYBP.vehicle,rep1

description: Library name: Sample 37


title: Sample_65_Gran29 ,DI6N_Control IgG

description: Library name: Sample_65_Gran29

value: Control IgG

value: Mtb infected


title: RYBP phase disruption, H2AK119ub1,rep2

description: Library name: Sample 36


title: smad1-cKO_PGC_1dpf_rep2

description:
Library name: smad1-cKO_PGC_1dpf_rep2
Column name in control_smad1-cKO_PGC_1dpf_TPM.csv: smad1-cKO_PGC_1dpf_rep2


title: RYBP phase disruption, H2AK119ub1,rep1

description: Library name: Sample 35


title: RYBP phase disruption, H3K4me3,rep2

description: Library name: Sample 34


title: Sample_64_Gran28 ,DI6N_Control IgG

description: Library name: Sample_64_Gran28


title: smad1-cKO_PGC_1dpf_rep1

description:
Library name: smad1-cKO_PGC_1dpf_rep1
Column name in control_smad1-cKO_PGC_1dpf_TPM.csv: smad1-cKO_PGC_1dpf_rep1


title: RYBP phase disruption, STAT3,rep2

description: Library name: Sample 32


title: Sample_63_Gran27 ,DI6N_Control IgG

description: Library name: Sample_63_Gran27


title: control_PGC_1dpf_rep3

description:
Library name: control_PGC_1dpf_rep3
Column name in control_smad1-cKO_PGC_1dpf_TPM.csv: control_PGC_1dpf_rep3


title: RYBP phase disruption, H3K4me3,rep1

description: Library name: Sample 33


title: RYBP phase disruption, STAT3,rep1

description: Library name: Sample 31


title: Sample_62_Gran26 ,DI6N_Control IgG

description: Library name: Sample_62_Gran26


title: Sample_61_Gran25 ,DI6N_Control IgG

description: Library name: Sample_61_Gran25


title: control_PGC_1dpf_rep1

description:
Library name: control_PGC_1dpf_rep1
Column name in control_smad1-cKO_PGC_1dpf_TPM.csv: control_PGC_1dpf_rep1


title: RYBP phase disruption, WDR5,rep1

description: Library name: Sample 27


title: Sample_60_Gran24 ,DI6N_Control IgG

description: Library name: Sample_60_Gran24


title: RYBP phase disruption, RING1B,rep2

description: Library name: Sample 30


title: RYBP phase disruption, WDR5,rep2

description: Library name: Sample 28


title: RYBP phase disruption, Input

description: Library name: Sample 26


title: control_PGC_1dpf_rep2

description:
Library name: control_PGC_1dpf_rep2
Column name in control_smad1-cKO_PGC_1dpf_TPM.csv: control_PGC_1dpf_rep2


title: WT cortex sample 2 (as a control for Lama4-/-)

description:
Library name: cont_cx2
10x Genomics

value: Brain cortical plate


title: WT.RYBP, H3K4me3,rep2

description: Library name: Sample 23


title: 22Rv1-dTAG-FOXA1 cells (Input)

city: La Jolla

first: Lauren

last: Hargis

address: 10650 N Torrey Pines Road, BCC526

institute: Scripps Research Institute

description: Library name: 22Rv1-dTAG-FOXA1, INPUT

data_processing:
Sequencing reads were aligned to human genome build hg19 and RefSeq genes by Bowtie2 with the following parameters: -N 1 -p 10 -x.
Using the unenriched input sample as background, the signal-enriched regions were identified by Model-based Analysis of ChIP-seq (MACS) peak-finding algorithm (v1.4.1) with the P value threshold of 1e-9.
Assembly: hg19
Supplementary files format and content: Genome-wide signal tracks in WIG format (.wig.gz) generated from hg19-aligned ChIP-seq BAM files using MACS. WIG files represent normalized read density (signal pileup) across the genome and are compressed using gzip. These files can be visualized in genome browsers (e.g., IGV or UCSC Genome Browser) to inspect ChIP-seq signal enrichment.

source_name: Prostate

extract_protocol:
Cells were washed with PBS, trypsinized, and crosslinked with 1.1 % formaldehyde (final) in 50 mM HEPES pH 7.5, 100 mM NaCl, 1 mM EDTA, and 0.5 mM EGTA for 10 minutes at room temperature. Crosslinking was quenched with 125 mM glycine for 5 minutes. Cells were washed three times with ice-cold PBS and snap-frozen at –80 °C until processing. For chromatin preparation, pellets were resuspended in Lysis Buffer 1 (LB1; 50 mM HEPES pH 7.5, 140 mM NaCl, 1 mM EDTA, 10 % glycerol, 0.5 % NP-40, 0.25 % Triton X-100, 1× Halt™ Protease Inhibitor Cocktail (Thermo Fisher)) and rotated for 10 minutes at 4 °C, followed by centrifugation at 1,400 × g for 5 minutes at 4 °C. Pellets were then washed with Lysis Buffer 2 (LB2; 10 mM Tris pH 7.5, 200 mM NaCl, 1 mM EDTA, 0.5 mM EGTA, 1× protease inhibitor) and resuspended in Sonication Buffer (50 mM HEPES pH 7.5, 140 mM NaCl, 1 mM EDTA, 1 mM EGTA, 1 % Triton X-100, 0.1 % sodium deoxycholate, 0.5 % SDS, 1× protease inhibitor). Chromatin was sheared using a Diagenode Bioruptor (25 cycles, 30 sec on/off, 10 °C). 50µL of whole cell extract (input) for the DMSO sample was moved to a new tube and stored at -20 °C until the reverse crosslinking step. Sheared chromatin was diluted to 0.1 % SDS and incubated overnight at 4 °C with antibodies conjugated to Dynabeads™ Protein G (Thermo Fisher): 10 µg FOXA1 (Novus Biologicals) or 5 µg H3K27ac (Diagenode). Beads were washed twice with Sonication Buffer (without SDS), once with High-Salt Sonication Buffer (500 mM NaCl, without SDS), once with LiCl Wash Buffer (20 mM Tris pH 7.5, 1 mM EDTA, 250 mM LiCl, 0.5 % NP-40, 0.5 % sodium deoxycholate), and once with TE + 50 mM NaCl. Bound chromatin was eluted in 200µL Elution Buffer (50 mM Tris pH 7.5, 10 mM EDTA, 1 % SDS) at 65 °C for 15 minutes. The input sample was thawed and 150µL of elution buffer was added before crosslinking with the other samples at 65 °C overnight (13 h). Samples were treated sequentially with 8µL 10mg/mL RNase A (37 °C, 2 h), 7µL of 300mM CaCl2 in 10mM Tris at pH 8, and 4µL 20mg/mL Proteinase K (55 °C, 30 min), followed by extraction with phenol:chloroform:isoamyl alcohol (25:24:1). The aqueous phase was isolated and DNA precipitated at -80 °C for 2-3 h.
DNA fragments (300-500 bp) were purified and processed for library preparation using the ThruPLEX® DNA-seq Kit (Takara Bio), indexed with DNA Unique Dual Index Kit -24U Set A (Takara), cleaned with AMPure XP beads (Beckman Coulter), and sequenced on an Illumina NextSeq 2000 (single-end, 75 bp).

value: Prostate

value: prostate carcinoma epithelial cell

value: DMSO

tag: chip-seq antibody


title: WT.RYBP, STAT3,rep2

description: Library name: Sample 21


title: 22Rv1-dTAG-FOXA1, DMSO, H3K27ac (ChIP)

description: Library name: 22Rv1-dTAG-FOXA1_DMSO, H3K27ac ChIP

value: H3K27ac (Diagenode, Cat#:C15410196)


title: Sample_58_Gran22 ,DI6N_Control IgG

description: Library name: Sample_58_Gran22


title: Sample_57_Gran21 ,DI6N_Control IgG

description: Library name: Sample_57_Gran21


title: 22Rv1-dTAG-FOXA1, dTAGv1, FOXA1 (ChIP)

description: Library name: 22Rv1-dTAG-FOXA1_dTAGv1, FOXA1 ChIP

value: 500nM dTAGv1

value: FOXA1 (Novus Biologicals, Cat#:NBP2-45354)


title: WT.RYBP, H2AK119ub1,rep2

description: Library name: Sample 25

value: embryonic stem cell

value: RYBPfl/fl Rosa26::CreERT2::WT RYBP overexpression


title: 22Rv1-dTAG-FOXA1, dTAGv1, H3K27ac (ChIP)

description: Library name: 22Rv1-dTAG-FOXA1_dTAGv1, H3K27ac ChIP


title: WT.RYBP, H2AK119ub1,rep1

description: Library name: Sample 24


title: WT.RYBP, RING1B,rep1

description: Library name: Sample 18


title: WT.RYBP, RING1B,rep2

description: Library name: Sample 19


title: WT.RYBP, H3K4me3,rep1

description: Library name: Sample 22


title: Sample_59_Gran23 ,DI6N_Control IgG

description: Library name: Sample_59_Gran23


title: Sample_56_Gran20 ,DI5F_Control IgG

description: Library name: Sample_56_Gran20


title: BT_04C_GEX

description:
Library name: BT_04C_mRNA
10x Genomics

value: SC

value: CD45+CD11b+ cells

value: Ly6G_pos_neg mice

value: EAE


title: RYBP phase disruption, RING1B,rep1

description: Library name: Sample 29


title: Sample_55_Gran19 ,DI5F_Control IgG

description: Library name: Sample_55_Gran19

value: granuloma

value: M


title: fish_SON_siSON_rep3

first: IBRAHIM

last: ILIK

address: Ihnestraße 63-73

institute: Max-Planck-Institut für molekulare Genetik

description: Library name: fishSON_siSON_rep3

data_processing:
Base calling, demultiplexing and FASTQ conversion
Read alignment to the human genome (GRCh38 assembly) using STAR 2.7.9a
Read alignments (.bam files) converted to bigWigs using bamCoverage 3.5.1
Assembly: hg38
Supplementary files format and content: RPKM normalized RNA-seq coverage in bigWig format

source_name: Flp-In T-Rex HEK293

extract_protocol:
Total RNA was extracted from cells with Quick-RNA MicroPrep kit (Zymo) after fractionation. Polyadenylated RNA was then isolated using Dynabeads™ mRNA Purification Kit. Purification was done twice to increase purity.
Strand-specific libraries were generated using KAPA Stranded RNA-seq Library Preparation Kit (Roche)

value: Flp-In T-Rex HEK293

value: siRNA against SON


title: WT.RYBP, Input

description: Library name: Sample 15


title: WT.RYBP, WDR5,rep1

description: Library name: Sample 16


title: fish_SON_siSON_rep2

description: Library name: fishSON_siSON_rep2


title: Sample_54_Gran18 ,DI5F_Control IgG

description: Library name: Sample_54_Gran18

value: Control IgG

value: Mtb infected


title: WT.RYBP, STAT3,rep1

description: Library name: Sample 20


title: TF-AA mutation, STAT3,rep2

description: Library name: Sample 14

value: TF-AA mutation


title: Sample_53_Gran17 ,DI5F_Control IgG

description: Library name: Sample_53_Gran17


title: TF-AA mutation, RING1B,rep2

description: Library name: Sample 12


title: WT.RYBP, WDR5,rep2

description: Library name: Sample 17


title: fish_SON_siSON_rep1

description: Library name: fishSON_siSON_rep1


title: TF-AA mutation, WDR5,rep2

description: Library name: Sample 10


title: TF-AA mutation, RING1B,rep1

description: Library name: Sample 11


title: Sample_52_Gran16 ,DI5F_Control IgG

description: Library name: Sample_52_Gran16


title: TF-AA mutation, WDR5,rep1

description: Library name: Sample 9


title: fly_SON_siSON_rep3

description: Library name: FeSHn470_siSON_rep3


title: WT ESC, STAT3,rep2

description: Library name: Sample 7

value: WT

value: control


title: TF-AA mutation, Input

description: Library name: Sample 8


title: WT ESC, STAT3,rep1

description: Library name: Sample 6


title: fly_SON_siSON_rep2

description: Library name: FeSHn470_siSON_rep2


title: Sample_50_Gran14 ,DI5F_Control IgG

description: Library name: Sample_50_Gran14


title: Sample_51_Gran15 ,DI5F_Control IgG

description: Library name: Sample_51_Gran15


title: fly_SON_siSON_rep1

description: Library name: FeSHn470_siSON_rep1


title: Sample_49_Gran13 ,DI5F_Control IgG

description: Library name: Sample_49_Gran13


title: WT ESC, RING1B,rep2

description: Library name: Sample 5


title: WT ESC, WDR5,rep2

description: Library name: Sample 3


title: SON_deltaC-term_siSON_rep3

description: Library name: FeSHn468_siSON_rep3


title: WT ESC, WDR5,rep1

description: Library name: Sample 2


title: WT ESC, Input

description: Library name: Sample 1


title: WT ESC, RING1B,rep1

description: Library name: Sample 4


title: SON_deltaC-term_siSON_rep2

description: Library name: FeSHn468_siSON_rep2


title: Sample_48_Gran12 ,DI5F_Control IgG

description: Library name: Sample_48_Gran12


title: Sample_47_Gran11 ,DI5F_Control IgG

description: Library name: Sample_47_Gran11