title: PTRH8_S16

city: Syracuse

first: Frank

last: Middleton

state: NY

address: 505 Irving Avenue

department: Neuroscience and Physiology

institute: SUNY Upstate Medical Univ

data_processing:
BaseSpace
Sequence reads were trimmed for adaptor sequence
Trimmed reads were mapped to hg38 transcriptome of the human genome using Salmon
Feature count mapping and filtering were performed in Partek Flow from quantified count data
TPM + 1, then quantile normalization, and log 2 transformation of filtered count data
Assembly: hg38
Supplementary files format and content: 2 tab-delimited text matrix files includes raw filtered Salmon feature counts and TPM quantile normalized values for all samples

extract_protocol:
Zymo Quick-RNA Viral Kit (R1035-E), with elution in 20 uL of nuclease free water or the Thermo MagMax Viral/Pathogen Nucleic Acid kit with the KingFisher instrument, with elution in 50 uL of nuclease free water.
Sequencing library preparation was done with the Illumina TruSeq Stranded Total RNA with RiboZero Gold kit following manufacturer's instructions.

tag: infection

value: Y

tag: vaccination

value: Male


title: HEK_icSHAPE_AS_Gadd45a_SINEB2a_del_92-101_NAI_rep1

status: Public on Sep 19 2023

type: SRA

city: Yokohama

first: Harshita

last: Sharma

state: Kanagawa

address: 1-7-22 Suehiro-cho, Tsurumi-ku

department: Division of Genomic Medicine

country: Japan

institute: RIKEN Center for Integrative Medical Sciences

library_source: transcriptomic

data_processing:
Standard icSHAPE bioinformatics pipeline was used (PMID:26766114).
After PCR duplicates removal and adapter (13 nt from 5ʹ end) trimming, sequencing reads were mapped to custom index of antisense Gadd45α SINEB2-a deletion mutants transcripts using Bowtie2. The mapping was focused on the region starting from 1 bp upstream of the SINE element till 88 bp downstream of it (to encompass all the reads with in SINE region). Following the icSHAPE pipeline, RT stops were calculated and normalized, and subsequently enrichment reactivity scores were calculated for each base by subtracting the background signal (DMSO data).
Assembly: Custom index:  >AS-Gadd45a-SINEB2a-del-27-36 GCAGCGACATCAGAAGAGGATATTGGAGATGGTTGAAGGCCACCATGTCGTTGCTGGGAATGAACTCAAGACCTCTGGAAGAGCAGTCAGTGCTCTTAACCTCTGAGCCATCTCTCCAGCCCATCGATGTCTCTTAAAAAACAAACAAACGAACGAACAGCAAGGGAGCTGGGTATGACAACACATACTATAATTCTAGTACTCAGGATG >AS-Gadd45a-SINEB2a-del-40-50 GCAGCGACATCAGAAGAGGATATTGGATCCCATTACAGATACCATGTCGTTGCTGGGAATGAACTCAAGACCTCTGGAAGAGCAGTCAGTGCTCTTAACCTCTGAGCCATCTCTCCAGCCCATCGATGTCTCTTAAAAAACAAACAAACGAACGAACAGCAAGGGAGCTGGGTATGACAACACATACTATAATTCTAGTACTCAGGATG >AS-Gadd45a-SINEB2a-del-66-76 GCAGCGACATCAGAAGAGGATATTGGATCCCATTACAGATGGTTGAAGGCCACCATGTCGTTGCTGAAGACCTCTGGAAGAGCAGTCAGTGCTCTTAACCTCTGAGCCATCTCTCCAGCCCATCGATGTCTCTTAAAAAACAAACAAACGAACGAACAGCAAGGGAGCTGGGTATGACAACACATACTATAATTCTAGTACTCAGGATG >AS-Gadd45a-SINEB2a-del-92-101 GCAGCGACATCAGAAGAGGATATTGGATCCCATTACAGATGGTTGAAGGCCACCATGTCGTTGCTGGGAATGAACTCAAGACCTCTGGAAGACTCTTAACCTCTGAGCCATCTCTCCAGCCCATCGATGTCTCTTAAAAAACAAACAAACGAACGAACAGCAAGGGAGCTGGGTATGACAACACATACTATAATTCTAGTACTCAGGATG
Supplementary files format and content: Valid enrichment reactivity score for each base of SINEB2. Format: Each base position is represented by a different row. Columns 1-4 correspond to SINE-transcript name, position of each base, valid enrichment reactivity score for each modified base (bases with null values were not detected by icSHAPE), and sequence of the modified base.
Library strategy: icSHAPE

molecule: total RNA

organism: Homo sapiens

growth_protocol: HEK293T/17 cells were grown in 6-well culture dish in DMEM (1×) + GlutaMAX-1 supplemented with 10% fetal bovine serum and 1% penicillin streptomycin solution at 37°C, 5% CO2 until ~80% confluent.

extract_protocol:
Total RNA was extracted using RNeasy Mini Kit (Qiagen) and digested with DNaseI to remove DNA contamination. Purified RNA was ribo-depleted and used for further library construction.
icSHAPE library preparation protocol was followed (PMID:26766114). Briefly, ribo-depleted RNA was biotin-clicked, fragmented and end-repaired. Next, RNA was 3' end ligated followed by cDNA synthesis and circularization. Final library was PCR amplified.

treatment_protocol: Different antisense Gadd45α SINEB2-a deletion mutants in SINEUP-EGFP constructs were co-transfected with pEGFP-C2 in 10-cm plates. 24 h post-transfection, 20 million cells were treated with either NAI-N3 or DMSO (mock) following the icSHAPE protocol (PMID:26766114).

tag: cell line

tag: cell type

value: Human embryonic kidney cell line

tag: treatment

value: Co-transfection with AS Gadd45a SINEB2a {delta}92-101 SINEUP-GFP and pEGFP-C2


title: HEK_icSHAPE_AS_Gadd45a_SINEB2a_del_92-101_DMSO_rep1

value: DMSO (mock)


title: PTRH6_S16

middle: A

country: USA

value: N

tag: age

tag: strain

tag: Sex


title: PTRH4_S8


title: PTRH5_S8

value: Female


title: HEK_icSHAPE_AS_Gadd45a_SINEB2a_del_66-76_DMSO_rep1

value: Co-transfection with AS Gadd45a SINEB2a {delta}66-76 SINEUP-GFP and pEGFP-C2


title: PTRH3_S16


title: PTRH1_S8


title: PTRH2_S8


title: PTRH11_S16

source_name: CONTROL

value: CONTROL


title: PTRH7_S8


title: PTRH10_S12


title: PTRG9_S7


title: PTRH9_S8


title: PTRG8_S15


title: PTRG7_S7


title: PTRG6_S15


title: PTRG3_S15


title: PTRG11_S15


title: PTRF9_S6


title: PTRG2_S7


title: PTRG10_S11


title: PTRF7_S6


title: PTRF8_S14


title: PTRG1_S7


title: PTRG5_S7


title: PTRF6_S14


title: PTRF5_S6


title: PTRF11_S14


title: PTRF10_S10


title: PTRE8_S13


title: PTRF3_S14


title: PTRE10_S9


title: PTRE5_S5


title: PTRE7_S5


title: PTRF2_S6


title: PTRD9_S4


title: PTRF1_S6


title: PTRE9_S5


title: PTRE11_S13


title: PTRE1_S5


title: PTRE4_S5


title: PTRD8_S12


title: PTRD6_S12


title: PTRD5_S4


title: PTRD4_S4


title: PTRD12_S16


title: PTRE6_S13


title: PTRD2_S4


title: PTRD1_S4


title: PTRF4_S6


title: PTRCH2_S16


title: PTRD11_S12


title: PTRD7_S4


title: PTRE3_S13


title: PTRE2_S5


title: PTRCG2_S15


title: PTRCF1_S6


title: PTRCG1_S7


title: PTRD3_S12


title: PTRD10_S12


title: PTRCD2_S12


title: PTRCC1_S3


title: PTRCF2_S14


title: PTRCE2_S13


title: PTRCD1_S4


title: PTRCB2_S10


title: PTRCE1_S5


title: PTRC7_S3


title: PTRC8_S11


title: PTRC9_S3


title: PTRC6_S11


title: PTRCA1_S1


title: PTRCC2_S11


title: PTRCB1_S2


title: PTRCA2_S9


title: PTRC4_S3


title: PTRC3_S11


title: PTRC2_S3


title: PTRC5_S3


title: PTRC12_S15


title: PTRC11_S11


title: PTRC10_S11


title: PTRCH1_S8


title: PTRC1_S3


title: PTRB9_S2


title: PTRB8_S10


title: PTRB2_S2


title: PTRB5_S14


title: PTRB3_S10


title: PTRB1_S2


title: PTRB4_S2


title: PTRB11_S10


title: PTRB6_S10


title: PTRA8_S9


title: PTRB7_S2


title: PTRB10_S10


title: PTRA4_S1


title: PTRA5_S1


title: PTRA9_S1


title: PTRA3_S9


title: PTRB12_S14


title: PTRA11_S9


title: OMEXH6_S48


title: PTRA1_S1


title: PTRA2_S1


title: OMEXH5_S40


title: OMEXH4_S32


title: PTRA12_S13


title: PTRA10_S9


title: OMEXH2_S16


title: OMEXG6_S47


title: OMEXH1_S8


title: OMEXG5_S39


title: PTRA7_S1


title: OMEXG3_S23


title: OMEXG1_S7


title: OMEXG2_S15


title: OMEXF6_S46


title: OMEXF3_S22


title: OMEXE6_S45


title: OMEXG4_S31


title: OMEXF4_S30


title: OMEXF2_S14


title: OMEXH3_S24


title: OMEXD4_S28


title: OMEXE3_S21


title: OMEXD3_S20


title: OMEXE4_S29


title: OMEXD2_S12


title: OMEXC6_S43


title: OMEXD5_S36


title: OMEXD6_S44


title: OMEXC5_S35


title: OMEXF1_S6


title: PTRA6_S9


title: OMEXC3_S19


title: OMEXE1_S5


title: OMEXC4_S27


title: OMEXF5_S38


title: OMEXC1_S3


title: OMEXE5_S37


title: OMEXB6_S42


title: OMEXE2_S13


title: OMEXA6_S41


title: OMEXB4_S26


title: OMEXB3_S18


title: OMEXA4_S25


title: OMEXD1_S4


title: OMEXB1_S2


title: OMEXA5_S33


title: OMEXA3_S17


title: DeltaH1


title: OMEXA1_S1


title: OMEXA2_S9


title: DeltaG3


title: DeltaG2


title: DeltaF4


title: DeltaG4


title: DeltaH2


title: DeltaF1


title: DeltaF3


title: DeltaF2


title: OMEXC2_S11


title: DeltaE4


title: DeltaE3


title: OMEXB5_S34


title: DeltaE2


title: DeltaD4


title: OMEXB2_S10


title: DeltaD3


title: DeltaD1


title: DeltaH4


title: DeltaC4


title: DeltaH3


title: DeltaC2


title: DeltaA4


title: DeltaB2


title: DeltaA3


title: DeltaB4


title: DeltaG1


title: DeltaB3


title: DeltaA1


title: BA5H5


title: BA5H2


title: DeltaC1


title: BA5H4


title: DeltaA2


title: BA5H1


title: BA5G6


title: BA5H3


title: BA5G5


title: BA5G4


title: BA5H6


title: DeltaC3


title: BA5G3


title: BA5G2


title: BA5F6


title: BA5F4


title: DeltaB1


title: BA5F2


title: BA5F3


title: DeltaD2


title: BA5F1


title: BA5G1


title: BA5E3


title: BA5E5


title: BA5E2


title: BA5E6


title: BA5E4


title: BA5D5


title: BA5D6


title: BA5E1


title: BA5D2


title: BA5D4


title: BA5D1


title: BA5C6


title: BA5C5


title: BA5C3


title: BA5F5


title: BA5C2


title: BA5C4


title: BA5B4


title: BA5B5


title: BA5B6


title: BA5C1


title: BA5B3


title: BA5B2


title: BA5B1


title: BA5A5


title: BA5A6


title: BA5A4


title: BA5A3


title: BA5A2


title: BA5D3


title: BA2H3


title: BA2H4


title: BA2H1


title: BA5A1


title: BA2H2


title: BA2F2


title: BA2F4


title: BA2G1


title: BA2F1


title: BA2G2


title: BA2F3


title: BA2E4


title: BA2E1


title: BA2E3


title: BA2E2


title: BA2D1


title: BA2D4


title: BA2D3


title: BA2C4


title: BA2D2


title: BA2G4


title: BA2C3


title: BA2C1


title: BA2B4


title: BA2B3


title: BA2B2


title: BA2A4


title: BA2A3


title: BA2C2


title: BA2B1


title: BA2G3


title: OMEXG6_S47

description:
matrix includes transcript ID, gene ID, and values for each sample ID
sample153

data_processing:
Partek Flow
Sequence reads were trimmed for adaptor sequence/low-quality sequence using Cutadapt 1.2.1
Trimmed sequence reads were quantified to hg38 Ensembl transcripts release 105 using Salmon, using minimum assigned fragments of 10, minimum score fraction of 0.65, match value 2, mismatch value -4, gap opening value 6 and gap extension value of 2
Quantified features were filtered to eliminate those with less than 1 count in 80% or more of the samples
Normalization performed on filtered features using TPM followed by quantile and log2 transformation
Assembly: Homo sapiens hg38
Supplementary files format and content: Tab-separated values matrix file containing raw Salmon feature counts
Supplementary files format and content: Tab-separated matrix file containing filtered and normalized feature abundances

source_name: saliva

extract_protocol:
RNA was purified from saliva swabs used for clinical PCR COVID-19 testing, using Zymo Quick-RNA Viral 96 Kit or the KingFisher MagMAX Viral/Pathogen Nucleic Acid Isolation Kit
RNA-seq libraries were synthesized using TruSeq Stranded Total RNA with Ribo-Zero Globin (Illumina) according to manufacturer protocol

tag: tissue

value: saliva

tag: group

value: Control-Vax

tag: race

value: Unknown/Other

tag: ethnicity


title: OMEXH6_S48

description:
matrix includes transcript ID, gene ID, and values for each sample ID
sample159

value: White or Caucasian


title: OMEXH5_S40

description:
matrix includes transcript ID, gene ID, and values for each sample ID
sample158

value: Not Hispanic


title: OMEXH3_S24

description:
matrix includes transcript ID, gene ID, and values for each sample ID
sample156

value: Infected-Unvax

value: Black or African American


title: OMEXH2_S16

description:
matrix includes transcript ID, gene ID, and values for each sample ID
sample155

value: Infected-Vax


title: OMEXH4_S32

description:
matrix includes transcript ID, gene ID, and values for each sample ID
sample157


title: OMEXG5_S39

description:
matrix includes transcript ID, gene ID, and values for each sample ID
sample152

value: Hispanic


title: OMEXG4_S31

description:
matrix includes transcript ID, gene ID, and values for each sample ID
sample151


title: OMEXG3_S23

description:
matrix includes transcript ID, gene ID, and values for each sample ID
sample150

value: Male


title: OMEXG2_S15

description:
matrix includes transcript ID, gene ID, and values for each sample ID
sample149


title: OMEXH1_S8

description:
matrix includes transcript ID, gene ID, and values for each sample ID
sample154


title: OMEXG1_S7

description:
matrix includes transcript ID, gene ID, and values for each sample ID
sample148


title: OMEXF5_S38

description:
matrix includes transcript ID, gene ID, and values for each sample ID
sample146


title: OMEXF6_S46

description:
matrix includes transcript ID, gene ID, and values for each sample ID
sample147


title: OMEXF3_S22

description:
matrix includes transcript ID, gene ID, and values for each sample ID
sample144


title: OMEXF2_S14

description:
matrix includes transcript ID, gene ID, and values for each sample ID
sample143


title: OMEXF4_S30

description:
matrix includes transcript ID, gene ID, and values for each sample ID
sample145


title: OMEXE6_S45

description:
matrix includes transcript ID, gene ID, and values for each sample ID
sample141


title: OMEXE3_S21

description:
matrix includes transcript ID, gene ID, and values for each sample ID
sample138


title: OMEXE4_S29

description:
matrix includes transcript ID, gene ID, and values for each sample ID
sample139


title: OMEXF1_S6

description:
matrix includes transcript ID, gene ID, and values for each sample ID
sample142

value: Asian


title: OMEXE5_S37

description:
matrix includes transcript ID, gene ID, and values for each sample ID
sample140


title: BA2A2

value: Y


title: BA2A1


title: OMEXE2_S13

description:
matrix includes transcript ID, gene ID, and values for each sample ID
sample137


title: OMEXE1_S5

description:
matrix includes transcript ID, gene ID, and values for each sample ID
sample136


title: OMEXD4_S28

description:
matrix includes transcript ID, gene ID, and values for each sample ID
sample133


title: OMEXD1_S4

description:
matrix includes transcript ID, gene ID, and values for each sample ID
sample130


title: OMEXC4_S27

description:
matrix includes transcript ID, gene ID, and values for each sample ID
sample127


title: OMEXD3_S20

description:
matrix includes transcript ID, gene ID, and values for each sample ID
sample132


title: OMEXD5_S36

description:
matrix includes transcript ID, gene ID, and values for each sample ID
sample134


title: OMEXD2_S12

description:
matrix includes transcript ID, gene ID, and values for each sample ID
sample131


title: OMEXC1_S3

description:
matrix includes transcript ID, gene ID, and values for each sample ID
sample124


title: OMEXC2_S11

description:
matrix includes transcript ID, gene ID, and values for each sample ID
sample125


title: OMEXC3_S19

description:
matrix includes transcript ID, gene ID, and values for each sample ID
sample126


title: OMEXB6_S42

description:
matrix includes transcript ID, gene ID, and values for each sample ID
sample123


title: OMEXB5_S34

description:
matrix includes transcript ID, gene ID, and values for each sample ID
sample122


title: OMEXD6_S44

description:
matrix includes transcript ID, gene ID, and values for each sample ID
sample135


title: OMEXB4_S26

description:
matrix includes transcript ID, gene ID, and values for each sample ID
sample121


title: OMEXB2_S10

description:
matrix includes transcript ID, gene ID, and values for each sample ID
sample119

value: American Indian or Alaska Native


title: OMEXB3_S18

description:
matrix includes transcript ID, gene ID, and values for each sample ID
sample120


title: OMEXB1_S2

description:
matrix includes transcript ID, gene ID, and values for each sample ID
sample118


title: OMEXA6_S41

description:
matrix includes transcript ID, gene ID, and values for each sample ID
sample117


title: OMEXA5_S33

description:
matrix includes transcript ID, gene ID, and values for each sample ID
sample116


title: OMEXA4_S25

description:
matrix includes transcript ID, gene ID, and values for each sample ID
sample115


title: BA5H5_S40

description:
matrix includes transcript ID, gene ID, and values for each sample ID
sample79


title: BA5H4_S32

description:
matrix includes transcript ID, gene ID, and values for each sample ID
sample78


title: BA5H6_S48

description:
matrix includes transcript ID, gene ID, and values for each sample ID
sample80


title: OMEXA3_S17

description:
matrix includes transcript ID, gene ID, and values for each sample ID
sample114


title: BA5H3_S24

description:
matrix includes transcript ID, gene ID, and values for each sample ID
sample77


title: OMEXA1_S1

description:
matrix includes transcript ID, gene ID, and values for each sample ID
sample112


title: OMEXA2_S9

description:
matrix includes transcript ID, gene ID, and values for each sample ID
sample113


title: OMEXC5_S35

description:
matrix includes transcript ID, gene ID, and values for each sample ID
sample128


title: BA5H2_S16

description:
matrix includes transcript ID, gene ID, and values for each sample ID
sample76


title: OMEXC6_S43

description:
matrix includes transcript ID, gene ID, and values for each sample ID
sample129


title: BA5H1_S8

description:
matrix includes transcript ID, gene ID, and values for each sample ID
sample75


title: BA5G6_S47

description:
matrix includes transcript ID, gene ID, and values for each sample ID
sample74


title: BA5G4_S31

description:
matrix includes transcript ID, gene ID, and values for each sample ID
sample72


title: BA5G3_S23

description:
matrix includes transcript ID, gene ID, and values for each sample ID
sample71


title: BA5F6_S46

description:
matrix includes transcript ID, gene ID, and values for each sample ID
sample68


title: BA5F5_S38

description:
matrix includes transcript ID, gene ID, and values for each sample ID
sample67


title: BA5G1_S7

description:
matrix includes transcript ID, gene ID, and values for each sample ID
sample69


title: BA5G2_S15

description:
matrix includes transcript ID, gene ID, and values for each sample ID
sample70


title: BA5F4_S30

description:
matrix includes transcript ID, gene ID, and values for each sample ID
sample66


title: BA5F2_S14

description:
matrix includes transcript ID, gene ID, and values for each sample ID
sample64


title: BA5F3_S22

description:
matrix includes transcript ID, gene ID, and values for each sample ID
sample65


title: BA5E6_S45

description:
matrix includes transcript ID, gene ID, and values for each sample ID
sample62


title: BA5F1_S6

description:
matrix includes transcript ID, gene ID, and values for each sample ID
sample63


title: BA5E4_S29

description:
matrix includes transcript ID, gene ID, and values for each sample ID
sample60


title: BA5E5_S37

description:
matrix includes transcript ID, gene ID, and values for each sample ID
sample61


title: BA5E3_S21

description:
matrix includes transcript ID, gene ID, and values for each sample ID
sample59


title: BA5E2_S13

description:
matrix includes transcript ID, gene ID, and values for each sample ID
sample58


title: BA5E1_S5

description:
matrix includes transcript ID, gene ID, and values for each sample ID
sample57


title: BA5D6_S44

description:
matrix includes transcript ID, gene ID, and values for each sample ID
sample56


title: BA5D5_S36

description:
matrix includes transcript ID, gene ID, and values for each sample ID
sample55


title: BA5D4_S28

description:
matrix includes transcript ID, gene ID, and values for each sample ID
sample54


title: BA5C6_S43

description:
matrix includes transcript ID, gene ID, and values for each sample ID
sample50


title: BA5D1_S4

description:
matrix includes transcript ID, gene ID, and values for each sample ID
sample51


title: BA5D2_S12

description:
matrix includes transcript ID, gene ID, and values for each sample ID
sample52


title: BA5C5_S35

description:
matrix includes transcript ID, gene ID, and values for each sample ID
sample49


title: BA5D3_S20

description:
matrix includes transcript ID, gene ID, and values for each sample ID
sample53


title: BA5C4_S27

description:
matrix includes transcript ID, gene ID, and values for each sample ID
sample48


title: BA5G5_S39

description:
matrix includes transcript ID, gene ID, and values for each sample ID
sample73


title: BA5C1_S3

description:
matrix includes transcript ID, gene ID, and values for each sample ID
sample45


title: BA5C3_S19

description:
matrix includes transcript ID, gene ID, and values for each sample ID
sample47


title: BA5B6_S42

description:
matrix includes transcript ID, gene ID, and values for each sample ID
sample44


title: BA5C2_S11

description:
matrix includes transcript ID, gene ID, and values for each sample ID
sample46


title: BA5B4_S26

description:
matrix includes transcript ID, gene ID, and values for each sample ID
sample42


title: BA5B3_S18

description:
matrix includes transcript ID, gene ID, and values for each sample ID
sample41


title: BA5B1_S2

description:
matrix includes transcript ID, gene ID, and values for each sample ID
sample39


title: BA5B2_S10

description:
matrix includes transcript ID, gene ID, and values for each sample ID
sample40


title: BA5A6_S41

description:
matrix includes transcript ID, gene ID, and values for each sample ID
sample38


title: BA5A4_S25

description:
matrix includes transcript ID, gene ID, and values for each sample ID
sample36


title: BA5A5_S33

description:
matrix includes transcript ID, gene ID, and values for each sample ID
sample37


title: BA5A2_S9

description:
matrix includes transcript ID, gene ID, and values for each sample ID
sample34


title: BA5A1_S1

description:
matrix includes transcript ID, gene ID, and values for each sample ID
sample33


title: BA2H4_S32

description:
matrix includes transcript ID, gene ID, and values for each sample ID
sample32


title: BA2H1_S8

description:
matrix includes transcript ID, gene ID, and values for each sample ID
sample29


title: BA2G4_S31

description:
matrix includes transcript ID, gene ID, and values for each sample ID
sample28


title: BA2G3_S23

description:
matrix includes transcript ID, gene ID, and values for each sample ID
sample27


title: BA2G1_S7

description:
matrix includes transcript ID, gene ID, and values for each sample ID
sample25


title: BA2F4_S30

description:
matrix includes transcript ID, gene ID, and values for each sample ID
sample24


title: BA2F2_S14

description:
matrix includes transcript ID, gene ID, and values for each sample ID
sample22


title: BA2F1_S6

description:
matrix includes transcript ID, gene ID, and values for each sample ID
sample21


title: BA2F3_S22

description:
matrix includes transcript ID, gene ID, and values for each sample ID
sample23


title: BA2E3_S21

description:
matrix includes transcript ID, gene ID, and values for each sample ID
sample19


title: BA2E4_S29

description:
matrix includes transcript ID, gene ID, and values for each sample ID
sample20


title: BA5B5_S34

description:
matrix includes transcript ID, gene ID, and values for each sample ID
sample43


title: BA2D4_S28

description:
matrix includes transcript ID, gene ID, and values for each sample ID
sample16


title: BA2D1_S4

description:
matrix includes transcript ID, gene ID, and values for each sample ID
sample13


title: BA2E2_S13

description:
matrix includes transcript ID, gene ID, and values for each sample ID
sample18


title: BA2D2_S12

description:
matrix includes transcript ID, gene ID, and values for each sample ID
sample14


title: BA2C4_S27

description:
matrix includes transcript ID, gene ID, and values for each sample ID
sample12


title: BA2D3_S20

description:
matrix includes transcript ID, gene ID, and values for each sample ID
sample15


title: BA2E1_S5

description:
matrix includes transcript ID, gene ID, and values for each sample ID
sample17


title: BA2C3_S19

description:
matrix includes transcript ID, gene ID, and values for each sample ID
sample11


title: BA5A3_S17

description:
matrix includes transcript ID, gene ID, and values for each sample ID
sample35


title: BA2C1_S3

description:
matrix includes transcript ID, gene ID, and values for each sample ID
sample09


title: BA2B4_S26

description:
matrix includes transcript ID, gene ID, and values for each sample ID
sample08


title: BA2B3_S18

description:
matrix includes transcript ID, gene ID, and values for each sample ID
sample07


title: BA2H3_S24

description:
matrix includes transcript ID, gene ID, and values for each sample ID
sample31


title: BA2H2_S16

description:
matrix includes transcript ID, gene ID, and values for each sample ID
sample30


title: BA2B1_S2

description:
matrix includes transcript ID, gene ID, and values for each sample ID
sample05


title: BA2A3_S17

description:
matrix includes transcript ID, gene ID, and values for each sample ID
sample03


title: BA2B2_S10

description:
matrix includes transcript ID, gene ID, and values for each sample ID
sample06


title: BA2G2_S15

description:
matrix includes transcript ID, gene ID, and values for each sample ID
sample26


title: BA2A4_S25

description:
matrix includes transcript ID, gene ID, and values for each sample ID
sample04


title: BA2A2_S9

description:
matrix includes transcript ID, gene ID, and values for each sample ID
sample02


title: in situ Hi-C on globose cell of olfactory epithelium with DpnII - 4DNEXCDN8ONW

city: Boston

last: DCIC

state: MA

address: 10 Shattuck St

institute: 4D Nucleome - Data Coordination and Integration Center

description:
lab: Stavros Lomvardas, COLUMBIA
award: 1U01DA040582-01
4DN accession: 4DNEXCDN8ONW
description: HiC from globose basal cells - bioreplicate 1
submitted_by: Adan Horta
ligation_time: 240
digestion_time: 960
tagging_method: Biotin-11-GTP
experiment_type: in situ Hi-C
ligation_volume: 1.2
digestion_enzyme: DpnII
crosslinking_time: 10
biosample_quantity: 67000 cells
crosslinking_method: 1% Formaldehyde
fragmentation_method: sonication
ligation_temperature: 25
digestion_temperature: 37
crosslinking_temperature: 25
fragment_size_selection_method: SPRI beads
url: https://data.4dnucleome.org/experiments-hi-c/4DNEXCDN8ONW/

library_source: genomic

data_processing:
https://data.4dnucleome.org/resources/data-analysis/hi_c-processing-pipeline
***************
workflow_run: https://data.4dnucleome.org/workflow-runs-awsem/12a1e42c-8b0e-4f60-8c09-75c9a28d226f/
genome_assembly: GRCm38
derived_from: 4DNFITH9BEAA.bam, 4DNFI3UBJ3HZ.chrom.sizes
description: This is an output file of the Hi-C processing pipeline
file_type: contact list-replicate
file_format: pairs
file name: 4DNFI4PDERVK.pairs.gz

molecule: genomic DNA

organism: Mus musculus

source_name: biosource_summary: globose cell of olfactory epithelium

extract_protocol:
description: The Official 4DN Standard in situ Hi-C protocol adapted from Rao et al. 2014 PMID: 25497547 - with accepted deviations approved by SC 02/21/2017
download: https://data.4dnucleome.org/protocols/fdc20e37-f22e-42dc-8026-0a132739bad1/@@download/attachment/4DN_in_situ_Hi-C_protocol_20170729.pdf

treatment_protocol:
description: FACS plots for multipotent progenitors from Mash1-Cre; Rosa26-TdTomato; Ngn1-GFP mice. HiC from P6 in FACS plot
download: https://data.4dnucleome.org/protocols/8d3e8999-0b82-4406-a842-385b5ee46ef7/@@download/attachment/FACS.Mash.170802.pdf

value: globose cell of olfactory epithelium

value: olfactory epithelium

tag: description

value: FACS-sorted globose basal cells - biological replicate 1

value: mixed

value: pup

value: primary cells

tag: url


title: in situ Hi-C on olfactory receptor cell with DpnII - 4DNEX5ICY4Q2

description:
lab: Stavros Lomvardas, COLUMBIA
award: 1U01DA040582-01
4DN accession: 4DNEX5ICY4Q2
description: HiC from mature olfactory sensory neurons - bioreplicate 1
submitted_by: Adan Horta
ligation_time: 240
digestion_time: 960
tagging_method: Biotin-11-GTP
experiment_type: in situ Hi-C
ligation_volume: 1.2
digestion_enzyme: DpnII
crosslinking_time: 10
biosample_quantity: 3000000 cells
crosslinking_method: 1% Formaldehyde
fragmentation_method: sonication
ligation_temperature: 25
digestion_temperature: 37
crosslinking_temperature: 25
fragment_size_selection_method: SPRI beads
url: https://data.4dnucleome.org/experiments-hi-c/4DNEX5ICY4Q2/

data_processing:
https://data.4dnucleome.org/resources/data-analysis/hi_c-processing-pipeline
***************
workflow_run: https://data.4dnucleome.org/workflow-runs-awsem/0a6e3ef2-b16e-410d-8937-740de9ec93d6/
genome_assembly: GRCm38
derived_from: 4DNFI64U1TVD.bam, 4DNFI3UBJ3HZ.chrom.sizes
description: This is an output file of the Hi-C processing pipeline
file_type: contact list-replicate
file_format: pairs
file name: 4DNFIVN95UEZ.pairs.gz

source_name: biosource_summary: olfactory receptor cell

treatment_protocol:
description: FACS plots for mature olfactory sensory neurons from OMP-GFP mice. HiC from P3 in FACS plot
download: https://data.4dnucleome.org/protocols/6ba69564-e104-41b0-a3c9-f3df252efd45/@@download/attachment/FACS.OMP.180305.pdf

value: olfactory receptor cell

value: FACs-sorted mature olfactory sensory neurons - biological replicate 1

value: adult


title: Psoriatic Lesional Skin Replicate 3

type: RNA

city: Singapore

first: Candida

last: Vaz

address: 30 Medical drive

department: Human Development

country: Singapore

institute: Singapore Institute for Clinical Sciences

description:
Biological replicate 3 of 4. Psoriatic Lesional Skin
BP02 LS RNA

hyb_protocol: Hybridized on the miRCURU LNA microRNA array (7th Gen) using Tecan Hybridization stations and automated washing steps were performed as per manufacturers standard protocol

scan_protocol: Arrays were scanned in ozone free environment as per Exiqons standard protocol

data_processing:
The Exiqon files pertaining to the samples were imported into Partek Genomics Suite using the microRNA Expression workflow. Once imported, the data was subjected to background subtraction (normalised to baseline) and LOESS transformation. The lesional samples were then compared to the healthy samples (Lesional vs Healthy) using ANOVA.  Significant differentially expressed miRNA were obtained using p-value with FDR <0.05 and a two-fold change cut-off.
Lowess Normalized log2 ratio (Cy5/Cy3)

source_name: Psoriatic Lesional Skin

label_protocol: Samples were labled using miRCURY LNA microRNA Hi-Power Labeling Kit (Exiqon)

growth_protocol: 4mm skin biopsies were collected from Psoriatic lesional skin and healthy controls

extract_protocol: Total RNA from skin biopsies were carried out using Trizol extraction procedure combined with Exiqon miRCURY total RNA isolation kit

treatment_protocol: Biopsies were snap frozen immediately in Trizol prior to RNA isolation

tag: disease

value: Psoriatic Lesional Skin


title: in situ Hi-C on olfactory receptor cell with DpnII - 4DNEXVCPZOH3

description:
lab: Stavros Lomvardas, COLUMBIA
award: 1U01DA040582-01
4DN accession: 4DNEXVCPZOH3
description: HiC from mature olfactory sensory neurons - bioreplicate 2
submitted_by: Adan Horta
ligation_time: 240
digestion_time: 960
tagging_method: Biotin-11-GTP
experiment_type: in situ Hi-C
ligation_volume: 1.2
digestion_enzyme: DpnII
crosslinking_time: 10
biosample_quantity: 1500000 cells
crosslinking_method: 1% Formaldehyde
fragmentation_method: sonication
ligation_temperature: 25
digestion_temperature: 37
crosslinking_temperature: 25
fragment_size_selection_method: SPRI beads
url: https://data.4dnucleome.org/experiments-hi-c/4DNEXVCPZOH3/

data_processing:
https://data.4dnucleome.org/resources/data-analysis/hi_c-processing-pipeline
***************
workflow_run: https://data.4dnucleome.org/workflow-runs-awsem/53550575-f343-47d5-b252-ad5d049bbb7a/
genome_assembly: GRCm38
derived_from: 4DNFIETUPUDJ.bam, 4DNFI3UBJ3HZ.chrom.sizes
description: This is an output file of the Hi-C processing pipeline
file_type: contact list-replicate
file_format: pairs
file name: 4DNFI2HQA2EE.pairs.gz

value: FACs-sorted mature olfactory sensory neurons - biological replicate 2


title: Healthy Skin Replicate 4

description:
Biological replicate 4 of 4. Healthy Skin
Healthy BH2 RNA

source_name: Healthy Skin

value: Healthy Skin


title: Psoriatic Lesional Skin Replicate 2

description:
Biological replicate 2 of 4. Psoriatic Lesional Skin
BP04 LS RNA


title: in situ Hi-C on olfactory receptor cell with DpnII - 4DNEXH98PC96

description:
lab: Stavros Lomvardas, COLUMBIA
award: 1U01DA040582-01
4DN accession: 4DNEXH98PC96
description: HiC from conditional OMP-Cre; Ldb1-KO mature olfactory sensory neurons - bioreplicate 2
submitted_by: Adan Horta
ligation_time: 240
digestion_time: 960
tagging_method: Biotin-11-GTP
experiment_type: in situ Hi-C
ligation_volume: 1.2
digestion_enzyme: DpnII
crosslinking_time: 10
biosample_quantity: 1000000 cells
crosslinking_method: 1% Formaldehyde
fragmentation_method: sonication
ligation_temperature: 25
digestion_temperature: 37
crosslinking_temperature: 25
fragment_size_selection_method: SPRI beads
url: https://data.4dnucleome.org/experiments-hi-c/4DNEXH98PC96/

data_processing:
https://data.4dnucleome.org/resources/data-analysis/hi_c-processing-pipeline
***************
workflow_run: https://data.4dnucleome.org/workflow-runs-awsem/631a02af-d4fc-46af-a7d5-22acc58dc220/
genome_assembly: GRCm38
derived_from: 4DNFIITCV39H.bam, 4DNFI3UBJ3HZ.chrom.sizes
description: This is an output file of the Hi-C processing pipeline
file_type: contact list-replicate
file_format: pairs
file name: 4DNFIPWEWCY3.pairs.gz

extract_protocol:
description: The Official 4DN Standard in situ Hi-C protocol adapted from Rao et al. 2014 PMID: 25497547 - with accepted deviations approved by SC 02/21/2017
download: https://data.4dnucleome.org/protocols/fdc20e37-f22e-42dc-8026-0a132739bad1/@@download/attachment/4DN_in_situ_Hi-C_protocol_20170729.pdf
description: in situ HiC protocol for primary cells
download: https://data.4dnucleome.org/protocols/de9c3f44-aa10-427e-83b8-566a4b6f5c4a/@@download/attachment/171004.insituHiC.pdf

value: Not Specified

value: FACs-sorted mOSNs with conditional Ldb1-KO - biological replicate 2


title: in situ Hi-C on olfactory receptor cell with DpnII - 4DNEXVJSLZI5

description:
lab: Stavros Lomvardas, COLUMBIA
award: 1U01DA040582-01
4DN accession: 4DNEXVJSLZI5
description: HiC from conditional OMP-Cre; Ldb1-KO mature olfactory sensory neurons - bioreplicate 1
submitted_by: Adan Horta
ligation_time: 240
digestion_time: 960
tagging_method: Biotin-11-GTP
experiment_type: in situ Hi-C
ligation_volume: 1.2
digestion_enzyme: DpnII
crosslinking_time: 10
biosample_quantity: 1000000 cells
crosslinking_method: 1% Formaldehyde
fragmentation_method: sonication
ligation_temperature: 25
digestion_temperature: 37
crosslinking_temperature: 25
fragment_size_selection_method: SPRI beads
url: https://data.4dnucleome.org/experiments-hi-c/4DNEXVJSLZI5/

data_processing:
https://data.4dnucleome.org/resources/data-analysis/hi_c-processing-pipeline
***************
workflow_run: https://data.4dnucleome.org/workflow-runs-awsem/08b92936-c3ca-4d01-9131-b7eb97201061/
genome_assembly: GRCm38
derived_from: 4DNFIHMY7KMH.bam, 4DNFI95DH3QJ.bam, 4DNFI3UBJ3HZ.chrom.sizes
description: This is an output file of the Hi-C processing pipeline
file_type: contact list-replicate
file_format: pairs
file name: 4DNFIC2O325X.pairs.gz

value: FACs-sorted mOSNs with conditional Ldb1-KO - biological replicate 1


title: BA2C2_S11

description:
matrix includes transcript ID, gene ID, and values for each sample ID
sample10

value: saliva

value: Infected-Unvax

value: Male

value: White or Caucasian

value: Not Hispanic


title: BA2A1_S1

description:
matrix includes transcript ID, gene ID, and values for each sample ID
sample01


title: Healthy Skin Replicate 1

description:
Biological replicate 1 of 4. Healthy Skin
Healthy BH4 RNA


title: Grem1 lineage traced cells - plate9

city: Adelaide

first: Susan

last: Woods

state: Select State

address: Level 5 South, SAHMRI building, North Terrace

department: School of Medicine

country: Australia

institute: The University of Adelaide

data_processing:
1) extract UMIs and barcodes with "umi_tools extract"
2) align reads with STAR
3) assign alignments to genes with featureCounts
4) sort & index bam with samtools
6) make count matrix from bam with "umi_tools count", pandas, and scipy
7) We applied the Seurat [https://satijalab.org/seurat/] package for cell normalization and cell filtering considering the MT percentage, minimum and maximum gene numbers under following criteria:  MT% < 20%;  Cell Gene Number < Median Gene Number * 2;  Cell Gene Number > 200. PCA and tSNE analysis was used for the single cell to cell relation description. Graphcluster and K-mean was utilized for cell clustering and based on the marker gene achieved some cluster was combined. ROC is used for marker gene analysis.
Genome_build: mm10
Supplementary_files_format_and_content: raw counts

source_name: Grem1-TDT hind limbs

extract_protocol:
Hind limbs were collected, and all muscles and ligaments removed. AC and GP from Grem1-TdT mice were excised under a dissection microscope and minced using a scalpel before being digested in 2.5mg/mL collagenase type II (#CLS-2, Worthington). Cleaned LepR-TdT whole bones were gently disrupted using a mortar and pestle, minced, and digested in 2.5mg/mL collagenase type I (#CLS-1, Worthington). The following antibodies were used: anti-CD45 (#103111, BioLegend), anti-Ter119 (#116211, BioLegend), anti-CD31 (#102509, BioLegend), and DAPI (#D9542, Sigma-Aldrich). LepR cells were sorted based on forward and side scatter, single cells, live cells (DAPI negative), trilineage negative expression (CD45-Ter119-CD31-) and TdTomato positive fluorescence. Grem1 cells were sorted based on forward and side scatter, single cells, live cells (DAPI negative), and TdTomato positive fluorescence. Individual cells were collected into single well in a 96-well plate with lysis buffer previously prepared by the Sulzberger Genome Center (Columbia University) and sequenced. Cells were randomly allocated into 96-well plates to avoid batch effects.
Sequencing libraries were constructed using Nextera XT (Illumina) with modifications. A custom i5 primer was used (NexteraPCR) with 0.6ng input cDNA and 10 cycles of amplification was performed. Unique i7 indexes were used for each plate. After amplification, the library was purified with two rounds of AMPure XP beads, visualized on the TapeStation and quantified using the Qubit II fluorometer. Libraries were sequenced on an Illumina NextSeq 500 using the 75 cycle High Output kit (read lengths 26(R1) x 8(i) x 58(R2)). With each plate we targeted ~70M reads. Library pools were loaded at 1.8pM with 30% PhiX

treatment_protocol: Grem1-TdT mice at 5 – 6 weeks of age were subjected to tamoxifen chow for 2 weeks before they were sacrificed. Age paired LepR-TdT mice were used for this analysis.

tag: lineage

value: hind limbs


title: in situ Hi-C on immediate neuronal precursor cell with DpnII - 4DNEXTDMNUOO

description:
lab: Stavros Lomvardas, COLUMBIA
award: 1U01DA040582-01
4DN accession: 4DNEXTDMNUOO
description: HiC from immediate neural precursors - bioreplicate 2
submitted_by: Adan Horta
ligation_time: 240
digestion_time: 960
tagging_method: Biotin-11-GTP
experiment_type: in situ Hi-C
ligation_volume: 1.2
digestion_enzyme: DpnII
crosslinking_time: 10
biosample_quantity: 2100000 cells
crosslinking_method: 1% Formaldehyde
fragmentation_method: sonication
ligation_temperature: 25
digestion_temperature: 37
crosslinking_temperature: 25
fragment_size_selection_method: SPRI beads
url: https://data.4dnucleome.org/experiments-hi-c/4DNEXTDMNUOO/

data_processing:
https://data.4dnucleome.org/resources/data-analysis/hi_c-processing-pipeline
***************
workflow_run: https://data.4dnucleome.org/workflow-runs-awsem/5bd9ec3e-9907-4d07-9231-fbcb1cfbae3b/
genome_assembly: GRCm38
derived_from: 4DNFIKHEJR3T.bam, 4DNFI3UBJ3HZ.chrom.sizes
description: This is an output file of the Hi-C processing pipeline
file_type: contact list-replicate
file_format: pairs
file name: 4DNFIBO9M2WY.pairs.gz

source_name: biosource_summary: immediate neuronal precursor cell

treatment_protocol:
description: FACS plots for immature olfactory sensory neurons from Ngn1-GFP mice. HiC from P4 in FACS plot
download: https://data.4dnucleome.org/protocols/0974d1b7-23f7-45ab-b22a-bf394a995cf4/@@download/attachment/FACS.NgnBright.170717.P0.pdf

value: immediate neuronal precursor cell

value: FVB/NTac

value: olfactory epithelium

value: FACS-sorted immediate neural precursor cells - biological replicate 2

value: mixed

value: pup


title: Healthy Skin Replicate 3

description:
Biological replicate 3 of 4. Healthy Skin
Healthy BH05


title: Grem1-lineage articular cartilage cells from mouse knee shown in figure 3m

city: NEW YORK

first: Abdullah

last: Ali

address: 1130 SAINT NICHOLAS AVE, ICRC 601

description: 10X Genomics

library_source: transcriptomic single cell

data_processing:
Raw Illumina data were processed to convert Illumina basecall files to FASTQ format. Reads were alignedto the mouse genome (mm10) version 2020-A and gene counting was performed using the 10× Genomics Cell Ranger pipeline.
Assembly: mm10/2020-A
Supplementary files format and content: h5 file format containing filtered feature and count matrix

source_name: Articular cartilage

extract_protocol:
The AC femur-tibia joint tissue from 4 Grem1-CreErt mice were shaved with a scalpel under the microscope, and then enzymatically digested with 4mg/ml Collagenase ii (Worthington Biochemical Corporation, LS004176) in alphaMEM (#M5650, Sigma) for 1h at room temperature and filtered with a 75um strainer to achieve single cells suspension and labeled with DAPI and kept on ice. Single cell suspensions were sorted by fluorescence activated cell sorting based forward and side scatter, dTomato fluorescence (positive) and DAPI (negative). Sorted cells were collected in Alpha-Mem media and submitted to the Sulzberger Columbia Genome Center at Columbia University Irving Medical Center for library preparation and sequencing.
Library preparation was performed using Chromium Single Cell 3' Library & Gel Bead Kit v3

value: Articular cartilage

tag: developmental stage

value: young adult

value: primary cells

value: 10 weeks


title: Grem1 lineage traced cells - plate7


title: Grem1 lineage traced cells - plate8


title: 7363M

city: Palo Alto

first: Andrew

last: Gentles

state: CA

address: 1265 Welch Rd

institute: Stanford University

description: Mechanical digestion

data_processing:
Sequences were filtered and aligned using the CellRanger software (v3.3, 10× Genomics).
Low quality cells were filtered out by removing cells with less than 200 counts,more than 2,500 counts and more than 15% of UMIs in the mitochondrial genes.
Genes that are detected in at least 3 cells were kept.
Assembly: GRCh38.p14
Supplementary files format and content: Tab-separated value files and matrix files.

source_name: Head and neck squamous cell carcinoma

extract_protocol:
Tumor tissue was thoroughly diced with a sterile scalpel and placed in a GentleMACs C-tube containing one milliliter of tissue digestion media. Tissue was mechanically digested on the GentleMACs dissociator five times under the human tumor tissue program “h_tumor_01”.The remaining solid tissue in the strainer, enzymatic sample, was collected and placed back in the C-tube with 4 mls of tissue digestion media, 0.5 ml of 3000 U/ml collagenase/ 1000 U/ml hyaluronidase.
After FACS sorting for live cells, library prep was performed using Chromium Next GEM Single Cell 3' Kit v3 (10x Genomics, San Francisco, CA) according to manufacturer’s instructions and send to Medgenome for sequencing on the Novaseq.

value: Head and neck squamous cell carcinoma


title: Psoriatic Lesional Skin Replicate 1

description:
Biological replicate 1 of 4. Psoriatic Lesional Skin
BP03 LS RNA

value: Psoriatic Lesional Skin


title: Grem1 lineage traced cells - plate6


title: 7363E

description: Enzymatic digestion


title: Psoriatic Lesional Skin Replicate 4

description:
Biological replicate 4 of 4. Psoriatic Lesional Skin
BP05 LS


title: DLD1-expressing dnTCF7L2 and IGF2BP3, Dox, Biol rep 3

city: Hershey

first: Vonn

last: Walter

state: PA

address: 500 University Drive

department: Public Health Sciences

institute: Penn State College of Medicine

data_processing:
De-multiplexed sequencing reads were generated using Illumina bcl2fastq (released version 2.18.0.12, Illumina), allowing no mismatches in the index read. After the quality and polyA trimming by BBDuk and alignment by STAR (version 2.5.3a), read counts were calculated using HTSeq by supplementing Ensembl gene annotation (GRCh38.78).
Assembly: GRCh38
Supplementary files format and content: raw read counts are provided in txt file

source_name: Colon

growth_protocol: Cells were cultured in RPMI-1640 Medium supplemented with 10% fetal bovine serum

extract_protocol:
Total RNA was isolated using RNeasy Mini Kit from Qiagen (74104)
The cDNA libraries were prepared using the QuantSeq 3’mRNA-Seq Library Prep Kit FWD for Illumina (Lexogen) as per the manufacturer’s instructions. Briefly, total RNA was reverse transcribed using oligo (dT) primers. The second cDNA strand was synthesized by random priming, in a manner that DNA polymerase is efficiently stopped when reaching the next hybridized random primer, so only the fragment close to the 3’ end gets captured for later indexed adapter ligation and PCR amplification. The processed libraries were assessed for their size distribution and concentration using BioAnalyzer High Sensitivity DNA Kit (Agilent Technologies).

treatment_protocol: 90% confluent cells were treated/untreated with Doxycycline (2µg/ml) for 48hrs to induce the expression of dnTCF7L2+GFP and dnTCF7L2+IGF2BP1

value: Colon

tag: biological repeat

value: Biol rep 3

value: Epithelial cell

value: Doxycycline


title: Grem1 lineage traced cells - plate4

value: hind limbs


title: DLD1-expressing dnTCF7L2 and IGF2BP1-Dox, Biol rep 1

value: Biol rep 1


title: DLD1-expressing dnTCF7L2 and IGF2BP2, Dox, Biol rep 2

value: Biol rep 2


title: Grem1 lineage traced cells - plate5


title: Grem1 lineage traced cells - plate2


title: in situ Hi-C on immediate neuronal precursor cell with DpnII - 4DNEXKO3TRJT

description:
lab: Stavros Lomvardas, COLUMBIA
award: 1U01DA040582-01
4DN accession: 4DNEXKO3TRJT
description: HiC from immediate neural precursors - bioreplicate 1
submitted_by: Adan Horta
ligation_time: 240
digestion_time: 960
tagging_method: Biotin-11-GTP
experiment_type: in situ Hi-C
ligation_volume: 1.2
digestion_enzyme: DpnII
crosslinking_time: 10
biosample_quantity: 2200000 cells
crosslinking_method: 1% Formaldehyde
fragmentation_method: sonication
ligation_temperature: 25
digestion_temperature: 37
crosslinking_temperature: 25
fragment_size_selection_method: SPRI beads
url: https://data.4dnucleome.org/experiments-hi-c/4DNEXKO3TRJT/

data_processing:
https://data.4dnucleome.org/resources/data-analysis/hi_c-processing-pipeline
***************
workflow_run: https://data.4dnucleome.org/workflow-runs-awsem/48e3efd2-1dc3-437f-84fe-1df4ff9fb127/
genome_assembly: GRCm38
derived_from: 4DNFIA66NTFV.bam, 4DNFI3UBJ3HZ.chrom.sizes
description: This is an output file of the Hi-C processing pipeline
file_type: contact list-replicate
file_format: pairs
file name: 4DNFIDFRSE2G.pairs.gz

value: immediate neuronal precursor cell

value: FVB/NTac

value: olfactory epithelium

value: FACS-sorted immediate neural precursor cells - biological replicate 1


title: DLD1-Dox, Biol rep 3

value: Untreated


title: Healthy Skin Replicate 2

description:
Biological replicate 2 of 4. Healthy Skin
Healthy BH3 RNA

value: Healthy Skin


title: Lepr lineage traced cells - plate2

source_name: Lepr-TDT hind limbs

value: Lepr-TdT


title: DLD1-Dox, Biol rep 2


title: Grem1 lineage traced cells - plate1


title: DLD1-Dox, Biol rep 1


title: Lepr lineage traced cells - plate1


title: DLD1-expressing dnTCF7L2, Untr, Biol rep 1


title: DLD1-expressing dnTCF7L2, Untr, Biol rep 3


title: DLD1-expressing dnTCF7L2, Untr, Biol rep 2


title: rep1

city: Wako

first: Shintaro

last: Iwasaki

address: 2-1 Hirosawa

department: Cluster for Pioneering Research

institute: RIKEN

description: TCP seq

library_source: other

data_processing:
Basecalling with RTA(Real-Time Analysis): ver2.7.7
3' adapter trimming with FastX-toolkit
Library sorting based on sample barcode sequence with custom script
Random barcode triming with custom script
rRNA and other non-coding RNA alignment with STAR(2.7.0a)
Alignment with STAR(2.7.0a)
Read quantitation using fp-framing
Assembly: Custom reporter sequence
Supplementary files format and content: Text files contain 66 columns: 1. Distance from start codon (nt);2. Number of reads smaller than 17 nt;3-66. Number of reads whose length are 17 to 80 nt
Library strategy: TCP-seq

molecule: other

organism: synthetic construct

source_name: in vitro translated mRNA in WGL (Promega)

extract_protocol:
Crosslink, MNase footprinting, 40S bound RNA fragemnt separation, reverse crosslink, RNA purification
17-80 nt gel excision, preadenylated linker ligation, rRNA depeletion, reverse transcription, cDNA circularization, PCR amplification

tag: fraction

value: 40S ribosme bound RNA fragment


title: rep2

description: TCP seq


title: DLD1-UT, Biol rep 3

tag: cell line


title: DLD1-UT, Biol rep 1

tag: cell type


title: NHBE cells, pre-treated with DiMNF, HCoV-OC43 infected, rep 3

first: Wharton

middle: O Y

last: Chan

state: Singapore

address: 8 College Road

department: Emerging Infectious Disease

institute: Duke-NUS Medical School

description:
Sequenced paired-end on two different lane (L5 and L6)
NDIOC3

data_processing:
Demultiplexing of the raw output data, quality control with FastQC.
Removal of adapter and rDNA reads using BBDuk.
Alignment to human reference genome hg38 using STAR aligner.
Read counts were generated using featureCounts from subread software.
Assembly: hg38 (release 13)
Supplementary files format and content: Tab delimited file containing gene level counts (non-normalized) of each sample.

source_name: NHBE

growth_protocol: NHBE cells were maintained in BEGM BulletKit Growth Media.

extract_protocol:
At 48 h post-infection, total RNA was extracted using RNeasy Mini Kit.
Library prep was performed using Truseq stranded total RNA kit with 1000ng sample as its starting material, with ribozero gold.

treatment_protocol: NHBE cells were pre-treated with 2 ml medium containing 1 μM of DiMNF or 0.003% DMSO for 48 h. NHBE cells were then inoculated with 2 ml of HCoV-OC43 inoculum (MOI 5) and incubated for 3 h. Subsequently, the inoculum was removed from the cells and 2 ml fresh medium containing 1 μM of DiMNF or 0.003% DMSO was added. Cells were incubated for 48 h before RNA extraction.

value: NHBE

value: Bronchial Epithelial Cells

tag: genotype

value: WT

tag: treatment

value: OC43 infected + DiMNF


title: NHBE cells, pre-treated with DiMNF, HCoV-OC43 infected, rep 2

description:
Sequenced paired-end on two different lane (L5 and L6)
NDIOC2


title: DLD1-UT, Biol rep 2

value: Colon

value: Epithelial cell


title: PBS + IgG replicate 3

city: Lausanne

first: Nadine

last: Fournier

state: Vaud

address: Agora Cancer Research Center, Bugon 25A

country: Switzerland

institute: Agora Cancer Research Center & Swiss Institute of Bioinformatics

data_processing:
The TCR sequences were further processed using ad hoc Perl scripts to: (i) pool all TCR sequences coding for the same protein sequence; (ii) correct for amplification and sequencing errors using 9mers UMI; (iii) filter out all out-frame sequences; (iv) determine the abundance of each distinct TCR sequence. TCR with a single read were removed for the analysis.
TCR clones which were considered out of frame were filtered out from the datasets.
Analysis of the TCR clones was performed by using the immunarch library [ImmunoMind Team. (2019). immunarch: An R Package for Painless Bioinformatics Analysis of T-C ImmunoMind Team. (2019)] in R 4.2.1.
The diversity of the TCR diversity was estimated by computing the TCR richness of each tumor, defined as the number of unique clonotypes in each dataset.
Tumors treated with Cis+DCP-IL-12/FLT3L+aPD-1and Cis+DCP-IL-12/FLT3L+IgG were pooled together and TCR richness was compared with unvaccinated samples (Cis+PBS+PD-1 and Vehicle+PBS+IgG). The proportion of each V gene was also compared between the two groups. Tumors were correlated based on their V genes usage with the Jansen Shannon divergence and clustered by multidimensional scaling and k-means clustering.
Assembly: TCR reference
Supplementary files format and content: tab separated, raw counts
Supplementary files format and content: tab separated, processed counts
Library strategy: TCR-Seq

source_name: Tumor

growth_protocol: We inoculated MC38 tumors s.c. and treated the mice with a single dose of cisplatin (Cis) on day 8 post-tumor injection. In some mice, this was followed by i.v. injection of DCP-IL-12/FLT3L on day 11 and 13, with or without PD-1 blocking antibodies (aPD-1) starting on day 14 twice weekly. Control mice received PBS plus irrelevant IgG.

extract_protocol:
Snap-frozen samples of tumors were lysed in Qiazol with a TissueLyser II (Qiagen). RNA was then isolated using the miRNeasy Micro Kit from Qiagen, according to the manufacturer’s instructions.
Extracted RNA was then amplified using the MessageAmp II aRNA Amplification Kit (Ambion) with the following modifications: in vitro transcription was performed at 37°C for 16h. The resulting cRNA was converted to ssDNA using the Superscript III (Thermofisher) and a collection of TRBV specific primers containing UMI and Illumina adapters. TCRs were then amplified by PCR (20 cycles with the Phusion from NEB) with a single primer pair binding to the constant region and the adapter linked to the TRAV/TRBV primers added during the reverse transcription. A second round of PCR (25 cycles with the Phusion from NEB) was performed to add the Illumina adapters containing the different indexes.

treatment_protocol: We terminated the experiment on day 18 (control mice) or day 27 (other groups) post-tumor injection to harvest tumors for TCR sequencing (TCR-Seq), without prior enrichment or exclusion of specific cell types.

value: Tumor

value: PBS + IgG


title: PBS + IgG replicate 2


title: NHBE cells, pre-treated with DiMNF, HCoV-OC43 infected, rep 1

description:
Sequenced paired-end on two different lane (L5 and L6)
NDIOC1


title: Cis + DCP-IL-12/FLT3L + IgG replicate 7

value: Cis + DCP-IL-12/FLT3L + IgG


title: Cis + PBS + aPD-1 replicate 5

value: Cis + PBS + aPD-1


title: PBS + IgG replicate 1


title: NHBE cells, pre-treated with DMSO, HCoV-OC43 infected, rep 3

description:
Sequenced paired-end on two different lane (L5 and L6)
NDMOC3

value: OC43 infected + DMSO cntrl


title: Cis + DCP-IL-12/FLT3L + ɑPD-1 replicate 6

value: Cis + DCP-IL-12/FLT3L + ɑPD-1


title: NHBE cells, pre-treated with DMSO, HCoV-OC43 infected, rep 1

description:
Sequenced paired-end on two different lane (L5 and L6)
NDMOC1


title: Cis + DCP-IL-12/FLT3L + IgG replicate 6


title: Cis + DCP-IL-12/FLT3L + IgG replicate 5


title: Cis + PBS + aPD-1 replicate 4


title: NHBE cells, pre-treated with DiMNF, uninfected, rep 3

description:
Sequenced paired-end on two different lane (L5 and L6)
NDI3

value: Mock infected + DiMNF


title: NHBE cells, pre-treated with DiMNF, uninfected, rep 2

description:
Sequenced paired-end on two different lane (L5 and L6)
NDI2


title: NHBE cells, pre-treated with DiMNF, uninfected, rep 1

description:
Sequenced paired-end on two different lane (L5 and L6)
NDI1


title: Cis + DCP-IL-12/FLT3L + ɑPD-1 replicate 7


title: Cis + DCP-IL-12/FLT3L + IgG replicate 4


title: NHBE cells, pre-treated with DMSO, uninfected, rep 3

description:
Sequenced paired-end on two different lane (L5 and L6)
NDM3

value: Mock infected + DMSO cntrl


title: NHBE cells, pre-treated with DMSO, uninfected, rep 2

description:
Sequenced paired-end on two different lane (L5 and L6)
NDM2


title: NHBE cells, pre-treated with DMSO, uninfected, rep 1

description:
Sequenced paired-end on two different lane (L5 and L6)
NDM1


title: Cis + DCP-IL-12/FLT3L + ɑPD-1 replicate 5


title: NHBE cells, pre-treated with DMSO, HCoV-OC43 infected, rep 2

description:
Sequenced paired-end on two different lane (L5 and L6)
NDMOC2


title: Cis + DCP-IL-12/FLT3L + ɑPD-1 replicate 3


title: Cis + PBS + aPD-1 replicate 2


title: Cis + DCP-IL-12/FLT3L + IgG replicate 2


title: CagA KO+GES-1, 24h, rep3

city: Shen Zhen

first: Zhiyong

last: Zhai

state: Guang Dong

address: No.1333, XinAn Street, BaoAn District

country: China

institute: Shenzhen Hospital of Southern Medical University

data_processing:
www.genedenovo.com
Reads were filtered by fastp (version 0.18.0).The parameters were as follows: 1) removing reads containing adapters; 2) removing reads containing more than 10% of unknown nucleotides(N); 3) removing low quality reads containing more than 50% of low quality (Q-value≤20) bases.
Short reads alignment tool Bowtie2 (version 2.2.8) was used for mapping reads to ribosome RNA (rRNA) database.The rRNA mapped reads then will be removed. The remaining clean reads were further used in assembly and gene abundance calculation.
An index of the reference genome was built, and paired-end clean reads were mapped to the reference genome using HISAT2. 2.4 and other parameters set as a default.
The mapped reads of each sample were assembled by using StringTie v1.3.1 in a reference-based approach.
Supplementary files format and content: tab-delimited text file includes raw counts for each sample.
Supplementary files format and content: tab-delimited text file includes FPKM values for each sample.

organism:
Helicobacter pylori
Homo sapiens

growth_protocol: Helicobacter pylori were maintained in columbia blood agar medium at 37℃.GES-1 cells were maintained in 1640 supplemented with 10% fetal bovine serum(FBS) in humidified atmosphere with 5% CO2 at 37℃.

extract_protocol:
Total RNA was extracted using Trizol reagent kit (Invitrogen, Carlsbad, CA,USA) according to the manufacturer’s protocol.
After total RNA was extracted, eukaryotic mRNA was enriched by Oligo(dT)beads(Pronucleus：After total RNA was extracted, prokaryotic mRNA was enriched by removing rRNA by Ribo-ZeroTM Magnetic Kit (Epicentre, Madison, WI, USA)). Then the enriched mRNA was fragmented into short fragments using fragmentation buffer and reversly transcribed into cDNA by using NEBNext Ultra RNA Library Prep Kit for Illumina(NEB#7530,New England Biolabs, Ipswich, MA, USA)

value: Helicobacter pylori+GES-1


title: Cis + DCP-IL-12/FLT3L + IgG replicate 1


title: Cis + PBS + aPD-1 replicate 1


title: L36_H3K4me3_rep2

city: Stuttgart

first: Cristiana

last: Lungu

state: BW

address: Allmandring 31

department: Institute of Cell Biology and Immunology

country: Germany

institute: University of Stuttgart

data_processing:
The fastq files were mapped to the human reference genome assembly hg19 using Bowtie2 with very-sensitive end-to-end mode.
The BAM files were filtered with MAPQ≥2 and PCR duplicates were removed using SAMTOOLS 1.9. The filtered BAM files from each replicate were merged within one condition using SAMTOOLS and the merged BAM files were normalized to 1x depth of coverage (reads per genomic content, RPGC) using Deeptools (3) 3.0.1 bamCoverage to generate bigwig files.
he filtered BAM files from each replicate were merged within one condition using SAMTOOLS and the merged BAM files were normalized to 1x depth of coverage (reads per genomic content, RPGC) using Deeptools (3) 3.0.1 bamCoverage to generate bigwig files.
Assembly: hg19
Supplementary files format and content: normalized bigwig files

growth_protocol: L3.6pl cells were cultured in phenol-free minimum essential medium (MEM) supplemented with 10% FBS, 1% penicillin/streptomycin, and 1% glutamine.

extract_protocol:
PDX tissue samples were homogenized on dry-ice using the Sciences BioMascher® II Micro Tissue homogenizers. Powdered tissue and cell pellets from L3.6pl cells were fixed in 1% formaldehyde in PBS for 20 min and quenched with 125 mM glycine for 5 min at room temperature. Sonicated chromatin extract was immunoprecipitated overnight with corresponding antibodies. Protein A sepharose was used to capture immune complexes. Immune complexes were washed, de-crosslinked and DNA was extracted.
ChIP-seq libraries except the H3K4me1 and H3K4me3 were prepared using the KAPA HyperPrep (Roche) kit. H3K4me1 and H3K4me3 libraries were prepared using the MicroPlex Library Preparation Kit (Diagenode) according to the manufacturer's instructions. The library size was estimated using a Bioanalyzer 2100.

treatment_protocol: Transfection of siRNAs was achieved using Lipofectamine RNAiMAX (Invitrogen) according to manufacturer’s instructions. Control non-targeting siRNA #5 (NT5) (siGENOME, #D-001210-05-20) and TP63 siRNA pool (siGENOME; #M-003330-01-0005 SMARTpool) were purchased from Dharmacon, ThermoScientific.

value: Pancreatic adenocarcinoma cell line

tag: antibody

value: H3K4me3 (Diagenode #C15410003)


title: L36_H3K4me3_rep3


title: Cis + PBS + aPD-1 replicate 3


title: L36_H3K4me1_rep2

value: H3K4me1 (Diagenode #C15410194)


title: Cis + DCP-IL-12/FLT3L + ɑPD-1 replicate 2


title: IGROV-1 cellsCRISPR Brunello libray, infected with HCoV-OC43

data_processing:
Demultiplexing of the raw output data, quality control with FastQC.
Alignment of the DNA to the set of gRNAs in the Brunello CRISPR library, using MAGeCK.
Assembly: hg38
Supplementary files format and content: Tab delimited file containing guide RNA counts (non-normalized) of each sample.
Library strategy: DNA-Seq

source_name: Ovary

growth_protocol: IGROV-1 cells were maintained in Dulbecco’s modified Eagle medium (DMEM) supplemented with 1× penicillin-streptomycin, 1× L-glutamine, and 10% heat-inactivated fetal bovine serum.

extract_protocol:
Total genomic DNA from both virus-resistant and uninfected control cells was respectively extracted using QIAamp DNA Mini Kit.
The inserted guide RNA sequences were retrieved from the genomic DNA by PCR amplification using the forward 5'-AATGGACTATCATATGCTTACCGTAACTTGAAAGTATTTCG-3' and reverse 5'-CTTTAGTTTGTATGTCTGTTGCTATTATGTCTACTATTCTTTCC-3' primers. The PCR products were further barcoded by an additional round of PCR amplification using primers containing illumina i5 and i7 barcodes. The PCR products were then gel purified and subjected to next-generation sequencing on illumina MiSeq platform using a custom sequencing primer.

treatment_protocol: IGROV-1 cells were stably transduced with lentiCas9-Blast and selected using blasticidin (15 μg/ml) to generate a population of Cas9 expressing IGROV-1 cells, IGROV-1-Cas9. These cells were subsequently transduced with the Human CRISPR Knockout Pooled Library (Brunello) at MOI of 0.3. Cells were selected using puromycin (1.5 μg/ml) and heterogeneous knockout cell populations were subsequently pooled together. The CRISPR genetic screens were started 10 days post transduction. Cell libraries displaying a >700-fold coverage of mutagenized cells were infected with SARS-CoV-2 at a MOI of 0.1, and HCoV-OC43 at a MOI of 0.05. SARS-CoV-2 infection was repeated for an additional round at two weeks post-infection. HCoV-OC43 infection was also repeated for two additional rounds at 5 and 10 days post-infection.

value: Ovary

value: Ovarian carcinoma cell line

value: Genome-wide CRISPR KO library (pooled)

value: HCoV-OC43 infection


title: IGROV-1 cellsCRISPR Brunello libray, uninfected


title: IGROV-1 cellsCRISPR Brunello libray, infected with SARS-CoV-2

value: SARS-CoV-2 infection


title: WT+GES-1, 24h, rep3


title: L36_H3K4me1_rep1

value: WT


title: CagA KO+GES-1, 24h, rep2


title: WT+GES-1, 24h, rep2


title: Cis + DCP-IL-12/FLT3L + ɑPD-1 replicate 4

value: Tumor


title: Cis + DCP-IL-12/FLT3L + IgG replicate 3

value: Cis + DCP-IL-12/FLT3L + IgG


title: WT+GES-1, 24h, rep1


title: CagA KO+GES-1, 12h, rep3


title: CagA KO+GES-1, 12h, rep2


title: PP_RNASeq_Rep1

city: XIAMEN

first: XIAOWEN

last: LYU

state: FUJIAN

address: No.4221, Xiang'an South Road, Xiang'an District

institute: XIAMEN UNIVERSITY

description: processed file: PP_RNASeq.2Reps.RPM.bw

data_processing:
ChIP-seq and CUT&Tag data processing: All reads were mapped to unique genomic regions using Bowtie2 and the hg38 human genome. PCR duplicates were removed manually. Bedtools genome Coverage function was used to derive bedgraph files for further analysis. To compare changes in ChIP-Seq signals, libraries were normalized by random picking to obtain the same numbers of reads. Normalized reads were used to derive bedgraph files for comparison in IGV. MACS2 was used to call peaks using default parameters with IgG ChIP-Seq data as control. Differential peaks were found using the edgeR (Robinson et al., 2010) R package at p<0.05, changes over 20% up/down.
Analysis of ATAC-seq data: ATAC-Seq data was processed by our in-house pipeline. First, paired end reads were aligned to the hg38 human reference genome using Bowtie2 with default parameters except -X 2000 -m 1. PCR     duplicates     were     removed using     Picard     Tools (http://picard.sourceforge.net;https://broadinstitute.github.io/picard/).  To adjust for fragment sizes, reads mapped to + strands and -strands were offset by +4 bp and -5 bp respectively. For all ATAC-seq datasets, sub-nucleosome and mono-nucleosome reads were separated based on fragment sizes: THSSs (transposases hypersensitive sites, bound by TFs, <115bp) and mono-nucleosomes (180~247bp). To obtain the exact positioning of nucleosomes, DANPOS (Chen et al., 2013) was used to derive the nucleosomal signals genome wide by dpos function using 180~247 bp fragments as input and 115 bp fragments as background using -p 1 -a 1 -jd 20 -u 0 -m 1. Reads were normalized between samples before running DANPOS. THSSs bedgraphs were made using the bedtools genomeCoverage function.   MACS2 was used to call peaks for subnucleosomal reads, which were bound by transcription factors.   To analyze the footprints of TFs in ATAC-seq data, motifs on a set of peaks or loop anchors were used as anchors for running dnase_average_profile.py scripts of the Wellington program in ATAC-seq mode. To compare between Ctrl and HS samples, read-normalized ATAC-seq THSSs (<115 bp) fragments were used as input to obtain the footprint average profiles. The footprint p values of all motifs on a set of peaks or anchors were derived using the wellington_footprints.py scripts of the Wellington program in ATAC-seq mode on read-normalized ATAC-seq THSSs (<115 bp) fragments.
RNA-seq data processing: RNA-seq raw reads were aligned using HISAT2 v2.2.0 to the hg38 human genome with default parameters. Transcripts per million (TPM) counts for all annotated human genes and transcripts were calculated by StringTie v2.1.6. Differentially expressed genes were identified using the R package “edgeR” with a cut-off p value ≤0.05 and fold change over 20% up/down.
Assembly: hg38
Supplementary files format and content: .bw; bigwig files including processed signals of RNA-Seq, ATAC-Seq, CUT&Tag and ChIP-Seq data
Supplementary files format and content: .genenamesorted; txt files including TPM counts for all genes calculated from RNA-Seq data

source_name: H9 hESCs

extract_protocol:
For ChIP-seq, H9 cells and their in vitro differentiated organoids were collected, fixed with 1% formaldehyde and homogenized to prepare for the ChIP-Seq libraries. After cell lysis, whole nuclear lysates were sonicated to shear the chromatin into fragments with an average size of around 200-500 bp in length. Chromatin was precleared with Protein A or G Dynabeads at 4°C for 2 hours and precipitated with antibody overnight at 4°C. Immunoprecipitated chromatin was tagmented with Tn5 transposes mixture on beads and then eluted, reverse crosslinked and purified by standard methods, followed by PCR amplification. For ATAC-seq, H9 cells and their in vitro differentiated organoids were collected for performing the OMNI-ATAC protocol. For OMNI-ATAC, organoids were homogenized with electric homogenizer for 10 seconds into small clusters of cells to perform standard OMNI-ATAC protocol. Briefly, cells were washed with PBS and nuclear membrane was disrupted by soaking in lysis buffer (10 mM Tris-HCl pH 7.4, 10 mM NaCl, 3mM MgCl2, 0.1% NP40, 0.1% Tween-20, and 0.01% Digitonin) on ice, nuclei was washed once in cold lysis buffer without NP40 or digitonin, and then incubated in Tn5 transposes mixture (25 ul 2x TD buffer, 2.5 ul transposase (100nM final), 16.5 ul PBS, 0.5 ul 1% digitonin, 0.5 ul 10% Tween-20, 5 ul H2O) at 37°C for 20 min with occasional shaking. After the reaction is over, DNA was directly extracted by Minelute Kit (Qiagen). Purified tagmented DNA were used to make Illumina Nextera libraries. For RNA-Seq, total RNA was isolated from H9 cells and their in vitro differentiated organoids using Trizol reagent (Invitrogen) and ribosomal RNA was removed using the Ribo Minus Transcriptome isolation kit (Invitrogen, K1550). Strand-specific RNA library prepared by TruSeq Stranded mRNA Library Prep Kit was amplified with barcoded primers for Illumina sequencing. For CUT&Tag, H9 cells and their in vitro differentiated organoids were harvested, gently homogenized with pestle A for standard library preparation. Briefly, cells were washed twice in 1.5 mL Wash Buffer (20 mM HEPES pH 7.5, 150 mM NaCl, 0.5 mM Spermidine, 1 × Protease inhibitor cocktail, EDTA free), immobilized to concanavalin A coated magnetic beads (Bangs Laboratories), and then resuspended in 50 μL Dig-wash Buffer (20 mM HEPES pH 7.5, 150 mM NaCl, 0.5 mM Spermidine, 1 × Protease inhibitor cocktail, 0.05% Digitonin) containing 2 mM EDTA. After sequential incubation in the primary antibody of CHD4 (abcam, #ab72418, diluted 1:50 in 50 μL of Dig-Wash buffer) , the appropriate secondary antibody (diluted 1:100 in 100 μL of Dig-Wash buffer) and a 1:200 dilution of pAG-Tn5 (gift from Henikoff Lab) in Dig-300 Buffer (0.05% digitonin, 20 mM HEPES, pH7.5, 300 mM NaCl, 0.5 mM Spermidine, 1 × Protease inhibitor cocktail) , bead-bound cells were resuspended in 50μL tagmentation buffer (10 mM MgCl2 in Dig-wash Buffer) to tagment genomic DNA. The tagmented DNA was cleaned up by 1.5 × Ampure XP beads (Beckman Counter), amplified with Illumina Nextera barcoded primers, purified by 1.1 × Ampure XP beads for Illumina sequencing.
Truseq libraries were constructed using the standard protocol. Genomic fragments were end repaired (NEBNext End Repair Module), A-tailed by adding adenosine to the 3’ ends of fragment using Klenow fragment (3’ to 5’ exo minus, New England Biolabs), and adaptors were ligated at room temperature for 1 hr with T4 DNA ligase (New England Biolabs). Libraries were amplified with Illumina primers using the KAPA SYBR FAST qPCR Master Mix. Nextera libraries were amplified with Nextera barcoded primers using the KAPA SYBR FAST qPCR Master Mix. Illumina libraries were sequenced paired-end at 50 bp length on Illumina Hiseq2500  v4 or NovaSeq  6000  instruments.

value: PP stage

value: H9 hESCs

value: in vitro differentiated PP cells

value: Pancreatic differentiation


title: Cis + DCP-IL-12/FLT3L + ɑPD-1 replicate 1

value: Cis + DCP-IL-12/FLT3L + ɑPD-1


title: L36_H3K4me3_rep1


title: CagA KO+GES-1, 12h, rep1

value: Helicobacter pylori+GES-1


title: PH_RNASeq_Rep2

description: processed file: PH_RNASeq.2Reps.RPM.bw

value: PH stage

value: in vitro differentiated PH cells


title: WT+GES-1, 12h, rep3


title: PH_RNASeq_Rep1

description: processed file: PH_RNASeq.2Reps.RPM.bw


title: WT+GES-1, 12h, rep1


title: WT+GES-1, 12h, rep2


title: PGT_RNASeq_Rep2

description: processed file: PGT_RNASeq.2Reps.RPM.bw

value: PGT stage

value: in vitro differentiated PGT cells


title: GES-1, Control, rep3


title: GES-1, Control, rep2


title: CagA KO+GES-1, 24h, rep1


title: DE_RNASeq_Rep2

description: processed file: DE_RNASeq.2Reps.RPM.bw

value: DE stage

value: in vitro differentiated DE cells


title: TPF-resistant Fadu cell line, treated with TPF + Cinobufotalin, scRNAseq

city: Beijing

first: Meng

last: Lian

address: 1 Dongjiaomin Alley

institute: Beijing Tongren Hospital

description: 10x Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v7.0.
Assembly: hg38
Supplementary files format and content: Tab-separated values files and matrix files

source_name: TPF-resistant Fadu cell line

extract_protocol:
The cell suspension was centrifuged at 300r at 4℃ for 5min. Discard the supernatant and add 1mL of re-suspension to the centrifuge tube to re-suspend the cells, add 3mL of pre-cooled erythrocytes lysis liquid in tube (Solarbio), blowing and suction evenly. Incubate at 4℃ for 5-10min, centrifuge at 300r at 4℃ for 5min immediately after completion and remove the supernatant and add 1mL of re-suspension( Precooled 1X PBS) to fully re-suspend the cells. Test with cell counter（Countstar Rigel S2）, adjust the concentration according to the test result, the target concentration is 700-1200 cell/µL, the Cell activity is greater than 85%, and the agglomeration is less than 15%. Once the final cell concentration and activity were reached, the cells were placed on ice and 10x Genomics single cell transcriptome chip on-board experiment was carried out within 30 minutes.
Single cell RNA-seq libraries were performed with Chromium Next GEM Single Cell 3ʹ Reagent Kits v3.1 on the Chromium Controller(10× Genomics).The quality of libraries was assessed by Qubit 4.0 and the Agilent 2100. Sequencing was performed on the Illumina NovaSeq 6000 with a sequencing depth of at least 50,000 reads per cell and 150 bp (PE150) paired-end reads.

value: TPF-resistant Fadu cell line

value: TPF + Cinobufotalin


title: Fadu cell line, treated with Cinobufotalin, scRNAseq

description: 10x Genomics

source_name: Fadu cell line

value: Fadu cell line

value: Cinobufotalin


title: hESCs_RNASeq_Rep1

description: processed file: H9_RNASeq.2Reps.RPM.bw

value: undifferentiated hESCs

value: H9 human embryonic stem cells

value: WT

value: undifferentiated state


title: DE_RNASeq_Rep1

description: processed file: DE_RNASeq.2Reps.RPM.bw

value: H9 hESCs

value: Pancreatic differentiation


title: HAMEC, EndoMT, rep2

city: Charlottesville

first: Nicholas

middle: W

last: Chavkin

address: 415 Lane Road

institute: University of Virginia

description:
EndoMT_2
HAMEC_EndoMT_RNAseq.csv

data_processing:
Raw sequencing reads were demultiplexed into sample specific Fastq files, which were analyzed by aligning to reference genomes (mouse mm10 or human hg38) by Kallisto v0.46.2
Differential gene expression analysis was performed with Sleuth v0.30.0
Assembly: mm10 or hg38
Supplementary files format and content: Normalized read output per aligned gene as analyzed by Kallisto, statistical outputs of differential gene expression between groups as analyzed by Sleuth

source_name: HAMEC

extract_protocol:
RNA was purified using the RNeasy MinElute kit (Qiagen, Cat # 74204)
Purified RNA was submitted to the Yale Center for genome analysis for quality control analysis, low-input RNA sequencing amplification, PolyA RNA library preparation, and paired-end 100bp sequencing (NovaSeq v2, Illumina)

value: HAMEC

value: TGFb/TNFa/IFNg

tag: time point

value: 4 days


title: HAMEC, EndoMT, rep3

description:
EndoMT_3
HAMEC_EndoMT_RNAseq.csv


title: SC-β_RNASeq_Rep2

description: processed file: BETA_RNASeq.2Reps.RPM.bw

value: SC-beta stage

value: in vitro differentiated beta cells


title: HAMEC, Control, rep2

description:
CT_2
HAMEC_EndoMT_RNAseq.csv

value: Control


title: HAMEC, EndoMT, rep1

description:
EndoMT_1
HAMEC_EndoMT_RNAseq.csv


title: SC-β_RNASeq_Rep1


title: HAMEC, Control, rep1

description:
CT_1
HAMEC_EndoMT_RNAseq.csv


title: DLD1-expressing dnTCF7L2 3

data_processing:
We followed the pipeline detailed in Busch et al., Methods, 2022 178:49-62, PMID 31751605
Demultiplexing was performed with Flexbar 3.5.0 to produce the fastq files in this submission. Adapter trimming was also performed. No mismatches for barcode matching were allowed, and only 1 nucleotide of overlap between the read 3’ end and the beginning of the adapter was required.  Trimmed reads with length at least 15 were retained for further analyses.
The STAR 2.7.3a aligner was used to make index files based on the primary fasta file (GRCh38.primary_assembly.genome.fa) and gene annotation file (gencode.v35.annotation.gtf). The alignment was then performed with STAR to produce bam files based on the parameters in Busch et al. and a maximum read length of 52.
UMI-tools 1.0.0 was applied to remove technical duplicate reads from the bam files that arise during PCR amplification.  Duplicate reads were identified based on their read ID using the --method unique option.
Next, the duplicate-removed bam files were converted to bed format using Bedtools 2.29.2.  These bed files were shifted by 1 nucleotide in the 5’ direction in order to correctly identify crosslinked nucleotides.  The shifted bed files were used to create bedgraph coverage files, a process that was performed separately for each strand.  Bigwig format coverage files were also created.
Using PureCLIP 1.3.1, the bam files were processed to make bed files containing sites that were associated with a significant crosslinked signal.  Post-processing steps were applied to these bed files with the goal of resizing the binding sites to have uniform width 9 nucleotides, as was done in the Busch et al. manuscript. These bed files were the basis of numerous downstream analyses.
Assembly: hg38
Supplementary files format and content: As described in Busch et al., filtered bed files were created that contain information about cross-linking sites (sampleID_bs_clean.bed, where sampleID is a sample identifier).  The sampleID_coverage_20210708.txt files contain informationa above coverage.

extract_protocol: We followed the iCLIP protocol detailed in Huppertz et al., Methods, 2014 65(3):274–287, PMID 24184353

treatment_protocol: 90% confluent cells were treated/untreated with Doxycycline (2µg/ml) for 48hrs to induce the expression of dnTCF7L2/GFP

tag: biological repeats

value: Biol repe 2

tag: tissue

value: Colon

value: Epithelium

value: Doxycycline


title: DLD1-expressing dnTCF7L2 4

value: Biol repe 3


title: sample: E92_2

city: Irvine

first: ABEL

last: PLAZA FLORIDO

state: California

address: 101 Academy, Suite 150 Irvine

department: Department of Pediatrics, UC Irvine School of Medicine

institute: Pediatric Exercise and Genomics Research Center (PERC)

data_processing:
The STRTprep pipeline (which is an open-source pre-processing and analysis package for STRT RNA-seq), available at https://github.com/shka/STRTprep/tree/v3dev, was used for processing raw sequencing reads, aligning to the hg19 genome, quantitating the expression levels
Genome_build: hg19 genome
Supplementary_files_format_and_content: txt

source_name: Whole blood

extract_protocol:
Total RNA was isolated from the blood samples that contained RNA later using RiboPureTM-Blood Kit (Thermo Fisher Scientific; Waltham, Massachusetts, USA). Subsequently, GlobinLock molecular mechanism was applied to block the high globin mRNA content of erythrocytes, which is abundant in the blood and could hamper the whole blood RNA analyses
Full transcriptome analysis was performed following the modified version of single-cell tagged reverse transcription (STRT) protocol, where 10 ng of high-quality input RNA was converted into cDNA and amplified to form an Illumina-compatible library. The STRTprep pipeline, available at https://github.com/shka/STRTprep/tree/v3dev, was used for processing raw sequencing reads, aligning to the hg19 genome, quantitating the expression levels.

treatment_protocol: 500 μL blood was collected into the tube that contained 1.3 mL RNAlater solution (Ambion Inc; Austin, Texas, USA) for transcriptome analysis and was stored at -80ºC until further processing

value: Whole blood

tag: age

value: 9-11 years old

tag: Sex

value: female

tag: group

value: exercise


title: PGT_RNASeq_Rep1

description: processed file: PGT_RNASeq.2Reps.RPM.bw

value: PGT stage

value: H9 hESCs

value: in vitro differentiated PGT cells

value: WT


title: PP_RNASeq_Rep2

description: processed file: PP_RNASeq.2Reps.RPM.bw

value: PP stage

value: in vitro differentiated PP cells

value: Pancreatic differentiation


title: DLD1-expressing dnTCF7L2 2

value: Biol repe 1


title: hESCs_RNASeq_Rep2

description: processed file: H9_RNASeq.2Reps.RPM.bw

value: undifferentiated hESCs

value: H9 human embryonic stem cells

value: undifferentiated state


title: sample: E92_1


title: GES-1, Control, rep1


title: DLD1 2

value: Biol rep 2

value: Colon

value: Epithelium

value: Doxycycline


title: DLD1 1

value: Biol rep 1


title: DLD1 3

value: Biol rep 3


title: TPF-resistant Fadu cell line, treated with TPF, scRNAseq

description: 10x Genomics

value: TPF-resistant Fadu cell line

value: TPF


title: PCL12 cells, unstimulated, replicate 3

city: Milano

first: Michela

last: Riba

address: via Olgettina 60

department: COSR, Center for Omics Sciences

country: Italy

institute: IRCCS, Ospdale San Raffaele

data_processing:
COSR Center (Center for Omics Science, Ospedale San Raffaele custom pipeline
Quality checks have been done on raw data using FastQC and MultiQC
Sequence reads were trimmed for adaptor sequence/low-quality sequence using Trimmomatic
Trimmed sequence reads were mapped to Hg38 using STAR
Read count extraction has been made using Rsubread library, featureCounts function
Assembly: Hg38
Supplementary files format and content: text file contains raw counts data for all the samples

growth_protocol: 3*106 cells/ml of RPMI+10%FBS

extract_protocol:
RNA was extracted using ReliaPrep™ RNA Miniprep Systems (Promega, Madison, WI, USA) following manufacturer protocol
RNA libraries for RNA-seq were prepared using Lexogen Stranded Quantseq following manufacturer's protocols.

value: CLL (Chronic Lymphocytic Leukemia) cell line

value: unstimulated

tag: time

value: ctrl


title: PCL12 cells, unstimulated, replicate 2


title: HAMEC, Control, rep3

description:
CT_3
HAMEC_EndoMT_RNAseq.csv

value: HAMEC

value: Control

value: 4 days


title: sample: E82_1

value: Whole blood

value: 9-11 years old

value: female

value: exercise


title: PCL12 cells, unstimulated, replicate 1


title: PCL12 cells, 2.5 μg/ml CpG-ODN2006 stimulation, 4h, replicate 2

value: TLR9 stimulation with 2.5 microg/ml CpG-ODN2006


title: PCL12 cells, 2.5 μg/ml CpG-ODN2006 stimulation, 4h, replicate 3


title: PCL12 cells, 2.5 μg/ml CpG-ODN2006 stimulation, 4h, replicate 1


title: sample: E73_1


title: MEC2 cells, unstimulated, replicate 3


title: sample: E68_2


title: sample: E68_1


title: MEC2 cells, unstimulated, replicate 2


title: MEC2 cells, unstimulated, replicate 1


title: MEC2 cells, 2.5 μg/ml CpG-ODN2006 stimulation, 4h, replicate 3


title: MEC2 cells, 2.5 μg/ml CpG-ODN2006 stimulation, 4h, replicate 2


title: sample: E106_2


title: HG3 cells, unstimulated, replicate 3


title: MEC2 cells, 2.5 μg/ml CpG-ODN2006 stimulation, 4h, replicate 1


title: HG3 cells, unstimulated, replicate 1


title: sample: E106_1


title: sample: E82_2


title: HG3 cells, unstimulated, replicate 2


title: sample: C99_2

value: no exercise


title: HG3 cells, 2.5 μg/ml CpG-ODN2006 stimulation, 4h, replicate 3


title: HG3 cells, 2.5 μg/ml CpG-ODN2006 stimulation, 4h, replicate 2


title: sample: C85_2


title: sample: C99_1


title: sample: C85_1


title: sample: E73_2


title: sample: C78_1


title: sample: C78_2


title: sample: C74_1_2


title: sample: C28_1


title: sample: C70_2


title: sample: C28_2


title: sample: C74_1_1


title: sample: E93_1

value: male


title: sample: E88_2_1


title: sample: E88_2_2


title: sample: E88_1_1


title: sample: E88_1_2


title: sample: E93_2


title: sample: E84_1


title: sample: C90_2


title: sample: E84_2


title: HG3 cells, 2.5 μg/ml CpG-ODN2006 stimulation, 4h, replicate 1


title: sample: C96_1


title: sample: E69_1


title: sample: E69_2


title: sample: C74_2_2


title: sample: C90_1


title: sample: C96_2


title: sample: C71_2


title: sample: C71_1


title: sample: C67_2


title: sample: C70_1


title: sample: C74_2_1


title: sample: C110_2


title: sample: C107_2


title: sample: C67_1


title: sample: C104_1


title: sample: C110_1


title: SC-β_HDAC8_Rep2

description:
processed file: BETA_HDAC8.normbyinput.qnorm_100bp.bw
processed file: BETA_HDAC8_CPmnt_peaks.narrowPeak

value: SC-beta stage

value: H9 hESCs

value: in vitro differentiated beta cells

value: WT

value: Pancreatic differentiation


title: SC-β_HDAC8_Rep1


title: DE_HDAC8_Rep2

description:
processed file: DE_HDAC8.normbyinput.qnorm_100bp.bw
processed file: DE_HDAC8_CPmnt_peaks.narrowPeak

value: DE stage

value: in vitro differentiated DE cells


title: DE_HDAC8_Rep1


title: hESCs_HDAC8_Rep2

description:
processed file: H9_HDAC8.normbyinput.qnorm_100bp.bw
processed file: H9_HDAC8_CPmnt_peaks.narrowPeak

value: undifferentiated hESCs

value: H9 human embryonic stem cells

value: undifferentiated state


title: 12_p_C4

source_name: primary CLL cells, unstimulated

value: primary CLL cells

value: CLL (Chronic Lymphocytic Leukemia) patient-derived primary leukemic B-cells

value: NFKBIZ_plus_pairing 5

value: unstimulated

value: ctrl


title: 02_p_C4

value: NFKBIZ_plus_pairing 6


title: 09_p_CPG4

source_name: primary CLL cells, 2.5 μg/ml CpG-ODN2006 stimulation, 4h

value: NFKBIZ_plus_pairing 7

value: TLR9 stimulation with 2.5µg/ml CpG-ODN2006


title: PGT_HDAC8_Rep2

description:
processed file: PGT_HDAC8.normbyinput.qnorm_100bp.bw
processed file: PGT_HDAC8_CPmnt_peaks.narrowPeak

value: PGT stage

value: H9 hESCs

value: in vitro differentiated PGT cells


title: hESCs_HDAC8_Rep1

value: WT


title: 11_p_CPG4


title: PP_HDAC8_Rep2

description:
processed file: PP_HDAC8.normbyinput.qnorm_100bp.bw
processed file: PP_HDAC8_CPmnt_peaks.narrowPeak

value: PP stage

value: in vitro differentiated PP cells

value: Pancreatic differentiation


title: 04_p_C4

value: NFKBIZ_plus_pairing 4


title: PP_HDAC8_Rep1


title: sample: C107_1

value: Whole blood

value: 9-11 years old

value: male

value: no exercise


title: 06_m_C4

value: primary CLL cells

value: CLL (Chronic Lymphocytic Leukemia) patient-derived primary leukemic B-cells

value: NFKBIZ_minus_pairing 3

value: unstimulated


title: sample: C104_2


title: 03_p_CPG4

value: TLR9 stimulation with 2.5µg/ml CpG-ODN2006


title: 10_p_C4

value: NFKBIZ_plus_pairing 7

value: ctrl


title: SC-β_ESCO1_Rep1

description:
processed file: BETA_ESCO1.normbyinput.qnorm_100bp.bw
processed file: BETA_ESCO1_CPmnt_peaks.narrowPeak

value: SC-beta stage

value: H9 hESCs

value: in vitro differentiated beta cells


title: SC-β_ESCO1_Rep2

value: WT


title: DE_ESCO1_Rep2

description:
processed file: DE_ESCO1.normbyinput.qnorm_100bp.bw
processed file: DE_ESCO1_CPmnt_peaks.narrowPeak

value: DE stage

value: in vitro differentiated DE cells

value: Pancreatic differentiation


title: DE_ESCO1_Rep1


title: 05_m_CPG4


title: 01_p_CPG4

value: NFKBIZ_plus_pairing 6


title: hESCs_ESCO1_Rep2

description:
processed file: H9_ESCO1.normbyinput.qnorm_100bp.bw
processed file: H9_ESCO1_CPmnt_peaks.narrowPeak

value: undifferentiated hESCs

value: H9 human embryonic stem cells

value: undifferentiated state


title: PGT_HDAC8_Rep1

value: PGT stage

value: in vitro differentiated PGT cells


title: hESCs_ESCO1_Rep1


title: PGT_ESCO1_Rep2

description:
processed file: PGT_ESCO1.normbyinput.qnorm_100bp.bw
processed file: PGT_ESCO1_CPmnt_peaks.narrowPeak


title: 08_m_C4

value: primary CLL cells

value: CLL (Chronic Lymphocytic Leukemia) patient-derived primary leukemic B-cells

value: NFKBIZ_minus_pairing 2

value: unstimulated


title: 07_m_CPG4

value: TLR9 stimulation with 2.5µg/ml CpG-ODN2006


title: PGT_ESCO1_Rep1

value: H9 hESCs


title: 14_m_C4

value: NFKBIZ_minus_pairing 1

value: ctrl


title: PP_ESCO1_Rep1

description:
processed file: PP_ESCO1.normbyinput.qnorm_100bp.bw
processed file: PP_ESCO1_CPmnt_peaks.narrowPeak

value: PP stage

value: in vitro differentiated PP cells

value: WT


title: PP_YY1_Rep1

description:
processed file: PP_YY1.normbyinput.qnorm_100bp.bw
processed file: PP_YY1_CPmnt.p0.00001_peaks.narrowPeak

value: Pancreatic differentiation


title: PH_YY1_Rep2

description:
processed file: PH_YY1.normbyinput.qnorm_100bp.bw
processed file: PH_YY1_CPmnt.p0.00001_peaks.narrowPeak

value: PH stage

value: in vitro differentiated PH cells


title: PH_YY1_Rep1


title: 13_m_CPG4


title: DIPG25_2

city: Stanford

first: Michelle

last: Monje

address: 265 Campus Drive, SIM1 G3035

department: Neurology

description: polyA RNA

data_processing:
Reads were mapped to hg19 annotation using Tophat2 (Kim et al 2013) (version 2.0.13). Transcript expression was quantified against RefSeq gene annotations using featureCounts (Liao et al, 2014). Attached files indicate transcript expression via fpkm values.
Assembly: hg19
Supplementary files format and content: Raw fpkm counts of gene expression abundance for SU-DIPG21 and SU-DIPG25 cells (in csv format)
Supplementary files format and content: Metadata table with sample key (in csv format)

molecule: polyA RNA

source_name: Brain

growth_protocol: Cells are grown in Tumor Stem Media (TSM), consisting of Neurobasal (-A), DMEM F12, B27 (-A), bFGF, EGF, PDGF-AB, and heparin. See Grasso et al 2015.

extract_protocol:
RNA-seq samples were pelleted and lysed in Trizol reagent then subsequently precipitated. After extraction from Trizol, RNA-seq samples were poly(A) selected using Dynabeads mRNA Purification Kit (Life Tech) before fragmentation using Thermo AM8740 and Second Strand Synthesis. Libraries were sequenced at 1x75 on an Illumina NextSeq 500.
RNA-seq samples were poly(A) selected using Dynabeads mRNA Purification Kit (Life Tech) before fragmentation using Thermo AM8740 and Second Strand Synthesis.

value: Brain

value: Patient-derived DIPG culture


title: hESCs_YY1_Rep2

description:
processed file: H9_YY1.normbyinput.qnorm_100bp.bw
processed file: H9_YY1_CPmnt.p0.00001_peaks.narrowPeak

value: undifferentiated hESCs

value: H9 human embryonic stem cells

value: undifferentiated state


title: PGT_YY1_Rep1

description:
processed file: PGT_YY1.normbyinput.qnorm_100bp.bw
processed file: PGT_YY1_CPmnt.p0.00001_peaks.narrowPeak

value: PGT stage

value: in vitro differentiated PGT cells


title: DIPG25_1

description: polyA RNA


title: DIPG21_2

description: polyA RNA


title: SC-β_YY1_Rep2

description:
processed file: BETA_YY1.normbyinput.qnorm_100bp.bw
processed file: BETA_YY1_CPmnt.p0.00001_peaks.narrowPeak

value: SC-beta stage

value: in vitro differentiated beta cells


title: SC-β_YY1_Rep1

value: H9 hESCs


title: DE_YY1_Rep1

description:
processed file: DE_YY1.normbyinput.qnorm_100bp.bw
processed file: DE_YY1_CPmnt.p0.00001_peaks.narrowPeak

value: DE stage

value: in vitro differentiated DE cells


title: DE_YY1_Rep2


title: PP_WAPL_Rep1

description:
processed file: PP_WAPL.normbyinput.qnorm_100bp.bw
processed file: PP_WAPL_CPmnt.p0.00001_peaks.narrowPeak

value: PP stage

value: in vitro differentiated PP cells


title: PP_ESCO1_Rep2

value: WT

value: Pancreatic differentiation


title: PH_WAPL_Rep2

description:
processed file: PH_WAPL.normbyinput.qnorm_100bp.bw
processed file: PH_WAPL_CPmnt.p0.00001_peaks.narrowPeak

value: PH stage

value: in vitro differentiated PH cells


title: DIPG21_1

description: polyA RNA

value: Brain

value: Patient-derived DIPG culture


title: PTRH9_S8

city: Syracuse

first: Frank

last: Middleton

address: 505 Irving Avenue

institute: SUNY Upstate Medical Univ

description:
matrix includes transcript ID, gene ID, and values for each sample ID
sample266

data_processing:
Partek Flow
Sequence reads were trimmed for adaptor sequence/low-quality sequence using Cutadapt 1.2.1
Trimmed sequence reads were quantified to hg38 Ensembl transcripts release 105 using Salmon, using minimum assigned fragments of 10, minimum score fraction of 0.65, match value 2, mismatch value -4, gap opening value 6 and gap extension value of 2
Quantified features were filtered to eliminate those with less than 1 count in 80% or more of the samples
Normalization performed on filtered features using TPM followed by quantile and log2 transformation
Assembly: Homo sapiens hg38
Supplementary files format and content: Tab-separated values matrix file containing raw Salmon feature counts
Supplementary files format and content: Tab-separated matrix file containing filtered and normalized feature abundances

source_name: saliva

extract_protocol:
RNA was purified from saliva swabs used for clinical PCR COVID-19 testing, using Zymo Quick-RNA Viral 96 Kit or the KingFisher MagMAX Viral/Pathogen Nucleic Acid Isolation Kit
RNA-seq libraries were synthesized using TruSeq Stranded Total RNA with Ribo-Zero Globin (Illumina) according to manufacturer protocol

value: saliva

value: Infected-Vax

value: Male

tag: race

value: White or Caucasian

tag: ethnicity

value: Not Hispanic


title: PH_WAPL_Rep1

tag: developmental stage


title: PTRH8_S16

description:
matrix includes transcript ID, gene ID, and values for each sample ID
sample265

value: Unknown/Other


title: PGT_WAPL_Rep1

description:
processed file: PGT_WAPL.normbyinput.qnorm_100bp.bw
processed file: PGT_WAPL_CPmnt.p0.00001_peaks.narrowPeak

value: PGT stage

value: H9 hESCs

value: in vitro differentiated PGT cells


title: hESCs_WAPL_Rep2

description:
processed file: H9_WAPL.normbyinput.qnorm_100bp.bw
processed file: H9_WAPL_CPmnt.p0.00001_peaks.narrowPeak

value: undifferentiated hESCs

value: H9 human embryonic stem cells

value: undifferentiated state


title: DE_WAPL_Rep2

description:
processed file: DE_WAPL.normbyinput.qnorm_100bp.bw
processed file: DE_WAPL_CPmnt.p0.00001_peaks.narrowPeak

value: DE stage

value: in vitro differentiated DE cells

value: WT

value: Pancreatic differentiation


title: hESCs_WAPL_Rep1


title: PTRH7_S8

description:
matrix includes transcript ID, gene ID, and values for each sample ID
sample264


title: PTRH6_S16

description:
matrix includes transcript ID, gene ID, and values for each sample ID
sample263

value: Infected-Unvax


title: SC-β_WAPL_Rep2

description:
processed file: BETA_WAPL.normbyinput.qnorm_100bp.bw
processed file: BETA_WAPL_CPmnt.p0.00001_peaks.narrowPeak

value: SC-beta stage

value: in vitro differentiated beta cells


title: DE_WAPL_Rep1


title: SC-β_WAPL_Rep1


title: PH_S2P_Rep2

description:
processed file: PH_S2P.normbyinput.qnorm_100bp.bw
processed file: PH_S2P_ChIP_Rep_peaks.narrowPeak

value: PH stage

value: in vitro differentiated PH cells


title: hESCs_YY1_Rep1


title: PTRH4_S8

description:
matrix includes transcript ID, gene ID, and values for each sample ID
sample261

value: saliva

value: Male

value: White or Caucasian

value: Hispanic


title: PTRH5_S8

description:
matrix includes transcript ID, gene ID, and values for each sample ID
sample262

value: Female

value: Not Hispanic


title: SC-β_S2P_Rep2

description:
processed file: BETA_S2P.normbyinput.qnorm_100bp.bw
processed file: BETA_S2P_ChIP_Rep_peaks.narrowPeak

value: H9 hESCs


title: PP_S2P_Rep1

description:
processed file: PP_S2P.normbyinput.qnorm_100bp.bw
processed file: PP_S2P_ChIP_peaks.narrowPeak

value: PP stage

value: in vitro differentiated PP cells


title: PH_S2P_Rep1


title: PGT_S2P_Rep1

description:
processed file: PGT_S2P.normbyinput.qnorm_100bp.bw
processed file: PGT_S2P_ChIP_peaks.narrowPeak

value: PGT stage

value: in vitro differentiated PGT cells


title: PTRH3_S16

description:
matrix includes transcript ID, gene ID, and values for each sample ID
sample260


title: hESCs_S2P_Rep1

description:
processed file: H9_S2P.normbyinput.qnorm_100bp.bw
processed file: H9_S2P_ChIP_peaks.narrowPeak

value: undifferentiated hESCs

value: H9 human embryonic stem cells

value: WT

value: undifferentiated state


title: PTRH1_S8

description:
matrix includes transcript ID, gene ID, and values for each sample ID
sample258

value: Infected-Unvax


title: PTRH2_S8

description:
matrix includes transcript ID, gene ID, and values for each sample ID
sample259


title: PP_CTCF_Rep2

description:
processed file: PP_CTCF.normbyinput.qnorm_100bp.bw
processed file: PP-CTCF-CPmnt-Rep2_ChIP.p0.00001_peaks.narrowPeak

value: Pancreatic differentiation


title: DE_S2P_Rep1

description:
processed file: DE_S2P.normbyinput.qnorm_100bp.bw
processed file: DE_S2P_ChIP_peaks.narrowPeak

value: DE stage

value: in vitro differentiated DE cells


title: SC-β_S2P_Rep1

value: SC-beta stage

value: in vitro differentiated beta cells


title: PTRH11_S16

description:
matrix includes transcript ID, gene ID, and values for each sample ID
sample257

value: saliva

value: Control-Unvax

value: Female

value: White or Caucasian

value: Hispanic


title: DE_CTCF_Rep2

description:
processed file: DE_CTCF.normbyinput.qnorm_100bp.bw
processed file: DE-CTCF-CPmnt-Rep2_ChIP.p0.00001_peaks.narrowPeak

value: H9 hESCs


title: PGT_CTCF_Rep2

description:
processed file: PGT_CTCF.normbyinput.qnorm_100bp.bw
processed file: PGT-CTCF-CPmnt-Rep2_ChIP.p0.00001_peaks.narrowPeak

value: PGT stage

value: in vitro differentiated PGT cells


title: PTRG9_S7

description:
matrix includes transcript ID, gene ID, and values for each sample ID
sample255

value: Infected-Vax

value: Male

value: Not Hispanic


title: PGT_Rad21

description:
processed file: PGT_Rad21.normbyinput.qnorm_100bp.bw
processed file: PGT_Rad21_ChIP_peaks.narrowPeak

value: WT


title: PTRH10_S12

description:
matrix includes transcript ID, gene ID, and values for each sample ID
sample256

value: Control-Vax


title: PP_Rad21

description:
processed file: PP_Rad21.normbyinput.qnorm_100bp.bw
processed file: PP_Rad21_ChIP_peaks.narrowPeak

value: PP stage

value: in vitro differentiated PP cells

value: Pancreatic differentiation


title: hESCs_Rad21

description:
processed file: H9_Rad21.normbyinput.qnorm_100bp.bw
processed file: H9_Rad21_ChIP_peaks.narrowPeak

value: undifferentiated hESCs

value: H9 human embryonic stem cells

value: undifferentiated state


title: PH_Rad21

description:
processed file: PH_Rad21.normbyinput.qnorm_100bp.bw
processed file: PH_Rad21_ChIP_peaks.narrowPeak

value: PH stage

value: in vitro differentiated PH cells


title: DE_Rad21

description:
processed file: DE_Rad21.normbyinput.qnorm_100bp.bw
processed file: DE_Rad21_ChIP_peaks.narrowPeak

value: DE stage

value: in vitro differentiated DE cells


title: SC-β_Rad21

description:
processed file: BETA_Rad21.normbyinput.qnorm_100bp.bw
processed file: BETA_Rad21_ChIP_peaks.narrowPeak

value: SC-beta stage

value: H9 hESCs

value: in vitro differentiated beta cells


title: PP_NIPBL

description:
processed file: PP_NIPBL.normbyinput.qnorm_100bp.bw
processed file: PP_NIPBL_CPmnt.p0.00001_peaks.narrowPeak


title: PH_NIPBL_Rep2

description:
processed file: PH_NIPBL.normbyinput.qnorm_100bp.bw
processed file: PH_NIPBL_CPmnt.p0.00001_peaks.narrowPeak


title: PH_NIPBL_Rep1