title: spinal  tuberculosis patient 9

city: Xi’an

first: Zili

last: Wang

address: NO.737, Xitai Road, High-tech Zone

department: Spine Surgery

institute: Xi’an International Medical Center Hospital Affiliated to Northwest University

description:
XT18
After quality control, the miRCURY™ Hy3™/Hy5™ Power labeling kit (Exiqon, Vedbaek, Denmark) was used according to the manufacturer’s protocol. The Hy3™-labeled samples were hybridized on the miRCURYTM LNA Array (v.19.0) (Exiqon) according to the array manual. And the data were collected using the Axon GenePix 4000B microarray scanner (Axon Instruments, Foster City, CA).

data_processing: Scanned images were then imported into GenePix Pro 6.0 software (Axon) for grid alignment and data extraction. Replicated miRNAs were averaged and miRNAs that intensities>=30 in all samples were chosen for calculating normalization factor

source_name: Plasma

extract_protocol: Total RNA was isolated from 200 μl of plasma using a miRcute miRNA extraction kit (TIANGEN, China) according to the manufacturer’s protocol.

tag: diagnosis

value: spinal  tuberculosis

value: Plasma

tag: molecule subtype

value: microRNA


title: spinal  tuberculosis patient 10

status: Public on Feb 23 2023

type: RNA

country: China

description:
XT19
After quality control, the miRCURY™ Hy3™/Hy5™ Power labeling kit (Exiqon, Vedbaek, Denmark) was used according to the manufacturer’s protocol. The Hy3™-labeled samples were hybridized on the miRCURYTM LNA Array (v.19.0) (Exiqon) according to the array manual. And the data were collected using the Axon GenePix 4000B microarray scanner (Axon Instruments, Foster City, CA).

molecule: total RNA

organism: Homo sapiens

tag: cell type


title: spinal  tuberculosis patient 8

description:
XT16
After quality control, the miRCURY™ Hy3™/Hy5™ Power labeling kit (Exiqon, Vedbaek, Denmark) was used according to the manufacturer’s protocol. The Hy3™-labeled samples were hybridized on the miRCURYTM LNA Array (v.19.0) (Exiqon) according to the array manual. And the data were collected using the Axon GenePix 4000B microarray scanner (Axon Instruments, Foster City, CA).


title: spinal  tuberculosis patient 3

description:
XT5
After quality control, the miRCURY™ Hy3™/Hy5™ Power labeling kit (Exiqon, Vedbaek, Denmark) was used according to the manufacturer’s protocol. The Hy3™-labeled samples were hybridized on the miRCURYTM LNA Array (v.19.0) (Exiqon) according to the array manual. And the data were collected using the Axon GenePix 4000B microarray scanner (Axon Instruments, Foster City, CA).


title: spinal  tuberculosis patient 5

description:
XT12
After quality control, the miRCURY™ Hy3™/Hy5™ Power labeling kit (Exiqon, Vedbaek, Denmark) was used according to the manufacturer’s protocol. The Hy3™-labeled samples were hybridized on the miRCURYTM LNA Array (v.19.0) (Exiqon) according to the array manual. And the data were collected using the Axon GenePix 4000B microarray scanner (Axon Instruments, Foster City, CA).


title: spinal  tuberculosis patient 6

description:
XT13
After quality control, the miRCURY™ Hy3™/Hy5™ Power labeling kit (Exiqon, Vedbaek, Denmark) was used according to the manufacturer’s protocol. The Hy3™-labeled samples were hybridized on the miRCURYTM LNA Array (v.19.0) (Exiqon) according to the array manual. And the data were collected using the Axon GenePix 4000B microarray scanner (Axon Instruments, Foster City, CA).


title: spinal  tuberculosis patient 7

description:
XT14
After quality control, the miRCURY™ Hy3™/Hy5™ Power labeling kit (Exiqon, Vedbaek, Denmark) was used according to the manufacturer’s protocol. The Hy3™-labeled samples were hybridized on the miRCURYTM LNA Array (v.19.0) (Exiqon) according to the array manual. And the data were collected using the Axon GenePix 4000B microarray scanner (Axon Instruments, Foster City, CA).


title: DGAT2i treated APOB-/- organoids from donor 1

type: SRA

city: Utrecht

first: Delilah

last: Hendriks

address: Uppsalalaan 8

country: Netherlands

institute: Hubrecht Institute

library_source: transcriptomic

data_processing:
Quality control on the sequence reads from the raw FASTQ files was done with FastQC.
TrimGalore was used to trim reads based on quality and adapter presence after which FastQC was again used to check the resulting quality.
rRNA reads were filtered out using SortMeRNA after which the resulting reads were aligned to the reference genome fasta (genome.fa) using the STAR aligner.
Followup QC on the mapped (bam) files was done using Sambamba, RSeQC and PreSeq.
Read counts were then generated using the Subread FeatureCounts module with the Homo_sapiens.GRCh37.74.gtf file as annotation
Assembly: hg19
Supplementary files format and content: csv file including feature raw counts for all samples

source_name: Liver

growth_protocol: Organoids were cultured in a humidified atmosphere with 5% CO2 at 37C

extract_protocol:
total RNA was isolated using TRIzol Reagent (Thermo Fisher)
RNA libraries were prepared using TruSeq Stranded mRNA polyA kit (Illumina)

treatment_protocol: Organoids were treated for 7 days with the indicated drug or vehicle

tag: individual

value: donor 1

tag: tissue

value: Liver

tag: cell line

value: Human hepatocyte organoid

value: Hepatocyte

tag: genotype

value: APOB-mutant

tag: treatment

value: DGAT2i 7 days


title: FASi treated APOB-/- organoids from donor 1

value: FASi 7 days


title: healty volunteer 5

description:
X9
After quality control, the miRCURY™ Hy3™/Hy5™ Power labeling kit (Exiqon, Vedbaek, Denmark) was used according to the manufacturer’s protocol. The Hy3™-labeled samples were hybridized on the miRCURYTM LNA Array (v.19.0) (Exiqon) according to the array manual. And the data were collected using the Axon GenePix 4000B microarray scanner (Axon Instruments, Foster City, CA).

value: non-spinal tuberculosis


title: spinal  tuberculosis patient 11

description:
XT20
After quality control, the miRCURY™ Hy3™/Hy5™ Power labeling kit (Exiqon, Vedbaek, Denmark) was used according to the manufacturer’s protocol. The Hy3™-labeled samples were hybridized on the miRCURYTM LNA Array (v.19.0) (Exiqon) according to the array manual. And the data were collected using the Axon GenePix 4000B microarray scanner (Axon Instruments, Foster City, CA).


title: healty volunteer 3

description:
X13
After quality control, the miRCURY™ Hy3™/Hy5™ Power labeling kit (Exiqon, Vedbaek, Denmark) was used according to the manufacturer’s protocol. The Hy3™-labeled samples were hybridized on the miRCURYTM LNA Array (v.19.0) (Exiqon) according to the array manual. And the data were collected using the Axon GenePix 4000B microarray scanner (Axon Instruments, Foster City, CA).


title: healty volunteer 1

description:
X3
After quality control, the miRCURY™ Hy3™/Hy5™ Power labeling kit (Exiqon, Vedbaek, Denmark) was used according to the manufacturer’s protocol. The Hy3™-labeled samples were hybridized on the miRCURYTM LNA Array (v.19.0) (Exiqon) according to the array manual. And the data were collected using the Axon GenePix 4000B microarray scanner (Axon Instruments, Foster City, CA).


title: spinal  tuberculosis patient 1

description:
XT2
After quality control, the miRCURY™ Hy3™/Hy5™ Power labeling kit (Exiqon, Vedbaek, Denmark) was used according to the manufacturer’s protocol. The Hy3™-labeled samples were hybridized on the miRCURYTM LNA Array (v.19.0) (Exiqon) according to the array manual. And the data were collected using the Axon GenePix 4000B microarray scanner (Axon Instruments, Foster City, CA).


title: healty volunteer 4

description:
X6
After quality control, the miRCURY™ Hy3™/Hy5™ Power labeling kit (Exiqon, Vedbaek, Denmark) was used according to the manufacturer’s protocol. The Hy3™-labeled samples were hybridized on the miRCURYTM LNA Array (v.19.0) (Exiqon) according to the array manual. And the data were collected using the Axon GenePix 4000B microarray scanner (Axon Instruments, Foster City, CA).


title: healty volunteer 2

description:
X1
After quality control, the miRCURY™ Hy3™/Hy5™ Power labeling kit (Exiqon, Vedbaek, Denmark) was used according to the manufacturer’s protocol. The Hy3™-labeled samples were hybridized on the miRCURYTM LNA Array (v.19.0) (Exiqon) according to the array manual. And the data were collected using the Axon GenePix 4000B microarray scanner (Axon Instruments, Foster City, CA).


title: healty volunteer 8

description:
X15
After quality control, the miRCURY™ Hy3™/Hy5™ Power labeling kit (Exiqon, Vedbaek, Denmark) was used according to the manufacturer’s protocol. The Hy3™-labeled samples were hybridized on the miRCURYTM LNA Array (v.19.0) (Exiqon) according to the array manual. And the data were collected using the Axon GenePix 4000B microarray scanner (Axon Instruments, Foster City, CA).


title: spinal  tuberculosis patient 4

description:
XT11
After quality control, the miRCURY™ Hy3™/Hy5™ Power labeling kit (Exiqon, Vedbaek, Denmark) was used according to the manufacturer’s protocol. The Hy3™-labeled samples were hybridized on the miRCURYTM LNA Array (v.19.0) (Exiqon) according to the array manual. And the data were collected using the Axon GenePix 4000B microarray scanner (Axon Instruments, Foster City, CA).


title: healty volunteer 7

description:
X14
After quality control, the miRCURY™ Hy3™/Hy5™ Power labeling kit (Exiqon, Vedbaek, Denmark) was used according to the manufacturer’s protocol. The Hy3™-labeled samples were hybridized on the miRCURYTM LNA Array (v.19.0) (Exiqon) according to the array manual. And the data were collected using the Axon GenePix 4000B microarray scanner (Axon Instruments, Foster City, CA).


title: healty volunteer 6

description:
X10
After quality control, the miRCURY™ Hy3™/Hy5™ Power labeling kit (Exiqon, Vedbaek, Denmark) was used according to the manufacturer’s protocol. The Hy3™-labeled samples were hybridized on the miRCURYTM LNA Array (v.19.0) (Exiqon) according to the array manual. And the data were collected using the Axon GenePix 4000B microarray scanner (Axon Instruments, Foster City, CA).


title: P13_N716_S522_HSR

city: London

first: Simona

last: Parrinello

address: 72 Huntley Street

country: United Kingdom

institute: UCL Cancer Institute

data_processing:
STAR-2.7.10b was used perform sample de-multiplexing, barcode processing and single cell gene unique molecular identifier (UMI) counting, while a digital expression matrix was obtained for each experiment with default parameters, mapped to the edited mm10 reference, where tdTomato's sequence was added.
Assembly: Edited mm10 with added tdTomato-WPRE-bGH poly(A) signal sequence taken from Ai9 Addgene plasmid (Plasmid #22799) sequence.
Supplementary files format and content: There is processed files that are output from STAR-2.7.10b.

organism: Mus musculus

source_name: Acutely FACS-purified tdTomato+ astrocyte-derived cells from aged injured cortex

extract_protocol:
Cells were isolated from adult brain using Miltenyi Adult Brain Dissociation kit. Following FACS-purification of tdTomato cells into 384 well plates, libraries were generated using Smartseq3 method.
Smartseq3 Single-cell RNA-seq

treatment_protocol: Endoxifen intracortical injection at 2-3month old. Collected and FACS-purified at > 1 year old


title: spinal  tuberculosis patient 2

description:
XT3
After quality control, the miRCURY™ Hy3™/Hy5™ Power labeling kit (Exiqon, Vedbaek, Denmark) was used according to the manufacturer’s protocol. The Hy3™-labeled samples were hybridized on the miRCURYTM LNA Array (v.19.0) (Exiqon) according to the array manual. And the data were collected using the Axon GenePix 4000B microarray scanner (Axon Instruments, Foster City, CA).


title: P15_N719_S522_HSR


title: P16_N720_S522_HSR


title: P11_N714_S522_HSR


title: P17_N721_S522_HSR


title: P12_N715_S522_HSR


title: spinal  tuberculosis patient 12

description:
XT23
After quality control, the miRCURY™ Hy3™/Hy5™ Power labeling kit (Exiqon, Vedbaek, Denmark) was used according to the manufacturer’s protocol. The Hy3™-labeled samples were hybridized on the miRCURYTM LNA Array (v.19.0) (Exiqon) according to the array manual. And the data were collected using the Axon GenePix 4000B microarray scanner (Axon Instruments, Foster City, CA).


title: P10_N712_S522_HSR


title: P09_N711_S522_HSR


title: P08_N710_S522_HSR


title: P06_N706_S522_HSR


title: P05_N705_S522_HSR


title: P04_N704_S522_HSR


title: P14_N718_S522_HSR


title: P03_N703_S522_HSR


title: P02_N702_S522_HSR


title: P01_N701_S522_HSR


title: O16_N720_S521_HSR


title: O14_N718_S521_HSR


title: O13_N716_S521_HSR


title: O12_N715_S521_HSR


title: O10_N712_S521_HSR


title: O11_N714_S521_HSR


title: O07_N707_S521_HSR


title: O01_N701_S521_HSR


title: O03_N703_S521_HSR


title: O05_N705_S521_HSR


title: O04_N704_S521_HSR


title: N17_N721_S520_HSR


title: O06_N706_S521_HSR


title: N16_N720_S520_HSR


title: O02_N702_S521_HSR


title: N15_N719_S520_HSR


title: P07_N707_S522_HSR


title: N14_N718_S520_HSR


title: N12_N715_S520_HSR


title: N13_N716_S520_HSR


title: N11_N714_S520_HSR


title: N09_N711_S520_HSR


title: O17_N721_S521_HSR


title: N10_N712_S520_HSR


title: N08_N710_S520_HSR


title: O15_N719_S521_HSR


title: O09_N711_S521_HSR


title: N06_N706_S520_HSR


title: N07_N707_S520_HSR


title: N05_N705_S520_HSR


title: O08_N710_S521_HSR


title: N02_N702_S520_HSR


title: N01_N701_S520_HSR


title: M17_N721_S518_HSR


title: N03_N703_S520_HSR


title: M11_N714_S518_HSR


title: N04_N704_S520_HSR


title: M15_N719_S518_HSR


title: M14_N718_S518_HSR


title: M13_N716_S518_HSR


title: M16_N720_S518_HSR


title: L13_N716_S517_HSR


title: M01_N701_S518_HSR


title: M07_N707_S518_HSR


title: L15_N719_S517_HSR


title: M08_N710_S518_HSR


title: M10_N712_S518_HSR


title: L17_N721_S517_HSR


title: M02_N702_S518_HSR


title: L14_N718_S517_HSR


title: M04_N704_S518_HSR


title: L11_N714_S517_HSR


title: L12_N715_S517_HSR


title: M06_N706_S518_HSR


title: L16_N720_S517_HSR


title: M05_N705_S518_HSR


title: L09_N711_S517_HSR


title: M09_N711_S518_HSR


title: M03_N703_S518_HSR


title: M12_N715_S518_HSR


title: L06_N706_S517_HSR


title: L04_N704_S517_HSR


title: L05_N705_S517_HSR


title: L07_N707_S517_HSR


title: K17_N721_S516_HSR


title: L02_N702_S517_HSR


title: L08_N710_S517_HSR


title: L01_N701_S517_HSR


title: K16_N720_S516_HSR


title: L10_N712_S517_HSR


title: K10_N712_S516_HSR


title: K14_N718_S516_HSR


title: K13_N716_S516_HSR


title: K09_N711_S516_HSR


title: K15_N719_S516_HSR


title: J14_N718_S515_HSR


title: K05_N705_S516_HSR


title: K11_N714_S516_HSR


title: K06_N706_S516_HSR


title: K04_N704_S516_HSR


title: K07_N707_S516_HSR


title: L03_N703_S517_HSR


title: J17_N721_S515_HSR


title: K02_N702_S516_HSR


title: J15_N719_S515_HSR


title: K01_N701_S516_HSR


title: K03_N703_S516_HSR


title: J11_N714_S515_HSR


title: J16_N720_S515_HSR


title: J10_N712_S515_HSR


title: J09_N711_S515_HSR


title: J13_N716_S515_HSR


title: J08_N710_S515_HSR


title: J07_N707_S515_HSR


title: J05_N705_S515_HSR


title: J04_N704_S515_HSR


title: K08_N710_S516_HSR


title: K12_N715_S516_HSR


title: J02_N702_S515_HSR


title: J03_N703_S515_HSR


title: I17_N721_S513_HSR


title: I14_N718_S513_HSR


title: I16_N720_S513_HSR


title: J12_N715_S515_HSR


title: J06_N706_S515_HSR


title: J01_N701_S515_HSR


title: I11_N714_S513_HSR


title: I08_N710_S513_HSR


title: I03_N703_S513_HSR


title: I09_N711_S513_HSR


title: I15_N719_S513_HSR


title: I07_N707_S513_HSR


title: I02_N702_S513_HSR


title: I12_N715_S513_HSR


title: I01_N701_S513_HSR


title: I06_N706_S513_HSR


title: H17_N721_S511_HSR


title: I13_N716_S513_HSR


title: H16_N720_S511_HSR


title: H15_N719_S511_HSR


title: I04_N704_S513_HSR


title: H13_N716_S511_HSR


title: H14_N718_S511_HSR


title: I10_N712_S513_HSR


title: H11_N714_S511_HSR


title: H10_N712_S511_HSR


title: H12_N715_S511_HSR


title: H09_N711_S511_HSR


title: I05_N705_S513_HSR


title: H08_N710_S511_HSR


title: H07_N707_S511_HSR


title: H04_N704_S511_HSR


title: H06_N706_S511_HSR


title: H02_N702_S511_HSR


title: H05_N705_S511_HSR


title: H03_N703_S511_HSR


title: G17_N721_S510_HSR


title: G07_N707_S510_HSR


title: G09_N711_S510_HSR


title: G06_N706_S510_HSR


title: G16_N720_S510_HSR


title: G14_N718_S510_HSR


title: G03_N703_S510_HSR


title: G02_N702_S510_HSR


title: G05_N705_S510_HSR


title: G12_N715_S510_HSR


title: H01_N701_S511_HSR


title: G13_N716_S510_HSR


title: G08_N710_S510_HSR


title: G04_N704_S510_HSR


title: F17_N721_S508_HSR


title: F15_N719_S508_HSR


title: G01_N701_S510_HSR


title: F11_N714_S508_HSR


title: F14_N718_S508_HSR


title: F13_N716_S508_HSR


title: F12_N715_S508_HSR


title: G10_N712_S510_HSR


title: F10_N712_S508_HSR


title: G15_N719_S510_HSR


title: F08_N710_S508_HSR


title: G11_N714_S510_HSR


title: F09_N711_S508_HSR


title: F06_N706_S508_HSR


title: F05_N705_S508_HSR


title: F07_N707_S508_HSR


title: F04_N704_S508_HSR


title: F01_N701_S508_HSR


title: F03_N703_S508_HSR


title: E09_N711_S507_HSR


title: E08_N710_S507_HSR


title: E14_N718_S507_HSR


title: E12_N715_S507_HSR


title: E17_N721_S507_HSR


title: E15_N719_S507_HSR


title: E07_N707_S507_HSR


title: E11_N714_S507_HSR


title: E10_N712_S507_HSR


title: E04_N704_S507_HSR


title: E05_N705_S507_HSR


title: E06_N706_S507_HSR


title: E03_N703_S507_HSR


title: E02_N702_S507_HSR


title: F02_N702_S508_HSR


title: E01_N701_S507_HSR


title: E13_N716_S507_HSR


title: D15_N719_S506_HSR


title: D16_N720_S506_HSR


title: D14_N718_S506_HSR


title: D17_N721_S506_HSR


title: D07_N707_S506_HSR


title: D09_N711_S506_HSR


title: D10_N712_S506_HSR


title: D13_N716_S506_HSR


title: D12_N715_S506_HSR


title: D08_N710_S506_HSR


title: D11_N714_S506_HSR


title: D03_N703_S506_HSR


title: D01_N701_S506_HSR


title: D02_N702_S506_HSR


title: C13_N716_S505_HSR


title: C14_N718_S505_HSR


title: C15_N719_S505_HSR


title: C16_N720_S505_HSR


title: C11_N714_S505_HSR


title: C12_N715_S505_HSR


title: C09_N711_S505_HSR


title: C05_N705_S505_HSR


title: C10_N712_S505_HSR


title: C06_N706_S505_HSR


title: C07_N707_S505_HSR


title: D06_N706_S506_HSR


title: C03_N703_S505_HSR


title: C08_N710_S505_HSR


title: C04_N704_S505_HSR


title: C02_N702_S505_HSR


title: C01_N701_S505_HSR


title: B16_N720_S503_HSR


title: B15_N719_S503_HSR


title: B17_N721_S503_HSR


title: B14_N718_S503_HSR


title: B12_N715_S503_HSR


title: D05_N705_S506_HSR


title: D04_N704_S506_HSR


title: B13_N716_S503_HSR


title: B11_N714_S503_HSR


title: C17_N721_S505_HSR


title: B06_N706_S503_HSR


title: B05_N705_S503_HSR


title: B07_N707_S503_HSR


title: B08_N710_S503_HSR


title: B04_N704_S503_HSR


title: B02_N702_S503_HSR


title: B03_N703_S503_HSR


title: A17_N721_S502_HSR


title: A15_N719_S502_HSR


title: A14_N718_S502_HSR


title: A16_N720_S502_HSR


title: A10_N712_S502_HSR


title: A13_N716_S502_HSR


title: A09_N711_S502_HSR


title: A12_N715_S502_HSR


title: A11_N714_S502_HSR


title: B10_N712_S503_HSR


title: A05_N705_S502_HSR


title: A08_N710_S502_HSR


title: A06_N706_S502_HSR


title: A04_N704_S502_HSR


title: A07_N707_S502_HSR


title: B09_N711_S503_HSR


title: LB258-2-CTRL_S10

city: Alhambra

first: Eva

last: Janeckova

address: 2250 Alcazar street

country: USA

institute: USC, CCMB

data_processing:
Illumina Casava1.8 software used for basecalling.
Raw reads were trimmed and aligned using STAR with the mm10 genome
CPM was used to normalize the data and differential expression was calculated by selecting transcripts that changed with p < 0.05
Assembly: mm10
Supplementary files format and content: tab-delimited text files include lognormal with shrinkage mean value for each feature in individual sample.

source_name: Soft palate

growth_protocol: Mice were housed in pathogen-free conditions.

extract_protocol:
Palate samples from b-cateninfl/fl (control) and Osr2-Cre;b-cateninfl/fl (mutant) mice were collected at E14.0 for RNA isolation with RNeasy Micro Kit (Qiagen) according to the manufacturer’s protocol
cDNA library preparation and sequencing were performed at the UCLA Technology Center for Genomics and Bioinformatics.

tag: strain

value: wild type

value: Soft palate

tag: age


title: LB258-6-MUT_S14


title: LB258-7-MUT_S15


title: LB258-1-CTRL_S9


title: A01_N701_S502_HSR


title: A02_N702_S502_HSR


title: A03_N703_S502_HSR


title: LB258-5-MUT_S13


title: H2BK11ac ChIP in ESC rep1

city: Copenhagen N

first: Chunarum

last: Choudhary

state: --- Select a state ---

address: Blegdamsvej 3B

department: Novo Nordisk Foundation Center for Protein Research

country: Denmark

institute: University of Copenhagen

description:
H2BK11ac ChIP-seq. Control
ESC_Ctrl_TC0_H2BK11ac.RM456_CC20.n2.smooth.bw
ESC_Ctrl_TC0_H2BK11ac.RM456_CC20_peak.bed

library_source: genomic

data_processing:
Read alignment was performed using BWA with default parameters. Low mapping quality read (MAPQ 10) and duplicated reads were removed using samtools. The DAC Blacklisted Regions were also omitted from the bam file using bedtools. Peaks were called using Lanceotron with default model and filtered if the input subtracted peak height < 8rpm.
For H3K27ac ChIP-seq samples, the data in this data series are merged with the GSE146324 data sets and analyzed.
Assembly: mm10, hg19
Supplementary files format and content: bigWig

molecule: genomic DNA

source_name: mouse ES cells

growth_protocol: E14Tg2A Rosa26-Cre Oct4-IRES-Puro mouse ESCs were used for all experiments 11932748. ESCs were cultured in a custom-made N2B27 medium consisting of 1:1 mix of DMEM/F12 and Neurobasal medium, without L-arginine and L-lysine (C.C.Pro GmbH, Oberdorla). The media was supplemented with L-arginine, L-lysine, 1000 units/ml leukemia inhibitory factor (LIF) (Merck Millipore), 1µM PD0325901, 3µM CT-99021 (custom-made by ABCR), 100µM 2-mercaptoethanol, 150µM sodium pyruvate, 0.5x B27 supplement (Thermo Fisher Scientific), as well as with 0.5x N2 supplement (made in house; or from Thermo Fisher Scientific). Human SH-SY5Y cell line was cultured in RPMI1640 medium supplementated with 10%  fetal bovine serum, (100U/ml) penicillin and (100ug/ml) streptmycin.

extract_protocol:
Cells were cross-linked for 10 min at room temperature with 1% formaldehyde solution with gentle agitation and quenched with 0.125 M glycine. Cross-linked cells were washed once with PBS, added swelling buffer (10 mM Tris-HCl pH8.0, 1.5 mM MgCl2, 10 mM NaCl, 0.5% NP-40) and incubated on ice for 10 minutes. After centrifugation, pellets were suspended with RIPA buffer (10 mM Tris-HCl pH8.0, 1 mM EDTA, 140 mM NaCl, 1% Triton X-100, 0.1% SDS, 0.1% Sodium Deoxycholate) containing proteinase inhibitor cocktail (Roche), and then were sonicated by using a BioRuptor sonicator (Diagenode). After centrifugation, solubilized chromatin was recovered and incubated with 5 µg of antibody bound to protein A/G magnetic beads (Pierce). After overnight incubation at 4ºC, the magnetic beads were washed with RIPA buffer twice, RIPA high salt buffer (10 mM Tris-HCl pH8.0, 1 mM EDTA, 500 mM NaCl, 1% Triton X-100, 0.1% SDS, 0.1% Sodium Deoxycholate), LiCl buffer (10 mM Tris-HCl pH8.0, 1 mM EDTA, 250 mM LiCl, 0.5% NP-40, 0.5% Sodium Deoxycholate) and TE buffer. The bound materials were eluted with elution buffer (10 mM Tris-HCl pH8.0, 5 mM EDTA, 300 mM NaCl, 0.1% SDS) overnight at 65ºC and treated with RNaseA for 30 min for 37°C and further incubation with Proteinase K for 1 hour at 37ºC. Then DNA was purified with a PCR purification kit (Qiagen).
ChIP-seq libraries were prepared by using the NEBNext Ultra II DNA prep kit (NEB E7645) following the manufacturer's instruction and sequenced on a Next-Seq 500 Sequencer (Illumina).

treatment_protocol: A-485 (10uM) or NVP2 (10uM) were treated for indicated time. For control samples, 0.1 % DMSO was added.

value: ES cells

tag: chip antibody

value: H2BK11ac (RevMAb, RM456)


title: H2BK20ac (CST34156) ChIP in ESC after NVP2 120min treatment rep1

description:
H2BK20ac (CST34156)  ChIP-seq in ESC. Cells were treated with 100nM NVP2 for 120 min
ESC_NVP2_100nM_TC120_H2BK20ac.CST34156_CC27.n2.smooth.bw

value: H2BK20ac (CST, CST34156)


title: MLLAF9WTM3

city: Brisbane

first: Jasmin

last: Straube

state: QLD

address: 300 Herston Rd

country: Australia

institute: QIMR Berghofer

data_processing:
Reads were trimmed for adapter sequences using Cutadapt (version 1.11) and aligned using STAR (version 2.5.2a) to the GRCm38 assembly using the gene, transcript, and exon features of Ensembl (release 67) gene model. Expression was estimated using RSEM (version 1.2.30).
Transcripts with zero read counts across all samples were removed prior analysis. Normalisation of RSEM expected read counts was performed by dividing by million reads mapped to generate counts per million (CPM), followed by the trimmed mean of M-values (TMM) method from the edgeR package.
Assembly: GRCm38
Supplementary files format and content: tab-delimited text files include RSEM expected read count values for each sample

source_name: spleen

extract_protocol:
GFP+ splenocytes of secondary transplant leukemic C57BL/6J immunocompetent or Rag2-/-γc-/- immunodeficient  mice was isolated.
cDNA libraries were prepared using the NEBNext Ultra RNA Library Prep kit with the polyA selection module (New England Biolabs) and purified with AMPure beads (Agilent). Libraries were quantified with the KAPA Library Quantification Kit for Illumina (Kapa Biosystems) and pooled. Sequencing was performed on the Illumina NextSeq 500/550 Sequencer High Output mode (1 × 75 bp).

value: spleen

value: GFP+ splenocytes

tag: disease state

value: Secondary transplant acute myeloid leukemia


title: MLLAF9WTM4


title: H2BK20ac (CST34156) ChIP in ESC

description:
H2BK20ac (CST34156) ChIP-seq in ESC. Control
ESC_Ctrl_TC0_H2BK20ac.CST34156_CC27.n2.smooth.bw
ESC_Ctrl_TC0_H2BK20ac.ab177430.CST34156_CC8.CC15_peak.bed


title: MLLAF9WTM0


title: B01_N701_S503_HSR


title: MLLAF9RAGM4

value: Rag2-/- gamma c-/-


title: MLLAF9RAGM2


title: MLLAF9RAGM1


title: MLLAF9RAGM3


title: MLLAF9WTM1


title: Primary mouse astrocytes - p53 ChIP

data_processing:
Analysis was performed with nf-core/chipseq (v1.0dev) Nextflow pipeline (v0.32.0)
Adaptor trimming with TrimGalore
Alignment was performed using BWA (v0.7.12-r1039) against mm10 genome with blacklist filtering
Duplicate reads were removed with Picard (v2.18.9-SNAPSHOT)
Bigwigs were generated with bedtools (v2.25.0) genomecov
Peaks were called with MACS2 NarrowPeak setting (v2.1.1.20160309)
Genome_build: mm10
Supplementary_files_format_and_content: .narrowPeak file is MACS2 called peaks and .bw files are bigwigs

source_name: Primary mouse cortical astrocytes

growth_protocol: 2x10^7 wildtype primary cortical astrocytes from mouse brains were incubated in media supplemented with BMP4.

extract_protocol:
ChIP was performed using the EZ-Magna ChIP kit (Millipore). Lysates were sonicated with Bioruptor Pico with 10-20 cycles (30s on, 30s off at 4°C) until chromatin was average of 100-400bp. IP was performed overnight at 4°C with p53-CM5 antibody (Leica, 1:50) or 1mg Normal Rabbit IgG.
Libraries were prepared with NEBNext Ultra II DNA Library Prep kit per maufacturers instructions, with 13 cycles of PCR amplification. Libraries were pooled and sequenced on Illumina NextSeq 500 platform with NextSeq 500/550 Mid Output Kit v2.5 (150 cycles) with Paired End 2x75.

value: Astrocytes

value: untreated


title: MLLAF9RAGM0


title: Primary mouse astrocytes - Input


title: LB258-3-CTRL_S11


title: H3K27ac (ab4729) ChIP in ESC rep1

description:
H3K27ac ChIP-seq. Control.
ESC_Ctrl_TC0_H3K27ac.ab4729_CC1.CC11.n2.smooth.bw
ESC_Ctrl_TC0_H3K27ac.ab4729_CC1.CC11_peak.bed

growth_protocol: E14Tg2A Rosa26-Cre Oct4-IRES-Puro mouse ESCs were cultured in custom-made (C.C.Pro GmbH, Oberdorla) N2B27 medium consisting of 1:1 mix of DMEM/F12 and Neurobasal medium, but lacking Arginine and Lysine. Prior to use, the media was supplemented with 640 µM L-Arginine, 550 µM L-Lysine, 100 µM 2-mercaptoethanol, 150 µM sodium pyruvate, 0.5x B27 supplement (Thermo Fisher Scientific), 0.5x N2 supplement (Thermo Fisher Scientific), 1% penicillin/streptomycin, and cell type-specific growth factors or inhibitors. For mESCs the medium was supplemented with 1000 units/ml leukemia inhibitory factor (LIF) (Merck Millipore), 1 µM PD0325901, and 3 µM CT-99021 (custom-made by ABCR GmbH, Karlsruhe). mESCs were passaged regularly (every 2 to 4 days) with Accutase (PAA) or TrypLE (Thermo Fisher Scientific), and were occasionally selected for Oct4 expression with 1µg/ml puromycin (Sigma). K562 cells were cultured in RPMI-1640 media supplemented with 10% FBS, and 1% penicillin/streptomycin. All cells were cultured at 5% CO2, 37 oC.

treatment_protocol: A-485 (10uM) were treated for indicated time. For control samples, 0.1 % DMSO was added.

value: H3K27ac (Abcam, ab4729)


title: H3K27me3 ChIP in ESC rep1

description:
H3K27me3 ChIP-seq. Control.
ESC_Ctrl_TC0_H3K27me3_CC8.n2.smooth.bw
ESC_Ctrl_TC0_H3K27me3_CC8_peak.bed


title: H2BK20ac (ab177430) ChIP in ESC after A-485 15min treatment rep2

description:
H2BK20ac (ab177430) ChIP-seq in ESC. Cells were treated with 10uM A-485 for 15 min.
ESC_A485_10uM_TC15_H2BK20ac.ab177430_CC8.CC15.n2.smooth.bw

value: H2BK20ac (Abcam, ab177430)


title: H3K9ac ChIP in ESC rep1

description:
H3K9ac ChIP-seq. Control.
ESC_Ctrl_TC0_H3K9ac_CC14.n2.smooth.bw
ESC_Ctrl_TC0_H3K9ac_CC14_peak.bed

value: H3K9ac (CST, CST9671)


title: H2BK16ac (ab177427) ChIP in ESC rep2

description:
H2BK16ac ChIP-seq in ESC. Control.
ESC_Ctrl_TC0_H2BK16ac.ab177427_CC8.CC15.n2.smooth.bw
ESC_Ctrl_TC0_H2BK16ac.ab177427_CC8.CC15_peak.bed

value: H2BK16ac (Abcam, ab177427)


title: H2BK16ac (ab177427) ChIP in ESC after A-485 15min treatment rep2

description:
H2BK16ac ChIP-seq in ESC. Cells were treated with 10uM A-485 for 15 min.
ESC_A485_10uM_TC15_H2BK16ac.ab177427_CC8.CC15.n2.smooth.bw


title: H2BK20ac (ab177430) ChIP in ESC rep1

description:
H2BK20ac (ab177430) ChIP-seq in ESC. Control.
ESC_Ctrl_TC0_H2BK20ac.ab177430_CC8.CC15.n2.smooth.bw
ESC_Ctrl_TC0_H2BK20ac.ab177430.CST34156_CC8.CC15_peak.bed


title: H2BK20ac (ab177430) ChIP in ESC rep2


title: H2BK20ac (ab177430) ChIP in ESC after A-485 5min treatment rep1

description:
H2BK20ac (ab177430) ChIP-seq in ESC. Cells were treated with 10uM A-485 for 5 min.
ESC_A485_10uM_TC5_H2BK20ac.ab177430_CC8.n2.smooth.bw


title: H2BK20ac (ab177430) ChIP in ESC after A-485 15min treatment rep1


title: H2BK12ac(ab40883) ChIP in ESC after A-485 15min treatment, rep2

description:
H2BK12ac ChIP-seq in ESC. Cells were treated with 10uM A-485 for 15 min.
ESC_A485_10uM_TC15_H2BK12ac.ab40883_CC8.CC15.n2.smooth.bw

value: H2BK12ac (Abcam, ab40883)


title: H2BK20ac (CST34156) ChIP in ESC rep1

description:
H2BK20ac (CST34156) ChIP-seq in ESC. Control.
ESC_Ctrl_TC0_H2BK20ac.CST34156_CC15.n2.smooth.bw
ESC_Ctrl_TC0_H2BK20ac.ab177430.CST34156_CC8.CC15_peak.bed


title: H2BK16ac (ab177427) ChIP in ESC rep1


title: H2BK12ac(ab40883) ChIP in ESC after A-485 15min treatment, rep1


title: H2BK5ac (ab40866) ChIP in ESC after A-485 15min treatment, rep1

description:
H2BK5ac (Ab40866) ChIP-seq in ESC. Cells were treated with 10uM A-485 for 15 min.
ESC_A485_10uM_TC15_H2BK5ac.ab40886_CC8.n2.smooth.bw

value: H2BK5ac (Abcam, ab40866)


title: H2BK12ac (ab40883) ChIP in ESC rep2

description:
H2BK12ac ChIP-seq in ESC. Control
ESC_Ctrl_TC0_H2BK12ac.ab40883_CC8.CC15.n2.smooth.bw
ESC_Ctrl_TC0_H2BK12ac.ab40883_CC8.CC15_peak.bed


title: H3K4me3 ChIP in ESC rep1

description:
H3K4me3 ChIP-seq. Control.
ESC_Ctrl_TC0_H3K4me3_CC10.n2.smooth.bw
ESC_Ctrl_TC0_H3K4me3_CC10_peak.bed

value: H3K4me3 (Millipore, 04-745)


title: H2BK12ac(ab40883) ChIP in ESC after A-485 5min treatment, rep1

description:
H2BK12ac ChIP-seq in ESC. Cells were treated with 10uM A-485 for 5 min.
ESC_A485_10uM_TC5_H2BK12ac.ab40883_CC8.n2.smooth.bw


title: H2BK12ac (ab40883) ChIP in ESC rep1


title: H2BK5ac (ab40866) ChIP in ESC rep1

description:
H2BK5ac (Ab40866) ChIP-seq in ESC. Control
ESC_Ctrl_TC0_H2BK5ac.ab40886_CC8.n2.smooth.bw
ESC_Ctrl_TC0_H2BK5ac.ab40886_CC8_peak.bed


title: H2BK5ac (ab40866) ChIP in ESC after A-485 5min treatment, rep1

description:
H2BK5ac (Ab40866) ChIP-seq in ESC. Cells were treated with 10uM A-485 for 5 min.
ESC_A485_10uM_TC5_H2BK5ac.ab40886_CC8.n2.smooth.bw


title: H2BK5ac (CST12799) ChIP in ESC after A-485 15min treatment, rep2

description:
H2BK5ac (CST12799) ChIP-seq in ESC. Cells were treated with 10uM A-485 for 15 min.
ESC_A485_10uM_TC15_H2BK5ac.CST12799_CC1.n2.smooth.bw

value: H2BK5ac (CST, CST12799)


title: H2BK5ac (CST12799) ChIP in ESC after A-485 5min treatment, rep2

description:
H2BK5ac (CST12799)  ChIP-seq in ESC. Cells were treated with 10uM A-485 for 5 min.
ESC_A485_10uM_TC5_H2BK5ac.CST12799_CC1.n2.smooth.bw

value: ES cells


title: H2BK5ac (CST12799) ChIP in ESC after A-485 5min treatment, rep1

description:
H2BK5ac (CST12799) ChIP-seq in ESC. Cells were treated with 10uM A-485 for 5 min.
ESC_A485_10uM_TC5_H2BK5ac.CST12799_CC1.n2.smooth.bw


title: H2BK5ac (CST12799) ChIP in ESC rep4

description:
H2BK5ac (CST12799) ChIP-seq in ESC. Control
ESC_Ctrl_TC0_H2BK5ac.CST12799_CC1.CC11.CC15.n2.smooth.bw
ESC_Ctrl_TC0_H2BK5ac.CST12799_CC1.CC11.CC15_peak.bed


title: H2BK16ac (ab177427) ChIP in ESC after A-485 15min treatment rep1


title: H2BK16ac (ab177427) ChIP in ESC after A-485 5min treatment rep1

description:
H2BK16ac ChIP-seq in ESC. Cells were treated with 10uM A-485 for 5 min.
ESC_A485_10uM_TC5_H2BK16ac.ab177427_CC8.n2.smooth.bw


title: H2BK5ac (CST12799) ChIP in ESC rep2


title: Med1 ChIP in ESC rep2

description:
Med1 ChIP-seq in ESC. Control
ESC_Ctrl_TC0_Med1_dfix_CC10.CC12.n2.smooth.bw
ESC_Ctrl_TC0_Med1_dfix_Spike.HEK293_CC10.CC12_peak.bed

value: Med1 (Millipore, 17-10530)


title: H2BK5ac (CST12799) ChIP in ESC rep1


title: Med1 ChIP in ESC rep1


title: WT6

data_processing:
Reads were trimmed for adapter sequences using Cutadapt (version 1.11) and aligned using STAR (version 2.5.2a) to the GRCm38 assembly using the gene, transcript, and exon features of Ensembl (release 67) gene model. Expression was estimated using RSEM (version 1.2.30).
Transcripts with zero read counts across all samples were removed prior analysis. Normalisation of RSEM expected read counts was performed by dividing by million reads mapped to generate counts per million (CPM), followed by the trimmed mean of M-values (TMM) method from the edgeR package.
Genome_build: GRCm38
Supplementary_files_format_and_content: tab-delimited text files include RSEM expected read count values for each sample

source_name: GFP+

tag: genotype/strain

value: AML-1 ETO Nras G12D


title: WT5

value: spleen


title: WT4

value: GFP+ splenocytes


title: H2BK5ac (CST 12799) ChIP in ESC after A-485 15min treatment, rep1

description:
H2BK5ac (CST12799)  ChIP-seq in ESC. Cells were treated with 10uM A-485 for 15 min.
ESC_A485_10uM_TC15_H2BK5ac.CST12799_CC1.n2.smooth.bw


title: RAG10

value: Secondary transplant acute myeloid leukemia


title: RAG11


title: WT3


title: WT1


title: RAG8


title: RAG7


title: SFMC, AS, Feature barcode [SF2_FB]

city: Daejeon

first: Song

last: Woogil

address: KAIST, Daejeon 34141, Korea

department: Graduate School of Medical science and engineering

country: South Korea

institute: KAIST

description:
Antibody-derived oligonucleotide library: read1 file contains cell barcode and UMI; read2 file contains Antibody Derived Tag reads
Antibody-derived oligonucleotide (ADT)

data_processing:
library strategy: CITE-seq (5' Feature Barcode Kit)
All data were processed by cellranger v3.0.2 and manipulated and visualized by R v4.1.1 and Seurat v4.0.2.
Each Library(S1-S8) is composed of the SFMCs of AS and RA, and PBMCs of AS. We excluded the RA patients' data before merge.
The location of the processed data is /home/users/songwoogil/Assf/geo_data/processed_data/
Supplementary files format and content: 10x Genomics output files: barcodes.tsv.gz, features.tsv.gz, matrix.mtx.gz

source_name: Connective tissue

extract_protocol:
Synovial fluid mononuclear cells and peripheral mononuclear cells from 6 AS patients.
Chromium Next GEM Single Cell 5ʹ Kit v1, 5' Feature Barcode Kit, and Chromium Single Cell Human TCR Amplification Kit, 10X Genomics
5' Feature Barcode Kit

value: Synovium

value: Connective tissue

value: Mononuclear cells

tag: library type

value: Feature barcode


title: H2BK5ac (CST12799) ChIP in ESC rep3


title: PBMC, SFMC, AS, scRNAseq(TCRseq) [S7_TCR]

description: 10x Genomics

library_source: other

data_processing:
All data were processed by cellranger v3.0.2 and manipulated and visualized by R v4.1.1 and Seurat v4.0.2.
Each Library(S1-S8) is composed of the SFMCs and PBMCs of AS. But, "SFMC_1946", "SFMC_3098", "SFMC_3625", "SFMC_5210" demux data have nothing to do with this expreiment.
Supplementary files format and content: 10x Genomics output files: barcodes.tsv.gz, features.tsv.gz, matrix.mtx.gz

molecule: other

extract_protocol:
Synovial fluid mononuclear cells and peripheral mononuclear cells from 6 AS patients.
Chromium Next GEM Single Cell 5ʹ Kit v1, 5' Feature Barcode Kit, and Chromium Single Cell Human TCR Amplification Kit, 10X Genomics

value: Peripheral blood, Synovium


title: PBMC, SFMC, AS, scRNAseq(TCRseq) [S6_TCR]

description: 10x Genomics


title: PBMC, SFMC, AS, scRNAseq(TCRseq) [S5_TCR]

description: 10x Genomics


title: PBMC, SFMC, AS, scRNAseq(TCRseq) [S8_TCR]

description: 10x Genomics


title: SFMC, AS, Feature barcode [SF1_FB]


title: PBMC, AS, Feature barcode [PB_FB]

value: Peripheral blood

tag: antibodies/tags

value: First 10 Features among 30 Tags :CD3-TotalSeqC, PD-L1-TotalSeqC, CD270-TotalSeqC, CD4-TotalSeqC, CD8-TotalSeqC, CD19-TotalSeqC, CD45RA-TotalSeqC, CD14-TotalSeqC, CD56-TotalSeqC, CD25-TotalSeqC(Please see AS@assays[["FB"]])


title: PBMC, SFMC, AS, scRNAseq [S3_GEX]

description: 10x Genomics

library_source: transcriptomic single cell


title: PBMC, SFMC, AS, scRNAseq [S2_GEX]

description: 10x Genomics


title: SFMC, AS, scRNAseq(TCRseq) [SF2_TCR]

description: 10x Genomics


title: PBMC, SFMC, AS, scRNAseq [S1_GEX]

description: 10x Genomics


title: SFMC, AS, scRNAseq(TCRseq) [SF1_TCR]

description: 10x Genomics


title: SFMC, AS, scRNAseq [SF1_S1]

description: 10x Genomics


title: SFMC, AS, scRNAseq [SF2_S2]

description: 10x Genomics


title: RAG9


title: 472T2

city: Ann Arbor

first: Carlos

middle: Andres

last: Aguilar

state: MI

address: 2200 Bonisteel Blvd

department: Biomedical Engineering

institute: University of Michigan

description:
10x Genomics Visium
canis_merged_D0_D7_D14.RDS
Integrated_Merged_spGEX_SeuratObj_v3.RDS
Canis_ST_list.RDS

data_processing:
Manual alignment of spatial barcodes to tissue location was performed using 10x Genomics Loupe Browser version 6
De-multiplexing, genome alignment (mm10-2020-A or CanFam3.1.97), and count matrix generation was performed using 10x Genomics Space Ranger version 1.3.0
Count matrices were imported into R using Seurat v4. Data normalization was performed using SCTransform, followed by principal component analysis (top 30 dimensions), FindNeighbors, FindClusters, and RunUMAP with default conditions.
Mouse datasets were integrated with annotated scRNA-Seq matrices publically available at GSE163376
Assembly: mm10-2020-A and CanFam3.1.97
Supplementary files format and content: Process data files are provided as (1) a list of Seurat Objects for each sample and (2) a single Seurat Object with all of the samples from the given species merged.
Library strategy: Spatial transcriptomics

organism: Canis lupus familiaris

source_name: Skeletal Muscle

extract_protocol:
Tissues were simultaneously flash frozen and OCT embedded according to 10x Genomics demonstrated protocol CG000240
Libraries were prepared according to manufacturer's protocol (10x Genomics demonstrated protocol CG000239). Briefly, 10um tissue sections were placed onto capture areas of visium slides and stained with hematoxylin and eosin, imaged, then permeabilized for 18 minutes (murine) or 24 minutes (canine). cDNAs were synthesized and amplified, followed by library construction.

value: Skeletal Muscle

tag: days post_injury

tag: slide serial_number

tag: Sex

value: Female


title: 585T


title: 472T1


title: 600T


title: adult

data_processing:
CellRanger v3.1.0 and bcl2fastq v2.20.0 were used perform sample de-multiplexing, barcode processing and single cell gene unique molecular identifier (UMI) counting, while a digital expression matrix was obtained for each experiment with default parameters, mapped to the edited mm10 reference, where tdTomato's sequence was added.
Assembly: Edited mm10 with added tdTomato-WPRE-bGH poly(A) signal sequence taken from Ai9 Addgene plasmid (Plasmid #22799) sequence.
Supplementary files format and content: There is 1 processed file that was output from CellRanger.

source_name: adult astrocytes

growth_protocol: Primary astrocytes from adult GFAP-CreERT2;p53flox/flox;LSL-tdTomato mice were cultured in DMEM-F12, N2 (1/200), B27 (1/100), 5mM HEPES, 1x MEM NEAA. 50μM betamercaptoethanol, 0.012% BSA, 6.525mg/ml glucose, 100μg/ml kanamycin, 2μg/ml gentamicin) (Pollard et al., 2009)  supplemented with 20ng/mL EGF and 10ng/mL FGF-2 and 4OHT (Sigma, 200nM) for 5 days

extract_protocol:
Cells were harvested to single cell suspension by trypsinisation and washed and filtered as described in 10x Genomics manual
10x Genomics Chromium Next GEM Single Cell 3' Kit v3.1

treatment_protocol: EGF + FGF + 4OHT for 5 days to induce CreER mediated recombination and astrocyte dedifferentiation

value: Primary astrocytes from mice


title: mature, 4hr, X121119_97

city: La Jolla

first: Fred

middle: H

last: Gage

state: CA

address: 10010 N Torrey Pines Rd

institute: The Salk Institute for Biological Studies

data_processing:
Reads were trimmed using Solexa-QA++ dynamic trim
Read were aligned to the mm10 (GRCm38) reference genome with Ensembl gene annotation using RSEM (bowtie)
Transcripts per million values calculated by RSEM were log2+1 transformed
Assembly: mm10
Supplementary files format and content: comma-delimited txt file provides counts for each sample
Supplementary files format and content: comma-delimited txt file provides log2+1 transformed tpm values for each sample

molecule: polyA RNA

source_name: brain

growth_protocol: Hemizygous Ascl1tm1.1(Cre/ERT2)Jejo/J mice (Jackson Laboratory stock #012882, RRID: IMSR_JAX:012882) (Kim et al., 2011) were bred with homozygous B6;129-Gt(ROSA)26Sortm5(CAG-Sun1/sfGFP)Nat/MmbeJ (Jackson laboratory stock #030952, RRID:IMSR_JAX:030952).

extract_protocol:
The hippocampus was dissected bilaterally after deep anesthesia with ketamine/xylazine/acepromazine and cervical dislocation. Hippocampal tissue was immediately placed into a nuclei isolation medium (sucrose 0.25 M, KCl 25 mM, MgCl2 5 mM, TrisCl 10 mM, dithiothreitol 100 uM, 0.1% Triton, protease inhibitors). Tissue was dounce homogenized and then samples were washed, resuspended in nuclei storage buffer (0.167 M sucrose, MgCl2 5 mM, and TrisCl 10 mM, dithiothreitol 100 uM, protease inhibitors) and filtered. Antibody staining proceeded in the nuclei storage buffer. Solutions and samples were kept cold throughout the protocol. Tools and solutions were made RNAse-free and RNAse inhibitors were used (Ambion #AM2684 at 1:1000 in both isolation and storage buffers). Samples were run on a BD Influx cell sorter and collected directly into 384-well plates pre-filled with 1 uL lysis buffer (0.1% Triton-X, 1 U/ul RNAse inhibitor, 2.5 mM dNTP mix, 2.5 uM anchored oligo-dT primer) and frozen at -80C until further processing
Libraries were prepared using the Smart-seq2 protocol with minor modifications. First strand synthesis with ProtoScript II reverse transcriptase (New England Biolabs), PCR preamplification with KAPA Hifi HotStart ReadyMix (Kapa), and bead cleanup (Agencourt AMPure XP beads, Beckman Coulter) were performed with the aid of a Mosquito HV liquid handler (SPT Labtech). The quality of cDNA was assessed by Bioanalyzer chip (Agilent) and concentration quantified by Qubit assay (Invitrogen). Single nuclei libraries were prepared with a Nextera XT DNA library prep kit (Illumina) and pooled together for sequencing. The quality of pooled libraries was assessed by TapeStation assay (Agilent). Libraries were sequenced on an Illumina HiSeq using single-end 50bp reads by the Salk Institute Next Generation Sequencing Core.

treatment_protocol: To induce Cre-recombination and label immature cells, tamoxifen (Sigma, T5648) was delivered at 200 mg/kg in 90% corn oil/10% ethanol by oral gavage daily for 7 days. Approximately 5 weeks later, mice were exposed to a novel environment for 1 hr to stimulate neuronal activity. Nuclear isolation was then performed either immediately (1 hr time point) or after a delay (4 hr time point).

value: brain

tag: cell state

value: mature

value: dentate granule cell

value: F

tag: mouseid

tag: time point


title: immatureactive, 4hr, X121119_98

tag: tissue

value: immatureactive

tag: cell type

value: M


title: PBMC, SFMC, AS, scRNAseq [S4_GEX]

description: 10x Genomics


title: immature, 4hr, X121119_94

value: immature


title: immature, 4hr, X121119_92


title: immature, 4hr, X121119_87


title: immature, 4hr, X121119_90


title: immature, 4hr, X121119_86


title: immature, 4hr, X121119_85


title: 426T

description:
10x Genomics Visium
Canis_ST_list.RDS
canis_merged_414T_415T_425T_426T.RDS


title: 425T


title: mature, 4hr, X121119_81


title: immature, 4hr, X121119_91


title: immature, 4hr, X121119_83


title: immature, 4hr, X121119_95


title: immature, 4hr, X121119_88


title: PBMC, AS, scRNAseq(TCRseq) [PB_TCR]

description: 10x Genomics


title: PBMC, AS, scRNAseq [PB_S3]

description: 10x Genomics


title: immature, 4hr, X121119_84


title: 415T


title: 414T


title: matureactive, 4hr, X121119_79

value: matureactive


title: matureactive, 4hr, X121119_77


title: matureactive, 4hr, X121119_78


title: matureactive, 4hr, X121119_71


title: matureactive, 4hr, X121119_68


title: matureactive, 4hr, X121119_66


title: mature, 4hr, X121119_65


title: mature, 4hr, X121119_60


title: mature, 4hr, X121119_58


title: mature, 4hr, X121119_62


title: mature, 4hr, X121119_63


title: immatureactive, 4hr, X121119_56


title: immatureactive, 4hr, X121119_55


title: immatureactive, 4hr, X121119_52


title: immatureactive, 4hr, X121119_53


title: immatureactive, 4hr, X121119_50


title: immatureactive, 4hr, X121119_48


title: immatureactive, 4hr, X121119_46


title: immature, 4hr, X121119_38


title: immatureactive, 4hr, X121119_43


title: immatureactive, 4hr, X121119_42


title: immature, 4hr, X121119_37


title: immature, 4hr, X121119_39


title: immature, 4hr, X121119_35


title: immature, 4hr, X121119_31


title: immature, 4hr, X121119_30


title: immature, 4hr, X121119_29


title: immature, 4hr, X121119_34


title: immature, 4hr, X121119_27


title: immature, 4hr, X121119_28


title: immature, 4hr, X121119_26


title: H2BK20ac (CST34156) ChIP in ESC after A-485 15min treatment rep1

description:
H2BK20ac (CST34156) ChIP-seq in ESC. Cells were treated with 10uM A-485 for 15 min.
ESC_A485_10uM_TC15_H2BK20ac.CST34156_CC15.n2.smooth.bw

value: ES cells

value: H2BK20ac (CST, CST34156)


title: immatureactive, 4hr, X121119_24


title: matureactive, 4hr, X121119_23


title: matureactive, 4hr, X121119_22


title: immatureactive, 4hr, X121119_51


title: matureactive, 4hr, X121119_18


title: immatureactive, 4hr, X121119_47


title: matureactive, 4hr, X121119_15


title: matureactive, 4hr, X121119_13


title: immatureactive, 4hr, X121119_16


title: matureactive, 4hr, X121119_12


title: matureactive, 4hr, X121119_119


title: matureactive, 4hr, X121119_106


title: mature, 4hr, X121119_105


title: immature, 4hr, X121119_104


title: immatureactive, 4hr, X121119_102


title: matureactive, 4hr, X121119_21


title: mature, 4hr, X121119_09


title: immatureactive, 4hr, X121119_100


title: immatureactive, 4hr, X121119_101


title: immature, 4hr, X121119_17


title: PTCL_Case34

city: Omaha

first: Javeed

last: Iqbal

state: NE

address: 601 S 42nd St

institute: UNMC

hyb_protocol: 65 degrees C for 16 hours

scan_protocol: Max

data_processing: Counts were normalized by dividing the counts for each gene for a given sample by the geometric mean of the counts for the housekeeping genes in that sample. The normalized counts  were then log2 transformed.

source_name: Peripheral T cell Lymphoma

extract_protocol: Total RNA was extracted from 1-3 10 uM FFPE curls using the RNAstorm™ Kit

value: Peripheral T cell Lymphoma

tag: case # from supplemental table9 (pmid35839444)

tag: hg-u133plus2.0 platform_id geo identifier

tag: affymetrix data geo series

tag: tumor

value: Lymphoma

tag: nanostringclass

value: AITL


title: PTCL_Case33


title: PTCL_Case32


title: PTCL_Case36

value: ALCL-neg


title: PTCL_Case31


title: PTCL_Case29


title: PTCL_Case28


title: PTCL_Case25


title: PTCL_Case26


title: PTCL_Case27


title: mature, 4hr, X121119_06


title: mature, 4hr, X121119_05


title: immature, 4hr, X121119_08


title: mature, 4hr, X121119_04


title: mature, 4hr, X121119_03


title: PTCL_Case37

value: ALCL-pos


title: PTCL_Case20


title: mature, 4hr, X121119_02


title: immatureactive, 4hr, X100119_99


title: PTCL_Case24


title: PTCL_Case23


title: PTCL_Case22


title: immatureactive, 4hr, X100119_97


title: immatureactive, 4hr, X121119_07


title: mature, 4hr, X100119_91


title: mature, 4hr, X100119_94


title: PTCL_Case19

value: Intermediate AITL/TBX21


title: mature, 4hr, X100119_92


title: mature, 4hr, X100119_89


title: immature, 4hr, X100119_90


title: PTCL_Case16


title: PTCL_Case17


title: PTCL_Case18


title: immature, 4hr, X100119_83


title: PTCL_Case15


title: immature, 4hr, X100119_81


title: PTCL_Case21


title: immature, 4hr, X100119_79


title: PTCL_Case12


title: PTCL_Case13


title: PTCL_Case7


title: PTCL_Case8


title: immature, 4hr, X100119_76


title: PTCL_Case9


title: immature, 4hr, X100119_77


title: PTCL_Case10


title: immature, 4hr, X100119_71


title: immature, 4hr, X100119_70


title: PTCL_Case4


title: immature, 4hr, X100119_68


title: PTCL_Case6


title: immature, 4hr, X100119_69


title: PTCL_Case5


title: PTCL_Case11


title: PTCL_Case3


title: immature, 4hr, X100119_66


title: immature, 4hr, X100119_67


title: immature, 4hr, X100119_80


title: PTCL_Case2


title: immature, 4hr, X100119_65


title: PTCL_Case441

tag: nanosstringclass


title: PTCL_Case437


title: immature, 4hr, X100119_63


title: PTCL_Case435


title: reactive hyperplasia_Case433

source_name: reactive hyperplasia

value: reactive hyperplasia


title: PTCL_Case439


title: immature, 4hr, X100119_62

value: brain


title: reactive hyperplasia_Case432


title: immature, 4hr, X100119_64


title: reactive hyperplasia_Case431


title: immature, 4hr, X100119_61


title: matureactive, 4hr, X100119_55


title: reactive hyperplasia_Case428


title: reactive hyperplasia_Case427


title: reactive hyperplasia_Case430


title: matureactive, 4hr, X100119_51


title: matureactive, 4hr, X100119_48


title: reactive hyperplasia_Case426

value: Intermediate AITL/GATA3


title: reactive hyperplasia_Case425


title: reactive hyperplasia_Case424


title: matureactive, 4hr, X100119_47

value: dentate granule cell


title: reactive hyperplasia_Case423


title: matureactive, 4hr, X100119_41


title: matureactive, 4hr, X100119_46


title: PTCL_Case405

value: ATLL


title: matureactive, 4hr, X100119_37


title: PTCL_Case391


title: matureactive, 4hr, X100119_38


title: matureactive, 4hr, X100119_36


title: matureactive, 4hr, X100119_40


title: matureactive, 4hr, X100119_34


title: matureactive, 4hr, X100119_53


title: PTCL_Case380


title: PTCL_Case389


title: matureactive, 4hr, X100119_49


title: PTCL_Case376


title: matureactive, 4hr, X100119_35


title: PTCL_Case387


title: PTCL_Case378


title: matureactive, 4hr, X100119_33


title: matureactive, 4hr, X100119_29


title: PTCL_Case374


title: PTCL_Case377


title: matureactive, 4hr, X100119_28


title: matureactive, 4hr, X100119_31


title: PTCL_Case372


title: mature, 4hr, X100119_27

value: mature


title: PTCL_Case369


title: mature, 4hr, X100119_25

value: M


title: PTCL_Case379


title: PTCL_Case368


title: PTCL_Case371

value: ENKTL


title: PTCL_Case367


title: matureactive, 4hr, X100119_228

value: matureactive

value: F


title: immature, 4hr, X100119_234

value: immature


title: PTCL_Case366


title: PTCL_Case365


title: immature, 4hr, X100119_222


title: matureactive, 4hr, X100119_227


title: mature, 4hr, X100119_22


title: PTCL_Case364


title: PTCL_Case363


title: PTCL_Case373


title: immatureactive, 4hr, X100119_215

value: immatureactive


title: matureactive, 4hr, X100119_214


title: PTCL_Case360

value: Lymphoma


title: PTCL_Case361


title: PTCL_Case357


title: PTCL_Case345


title: immature, 4hr, X100119_236


title: matureactive, 4hr, X100119_211


title: matureactive, 4hr, X100119_210


title: PTCL_Case342


title: PTCL_Case341


title: immatureactive, 4hr, X100119_206


title: matureactive, 4hr, X100119_208


title: immatureactive, 4hr, X100119_200


title: PTCL_Case339

value: AITL


title: immatureactive, 4hr, X100119_199


title: PTCL_Case336


title: immatureactive, 4hr, X100119_196


title: immatureactive, 4hr, X100119_218


title: immatureactive, 4hr, X100119_198


title: PTCL_Case334


title: PTCL_Case335

value: ALCL-neg


title: PTCL_Case333

value: ALCL-pos


title: immatureactive, 4hr, X100119_195


title: matureactive, 4hr, X100119_213


title: matureactive, 4hr, X100119_194


title: PTCL_Case331


title: immature, 4hr, X100119_191


title: immature, 4hr, X100119_190


title: PTCL_Case328


title: PTCL_Case329


title: PTCL_Case343


title: immature, 4hr, X100119_188


title: immature, 4hr, X100119_187


title: PTCL_Case325


title: immature, 4hr, X100119_185


title: PTCL_Case322


title: immature, 4hr, X100119_184


title: PTCL_Case318


title: PTCL_Case311


title: PTCL_Case332


title: immature, 4hr, X100119_182


title: mature, 4hr, X100119_18


title: immature, 4hr, X100119_189


title: PTCL_Case310


title: PTCL_Case307


title: PTCL_Case309


title: PTCL_Case296


title: PTCL_Case295


title: immature, 4hr, X100119_166


title: immatureactive, 4hr, X100119_165


title: PTCL_Case293


title: mature, 4hr, X100119_179


title: immature, 4hr, X100119_177


title: PTCL_Case292


title: immature, 4hr, X100119_176


title: immature, 4hr, X100119_167


title: PTCL_Case321


title: matureactive, 4hr, X100119_159


title: mature, 4hr, X100119_16


title: matureactive, 4hr, X100119_161


title: PTCL_Case288


title: PTCL_Case290


title: matureactive, 4hr, X100119_157


title: PTCL_Case291


title: PTCL_Case289


title: matureactive, 4hr, X100119_156


title: matureactive, 4hr, X100119_155


title: matureactive, 4hr, X100119_154


title: PTCL_Case284


title: PTCL_Case286


title: PTCL_Case285


title: matureactive, 4hr, X100119_152


title: matureactive, 4hr, X100119_145


title: matureactive, 4hr, X100119_142


title: PTCL_Case282


title: PTCL_Case278


title: PTCL_Case277


title: matureactive, 4hr, X100119_137


title: PTCL_Case274

value: Intermediate AITL/TBX21


title: PTCL_Case272


title: immature, 4hr, X100119_133


title: mature, 4hr, X100119_131


title: immature, 4hr, X100119_134


title: PTCL_Case287


title: PTCL_Case271


title: PTCL_Case269


title: PTCL_Case270


title: immature, 4hr, X100119_149


title: mature, 4hr, X100119_128


title: mature, 4hr, X100119_125


title: PTCL_Case265


title: mature, 4hr, X100119_130


title: PTCL_Case258


title: mature, 4hr, X100119_124


title: mature, 4hr, X100119_122


title: PTCL_Case276


title: matureactive, 4hr, X100119_138


title: mature, 4hr, X100119_121


title: PTCL_Case257


title: PTCL_Case275


title: immatureactive, 4hr, X100119_117


title: PTCL_Case255


title: PTCL_Case273


title: mature, 4hr, X100119_12


title: immatureactive, 4hr, X100119_115


title: PTCL_Case253


title: PTCL_Case252


title: PTCL_Case251


title: immatureactive, 4hr, X100119_113


title: mature, 4hr, X100119_110


title: mature, 4hr, X100119_11


title: PTCL_Case247


title: PTCL_Case242


title: matureactive, 4hr, X100119_104


title: PTCL_Case235


title: mature, 4hr, X100119_09


title: matureactive, 4hr, X100119_103


title: PTCL_Case232


title: PTCL_Case254


title: PTCL_Case233


title: mature, 4hr, X100119_08


title: PTCL_Case234


title: mature, 4hr, X100119_07


title: mature, 4hr, X100119_05


title: PTCL_Case231


title: mature, 4hr, X100119_04


title: PTCL_Case229


title: PTCL_Case228


title: PTCL_Case227


title: mature, 4hr, X100119_03


title: PTCL_Case230


title: PTCL_Case224


title: mature, 4hr, X100119_02


title: PTCL_Case223


title: immature, 1hr, X043019_98


title: immature, 1hr, X043019_99


title: PTCL_Case215


title: mature, 4hr, X100119_10


title: PTCL_Case212


title: PTCL_Case211


title: immature, 1hr, X043019_97


title: mature, 4hr, X100119_06


title: immature, 1hr, X043019_96


title: immature, 1hr, X043019_94


title: PTCL_Case208


title: immature, 1hr, X043019_92


title: PTCL_Case207


title: PTCL_Case206


title: immature, 1hr, X043019_89


title: immature, 1hr, X043019_90


title: immature, 1hr, X043019_87


title: PTCL_Case222


title: mature, 4hr, X100119_01


title: PTCL_Case209


title: PTCL_Case202


title: PTCL_Case197


title: PTCL_Case199


title: immature, 1hr, X043019_91


title: PTCL_Case201


title: PTCL_Case204


title: immature, 1hr, X043019_86


title: immature, 1hr, X043019_88


title: PTCL_Case196


title: immature, 1hr, X043019_85


title: immature, 1hr, X043019_84


title: PTCL_Case191


title: immature, 1hr, X043019_82


title: PTCL_Case189


title: immature, 1hr, X043019_93


title: PTCL_Case190


title: immature, 1hr, X043019_81


title: immature, 1hr, X043019_80


title: immature, 1hr, X043019_78


title: immature, 1hr, X043019_76


title: PTCL_Case184


title: immature, 1hr, X043019_75


title: immature, 1hr, X043019_77


title: immature, 1hr, X043019_74


title: PTCL_Case183


title: matureactive, 1hr, X043019_70


title: immature, 1hr, X043019_73


title: PTCL_Case179


title: PTCL_Case178


title: matureactive, 1hr, X043019_71


title: PTCL_Case174


title: matureactive, 1hr, X043019_69


title: matureactive, 1hr, X043019_67


title: PTCL_Case170


title: matureactive, 1hr, X043019_65


title: PTCL_Case167


title: PTCL_Case169


title: matureactive, 1hr, X043019_63


title: PTCL_Case166


title: PTCL_Case188


title: PTCL_Case187


title: immature, 1hr, X043019_79


title: PTCL_Case165


title: matureactive, 1hr, X043019_62


title: PTCL_Case163


title: PTCL_Case164


title: PTCL_Case180


title: matureactive, 1hr, X043019_60


title: matureactive, 1hr, X043019_59


title: matureactive, 1hr, X043019_57


title: PTCL_Case168


title: PTCL_Case161


title: PTCL_Case162


title: matureactive, 1hr, X043019_52


title: matureactive, 1hr, X043019_53


title: PTCL_Case160


title: PTCL_Case159


title: PTCL_Case158


title: matureactive, 1hr, X043019_51


title: matureactive, 1hr, X043019_50


title: matureactive, 1hr, X043019_48


title: PTCL_Case156


title: matureactive, 1hr, X043019_47


title: matureactive, 1hr, X043019_49


title: PTCL_Case157


title: PTCL_Case155


title: PTCL_Case154


title: matureactive, 1hr, X043019_45


title: PTCL_Case151


title: PTCL_Case153


title: PTCL_Case150


title: matureactive, 1hr, X043019_46


title: PTCL_Case147


title: matureactive, 1hr, X043019_44


title: PTCL_Case146


title: matureactive, 1hr, X043019_55


title: matureactive, 1hr, X043019_43


title: PTCL_Case144


title: PTCL_Case143


title: matureactive, 1hr, X043019_39


title: matureactive, 1hr, X043019_41


title: PTCL_Case142


title: matureactive, 1hr, X043019_40


title: PTCL_Case140


title: matureactive, 1hr, X043019_38


title: matureactive, 1hr, X043019_37


title: PTCL_Case123


title: mature, 1hr, X043019_33


title: mature, 1hr, X043019_35


title: mature, 1hr, X043019_31


title: mature, 1hr, X043019_30


title: mature, 1hr, X043019_32


title: mature, 1hr, X043019_29


title: mature, 1hr, X043019_34


title: PTCL_Case122


title: matureactive, 1hr, X043019_42


title: mature, 1hr, X043019_27


title: mature, 1hr, X043019_28


title: PTCL_Case119


title: PTCL_Case120


title: PTCL_Case118


title: PTCL_Case115


title: mature, 1hr, X043019_26


title: immatureactive, 1hr, X043019_250


title: PTCL_Case114


title: PTCL_Case141


title: mature, 1hr, X043019_25


title: ASTROCYTE #2 CO-CULTURED WITH DU145 CELLS

city: Rio de Janeiro

first: Pedro

last: Nicolau Neto

state: RJ

address: 37 Andre Cavalcanti Street

department: PCM

country: Brazil

institute: INCA

description: GENE EXPRESSION FROM HUMAN ASTROCYTE CO-CULTURED WITH DU145 CELLS

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Human gene 1.0 ST. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: Genechip Scanner 3000 7G

data_processing: The data were analyzed with Expression console (Affymetrix) (RMA) using Affymetrix default analysis settings and global scaling as normalization method.

label: Biotin

source_name: HUMAN_ASTROCYTE_ COCULTURED DU145 CELLS

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 1 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

extract_protocol: RNEAsy mini kit Qiagen

value: HUMAN ASTROCYTE


title: PTCL_Case113


title: ASTROCYTE CONTROL #2

description: GENE EXPRESSION FROM HUMAN ASTROCYTE

source_name: HUMAN ASTROCYTE CONTROL


title: ASTROCYTE CONTROL #1

description: GENE EXPRESSION FROM HUMAN ASTROCYTE


title: ASTROCYTE #1 CO-CULTURED WITH LNCAP CELLS

description: GENE EXPRESSION FROM HUMAN ASTROCYTE CO-CULTURED WITH LNCAP CELLS

source_name: HUMAN_ASTROCYTE_ COCULTURED LNCAP CELLS


title: immatureactive, 1hr, X043019_247

value: brain


title: ASTROCYTE #2 CO-CULTURED WITH LNCAP CELLS


title: ASTROCYTE #1 CO-CULTURED WITH DU145 CELLS


title: immatureactive, 1hr, X043019_246


title: immatureactive, 1hr, X043019_245


title: immatureactive, 1hr, X043019_243


title: immatureactive, 1hr, X043019_244


title: PTCL_Case98


title: LNCAP CELLS CO-CULTURED WITH ASTROCYTE #2

description: GENE EXPRESSION FROM LNCAP CELLS CO-CULTURED WITH HUMAN ASTROCYTE

source_name: LNCAP CELLS CO-CULTURED WITH ASTROCYTE

value: PROSTATE TUMOR CELL LINE


title: immatureactive, 1hr, X043019_238

value: dentate granule cell


title: immatureactive, 1hr, X043019_236


title: immatureactive, 1hr, X043019_249


title: immatureactive, 1hr, X043019_235


title: PTCL_Case67


title: DU145 CONTROL #1

description: GENE EXPRESSION FROM DU145 CELLS

source_name: DU145 CELLS CONTROL


title: PTCL_Case46


title: DU145 CONTROL #2

description: GENE EXPRESSION FROM DU145 CELLS


title: immatureactive, 1hr, X043019_248


title: immatureactive, 1hr, X043019_234


title: DU145 CELLS CO-CULTURED WITH ASTROCYTE #1

description: GENE EXPRESSION FROM DU145 CELLS CO-CULTURED WITH HUMAN ASTROCYTE

source_name: DU145 CELLS CO-CULTURED WITH ASTROCYTE


title: DU145 CELLS CO-CULTURED WITH ASTROCYTE #2


title: immatureactive, 1hr, X043019_233


title: PTCL_Case138

value: Peripheral T cell Lymphoma

value: Not deposited


title: immature, 1hr, X043019_232

value: M


title: immature, 1hr, X043019_231


title: immature, 1hr, X043019_230


title: PTCL_Case136


title: mature, 1hr, X043019_23

value: mature


title: PTCL_Case135


title: immature, 1hr, X043019_229


title: LNCAP CONTROL #1

description: GENE EXPRESSION FROM LNCAP CELLS

source_name: LNCAP CELLS CONTROL


title: immature, 1hr, X043019_228


title: immature, 1hr, X043019_227


title: PTCL_Case132


title: PTCL_Case131


title: LNCAP CELLS CO-CULTURED WITH ASTROCYTE #1


title: immature, 1hr, X043019_224


title: immature, 1hr, X043019_225


title: immature, 1hr, X043019_223


title: immature, 1hr, X043019_221


title: immature, 1hr, X043019_222


title: PTCL_Case130


title: PTCL_Case129


title: PTCL_Case128


title: immature, 1hr, X043019_219


title: immature, 1hr, X043019_217


title: PTCL_Case126


title: PTCL_Case112

value: ENKTL


title: immature, 1hr, X043019_215

value: F


title: immature, 1hr, X043019_214

value: immature


title: immature, 1hr, X043019_213


title: PTCL_Case125

value: Not Done


title: HDLEC treated with liposomes, rep2

city: Tel Aviv

first: Guy

last: Shapira

address: Chaim Levanon 30

country: Israel

institute: Tel Aviv University

hyb_protocol: Hybridization was performed at 58 °C in GEX-HCB buffer (Illumina) at a concentration of 100 ng cRNA μl-1, unsealed, in a humidified chamber for 20 h

scan_protocol: array signals were developed by a 10-min incubation in a 1 μg ml-1 Cy3-labeled streptavidin (Amersham Biosciences) and 1% blocking solution. Microarray scanning was performed in an iScan array scanner

data_processing: The data were processed using R/Bioconductor scripts (Ritchie et al., 2011)

source_name: cell line

label_protocol: Illumina protocol.

growth_protocol: HDLECs were purchased from PromoCell and cultured in EGM-2, which consists of EBM-2 (Lonza) and 20% FBS (Lonza). Cells were grown in culture flasks with 0.1% gelatin (Sigma) at 37 °C, 5% CO2

extract_protocol: Total RNA  (three independent experiments) was isolated using Trizol (Invitrogen).

treatment_protocol: 24hr incubation of HDLEC with melanosomes isolated from MNT-1 cells or liposomes.

value: HDLEC

tag: treatment

value: liposomes


title: LNCAP CONTROL #2

description: GENE EXPRESSION FROM LNCAP CELLS


title: HDLEC treated with liposomes, rep3


title: PTCL_Case124

value: Lymphoma


title: mature, 1hr, X043019_22


title: HDLEC treated with liposomes, rep1


title: immature, 1hr, X043019_210


title: immature, 1hr, X043019_211


title: HDLEC treated with melanosomes, rep3

value: melanosomes


title: HDLEC treated with melanosomes, rep2


title: age related cataract-rep2 [8]

city: Shanghai

first: Yingying

last: Hong

address: No.83 Fenyang Road

department: Ophthalmology

institute: Eye and ENT hospital (Fudan university)

description: replicate 2

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were normalised using quantile normalisation with GenomeStudio Gene Expression Module v1.0

label: biotin

source_name: anterior lens capsules

label_protocol: Biotinylated cRNA were prepared with the Illumina TotalPrep RAN amplicaiton kit for Illumina arrays

extract_protocol: RNA was extracted with Trizol reagent, followed by clean-up and DNase I treatment with Illumina TotalPrep RAN amplicaiton kit in accordance with the prescribed protocol provided with the kit.

value: age related cataract


title: HDLEC treated with melanosomes, rep1


title: age related cataract-rep3 [M(5,6,9)]

description: replicate 3


title: PTCL_Case121


title: PTCL_Case117


title: immature, 1hr, X043019_216


title: immature, 1hr, X043019_208


title: immature, 1hr, X043019_209


title: immature, 1hr, X043019_212


title: age related cataract-rep1 [7]

description: replicate 1


title: PTCL_Case116


title: mature, 1hr, X043019_21


title: immature, 1hr, X043019_207


title: immature, 1hr, X043019_206


title: immature, 1hr, X043019_204


title: Keap1WT/WT MEF rep 2

city: Tampa

first: Chang

last: Jiang

state: FL

address: 16309 Hyde Manor Dr.

department: Cancer Physiology

institute: H. Lee Moffitt Cancer Center and Research Institute

data_processing:
QC, data filtering, cleaning (Novogene)
STAR for reference genome mapping (Novogene)
DESeq2 for analysis of differential expression (Novogene)
Assembly: mm10
Supplementary files format and content: excel file containing all genes, fold change, p-value, pfkm, and read count for Nrf2 D29H comparison
Supplementary files format and content: excel file containing all genes, fold change, p-value, pfkm, and read count for Keap1 R554Q comparison

source_name: MEF

growth_protocol: Pyruvate free DMEM, 10% FBS

extract_protocol:
Rneasy Plus mini kit (Qiagen)
Libraries were prepared by Novogene using the NEBNext® UltraTM RNA Library Prep Kit

treatment_protocol: Adenoviral Cre or Empty at a MOI of 500

tag: cell line

value: MEF

value: mouse embryonic fibroblast

tag: genotype

value: Adenoviral Empty


title: immature, 1hr, X043019_203

value: brain

value: dentate granule cell


title: PTCL_Case111

value: Peripheral T cell Lymphoma

value: ALCL-neg


title: PTCL_Case110

value: Intermediate AITL/TBX21


title: Human lens-rep1 [capx_2]

description: replicate 1

value: Human lens


title: Human lens-rep2 [capx_3]

description: replicate 2


title: immature, 1hr, X043019_201

value: F


title: immature, 1hr, X043019_200

value: immature


title: Human lens-rep3 [capx_m]

description: replicate 3


title: Keap1WT/WT MEF rep 1


title: PTCL_Case108

value: AITL


title: Keap1R554Q/R554Q MEF rep 3

value: Adenoviral Cre


title: mature, 1hr, X043019_20

value: mature


title: immature, 1hr, X043019_199


title: PTCL_Case106

value: Lymphoma

value: ALCL-pos


title: Keap1R554Q/R554Q MEF rep 2


title: immature, 1hr, X043019_205


title: Keap1R554Q/R554Q MEF rep 1


title: Keap1WT/WT MEF rep 3


title: PTCL_Case105


title: matureactive, 1hr, X043019_194

value: matureactive

value: M


title: immature, 1hr, X043019_197


title: immature, 1hr, X043019_198


title: Nrf2LSL/LSL (Nrf2 KO) MEF rep 3

value: MEF

value: mouse embryonic fibroblast


title: matureactive, 1hr, X043019_195

value: brain


title: matureactive, 1hr, X043019_192

value: dentate granule cell


title: matureactive, 1hr, X043019_191


title: Nrf2LSL/LSL (Nrf2 KO) MEF rep 2

value: Adenoviral Empty


title: PTCL_Case103

value: Peripheral T cell Lymphoma


title: PTCL_Case104


title: PTCL_Case102


title: Nrf2LSL/LSL (Nrf2 KO) MEF rep 1


title: matureactive, 1hr, X043019_189


title: Nrf2D29H/D29H MEF rep 3


title: matureactive, 1hr, X043019_188


title: matureactive, 1hr, X043019_187


title: matureactive, 1hr, X043019_190


title: matureactive, 1hr, X043019_186


title: Nrf2D29H/D29H MEF rep 2


title: mature, 1hr, X043019_19


title: matureactive, 1hr, X043019_196


title: matureactive, 1hr, X043019_185


title: matureactive, 1hr, X043019_184


title: Nrf2D29H/D29H MEF rep 1


title: matureactive, 1hr, X043019_183


title: PTCL_Case100


title: PTCL_Case101


title: matureactive, 1hr, X043019_181


title: matureactive, 1hr, X043019_180


title: matureactive, 1hr, X043019_182


title: PTCL_Case99


title: PTCL_Case97


title: PTCL_Case96


title: mature, 1hr, X043019_18


title: matureactive, 1hr, X043019_179


title: matureactive, 1hr, X043019_176


title: matureactive, 1hr, X043019_178


title: matureactive, 1hr, X043019_175


title: PTCL_Case93


title: matureactive, 1hr, X043019_172


title: PTCL_Case92


title: HLC-d6DEd14-rep1

city: Tokyo

first: Syusaku

last: Tsuzuki

address: 4-6-1, Shirokanedai, Minato-Ku

department: Center for Stem Cell Biology and Regenerative Medicine

country: Japan

institute: The University of Tokyo Institute of Medical Science Division of Regenerative Medicine

hyb_protocol: 1.5 ug of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 250 ml containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 250 ml of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Whole Human Genome Oligo Microarrays (G4112A) for 17 hours at 65°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using one color scan setting for 1x44k array slides (Scan Area 61x21.6 mm, Scan resolution 10um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 9.1 (Agilent) using default parameters (protocol GE v2 8x60K and Grid: 039494_D_F_20190204) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

source_name: Hepatocyte-like cells derived from hiPSC, d4DE, day14

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.5 ug RNA using the One-Color Low RNA Input Linear Amplification PLUS kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

extract_protocol: RNA was prepared using the RNeasy mini kit (Qiagen) following the manufacturer's recommendations. RNA was quantified using a NanoDrop-1000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

tag: differentiation protocol

tag: time

value: 14 culture days


title: HLC-Exd6DEd8-rep1

source_name: Hepatocyte-like cells derived from hiPSC, d4DE, Ex-day8

value: 8 culture days


title: matureactive, 1hr, X043019_174

tag: Sex


title: matureactive, 1hr, X043019_171

tag: cell state

value: F


title: PTCL_Case91.rep2

value: Intermediate AITL/TBX21


title: matureactive, 1hr, X043019_170

tag: mouseid


title: PTCL_Case95

value: ALCL-neg


title: HLC-d4DEd10-rep1

source_name: Hepatocyte-like cells derived from hiPSC, d4DE, day10

value: 10 culture days


title: HLC-d6DEd12-rep1

source_name: Hepatocyte-like cells derived from hiPSC, d6DE, day12

value: 12 culture days


title: HLC-d4DEd12-rep1

source_name: Hepatocyte-like cells derived from hiPSC, d4DE, day12


title: HLC-d6DEd10-rep1

source_name: Hepatocyte-like cells derived from hiPSC, d6DE, day10


title: mature, 1hr, X043019_17

source_name: brain

value: mature

tag: time point


title: TCR KIR+ CD8+ T cell 03

city: Bundang-gu, Seongnam-si

first: Seong Jin

last: Choi

state: Gyeonggi-do

address: Dolma-ro, 172

department: Internal Medicine

institute: Seoul National University Bundang Hospital

description: TCR-seq

data_processing:
For RNA sequencing, single-end reads with 75 base pairs were aligned to the human reference genome using STAR (v 2.7.2)
For TCR sequencing, paired-end reads with 300 base pairs were aligned using MiXCR (v 3.0.3)
Genome_build: GRCh38
Supplementary_files_format_and_content: csv files include read counts for each Sample ...
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample
Supplementary_files_format_and_content: txt files include clonal information for each Sample …

source_name: PBMC

extract_protocol:
Naïve, memory, NKG2A+, and KIR+ CD8+ T cells were isolated using a FACSAria II cell sorter (BD Biosciences).
RNA-seq libraries were prepared using the QuantSeq 3’ mRNA-Seq Library Prep Kit (Lexogen) and sequenced on an Illumina NextSeq 500 for RNA sequencing. The TCR library was prepared using the SMARTer® Human TCR a/b Profiling Kit (Takara Bio, USA) and sequenced on an Illumina MiSeq

tag: disease

value: healthy

tag: clonotypes

value: KIR+ CD8+


title: PTCL_Case89

source_name: Peripheral T cell Lymphoma

tag: tissue

tag: case # from supplemental table9 (pmid35839444)

value: Lymphoma

value: AITL


title: PTCL_Case90

tag: hg-u133plus2.0 platform_id geo identifier

tag: affymetrix data geo series


title: PTCL_Case88

tag: tumor

tag: nanostringclass

value: ATLL


title: matureactive, 1hr, X043019_166

value: brain

value: matureactive

tag: cell type


title: TCR KIR+ CD8+ T cell 02

description: TCR-seq


title: HLC-d4DEd8-rep1

source_name: Hepatocyte-like cells derived from hiPSC, d4DE, day8


title: matureactive, 1hr, X043019_173

value: dentate granule cell

value: M


title: matureactive, 1hr, X043019_164


title: HLC-d6DEd8-rep1

source_name: Hepatocyte-like cells derived from hiPSC, d6DE, day8


title: TCR KIR+ CD8+ T cell 01

description: TCR-seq


title: matureactive, 1hr, X043019_163


title: PTCL_Case91.rep1

value: Peripheral T cell Lymphoma


title: PTCL_Case87


title: matureactive, 1hr, X043019_161


title: mature, 1hr, X043019_160


title: matureactive, 1hr, X043019_169


title: TCR NKG2A+ CD8+ T cell 03

description: TCR-seq

value: NKG2A+ CD8+


title: matureactive, 1hr, X043019_168

value: F


title: matureactive, 1hr, X043019_167


title: mature, 1hr, X043019_16


title: PTCL_Case85


title: PTCL_Case86

value: ENKTL


title: mature, 1hr, X043019_159


title: mature, 1hr, X043019_155


title: TCR NKG2A+ CD8+ T cell 02

description: TCR-seq


title: mature, 1hr, X043019_154


title: TCR NKG2A+ CD8+ T cell 01

description: TCR-seq


title: PTCL_Case84


title: mature, 1hr, X043019_152


title: matureactive, 1hr, X043019_165


title: PTCL_Case83


title: mature, 1hr, X043019_151


title: PTCL_Case81


title: mature, 1hr, X043019_150


title: mature, 1hr, X043019_15


title: mature, 1hr, X043019_146


title: mature, 1hr, X043019_145


title: mature, 1hr, X043019_144


title: mature, 1hr, X043019_143


title: TCR Naïve CD8+ T cell 02

description: TCR-seq

value: Naïve CD8+


title: PTCL_Case80


title: TCR Naïve CD8+ T cell 03

description: TCR-seq


title: TCR Memory CD8+ T cell 01

description: TCR-seq

value: Memory CD8+


title: mature, 1hr, X043019_158


title: TCR Naïve CD8+ T cell 01

description: TCR-seq


title: immatureactive, 1hr, X043019_141

value: immatureactive


title: immatureactive, 1hr, X043019_142


title: PTCL_Case77

value: ALCL-neg


title: immatureactive, 1hr, X043019_140


title: TCR Memory CD8+ T cell 02

description: TCR-seq

value: healthy


title: mature, 1hr, X043019_14

value: mature


title: PTCL_Case73

value: Lymphoma


title: PTCL_Case70


title: TCR Memory CD8+ T cell 03

description: TCR-seq


title: immatureactive, 1hr, X043019_137


title: immatureactive, 1hr, X043019_139


title: Cohort_4, omental, subject_5

city: Stockholm

first: Jiawei

last: Zhong

address: Blickagången 16, Flemingsberg

department: Department of Medicine, Huddinge

country: Sweden

institute: Karolinska Institutet

description: 10x Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v6.0 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: hg38
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Omental white adipose tissue

extract_protocol:
Paired samples of omental and subcutaneous WAT were obtained from female patients with obesity undergoing different bariatric surgery procedures (Roux-en-Y Gastric Bypass and sleeve gastrectomy). After collection, samples were washed using PBS, placed on ice until  the end of the surgery procedure, snap-frozen in liquid nitrogen and stored at -80°C for later use.
50 mg of fresh or frozen WAT was first minced into 1-3 mm pieces and then homogenized on ice in 0.1% CHAPS in CST buffer supplemented with 0.2U/μl RNAase inhibitor (RI) using a Dounce homogenizer. After homogenization, samples were left on ice for five minutes following which PBS supplemented with BSA and 0.2U/μl RI was added to obtain a final concentration of 1% BSA. The lysates were filtered through 40 μm cell strainers and centrifuged at 500 x g for five minutes at 4 °C. The nuclei pellets were resuspended with 1% BSA in PBS supplemented with 0.2U/μl RI and centrifuged again at 500 x g for five minutes at 4 °C. This step was repeated once more. After the final resuspension, nuclei were filtered through 20 μm cell strainers and loaded directly on a 10x Chip G. 10X-libraries were prepared with the Chromium Single Cell v3.1 reagent kit following the manufacturer’s protocol (10X Genomics). Suspensions containing around 1200 nuclei per μl were loaded on Chip G followed by reverse transcription to obtain cDNA, which subsequently was amplified and used for library construction. After preparation, the libraries were sequenced on a NovaSeq 6000 platform (Illumina).
snRNA-seq

value: Omental white adipose tissue

tag: cohort

value: Cohort_4, subject_5


title: Cohort_4, omental, subject_4

description: 10x Genomics

value: Cohort_4, subject_4


title: immatureactive, 1hr, X043019_136

value: brain


title: mature, 1hr, X043019_149

value: dentate granule cell


title: PTCL_Case69


title: mature, 1hr, X043019_147


title: Cohort_4, omental, subject_3

description: 10x Genomics

value: Cohort_4, subject_3


title: immatureactive, 1hr, X043019_135


title: PTCL_Case68

value: Peripheral T cell Lymphoma

value: AITL


title: PTCL_Case78

value: ATLL


title: immatureactive, 1hr, X043019_131

value: F


title: immatureactive, 1hr, X043019_132


title: Cohort_4, omental, subject_2

description: 10x Genomics

value: Cohort_4, subject_2


title: immatureactive, 1hr, X043019_130


title: PTCL_Case65


title: mature, 1hr, X043019_13

value: M


title: Cohort_4, omental, subject_1

description: 10x Genomics

value: Cohort_4, subject_1


title: immatureactive, 1hr, X043019_128

value: immatureactive


title: immatureactive, 1hr, X043019_129


title: Cohort_3, subcutaneous

description: 10x Genomics

source_name: Subcutaneous white adipose tissue

extract_protocol:
Subcutaneous WAT from the periumbilical region was taken by needle biopsy
50 mg of fresh or frozen WAT was first minced into 1-3 mm pieces and then homogenized on ice in 0.1% CHAPS in CST buffer supplemented with 0.2U/μl RNAase inhibitor (RI) using a Dounce homogenizer. After homogenization, samples were left on ice for five minutes following which PBS supplemented with BSA and 0.2U/μl RI was added to obtain a final concentration of 1% BSA. The lysates were filtered through 40 μm cell strainers and centrifuged at 500 x g for five minutes at 4 °C. The nuclei pellets were resuspended with 1% BSA in PBS supplemented with 0.2U/μl RI and centrifuged again at 500 x g for five minutes at 4 °C. This step was repeated once more. After the final resuspension, nuclei were filtered through 20 μm cell strainers and loaded directly on a 10x Chip G. 10X-libraries were prepared with the Chromium Single Cell v3.1 reagent kit following the manufacturer’s protocol (10X Genomics). Suspensions containing around 1200 nuclei per μl were loaded on Chip G followed by reverse transcription to obtain cDNA, which subsequently was amplified and used for library construction. After preparation, the libraries were sequenced on a NovaSeq 6000 platform (Illumina).
snRNA-seq

value: Subcutaneous white adipose tissue


title: PTCL_Case63

value: Not deposited


title: Cohort_2, subcutaneous, subject_2

description: 10x Genomics

value: Cohort_2, subject_2


title: immatureactive, 1hr, X043019_124


title: immatureactive, 1hr, X043019_125


title: Cohort_2, subcutaneous, subject_1

description: 10x Genomics

value: Cohort_2, subject_1


title: immatureactive, 1hr, X043019_127


title: immatureactive, 1hr, X043019_123


title: PTCL_Case62

value: Lymphoma

value: ALCL-pos


title: Cohort_1, subcutaneous

description: 10x Genomics


title: immatureactive, 1hr, X043019_122

value: brain


title: immatureactive, 1hr, X043019_120

value: dentate granule cell


title: mature, 1hr, X043019_12

value: mature


title: immatureactive, 1hr, X043019_118


title: PTCL_Case59

value: Peripheral T cell Lymphoma


title: PTCL_Case61

value: ALCL-neg


title: PTCL_Case58


title: PTCL_Case57

value: ENKTL


title: PTCL_Case56


title: immatureactive, 1hr, X043019_115

value: F


title: immatureactive, 1hr, X043019_116


title: immatureactive, 1hr, X043019_114


title: immatureactive, 1hr, X043019_112


title: PTCL_Case55


title: Donor3_TGFb_2 (RNA-seq)

city: Philadelphia

first: Inyoung

last: Jung

state: PA

address: SPE, 9-304, 3400 Civic Center Blvd, Bldg. 421

institute: University of Pennsylvania

data_processing:
Transcriptome sequencing was performed by Novogene using the NovaSeq 6000 system (Illumina, 150bp paired end reads). Paired-end reads were pseudoaligned to the human genome (GRCh38) using kallisto v0.46.0, and count estimates at the gene level were summarized using tximport 1.24.0.
Supplementary files format and content: tsv files include TPM values for each Sample
Assembly: GRCh38

source_name: blood

growth_protocol: Peripheral blood mononuclear cells (PBMCs) were obtained from healthy subjects via leukapheresis. Written informed consent for leukocyte collection was provided by study subjects according to the Declaration of Helsinki and the International Conference on Harmonization Guidelines for Good Clinical Practice. PBMCs were isolated from buffy coats and cryopreserved at 4 × 107 cells per vial. Cryopreserved PBMCs were thawed, and T-cell purification was carried out using the Pan T Cell Isolation Kit according to the manufacturer’s instructions (Miltenyi Biotec). For CAR-TCONV manufacturing, T-cells were activated with Cell Therapy Systems CD3/CD28 Dynabeads™ (Thermo Fisher Scientific) at a bead to cell ratio of 3:1 for three days in T-cell OpTmizer CTS SFM media (Gibco) supplemented with 5% human AB serum and 100U/mL human IL-2 (T-cell media). At 24-hours post-T-cell activation, T-cells were transduced with the lentiviral vector (M5bbz CAR) at a multiplicity of infection (MOI) of 3. T-cell media was added to cultures every two days, and on day nine, CAR T-cells were cryopreserved in T-cell media supplemented with 20% human AB serum and 10% dimethyl sulfoxide. For CAR-TRM production, T-cell culture media was supplemented with 2ng/mL of TGFβ (R&D Systems or Cell Signaling Technology) in addition to IL-2, and the CAR T-cell engineering process was carried out.

extract_protocol: Anti-mesothelin M5 CAR-TCONV and CAR-TRM cells were harvested after nine days of in vitro expansion. CD8+ CAR T-cells were magnetically isolated using anti-mesothelin-coated beads (ACROBiosystems) and anti-CD8 microbeads (Miltenyi Biotec), followed by resuspension in 500µL of TRIzol (Invitrogen). Total RNA was prepared using RNA Clean & Concentrator™ kits (Zymo Research) following the manufacturer’s instructions.

value: blood

tag: cell subtype

value: T-cell

tag: individual

tag: treatment

value: TGFb

tag: biological replication

value: Normal donor 3_rep2


title: immatureactive, 1hr, X043019_111

tag: cell state

value: immatureactive

tag: Sex


title: Donor3_IL2_2 (RNA-seq)


title: immatureactive, 1hr, X043019_121

value: M

tag: mouseid

tag: time point


title: immatureactive, 1hr, X043019_110


title: mature, 1hr, X043019_11


title: PTCL_Case52


title: PTCL_Case53


title: Donor2_TGFb_2 (RNA-seq)

value: Normal donor 2_rep2


title: immatureactive, 1hr, X043019_109


title: Donor3_IL2_1 (RNA-seq)

value: Normal donor 3_rep1


title: immatureactive, 1hr, X043019_117


title: PTCL_Case51

value: Lymphoma


title: immature, 1hr, X043019_106

value: immature


title: PTCL_Case50

value: AITL


title: immature, 1hr, X043019_105

value: brain

value: dentate granule cell


title: Donor2_TGFb_1 (RNA-seq)

value: Normal donor 2_rep1


title: Donor3_TGFb_1 (RNA-seq)


title: PTCL_Case49

value: Peripheral T cell Lymphoma


title: immatureactive, 1hr, X043019_113


title: immature, 1hr, X043019_100


title: immature, 1hr, X043019_102


title: Donor2_IL2_2 (RNA-seq)


title: immature, 1hr, X043019_103


title: PTCL_Case54

value: ALCL-pos


title: PTCL_Case48


title: mature, 1hr, X043019_10

value: mature

value: F


title: Donor2_IL2_1 (RNA-seq)

value: blood

value: T-cell


title: mature, 1hr, X043019_09


title: mature, 1hr, X043019_08


title: Donor1_TGFb_2 (RNA-seq)

value: TGFb

value: Normal donor 1_rep2


title: PTCL_Case47


title: Donor1_TGFb_1 (RNA-seq)

value: Normal donor 1_rep1


title: mature, 1hr, X043019_03


title: mature, 1hr, X043019_07


title: mature, 1hr, X043019_02


title: A26

data_processing:
CellRanger v3.1.0 and bcl2fastq v2.20.0 were used perform sample de-multiplexing, barcode processing and single cell gene unique molecular identifier (UMI) counting, while a digital expression matrix was obtained for each experiment with default parameters, mapped to the edited mm10 reference, where tdTomato's sequence was added.
Basic processing and visualization of the scRNA-seq data were performed using the bayNorm (version 1.8.0) and Seurat package (version 4.0.4) in R (version 4.0.4).
Genome_build: Edited mm10 with added tdTomato-WPRE-bGH poly(A) signal sequence taken from Ai9 Addgene plasmid (Plasmid #22799) sequence.
Supplementary_files_format_and_content: There are 2 processed files that are output from CellRanger.

source_name: Primary astrocytes

growth_protocol: Primary astrocytes from GFAP-CreERT2;p53flox/flox;LSL-tdTomato mice were cultured in DMEM-F12, N2 (1/200), B27 (1/100), 5mM HEPES, 1x MEM NEAA. 50μM betamercaptoethanol, 0.012% BSA, 6.525mg/ml glucose, 100μg/ml kanamycin, 2μg/ml gentamicin) (Pollard et al., 2009)  supplemented with 20ng/mL EGF and 10ng/mL FGF-2 and 4OHT (Sigma, 200nM) for 5 days

extract_protocol:
Cells were harvested to single cell suspension by trypsinisation and washed and filtered as described in 10x Genomics manual
10x Genomics Single Cell 3’ v2

value: Primary astrocytes from mice

tag: strain


title: A19


title: PTCL_Case43

tag: tissue

value: ALCL-neg


title: PTCL_Case44

tag: case # from supplemental table9 (pmid35839444)

value: Lymphoma


title: immature, 1hr, X043019_104

value: immature

value: M


title: Donor1_IL2_1 (RNA-seq)


title: PTCL_Case42

tag: hg-u133plus2.0 platform_id geo identifier


title: PTCL_Case41

tag: affymetrix data geo series


title: Donor2_TGFb_2 (ATAC-seq)

data_processing:
Cutadapt (https://github.com/marcelm/cutadapt/) was used to trim FASTQ files of adapter contamination. Reads were aligned to the hg19 reference genome using Bowtie2, retaining only properly aligned and paired reads from 10 and 1000 base pairs. Mitochondrial reads were then eliminated (https://github.com/jsh58/harvard/blob/master/removeChrom.py). Aligned reads were converted to BAM files and sorted with samtools, and Picard was used to remove PCR duplicates. BAM files were indexed using samtools to display tracks in the Integrative Genome Viewer (IGV). MACS2 was used to call peaks with an FDR q-value cutoff of 0.01. The R package Diffbind was used to remove ENCODE blacklisted regions (https://sites.google.com/site/anshulkundaje/projects/blacklists), then to identify peaks differentially opened between the CAR-TCONV and -TRM populations.
Supplementary files format and content: narrowPeak files
Assembly: GRCh38

growth_protocol: Peripheral blood mononuclear cells (PBMCs) were obtained from healthy subjects via leukapheresis. Written informed consent for leukocyte collection was provided by study subjects according to the Declaration of Helsinki and the International Conference on Harmonization Guidelines for Good Clinical Practice. PBMCs were isolated from buffy coats and cryopreserved at 4 × 107 cells per vial. Cryopreserved PBMCs were thawed, and T-cell purification was carried out using the Pan T Cell Isolation Kit according to the manufacturer’s instructions (Miltenyi Biotec). For CAR-TCONV manufacturing, T-cells were activated with Cell Therapy Systems CD3/CD28 Dynabeads™ (Thermo Fisher Scientific) at a bead to cell ratio of 3:1 for three days in T-cell OpTmizer CTS SFM media (Gibco) supplemented with 5% human AB serum and 100U/mL human IL-2 (T-cell media). At 24-hours post-T-cell activation, T-cells were transduced with the lentiviral vectors (M5bbz CAR) at a multiplicity of infection (MOI) of 3. T-cell media was added to cultures every two days, and on day nine, CAR T-cells were cryopreserved in T-cell media supplemented with 20% human AB serum and 10% dimethyl sulfoxide. For CAR-TRM production, T-cell culture media was supplemented with 2ng/mL of TGFβ (R&D Systems or Cell Signaling Technology) in addition to IL-2, and the CAR T-cell engineering process was carried out.

extract_protocol: Anti-mesothelin M5 CAR-TCONV and CAR-TRM cells were harvested after nine days of in vitro expansion. CD8+ CAR T-cells were magnetically isolated using anti-mesothelin-coated beads (ACROBiosystems) and anti-CD8 microbeads (Miltenyi Biotec). After elimination of dead cells, 100,000 CD8+ CAR T-cells were cryopreserved. Library preparation was performed by Novogene as follows: a reaction mixture consisting of Tn5 transposase and equimolar adapter1 and adapter 2 was added to nuclei pellets and incubated at 37°C for thirty minutes. The library was enriched using PCR, and purification of final libraries was carried out using AMPure beads (Beckman Coulter). Paired-end sequencing (150bp reads) was conducted on a NovaSeq 6000 instrument.

value: Normal donor 2_rep2


title: Donor2_TGFb_1 (ATAC-seq)


title: PTCL_Case45

tag: tumor


title: Donor1_IL2_2 (RNA-seq)


title: Jurkat, BHLHE40_LV, stimulated, rep2, H3K27ac

city: Boston

first: Nauman

middle: Muhammad

last: Javed

state: MA

address: 450 BROOKLINE AVE

department: Cancer Biology

institute: DANA-FARBER CANCER INSTITUTE INC

description:
Stimulated Jurkats H3K27ac, BHLHE40OE_LV (BHLHE40 overexpressing lentivirus)
BHLHE40OE_H3K27Ac.pval.bigwig

data_processing:
Basecalls were performed using bcl2fastq v2.20. Alignment, filtering, peak calling and QC was performed using ENCODE ChIP-seq pipeline v. 2.1.6(https://github.com/ENCODE-DCC/chip-seq-pipeline2) with default parameters.
For GATA3, H3K27ac, BHLHE40 P258 (sgCtrl_P258, unedited)) WCE-P258-1 and WCE-P258-2 were used as input control. For GATA3, H3K27ac, BHLHE40 P260 (sg70_P260, unedited)) WCE-P260-1 and WCE-P260-2 were used as input control. For TAL1 P258, WCE-P258-1_batch2, WCE-P258-2_batch2 were used as input control samples. For TAL1 P260, WCE-P260-1_batch2, WCE-P260-2_batch2 were used as input control samples. For CtrlLV GATA3 and BHLHE40 ChIP, WCE-P258-1 and WCE-P258-2 were used as input control samples. No input controls were provided for H3K27ac/H3K27me3 processing
p-value bigWig files showing signal enrichment relative to input control were generated for merged filtered bams for each replicate using MACS2 bdgcmp -m FE and default parameters in the ENCODE pipeline
Assembly: hg38
Supplementary files format and content: Bigwigs contain enrichment p-value for merged replicates for each condition/treatment relative to the matched merged input controls generated using MACS2.
Supplementary files format and content: NarrowPeaks contain significant IDR peaks (0.05 cutoff) for BHLHE40 and GATA3 ChIP in Ctrl-LV (BHLHE40-WT) Jurkats, and pooled MACS2 raw peaks for H3K27ac ChIP

source_name: Jurkat

growth_protocol: Jurkat cells  were grown in 37C, 5%CO2 in complete RPM consisting of RPMI(GIBCO), 10% fetal bovine serum(FBS, heat inactivated, Peak Serum), 20 mM HEPES(GIBCO), 1% sodium pyruvate(GIBCO), 1% penicillin-streptomycin(GIBCO), 1% NEAA(GIBCO), at a maximum density of 2 x 10^6 cells. Cells were routinely tested for mycoplasma.

extract_protocol:
25 million cells per sample were pelleted and fixed using 1% formaldehyde and quenched with glycine. Pellets were washed with cold PBS+proteinase, resuspended in lysis buffer, and incubated on ice for 10 minutes. Sample was then diluted up to 1 ml in ChiP dilution buffer, sonicated using Covaris E220, and  incubated overnight with H3K27ac antibody(Active Motif, 39133), GATA3(CST-D13C9), or BHLHE40(Novus Biological NB100-1800) and incubated overnight.  Immunopreciitation was performed using protein G beads, and DNA fragments were purified using AMPure XP beads
Eluted fragments were then processed with DNA end-repair(Epicenter Biotech), Klenow a base adding(Klenow from NEB), adaptor ligation, PCR amplification, and purification using AMPure XP beads with final size of ~300 bp.

treatment_protocol: Jurkat cells were stimulated for 2 hours with 50 ng/ml PMA(Sigma-Aldrich) and 500 ng/ml ionomycin(Sigma,Aldrich). Lentivirus transduction was conducted using either  sgCtrl_P258(control guide RNA) or sg70_P260(RE4 base editing guide RNA) constructs. Cells were plated at a density of 2-5 x 10^5 cells and treated with lentiviral supernatant supplemented with 8 ug/ml polybrene, centrifuged at 2000g 32 C for 60 minutes, and incubated overnight at 37C 5%CO2. Cells were changed into complete RMPI the following day and puromycin selection was conducted using 5 ug/ml for 3 days.

tag: cell line

value: Jurkat

value: T-ALL

tag: chip antibody

value: H3K27ac (Active Motif 39133)

tag: genotype

value: stimulated(PMA/ionomycin 5 hours)


title: Jurkat, BHLHE40_LV, stimulated, rep1, H3K27ac

tag: cell type


title: Jurkat, BHLHE40_LV, stimulated, rep1, H3K27me3

description:
Stimulated Jurkats H3K27me3, BHLHE40OE_LV (BHLHE40 overexpressing lentivirus)
BHLHE40OE_H3K27Me3.pval.bigwig

value: H3K27me3(Active Motif 39155)


title: PTCL_Case40

value: Peripheral T cell Lymphoma

tag: nanostringclass

value: ALCL-pos


title: Jurkat, BHLHE40_LV, stimulated, rep1, BHLHE40

description:
Stimulated Jurkats BHLHE40, BHLHE40OE_LV (BHLHE40 overexpressing lentivirus)
BHLHE40OE_BHLHE40.pval.bigwig

value: BHLHE40 ( Novus Biological, NB100-1800)

tag: treatment


title: Donor2_IL2_2 (ATAC-seq)

value: blood

tag: cell subtype

value: T-cell

tag: individual

tag: biological replication


title: Jurkat, BHLHE40_LV, stimulated, rep2, BHLHE40


title: PTCL_Case39


title: Jurkat, BHLHE40_LV, stimulated, rep2, H3K27me3


title: Jurkat, Ctrl_LV, stimulated, rep2, H3K27me3

description:
Stimulated Jurkats H3K27me3, Ctrl_LV (control lentivirus)
CtrlLV_H3K27Me3.pval.signal.bigwig


title: Jurkat, Ctrl_LV, stimulated, rep1, H3K27me3


title: Donor2_IL2_1 (ATAC-seq)

value: Normal donor 2_rep1


title: Jurkat, Ctrl_LV, stimulated, rep2, H3K27ac

description:
Stimulated Jurkats H3K27ac, Ctrl_LV (control lentivirus)
CtrlLV_H3K27Ac.pval.signal.bigwig
CtrlLV_H3K27ac.pooled.narrowPeak.gz


title: Jurkat, Ctrl_LV, stimulated, rep2, GATA3

description:
Stimulated Jurkats GATA3, Ctrl_LV (control lentivirus)
CtrlLV_GATA3.idr0.05.narrowPeak.gz


title: Jurkat, Ctrl_LV, stimulated, rep1, GATA3


title: Donor1_TGFb_2 (ATAC-seq)

value: TGFb

value: Normal donor 1_rep2


title: PTCL_Case38

value: Lymphoma

value: ALCL-neg


title: Jurkat, Ctrl_LV, stimulated, rep1, BHLHE40

description:
Stimulated Jurkats BHLHE40, Ctrl_LV (control lentivirus)
CtrlLV_BHLHE40.pval.signal.bigwig
CtrlLV_BHLHE40.idr0.05.narrowPeak.gz


title: Donor1_IL2_2 (ATAC-seq)


title: Jurkat, sg70_P260, stimulated, rep2, TAL1

description:
Stimulated Jurkats TAL1, BHLHE40OE_LV (BHLHE40 overexpressing lentivirus)
TAL1_p260.pval.bigwig

value: TAL1 (Santa Cruz Biotechnology, # SC-393287)


title: Jurkat, sg70_P260, stimulated, rep1, TAL1


title: Jurkat, sgCtrl_P258, stimulated, rep1, TAL1

description:
Stimulated Jurkats TAL1, Ctrl_LV (control lentivirus)
TAL1_p258.pval.bigwig


title: Jurkat, sg70_P260, stimulated, rep1, batch2, WCE

description: Stimulated Jurkats input control, sg70_P260(targeting guide), second batch WCE used for TAL1 and H3K27me3 Ctrl_P258 sample normalization